https://wiki.bwhpc.de/wiki/api.php?action=feedcontributions&feedformat=atom&user=J+KucerabwHPC Wiki - User contributions [en]2026-05-13T03:08:15ZUser contributionsMediaWiki 1.39.17https://wiki.bwhpc.de/wiki/index.php?title=Software_Modules_Lmod&diff=13016Software Modules Lmod2024-10-10T12:38:13Z<p>J Kucera: </p>
<hr />
<div>Software Module System - Lmod<br />
<br />
= Preface =<br />
<br />
This guide provides a general overview and introduction to the software system management via Lmod on JUSTUS 2 for new users as well as for experienced users coming, e.g. from sites planted with different Environment modules systems.<br />
<br />
= Scientific Software management through the module system Lmod =<br />
The following sections covers the basic module commands needed to find and load the scientific applications installed on the JUSTUS 2.<br><br />
<br />
JUSTUS 2 uses Linux operating system. The standard Linux packages are installed on the front end nodes (login and visualisation nodes).<br />
The '''scientific software is accessible via so called module system'''.<br><br />
'''To find and load an scientific application, one needs to use module commands.''' For example the following command sequence:<br />
<pre><br />
module load chem/gaussian/g16.C.01<br />
module list<br />
module help chem/gaussian/g16.C.01<br />
cp $GAUSSIAN_EXA_DIR/bwforcluster-gaussian-example.sbatch .<br />
</pre><br />
<pre><br />
1. loads the module with gaussian software package of version 16, revision C.01<br />
2. prints out the list of currently load modules<br />
3. provides the user help for the particular gaussian module<br />
4. copies the template batch script which was specifically designed for submission of g16 jobs into SLURM workload manager on JUSTUS 2.<br />
</pre><br />
<br />
<br />
=== Why we use module system? Modules load scientific software ===<br />
The module system on JUSTUS 2 is managed by '''[https://lmod.readthedocs.io/en/latest/ Lmod]''' (https://lmod.readthedocs.io/en/latest/).<br />
The module system incorporates majority of the computational software available - this includes among others compilers, mpi libraries, numerical libraries, computational<br />
chemistry packages, python specific libraries etc.. <br><br>'''The programs managed by the module system are by default not utilizable. It has to be "loaded" to become executable.'''<br />
<br><br><br />
The use of '''module system''' provide among others the following '''functionalities''':<br />
<br />
'''1.''' When '''loading a module''', it automatically '''sets the appropriate environment variables required by the application to run properly'''.<br><br />
'''2.''' It also takes care about the '''module dependency'''. It either loads all additional modules required for the application, or it informs the user if additional dependency modules need to be manually loaded.<br><br />
'''3.''' It '''prevents loading of modules''' that could be '''in conflicts''' and can '''cause instability or unexpected behavior'''.<br><br />
<br><br />
<br />
Among the main functionalities of Lmod belongs '''module load''' to make variety of the software packages pre-installed on the cluster accessible. '''This is feasible by only a single command''': <br />
<br><br />
<pre><br />
module load <module_name><br />
</pre><br />
The activation is realized by '''dynamical modification of the user's shell environment'''. This simply includes '''adding new paths''' to bin directories with the specific software '''into the PATH environmental variable'''. Typically, Lmod modifies '''PATH''' and '''LD_LIBRARY_PATH''' as well as it '''sets new variables''' as, for example '''<SOFTWARE_NAME>_EXA_DIR''' containing path to directory with the examples for a specific software.<br />
<br><br><br />
Example: compare the content of $PATH environmental variable before and after the load of the gaussian module:<br />
<br>Before the load of gaussian module: <br />
<pre><br />
echo $PATH<br />
/home/software/common/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin<br />
</pre><br />
<pre><br />
which g16<br />
/usr/bin/which: no g16 in (/home/software/common/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin)<br />
</pre><br />
<pre><br />
ml chem/gaussian<br />
</pre><br />
After gaussian is loaded:<br />
<pre><br />
echo $PATH<br />
/.../chem/gaussian/g16.C.01/x86_64-Intel-avx2-source/g16/bsd:/.../chem/gaussian/g16.C.01/x86_64-Intel-avx2-source/g16:/home/software/common/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin<br />
</pre><br />
<pre><br />
which g16<br />
/.../chem/gaussian/g16.C.01/x86_64-Intel-avx2-source/g16/g16<br />
</pre><br />
<br />
=== Basic functions of Lmod and commands ===<br />
<br>The module system has other useful capabilities then just the managing the environment.<br><br><br />
''' (i) to list available software'''<br><br />
<pre><br />
module available<br />
</pre><br />
'''<br> (ii) to load (activate) modules (particular software)'''<br><br />
<pre><br />
module load<br />
</pre><br />
'''<br> (iii) to unload (inactivate) modules (particular software)'''<br><br />
<pre><br />
module unload<br />
</pre><br />
<pre><br />
module purge<br />
</pre><br />
''' (iv) to list currently loaded modules'''<br><br />
<pre><br />
module list<br />
</pre><br />
<br />
'''<br> (v) to search through all packages within the module system'''<br><br />
<pre><br />
module available<br />
</pre><br />
<pre><br />
module spider<br />
</pre><br />
<pre><br />
module keyword<br />
</pre><br />
'''<br> (vi) to provide specific help information for a particular module system<br>'''<br />
<pre><br />
module help<br />
</pre><br />
<pre><br />
module whatis<br />
</pre><br />
<br />
== Elementary Lmod Commands ==<br />
The module commands below might be used interactively (in shells' current session), as well as in the shell scripts, in particular in the sbatch scripts used for submission of the computational jobs into SLURM (workload manager on JUSTUS2).<br />
=== List of available software modules ===<br />
<pre><br />
module available<br />
</pre><br />
alternatively also in a short form<br />
<pre><br />
ml av<br />
</pre><br />
<br />
=== Module naming convention: Category/Name/Version ===<br />
On JUSTUS 2 (similarly as on other HPC sites of bwHPC), the software modules are grouped into<br />
several categories:<br />
<!--* [[:Category:Chemistry_software|chem]]--><br />
* chem<br />
<!--* [[:Category:Compiler_software|compiler]]--><br />
* compiler<br />
<!--* [[:Category:Debugger_software|devel]]--><br />
* devel<br />
<!--* [[:Category:Libraries|lib]]--><br />
* lib<br />
<!--* [[:Category:Numerical libraries|numlib]]--><br />
* numlib<br />
<!--* [[:Category:Physics software|phys]]--><br />
* phys<br />
<!--* [[:Category:System software|system]]--><br />
* system<br />
<!--* [[:Category:Visualization|vis]]--><br />
* vis<br />
<!--* [[:Category:Mathematical ecosystems|math]]--><br />
* math<br />
<br />
This makes it easier for<br />
users to get oriented within the module system. For example Gaussian 16 program allowing<br />
to calculate electronic structure of molecules is found in the category chem (together with other<br />
programs used by theoretical chemists).<br />
<br><br />
Each the category is further divided according to software packages and those finally according to software versions. <br />
<br><br />
The full '''name of a module''' always consists of three parts '''category, name, and version''' separated by slash '''category/name/version''' . Consequently, the<br />
full name of the module with Gaussian 16 package is '''chem/gaussian/g16.C.01'''. Analogously, gnu compiler of version 10.2 is addressed as '''compiler/gnu/10.2'''.<br />
<br><br><br />
See, for example, all modules of category chem with:<br />
<pre><br />
ml av chem<br />
</pre><br />
<pre><br />
---------------------------------------------- /opt/bwhpc/common/modulefiles/Core----------------------------------------------------------------------------------<br />
chem/adf/2019.304 chem/gaussian/g16.C.01 chem/molpro/2020.1 (D) chem/orca/5.0.1-xtb-6.4.1 chem/tmolex/4.6 (D)<br />
chem/ams/2020.101 chem/gaussview/6.1.1 chem/namd/2.14 chem/orca/5.0.1 (D) chem/turbomole/7.4.1<br />
chem/ams/2020.103 chem/gromacs/2020.2 chem/nbo/6.0.18_i4 chem/quantum_espresso/6.5 chem/turbomole/7.5 (D)<br />
chem/ams/2021.102 (D) chem/gromacs/2020.4 chem/nbo/6.0.18_i8 (D) chem/quantum_espresso/6.7_openmp-5 chem/vasp/5.4.4.3.16052018<br />
chem/cfour/2.1_openmpi chem/gromacs/2021.1 (D) chem/openbabel/3.1.1 chem/quantum_espresso/6.7 (D) chem/vmd/1.9.3<br />
chem/cp2k/7.1 chem/jmol/14.31.3 chem/openmolcas/19.11 chem/schrodinger/2020-2 chem/xtb/6.3.3<br />
chem/cp2k/8.0_devel (D) chem/lammps/stable_3Mar2020 chem/openmolcas/21.06 (D) chem/schrodinger/2021-1 (D) chem/xtb/6.4.1 (D)<br />
chem/dalton/2020.0 chem/molcas/8.4 chem/openmolcas/21.10 chem/siesta/4.1-b4<br />
chem/dftbplus/20.2.1-cpu chem/molden/5.9 chem/orca/4.2.1-xtb-6.3.3 chem/siesta/4.1.5 (D)<br />
chem/gamess/2020.2 chem/molpro/2019.2.3 chem/orca/4.2.1 chem/tmolex/4.5.2<br />
</pre><br />
or, analogously, all available versions of intel compilers:<br />
<br><br />
<pre><br />
ml av compiler/intel<br />
</pre><br />
<pre><br />
--------------------------------------------------------------------------------/opt/bwhpc/common/modulefiles/Core--------------------------------------------------------------<br />
compiler/intel/19.0 compiler/intel/19.1 compiler/intel/19.1.2 (D)<br />
</pre><br />
<br />
=== Load specific software ===<br />
<pre><br />
module load <module_name><br />
</pre><br />
or shortly<br />
<pre><br />
ml <module_name><br />
</pre><br />
For example to load gaussian of version 16 one has to run<br />
<pre><br />
ml chem/gaussian/g16.C.01<br />
</pre><br />
=== List of the loaded modules ===<br />
<pre><br />
module list<br />
</pre><br />
or simply<br />
<pre><br />
ml<br />
</pre><br />
<br />
=== Default module version ===<br />
In case of there is multiple software versions, one version is always pre-determined as the '''default'''<br />
version. To address a default version, ''version'' can be omitted in the module identifier.<br />
For example, the loading of the default intel compiler module is realized via<br />
<pre><br />
ml compiler/intel<br />
</pre><br />
<pre><br />
ml<br />
<br />
Currently Loaded Modules:<br />
1) compiler/intel/19.1.2<br />
</pre><br />
<br />
=== Unload a specific software from the environment ===<br />
<pre><br />
module unload <module_name><br />
</pre><br />
or equivalently<br />
<pre><br />
ml -<module_name><br />
</pre><br />
for example to unload previously loaded vasp module chem/vasp/5.4.4.3.16052018<br />
use<br />
<pre><br />
ml -chem/vasp/5.4.4.3.16052018<br />
</pre><br />
=== Unload all the loaded modules ===<br />
<pre><br />
$ module purge<br />
</pre><br />
or<br />
<pre><br />
ml purge<br />
</pre><br />
=== Providing a specific help for a particular module ===<br />
<pre><br />
module help <module_name><br />
</pre><br />
or<br />
<pre><br />
ml help <module_name><br />
</pre><br />
=== Software job examples and batch script templates === <br />
Majority of the software modules provides examples, including job queueing system examples (batch scripts)<br />
for slurm. A full path the directory with examples is normally contained in <SOFTWARE_NAME>_EXA_DIR<br />
environmental variable. For example the examples for Gromacs-2021.1 are located in (after the loading of the module).<br />
<pre><br />
ml chem/gromacs/2021.1<br />
</pre><br />
<pre><br />
echo $GROMACS_EXA_DIR/<br />
/opt/bwhpc/common/chem/gromacs/2021.1-openmpi-4.0/bwhpc-examples/<br />
</pre><br />
<pre><br />
ls $GROMACS_EXA_DIR<br />
GROMACS_TestCaseA Performance-Tuning-and-Optimization-of-GROMACS.pdf README<br />
</pre><br />
<pre><br />
ls $GROMACS_EXA_DIR/GROMACS_TestCaseA/<br />
gromacs-2021.1_gpu.slurm gromacs-2021.1.slurm ion_channel.tpr<br />
</pre><br />
Users may make a copy of these examples and use it as template for their own job scripts:<br />
<pre><br />
cp $GROMACS_EXA_DIR/GROMACS_TestCaseA/gromacs-2021.1_gpu.slurm .<br />
</pre><br />
'''Note: All the batch scripts examples are fully functional, i.e. the example scripts could be directly submitted into the queuing system, to launch a test job.'''<br />
Typically, the scripts launch a short, simple calculation of the given software. Moreover, most of the sbatch scripts contain<br />
general submit instructions, as well as hints specific for the particular program.<br />
<br />
=== Searching through module names ===<br />
<pre><br />
module available <module_name><br />
</pre><br />
or shortly<br />
<pre><br />
ml av <module_name><br />
</pre><br />
For example, searching for python modules is realized via<br />
<pre><br />
ml av python<br />
</pre><br />
with the following output:<br />
<pre><br />
----------------------------------------------------------------------------------- /opt/bwhpc/common/modulefiles/Core ------------------------------------------------------------------------------------<br />
devel/python/3.8.3 lib/python_matplotlib/3.2.2_numpy-1.19.0_python-3.8.3 numlib/python_numpy/1.19.0_python-3.8.3 numlib/python_scipy/1.5.0_numpy-1.19.0_python-3.8.3<br />
<br />
Use "module spider" to find all possible modules and extensions.<br />
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys"<br />
</pre><br />
<br />
=== What does this software do? Command when you don't know this software ===<br />
<pre><br />
ml whatis <modulename><br />
</pre><br />
provides the short description of the software package.<br />
<br />
=== Finding detailed information about a specific module ===<br />
<pre><br />
module spider <searching_pattern><br />
</pre><br />
or just<br />
<pre><br />
ml spider <searching_pattern><br />
</pre><br />
<br />
=== Extended searching through entire module system ===<br />
<pre><br />
module keyword <searching_pattern><br />
</pre><br />
For example, to find out which modules contain fftw library:<br />
<pre><br />
ml keyword fftw<br />
</pre><br />
which gives the following info:<br />
<pre><br />
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------<br />
<br />
The following modules match your search criteria: "fftw"<br />
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------<br />
<br />
numlib/mkl: numlib/mkl/2019, numlib/mkl/2020, numlib/mkl/2020.2<br />
<br />
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------<br />
</pre><br />
<br />
== Best Practices when working with modules ==<br />
=== Always load modules with the entire module name === <br />
The software stack is updated regularly. The adding of the new software version usually revokes which version is marked as default. <br />
The newer software is not always backwards compatible, including the existing scripts, workflow, or even input files.<br />
Therefore it is strongly recommended to avoid the loading based on just category and software name. Instead, one should always use the entire module name (including the version) to make sure the same module is loaded each time.<br />
<br />
=== Load only those modules that are needed for the current application === <br />
Only load modules that are needed for the current script or workflow you are running, to reduce the chance of unexpected behavior caused by module conflicts.<br />
<br />
'''Typical error''' sometimes seen on the cluster by loading of vasp module is this:<br />
<pre><br />
ml compiler/intel/19.1.2<br />
ml mpi/impi/2019.8<br />
ml chem/vasp/5.4.4.3.16052018<br />
</pre><br />
<br />
'''The correct way''' is indeed only:<br />
<pre><br />
ml chem/vasp/5.4.4.3.16052018<br />
</pre><br />
<br />
=== Do not use module commands in .bashrc, .bash_profile etc. scripts ===<br />
Avoid including “module load” commands in your .bashrc or .bash_profile files. As an alternative, create a bash script with the module load commands and source it each time, to load the modules needed.<br />
<br />
=== Use 'module help' command ===<br />
see [[Software_Modules_Lmod#Providing_a_specific_help_for_a_particular_module]]<br />
<br />
=== Check content of $<SOFTWARE_NAME>_EXA_DIR folder ===<br />
see [[//wiki.bwhpc.de/e/Software_Modules_Lmod#Software_job_examples_and_batch_script_templates]]<br />
<br />
=== Use 'ml purge' in sbatch scripts before the first 'ml load' ===<br />
The environment in effect at the time of the sbatch, salloc, or srun commands is executed are propagated <br />
to the spawned processes, i.e. also to the job-script. Consequently, should be some module loaded at the<br />
time of the 'sbatch <job-script>' command execution, its state, i.e. "loaded", as well as the values of<br />
the set environmental variables will be propagated with the job.<br><br><br />
Thus, consider to put 'ml purge' command as the first module command when you are designing your job-scripts.<br />
This might prevent variety of module conflict situations.<br />
<br />
Imagine for example, in the following scenario<br />
<pre><br />
On the login node:<br />
<br />
ml compiler/intel/19.1.2<br />
salloc --nodes=1 --ntasks-per-node=1<br />
<br />
... waiting for the allocation of the resources ...<br />
Once on the compute node execute<br />
<br />
ml compiler/gnu/10.2<br />
</pre><br />
the load of compiler/gnu/10.2 module on the compute node fails with following error:<br />
<pre><br />
Lmod has detected the following error: Cannot load module "compiler/gnu/10.2" because these module(s) are loaded:<br />
compiler/intel<br />
<br />
While processing the following module(s):<br />
Module fullname Module Filename<br />
--------------- ---------------<br />
compiler/gnu/10.2 /opt/bwhpc/common/modulefiles/Core/compiler/gnu/10.2.lua<br />
<br />
[ul_l_tkz12@login02 ~]$ ml<br />
<br />
Currently Loaded Modules:<br />
1) compiler/intel/19.1.2<br />
</pre><br />
<br />
== Useful Extras ==<br />
=== Conflicts between modules ===<br />
Some modules cannot be loaded together at the same time. For example two different versions of the same package cannot<br />
be activated simultaneously. The modules might already built-in this functionality. In such circumstances, Lmod, during the loading, either<br />
prints an error message and no module is loaded, or the module is reloaded - the old module is unloaded and only the new module is become activated.<br><br><br />
'''Example of two versions of the intel compiler - module reload:'''<br />
<pre><br />
ml compiler/intel/19.1<br />
</pre><br />
<pre><br />
ml<br />
<br />
Currently Loaded Modules:<br />
1) compiler/intel/19.1<br />
</pre><br />
<pre><br />
ml compiler/intel/19.1.2 <br />
<br />
The following have been reloaded with a version change:<br />
1) compiler/intel/19.1 => compiler/intel/19.1.2<br />
</pre><br />
<pre><br />
ml<br />
<br />
Currently Loaded Modules:<br />
1) compiler/intel/19.1.2<br />
</pre><br />
<br><br><br />
'''Example of two different compilers intel and gnu triggers the module conflict with the error during the load of gnu - the new module is not loaded:'''<br />
<br />
<pre><br />
ml compiler/intel/19.1.2<br />
</pre><br />
<pre><br />
ml<br />
<br />
Currently Loaded Modules:<br />
1) compiler/intel/19.1.2<br />
</pre><br />
<pre><br />
ml compiler/gnu/10.2 <br />
Lmod has detected the following error: Cannot load module "compiler/gnu/10.2" because these module(s) are loaded:<br />
compiler/intel<br />
<br />
While processing the following module(s):<br />
Module fullname Module Filename<br />
--------------- ---------------<br />
compiler/gnu/10.2 /opt/bwhpc/common/modulefiles/Core/compiler/gnu/10.2.lua<br />
</pre><br />
<pre><br />
ml<br />
<br />
Currently Loaded Modules:<br />
1) compiler/intel/19.1.2<br />
</pre><br />
<br><br />
'''Solution:''' intel compiler must be unloaded prior the load of gnu module.<br />
<pre><br />
ml -compiler/intel/19.1.2<br />
</pre><br />
<pre><br />
ml compiler/gnu/10.2<br />
</pre><br />
<pre><br />
ml<br />
<br />
Currently Loaded Modules:<br />
1) compiler/gnu/10.2<br />
</pre><br />
<br />
=== Module dependencies (why there is no mpi module?) ===<br />
Some modules can depends on other modules. Typically, many modules depends on mpi library, Mpi library depends on a compiler, etc.. The user does not need<br />
to care about these fundamental dependencies. Majority of modules automatically take care about loading of all necessary packages it is depending on.<br />
However, there is an eminent exception - mpi library. While the most of the installed parallel applications exist for only one compiler-mpi combination,<br />
there are variety of mpi libraries of the same versions built with different compilers. For example there are two sets of OpenMPI 4.0 modules for intel and gnu compilers.<br />
Thus, an user who wants to load a specific mpi must chose (load) a particular compiler prior the mpi module load. Note, that the mpi modules also remains<br />
"invisible" for "module av <mpi_name>" command until a certain compiler is not loaded. This due to the module hierarchy of Lmod. More details about the hierarchy<br />
is below in [[Software_Modules_Lmod#Semi_hierarchical_layout_of_modules_on_JUSTUS_2]]<br />
<br />
<br />
==== Consequences of the partial module hierarchy for mpi modules ====<br />
Mpi modules remains invisible for a user (prompted ''module avail'') until some compiler module has been loaded. Once the compiler module has been activated corresponding mpi modules, i.e. built with the particular compiler, become visible.<br><br />
<br><br />
E.g., with the originally empty list of the loaded modules, the module command <br />
<pre><br />
$ module avail<br />
</pre><br />
or its shorthand analogue<br />
<pre> <br />
$ ml av<br />
</pre><br />
displays no mpi module available. After running<br />
<pre><br />
ml compiler/intel/19.1<br />
ml av<br />
</pre><br />
mpi packages compatible with the intel 19.1 compiler becomes visible<br />
<pre><br />
------------ /opt/bwhpc/common/modulefiles/Compiler/intel/19.1 --------------------<br />
mpi/impi/2019.7 mpi/openmpi/4.0<br />
</pre><br />
in the list of the available software.<br />
<br />
=== Online user guide of Lmod ===<br />
The complete user guide can be found on Lmod websites [https://lmod.readthedocs.io/en/latest/010_user.html]<br />
<br />
=== Additional Module System tasks ===<br />
Lmod offers more than 25 sub-commands plus various options to manage the modulefile system installed on JUSTUS 2. See, e.g. output of "module --help" command. Large majority of users will use only couple of them. A complete list of module sub-commands can be displayed by entering "module --help" command or in [https://lmod.readthedocs.io/en/latest/010_user.html Lmod online documentation]. The following text lists only a couple of them.<br />
<br />
== Other topics == <br />
=== Which shells supports module commands? ===<br />
So far Bash is only supported shell on JUSTUS 2 to interpret module commands.<br />
<br />
=== Semi hierarchical layout of modules on JUSTUS 2 ===<br />
<br />
==== Module hierarchy in Lmod ====<br />
The structure of software modules on JUSTUS 2 exploits a "semi" hierarchical structure. This is slightly different from what can be seen on another HPC systems with "full" hierarchical structure. The typical systems with full hierarchy put compiler modules (i.e., intel, gcc) in the uppermost (Core) level, depending libraries (e.g., MPI) on the second level, and more depending libraries on a third level. As a consequence, not all the modules contained in the module system are initially visible, namely the modules putted in the second and third layer. Only after a loading a compiler module, the modules of the second layer directly depending on the particular compiler will become available. And similarly, loading an MPI module will make the modules of the third layer depending on the loaded MPI library visible.<br><br />
<br />
==== Semi hierarchy of software stack on JUSTUS 2 ====<br />
JUSTUS 2 adopted the hierarchical structure of the modules layout only partially. In particular, there is only "Core" and the "second" level presented and there are only mpi modules contained in the second level. All other modules, i.e. for example those from the "chem" sub-cathegory such as ''vasp'', ''turbomole'', or ''gaussian'', or those located in the "numlib" sub-cathegory such as ''mkl'' or ''python_numpy'', are embodied in the "Core" level.<br />
<br><br />
<br />
==== Module dependency ====<br />
The adopted hierarchy models is not the only tool handling the module dependency. As a matter of fact, most of the modules on JUSTUS 2 require a provision of functionalities from another modules, albeit located in the "Core" level. Such provisioning is implemented in a modulefile either automatically without a need of any action from the user (the depending modulefile, while loading, loads all additional modules automatically) or the depending modulefile, while loading, informs the user about necessity to pre-load additional modules if those has not been activated yet (in this case the user must repeat the loading operation). Which of the solution is applied rests with the decision of the person who built the particular module.<br><br />
<br><br />
An example of module with the implemented automated pre-loading is ''orca'' module. With the pre-emptied list of the loading modules, i.e.<br />
<pre><br />
ml<br />
</pre><br />
shows <br />
<pre><br />
No modules loaded<br />
</pre><br />
, the command sequence<br />
<pre><br />
ml chem/orca<br />
ml<br />
</pre><br />
shows<br />
<pre><br />
Currently Loaded Modules:<br />
1) compiler/intel/19.1 2) chem/orca/4.2.1 <br />
</pre><br />
I.e., loading of the ''intel'' compiler is built-in the ''orca'' module.<br />
<br />
=== Complete list of Lmod options and sub-commands === <br />
The whole list of module options and all commands available can be displayed by running<br />
<pre><br />
man module<br />
</pre><br />
or<br />
<pre><br />
module --help<br />
</pre><br />
<br />
=== How do Modules work? ===<br />
The default shell on the bwHPC clusters is bash, so explanations and examples will be shown for bash. In general, programs cannot modify the environment of the shell they are being run from, so how can the module command do exactly that?<br />
<br><br />
The module command is not a program, but a bash-function.<br />
You can view its content using:<br />
<pre><br />
type module<br />
</pre><br />
and you will get the following result:<br />
<pre><br />
type module<br />
module is a function<br />
module ()<br />
{<br />
eval $($LMOD_CMD bash "$@");<br />
[ $? = 0 ] && eval $(${LMOD_SETTARG_CMD:-:} -s sh)<br />
}<br />
</pre><br />
In this function, lmod is called. Its output to stdout is then executed inside your current shell using the bash-internal ''eval'' command. As a consequence, all output that you see from the module is transmitted via stderr (output handle 2) or in so<br />
<br><br />
<br><br />
----<br />
[[#top|Back to top]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Orca&diff=12661JUSTUS2/Software/Orca2024-02-29T12:57:55Z<p>J Kucera: </p>
<hr />
<div>{{Softwarepage|chem/orca}}<br />
<br />
{| width=600px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/orca/5.0.4<br />
|-<br />
| Availability<br />
| [[bwUniCluster]] &#124; [[JUSTUS2]]<br />
|-<br />
| License<br />
| [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA]<br />
|-<br />
|Citing<br />
| As described in the [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf manual]. Refer to Chapter 'Publications Related to ORCA' for guidance on citation.<br />
|-<br />
| Links<br />
| [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Forum Portal] &#124; [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|}<br />
<br><br />
= Description =<br />
<br />
'''ORCA''' is a comprehensive, fully parallelized quantum chemistry package designed for advanced electronic structure methods. It encompasses density functional theory, many-body perturbation theory, coupled cluster methods, multireference methods, and semi-empirical quantum chemistry approaches. ORCA is capable of computing a wide range of molecular properties and serves as a fully integrated system for multi-level calculations, including QM/MM, ONIOM, and embedded crystals.<br />
<br />
Additionally, ORCA offers several advanced features to improve computational efficiency and accuracy. These include local correlation methods, starting with PNOs and expanded to DLPNO to reduce the computational cost of coupled cluster calculations. It also incorporates RIJCOSX for efficient handling of Hartree-Fock based methods.<br />
<br />
Furthermore, ORCA provides NEB-TS for studying reaction pathways and offers various methods for accurately calculating excited states, such as TD-DFT, EOM-CCSD, STEOM-CCSD, CASSCF with NEVPT2 or CASPT2, as well as molecular dynamics and multi-scale QM-MM models.<br />
<br />
Please refer to documentation provided by the ORCA developers in the first place for more detailed information, e.g.: <br />
<br />
[https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Orca Manual 5.0.4]<br />
<br><br />
[https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wcms.1606 Article Overview by Frank Nesse]<br />
<br><br />
[https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.81 Article about main improvement in the version 5.0]<br />
<br />
<br><br />
<br />
= Miscellaneous Notes to Usage = <br />
* ORCA utilizes MPI parallelization, specifically backed by OpenMPI. When configuring parallel jobs in the Slurm sbatch script, use appropriate directives such as --nodes and --ntasks-per-node.<br>Avoid using the --cpus-per-task directive. All the ORCA modules load the appropriate OpenMPI module automatically.<br />
* To ensure successful parallel runs, it is necessary to call ORCA with the full path, i.e. '$ORCA_BIN_DIR/orca <input_file>' <br />
* Due to potential large I/O operations, especially for post HF methods, it is advisable to place temporary files a local scratch directory.<br>To learn more about local disk space on [https://wiki.bwhpc.de/e/JUSTUS2 JUSTUS 2], please refer to the following [https://wiki.bwhpc.de/e/JUSTUS2/Hardware#.24SCRATCH_and_.24TMPDIR link].<br />
* The most preferable way to load ORCA is with the specific version included, i.e., 'module load chem/orca/<version>'.<br>The default version, which may change over time, can be loaded simply with the command 'module load chem/orca'.<br />
* The module includes the loading of all additional modules, especially an appropriate OpenMPI module in the case of ORCA, necessary for the proper functioning of the program, so there's no need to load additional modules separately. However, loading additional modules may be counterproductive.<br />
<br><br />
----<br />
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Quantum_ESPRESSO&diff=12660JUSTUS2/Software/Quantum ESPRESSO2024-02-29T12:57:39Z<p>J Kucera: </p>
<hr />
<div>{{Softwarepage|chem/quantum_espresso}}<br />
<br />
{| width=760px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/quantum_espresso/7.1<br />
|-<br />
| Availability<br />
| [https://wiki.bwhpc.de/e/JUSTUS2 BwForCluster JUSTUS2] <br />
|-<br />
| License<br />
| Open-source software, distributed under the GNU General Public License (GPL). [[#License|More...]]<br />
|-<br />
| Citing <br />
| As described [https://www.quantum-espresso.org/quote/ here]<br />
|-<br />
| Links<br />
| [https://www.quantum-espresso.org Homepage] &#124; [https://www.quantum-espresso.org/resources/users-manual Documentation] &#124; Main Portal to [https://www.quantum-espresso.org/users-forum/ Forum]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|-<br />
|}<br />
<br />
= Description =<br />
<br />
'''Quantum ESPRESSO''' is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.<br />
<br />
= License =<br />
<br />
Quantum ESPRESSO is free, open-source software released under the GNU General Public License (GPL). Anyone interested in using the Quantum ESPRESSO program suite must read the conditions described in its [https://www.quantum-espresso.org/project/manifesto manifesto].<br />
<br />
= Parallelization = <br />
QUANTUM ESPRESSO utilizes hybrid MPI/OpenMP parallelization. When configuring parallel jobs in the Slurm sbatch script, use appropriate directives such as --nodes, --ntasks-per-node, and --cpus-per-task. It is recommended to conduct benchmarks before submitting a large number of productive jobs.<br />
<br />
QUANTUM ESPRESSO implements several levels of MPI parallelization, distributing both calculations and data structures across processors. These processors are organized hierarchically into different groups identified by various MPI communicators (you might also refer to the following [https://www.quantum-espresso.org/Doc/user_guide/node20.html link]:<br />
<br />
* world: The group of all processors (MPI_COMM_WORLD).<br />
* images: Processors divided into different "images," each corresponding to a distinct self-consistent or linear-response calculation, loosely coupled to others.<br />
* pools: Each image can be subdivided into "pools," each responsible for a group of k-points.<br />
* bands: Each pool is further subdivided into "band groups," each handling a group of Kohn-Sham orbitals, especially useful for calculations with hybrid functionals.<br />
* PW: Orbitals in the PW basis set, charges, and density are distributed across processors. Linear-algebra operations on PW grids are automatically parallelized. 3D FFTs transform electronic wave functions between reciprocal and real space, with planes of the 3D grid distributed in real space to processors.<br />
* tasks: FFTs on Kohn-Sham states are redistributed to "task" groups to allow efficient parallelization of the 3D FFT when the number of processors exceeds the number of FFT planes.<br />
* linear-algebra group: A further level of parallelization involves subspace diagonalization/iterative orthonormalization, organized into a square 2D grid of processors. This group performs parallel diagonalization using standard linear algebra operations. Preferred options include ELPA and ScaLAPACK, with alternative built-in algorithms available.<br />
<br />
It's important to note that not all parallelization levels are implemented in all parts of the code.<br />
----<br />
[[Category:Chemistry software]][[Category:BwForCluster_Chemistry]][[Category:BwForCluster_JUSTUS_2]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Quantum_ESPRESSO&diff=12659JUSTUS2/Software/Quantum ESPRESSO2024-02-29T12:57:12Z<p>J Kucera: </p>
<hr />
<div>{{Softwarepage|chem/quantum_espresso}}<br />
<br />
{| width=760px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/quantum_espresso/7.1<br />
|-<br />
| Availability<br />
| [https://wiki.bwhpc.de/e/JUSTUS2 BwForCluster JUSTUS2] <br />
|-<br />
| License<br />
| Open-source software, distributed under the GNU General Public License (GPL). [[#License|More...]]<br />
|-<br />
| Citing <br />
| As described [https://www.quantum-espresso.org/quote/ here]<br />
|-<br />
| Links<br />
| [https://www.quantum-espresso.org Homepage] &#124; [https://www.quantum-espresso.org/resources/users-manual Documentation] &#124; Main Portal to [https://www.quantum-espresso.org/users-forum/ Forum]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|-<br />
|}<br />
<br />
= Description =<br />
<br />
'''Quantum ESPRESSO''' is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.<br />
<br />
= Availability =<br />
<br />
Quantum ESPRESSO is available on [https://wiki.bwhpc.de/e/JUSTUS2 JUSTUS 2].<br />
<br />
In order to check which versions of Quantum ESPRESSO are installed on the compute cluster, run the following command:<br />
<pre><br />
$ module avail chem/quantum_espresso<br />
</pre><br />
<br />
<pre><br />
-----------------------------------------------------------/opt/bwhpc/common/modulefiles/Core ---------------------------------------------------------------<br />
chem/quantum_espresso/6.5 chem/quantum_espresso/6.7_openmp-5 chem/quantum_espresso/6.7 chem/quantum_espresso/7.0 (D) chem/quantum_espresso/7.1<br />
</pre><br />
<br />
= License =<br />
<br />
Quantum ESPRESSO is free, open-source software released under the GNU General Public License (GPL). Anyone interested in using the Quantum ESPRESSO program suite must read the conditions described in its [https://www.quantum-espresso.org/project/manifesto manifesto].<br />
<br />
= Parallelization = <br />
QUANTUM ESPRESSO utilizes hybrid MPI/OpenMP parallelization. When configuring parallel jobs in the Slurm sbatch script, use appropriate directives such as --nodes, --ntasks-per-node, and --cpus-per-task. It is recommended to conduct benchmarks before submitting a large number of productive jobs.<br />
<br />
QUANTUM ESPRESSO implements several levels of MPI parallelization, distributing both calculations and data structures across processors. These processors are organized hierarchically into different groups identified by various MPI communicators (you might also refer to the following [https://www.quantum-espresso.org/Doc/user_guide/node20.html link]:<br />
<br />
* world: The group of all processors (MPI_COMM_WORLD).<br />
* images: Processors divided into different "images," each corresponding to a distinct self-consistent or linear-response calculation, loosely coupled to others.<br />
* pools: Each image can be subdivided into "pools," each responsible for a group of k-points.<br />
* bands: Each pool is further subdivided into "band groups," each handling a group of Kohn-Sham orbitals, especially useful for calculations with hybrid functionals.<br />
* PW: Orbitals in the PW basis set, charges, and density are distributed across processors. Linear-algebra operations on PW grids are automatically parallelized. 3D FFTs transform electronic wave functions between reciprocal and real space, with planes of the 3D grid distributed in real space to processors.<br />
* tasks: FFTs on Kohn-Sham states are redistributed to "task" groups to allow efficient parallelization of the 3D FFT when the number of processors exceeds the number of FFT planes.<br />
* linear-algebra group: A further level of parallelization involves subspace diagonalization/iterative orthonormalization, organized into a square 2D grid of processors. This group performs parallel diagonalization using standard linear algebra operations. Preferred options include ELPA and ScaLAPACK, with alternative built-in algorithms available.<br />
<br />
It's important to note that not all parallelization levels are implemented in all parts of the code.<br />
----<br />
[[Category:Chemistry software]][[Category:BwForCluster_Chemistry]][[Category:BwForCluster_JUSTUS_2]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Orca&diff=12658JUSTUS2/Software/Orca2024-02-29T12:55:44Z<p>J Kucera: /* Miscellaneous Notes to Usage */</p>
<hr />
<div>{{Softwarepage|chem/orca}}<br />
<br />
{| width=600px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/orca/5.0.4<br />
|-<br />
| Availability<br />
| [[bwUniCluster]] &#124; [[JUSTUS2]]<br />
|-<br />
| License<br />
| [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA]<br />
|-<br />
|Citing<br />
| As described in the [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf manual]. Refer to Chapter 'Publications Related to ORCA' for guidance on citation.<br />
|-<br />
| Links<br />
| [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Forum Portal] &#124; [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|}<br />
<br><br />
= Description =<br />
<br />
'''ORCA''' is a comprehensive, fully parallelized quantum chemistry package designed for advanced electronic structure methods. It encompasses density functional theory, many-body perturbation theory, coupled cluster methods, multireference methods, and semi-empirical quantum chemistry approaches. ORCA is capable of computing a wide range of molecular properties and serves as a fully integrated system for multi-level calculations, including QM/MM, ONIOM, and embedded crystals.<br />
<br />
Additionally, ORCA offers several advanced features to improve computational efficiency and accuracy. These include local correlation methods, starting with PNOs and expanded to DLPNO to reduce the computational cost of coupled cluster calculations. It also incorporates RIJCOSX for efficient handling of Hartree-Fock based methods.<br />
<br />
Furthermore, ORCA provides NEB-TS for studying reaction pathways and offers various methods for accurately calculating excited states, such as TD-DFT, EOM-CCSD, STEOM-CCSD, CASSCF with NEVPT2 or CASPT2, as well as molecular dynamics and multi-scale QM-MM models.<br />
<br />
Please refer to documentation provided by the ORCA developers in the first place for more detailed information, e.g.: <br />
<br />
[https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Orca Manual 5.0.4]<br />
<br><br />
[https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wcms.1606 Article Overview by Frank Nesse]<br />
<br><br />
[https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.81 Article about main improvement in the version 5.0]<br />
<br />
<br><br />
<br />
== Miscellaneous Notes to Usage == <br />
* ORCA utilizes MPI parallelization, specifically backed by OpenMPI. When configuring parallel jobs in the Slurm sbatch script, use appropriate directives such as --nodes and --ntasks-per-node.<br>Avoid using the --cpus-per-task directive. All the ORCA modules load the appropriate OpenMPI module automatically.<br />
* To ensure successful parallel runs, it is necessary to call ORCA with the full path, i.e. '$ORCA_BIN_DIR/orca <input_file>' <br />
* Due to potential large I/O operations, especially for post HF methods, it is advisable to place temporary files a local scratch directory.<br>To learn more about local disk space on [https://wiki.bwhpc.de/e/JUSTUS2 JUSTUS 2], please refer to the following [https://wiki.bwhpc.de/e/JUSTUS2/Hardware#.24SCRATCH_and_.24TMPDIR link].<br />
* The most preferable way to load ORCA is with the specific version included, i.e., 'module load chem/orca/<version>'.<br>The default version, which may change over time, can be loaded simply with the command 'module load chem/orca'.<br />
* The module includes the loading of all additional modules, especially an appropriate OpenMPI module in the case of ORCA, necessary for the proper functioning of the program, so there's no need to load additional modules separately. However, loading additional modules may be counterproductive.<br />
<br><br />
----<br />
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Orca&diff=12657JUSTUS2/Software/Orca2024-02-29T12:55:09Z<p>J Kucera: /* Miscellaneous Notes to Usage */</p>
<hr />
<div>{{Softwarepage|chem/orca}}<br />
<br />
{| width=600px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/orca/5.0.4<br />
|-<br />
| Availability<br />
| [[bwUniCluster]] &#124; [[JUSTUS2]]<br />
|-<br />
| License<br />
| [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA]<br />
|-<br />
|Citing<br />
| As described in the [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf manual]. Refer to Chapter 'Publications Related to ORCA' for guidance on citation.<br />
|-<br />
| Links<br />
| [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Forum Portal] &#124; [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|}<br />
<br><br />
= Description =<br />
<br />
'''ORCA''' is a comprehensive, fully parallelized quantum chemistry package designed for advanced electronic structure methods. It encompasses density functional theory, many-body perturbation theory, coupled cluster methods, multireference methods, and semi-empirical quantum chemistry approaches. ORCA is capable of computing a wide range of molecular properties and serves as a fully integrated system for multi-level calculations, including QM/MM, ONIOM, and embedded crystals.<br />
<br />
Additionally, ORCA offers several advanced features to improve computational efficiency and accuracy. These include local correlation methods, starting with PNOs and expanded to DLPNO to reduce the computational cost of coupled cluster calculations. It also incorporates RIJCOSX for efficient handling of Hartree-Fock based methods.<br />
<br />
Furthermore, ORCA provides NEB-TS for studying reaction pathways and offers various methods for accurately calculating excited states, such as TD-DFT, EOM-CCSD, STEOM-CCSD, CASSCF with NEVPT2 or CASPT2, as well as molecular dynamics and multi-scale QM-MM models.<br />
<br />
Please refer to documentation provided by the ORCA developers in the first place for more detailed information, e.g.: <br />
<br />
[https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Orca Manual 5.0.4]<br />
<br><br />
[https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wcms.1606 Article Overview by Frank Nesse]<br />
<br><br />
[https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.81 Article about main improvement in the version 5.0]<br />
<br />
<br><br />
<br />
== Miscellaneous Notes to Usage == <br />
* ORCA utilizes MPI parallelization, specifically backed by OpenMPI. When configuring parallel jobs in the Slurm sbatch script, use appropriate directives such as --nodes and --ntasks-per-node.<br>Avoid using the --cpus-per-task directive. All the ORCA modules (accessible via 'module avail orca') automatically load the appropriate OpenMPI module.<br />
* To ensure successful parallel runs, it is necessary to call ORCA with the full path, i.e. '$ORCA_BIN_DIR/orca <input_file>' <br />
* Due to potential large I/O operations, especially for post HF methods, it is advisable to place temporary files a local scratch directory.<br>To learn more about local disk space on [https://wiki.bwhpc.de/e/JUSTUS2 JUSTUS 2], please refer to the following [https://wiki.bwhpc.de/e/JUSTUS2/Hardware#.24SCRATCH_and_.24TMPDIR link].<br />
* The most preferable way to load ORCA is with the specific version included, i.e., 'module load chem/orca/<version>'.<br>The default version, which may change over time, can be loaded simply with the command 'module load chem/orca'.<br />
* The module includes the loading of all additional modules, especially an appropriate OpenMPI module in the case of ORCA, necessary for the proper functioning of the program, so there's no need to load additional modules separately. However, loading additional modules may be counterproductive.<br />
<br><br />
----<br />
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Orca&diff=12656JUSTUS2/Software/Orca2024-02-29T12:54:07Z<p>J Kucera: </p>
<hr />
<div>{{Softwarepage|chem/orca}}<br />
<br />
{| width=600px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/orca/5.0.4<br />
|-<br />
| Availability<br />
| [[bwUniCluster]] &#124; [[JUSTUS2]]<br />
|-<br />
| License<br />
| [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA]<br />
|-<br />
|Citing<br />
| As described in the [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf manual]. Refer to Chapter 'Publications Related to ORCA' for guidance on citation.<br />
|-<br />
| Links<br />
| [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Forum Portal] &#124; [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|}<br />
<br><br />
= Description =<br />
<br />
'''ORCA''' is a comprehensive, fully parallelized quantum chemistry package designed for advanced electronic structure methods. It encompasses density functional theory, many-body perturbation theory, coupled cluster methods, multireference methods, and semi-empirical quantum chemistry approaches. ORCA is capable of computing a wide range of molecular properties and serves as a fully integrated system for multi-level calculations, including QM/MM, ONIOM, and embedded crystals.<br />
<br />
Additionally, ORCA offers several advanced features to improve computational efficiency and accuracy. These include local correlation methods, starting with PNOs and expanded to DLPNO to reduce the computational cost of coupled cluster calculations. It also incorporates RIJCOSX for efficient handling of Hartree-Fock based methods.<br />
<br />
Furthermore, ORCA provides NEB-TS for studying reaction pathways and offers various methods for accurately calculating excited states, such as TD-DFT, EOM-CCSD, STEOM-CCSD, CASSCF with NEVPT2 or CASPT2, as well as molecular dynamics and multi-scale QM-MM models.<br />
<br />
Please refer to documentation provided by the ORCA developers in the first place for more detailed information, e.g.: <br />
<br />
[https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Orca Manual 5.0.4]<br />
<br><br />
[https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wcms.1606 Article Overview by Frank Nesse]<br />
<br><br />
[https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.81 Article about main improvement in the version 5.0]<br />
<br />
<br><br />
<br />
== Miscellaneous Notes to Usage == <br />
* ORCA utilizes MPI parallelization, specifically backed by OpenMPI. When configuring parallel jobs in the Slurm sbatch script, use appropriate directives such as --nodes and --ntasks-per-node.<br>Avoid using the --cpus-per-task directive.<br />
* To ensure successful parallel runs, it is necessary to call ORCA with the full path, i.e. '$ORCA_BIN_DIR/orca <input_file>'<br />
* The ORCA module (accessible via 'module avail orca') automatically loads the appropriate OpenMPI module.<br />
* Due to potential large I/O operations, especially for post HF methods, it is advisable to place temporary files a local scratch directory.<br>To learn more about local disk space on [https://wiki.bwhpc.de/e/JUSTUS2 JUSTUS 2], please refer to the following [https://wiki.bwhpc.de/e/JUSTUS2/Hardware#.24SCRATCH_and_.24TMPDIR link].<br />
* The most preferable way to load ORCA is with the specific version included, i.e., 'module load chem/orca/<version>'.<br>The default version, which may change over time, can be loaded simply with the command 'module load chem/orca'.<br />
* The module includes the loading of all additional modules, especially an appropriate OpenMPI module in the case of ORCA, necessary for the proper functioning of the program, so there's no need to load additional modules separately. However, loading additional modules may be counterproductive.<br />
<br><br />
----<br />
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Orca&diff=12655JUSTUS2/Software/Orca2024-02-29T12:53:41Z<p>J Kucera: </p>
<hr />
<div>{{Softwarepage|chem/orca}}<br />
<br />
{| width=600px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/orca/5.0.4<br />
|-<br />
| Availability<br />
| [[bwUniCluster]] &#124; [[JUSTUS2]]<br />
|-<br />
| License<br />
| [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA]<br />
|-<br />
|Citing<br />
| As described in the [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf manual]. Refer to Chapter 'Publications Related to ORCA' for guidance on citation.<br />
|-<br />
| Links<br />
| [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Forum Portal] &#124; [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|}<br />
<br><br />
= Description =<br />
<br />
'''ORCA''' is a comprehensive, fully parallelized quantum chemistry package designed for advanced electronic structure methods. It encompasses density functional theory, many-body perturbation theory, coupled cluster methods, multireference methods, and semi-empirical quantum chemistry approaches. ORCA is capable of computing a wide range of molecular properties and serves as a fully integrated system for multi-level calculations, including QM/MM, ONIOM, and embedded crystals.<br />
<br />
Additionally, ORCA offers several advanced features to improve computational efficiency and accuracy. These include local correlation methods, starting with PNOs and expanded to DLPNO to reduce the computational cost of coupled cluster calculations. It also incorporates RIJCOSX for efficient handling of Hartree-Fock based methods.<br />
<br />
Furthermore, ORCA provides NEB-TS for studying reaction pathways and offers various methods for accurately calculating excited states, such as TD-DFT, EOM-CCSD, STEOM-CCSD, CASSCF with NEVPT2 or CASPT2, as well as molecular dynamics and multi-scale QM-MM models.<br />
<br />
Please refer to documentation provided by the ORCA developers in the first place for more detailed information, e.g.: <br />
<br />
[https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Orca Manual 5.0.4]<br />
<br><br />
[https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wcms.1606 Article Overview by Frank Nesse]<br />
<br><br />
[https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.81 Article about main improvement in the version 5.0]<br />
<br />
<br><br />
<br />
= Versions and Availability =<br />
<br />
On the command line interface of any bwHPC cluster you'll get a list of available versions by using<br />
the command<br />
<br><br />
''''module avail chem/orca''''.<br />
<pre><br />
$ module avail chem/orca # JUSTUS 2<br />
------------------------------ ----------------/opt/bwhpc/common/modulefiles/Core --------------------------------------------------------<br />
chem/orca/4.2.1-xtb-6.3.3 chem/orca/5.0.1-xtb-6.4.1 chem/orca/5.0.2 chem/orca/5.0.3 chem/orca/5.0.4 (D)<br />
chem/orca/4.2.1 chem/orca/5.0.1 chem/orca/5.0.3-xtb-6.5.1 chem/orca/5.0.4_xtb-6.6.0<br />
</pre><br />
<br><br />
<br />
== Miscellaneous Notes to Usage == <br />
* ORCA utilizes MPI parallelization, specifically backed by OpenMPI. When configuring parallel jobs in the Slurm sbatch script, use appropriate directives such as --nodes and --ntasks-per-node.<br>Avoid using the --cpus-per-task directive.<br />
* To ensure successful parallel runs, it is necessary to call ORCA with the full path, i.e. '$ORCA_BIN_DIR/orca <input_file>'<br />
* The ORCA module (accessible via 'module avail orca') automatically loads the appropriate OpenMPI module.<br />
* Due to potential large I/O operations, especially for post HF methods, it is advisable to place temporary files a local scratch directory.<br>To learn more about local disk space on [https://wiki.bwhpc.de/e/JUSTUS2 JUSTUS 2], please refer to the following [https://wiki.bwhpc.de/e/JUSTUS2/Hardware#.24SCRATCH_and_.24TMPDIR link].<br />
* The most preferable way to load ORCA is with the specific version included, i.e., 'module load chem/orca/<version>'.<br>The default version, which may change over time, can be loaded simply with the command 'module load chem/orca'.<br />
* The module includes the loading of all additional modules, especially an appropriate OpenMPI module in the case of ORCA, necessary for the proper functioning of the program, so there's no need to load additional modules separately. However, loading additional modules may be counterproductive.<br />
<br><br />
----<br />
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Quantum_ESPRESSO&diff=12654JUSTUS2/Software/Quantum ESPRESSO2024-02-29T09:33:32Z<p>J Kucera: /* Parallelization */</p>
<hr />
<div>{{Softwarepage|chem/quantum_espresso}}<br />
<br />
{| width=760px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/quantum_espresso/7.1<br />
|-<br />
| Availability<br />
| [https://wiki.bwhpc.de/e/JUSTUS2 BwForCluster JUSTUS2] <br />
|-<br />
| License<br />
| Open-source software, distributed under the GNU General Public License (GPL). [[#License|More...]]<br />
|-<br />
| Citing <br />
| As described [https://www.quantum-espresso.org/quote/ here]<br />
|-<br />
| Links<br />
| [https://www.quantum-espresso.org Homepage] &#124; [https://www.quantum-espresso.org/resources/users-manual Documentation] &#124; Main Portal to [https://www.quantum-espresso.org/users-forum/ Forum]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|-<br />
|}<br />
<br />
= Description =<br />
<br />
'''Quantum ESPRESSO''' is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.<br />
<br />
= Availability =<br />
<br />
Quantum ESPRESSO is available on [https://wiki.bwhpc.de/e/JUSTUS2 JUSTUS 2].<br />
<br />
In order to check which versions of Quantum ESPRESSO are installed on the compute cluster, run the following command:<br />
<pre><br />
$ module avail chem/quantum_espresso<br />
</pre><br />
<br />
<pre><br />
-----------------------------------------------------------/opt/bwhpc/common/modulefiles/Core ---------------------------------------------------------------<br />
chem/quantum_espresso/6.5 chem/quantum_espresso/6.7_openmp-5 chem/quantum_espresso/6.7 chem/quantum_espresso/7.0 (D) chem/quantum_espresso/7.1<br />
</pre><br />
<br />
= License =<br />
<br />
Quantum ESPRESSO is free, open-source software released under the GNU General Public License (GPL). Anyone interested in using the Quantum ESPRESSO program suite must read the conditions described in its [https://www.quantum-espresso.org/project/manifesto manifesto].<br />
<br />
= Usage =<br />
== Loading the module ==<br />
<br />
The most preferable way to load Quantum Espresso (QE) is with the specific version included, i.e., 'module load chem/quantum_espresso/<version>'. <br />
<br />
<pre><br />
$ module load chem/quantum_espresso/7.1<br />
</pre><br />
<br />
<br />
The default version, which may change over time, can be loaded simply with the command 'module load chem/quantum_espresso'.<br />
The module includes the loading of all additional modules necessary for the proper functioning of the program, so there's no need to load additional modules separately. However, loading additional modules may be counterproductive.<br />
<br />
<br />
== Parallelization == <br />
QUANTUM ESPRESSO utilizes hybrid MPI/OpenMP parallelization. When configuring parallel jobs in the Slurm sbatch script, use appropriate directives such as --nodes, --ntasks-per-node, and --cpus-per-task. It is recommended to conduct benchmarks before submitting a large number of productive jobs.<br />
<br />
QUANTUM ESPRESSO implements several levels of MPI parallelization, distributing both calculations and data structures across processors. These processors are organized hierarchically into different groups identified by various MPI communicators (you might also refer to the following [https://www.quantum-espresso.org/Doc/user_guide/node20.html link]:<br />
<br />
* world: The group of all processors (MPI_COMM_WORLD).<br />
* images: Processors divided into different "images," each corresponding to a distinct self-consistent or linear-response calculation, loosely coupled to others.<br />
* pools: Each image can be subdivided into "pools," each responsible for a group of k-points.<br />
* bands: Each pool is further subdivided into "band groups," each handling a group of Kohn-Sham orbitals, especially useful for calculations with hybrid functionals.<br />
* PW: Orbitals in the PW basis set, charges, and density are distributed across processors. Linear-algebra operations on PW grids are automatically parallelized. 3D FFTs transform electronic wave functions between reciprocal and real space, with planes of the 3D grid distributed in real space to processors.<br />
* tasks: FFTs on Kohn-Sham states are redistributed to "task" groups to allow efficient parallelization of the 3D FFT when the number of processors exceeds the number of FFT planes.<br />
* linear-algebra group: A further level of parallelization involves subspace diagonalization/iterative orthonormalization, organized into a square 2D grid of processors. This group performs parallel diagonalization using standard linear algebra operations. Preferred options include ELPA and ScaLAPACK, with alternative built-in algorithms available.<br />
<br />
It's important to note that not all parallelization levels are implemented in all parts of the code.<br />
<br />
== Example Script ==<br />
<br />
A working example of the submission script for a parallel QE job is available, after loading the module, at $ESPRESSO_EXA_DIR/slurm_quantum_espresso-example.sbatch file.<br />
----<br />
[[Category:Chemistry software]][[Category:BwForCluster_Chemistry]][[Category:BwForCluster_JUSTUS_2]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Quantum_ESPRESSO&diff=12653JUSTUS2/Software/Quantum ESPRESSO2024-02-29T09:31:50Z<p>J Kucera: /* Parallelization */</p>
<hr />
<div>{{Softwarepage|chem/quantum_espresso}}<br />
<br />
{| width=760px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/quantum_espresso/7.1<br />
|-<br />
| Availability<br />
| [https://wiki.bwhpc.de/e/JUSTUS2 BwForCluster JUSTUS2] <br />
|-<br />
| License<br />
| Open-source software, distributed under the GNU General Public License (GPL). [[#License|More...]]<br />
|-<br />
| Citing <br />
| As described [https://www.quantum-espresso.org/quote/ here]<br />
|-<br />
| Links<br />
| [https://www.quantum-espresso.org Homepage] &#124; [https://www.quantum-espresso.org/resources/users-manual Documentation] &#124; Main Portal to [https://www.quantum-espresso.org/users-forum/ Forum]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|-<br />
|}<br />
<br />
= Description =<br />
<br />
'''Quantum ESPRESSO''' is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.<br />
<br />
= Availability =<br />
<br />
Quantum ESPRESSO is available on [https://wiki.bwhpc.de/e/JUSTUS2 JUSTUS 2].<br />
<br />
In order to check which versions of Quantum ESPRESSO are installed on the compute cluster, run the following command:<br />
<pre><br />
$ module avail chem/quantum_espresso<br />
</pre><br />
<br />
<pre><br />
-----------------------------------------------------------/opt/bwhpc/common/modulefiles/Core ---------------------------------------------------------------<br />
chem/quantum_espresso/6.5 chem/quantum_espresso/6.7_openmp-5 chem/quantum_espresso/6.7 chem/quantum_espresso/7.0 (D) chem/quantum_espresso/7.1<br />
</pre><br />
<br />
= License =<br />
<br />
Quantum ESPRESSO is free, open-source software released under the GNU General Public License (GPL). Anyone interested in using the Quantum ESPRESSO program suite must read the conditions described in its [https://www.quantum-espresso.org/project/manifesto manifesto].<br />
<br />
= Usage =<br />
== Loading the module ==<br />
<br />
The most preferable way to load Quantum Espresso (QE) is with the specific version included, i.e., 'module load chem/quantum_espresso/<version>'. <br />
<br />
<pre><br />
$ module load chem/quantum_espresso/7.1<br />
</pre><br />
<br />
<br />
The default version, which may change over time, can be loaded simply with the command 'module load chem/quantum_espresso'.<br />
The module includes the loading of all additional modules necessary for the proper functioning of the program, so there's no need to load additional modules separately. However, loading additional modules may be counterproductive.<br />
<br />
<br />
== Parallelization == <br />
QUANTUM ESPRESSO utilizes hybrid MPI/OpenMP parallelization. When configuring parallel jobs in the Slurm sbatch script, use appropriate directives such as --nodes, --ntasks-per-node, and --cpus-per-task. It is recommended to conduct benchmarks before submitting a large number of productive jobs.<br />
<br />
QUANTUM ESPRESSO implements several levels of MPI parallelization, distributing both calculations and data structures across processors. These processors are organized hierarchically into different groups identified by various MPI communicators:<br />
<br />
* world: The group of all processors (MPI_COMM_WORLD).<br />
* images: Processors divided into different "images," each corresponding to a distinct self-consistent or linear-response calculation, loosely coupled to others.<br />
* pools: Each image can be subdivided into "pools," each responsible for a group of k-points.<br />
* bands: Each pool is further subdivided into "band groups," each handling a group of Kohn-Sham orbitals, especially useful for calculations with hybrid functionals.<br />
* PW: Orbitals in the PW basis set, charges, and density are distributed across processors. Linear-algebra operations on PW grids are automatically parallelized. 3D FFTs transform electronic wave functions between reciprocal and real space, with planes of the 3D grid distributed in real space to processors.<br />
* tasks: FFTs on Kohn-Sham states are redistributed to "task" groups to allow efficient parallelization of the 3D FFT when the number of processors exceeds the number of FFT planes.<br />
* linear-algebra group: A further level of parallelization involves subspace diagonalization/iterative orthonormalization, organized into a square 2D grid of processors. This group performs parallel diagonalization using standard linear algebra operations. Preferred options include ELPA and ScaLAPACK, with alternative built-in algorithms available.<br />
<br />
It's important to note that not all parallelization levels are implemented in all parts of the code.<br />
<br />
== Example Script ==<br />
<br />
A working example of the submission script for a parallel QE job is available, after loading the module, at $ESPRESSO_EXA_DIR/slurm_quantum_espresso-example.sbatch file.<br />
----<br />
[[Category:Chemistry software]][[Category:BwForCluster_Chemistry]][[Category:BwForCluster_JUSTUS_2]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Quantum_ESPRESSO&diff=12652JUSTUS2/Software/Quantum ESPRESSO2024-02-29T09:31:20Z<p>J Kucera: /* Parallelization */</p>
<hr />
<div>{{Softwarepage|chem/quantum_espresso}}<br />
<br />
{| width=760px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/quantum_espresso/7.1<br />
|-<br />
| Availability<br />
| [https://wiki.bwhpc.de/e/JUSTUS2 BwForCluster JUSTUS2] <br />
|-<br />
| License<br />
| Open-source software, distributed under the GNU General Public License (GPL). [[#License|More...]]<br />
|-<br />
| Citing <br />
| As described [https://www.quantum-espresso.org/quote/ here]<br />
|-<br />
| Links<br />
| [https://www.quantum-espresso.org Homepage] &#124; [https://www.quantum-espresso.org/resources/users-manual Documentation] &#124; Main Portal to [https://www.quantum-espresso.org/users-forum/ Forum]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|-<br />
|}<br />
<br />
= Description =<br />
<br />
'''Quantum ESPRESSO''' is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.<br />
<br />
= Availability =<br />
<br />
Quantum ESPRESSO is available on [https://wiki.bwhpc.de/e/JUSTUS2 JUSTUS 2].<br />
<br />
In order to check which versions of Quantum ESPRESSO are installed on the compute cluster, run the following command:<br />
<pre><br />
$ module avail chem/quantum_espresso<br />
</pre><br />
<br />
<pre><br />
-----------------------------------------------------------/opt/bwhpc/common/modulefiles/Core ---------------------------------------------------------------<br />
chem/quantum_espresso/6.5 chem/quantum_espresso/6.7_openmp-5 chem/quantum_espresso/6.7 chem/quantum_espresso/7.0 (D) chem/quantum_espresso/7.1<br />
</pre><br />
<br />
= License =<br />
<br />
Quantum ESPRESSO is free, open-source software released under the GNU General Public License (GPL). Anyone interested in using the Quantum ESPRESSO program suite must read the conditions described in its [https://www.quantum-espresso.org/project/manifesto manifesto].<br />
<br />
= Usage =<br />
== Loading the module ==<br />
<br />
The most preferable way to load Quantum Espresso (QE) is with the specific version included, i.e., 'module load chem/quantum_espresso/<version>'. <br />
<br />
<pre><br />
$ module load chem/quantum_espresso/7.1<br />
</pre><br />
<br />
<br />
The default version, which may change over time, can be loaded simply with the command 'module load chem/quantum_espresso'.<br />
The module includes the loading of all additional modules necessary for the proper functioning of the program, so there's no need to load additional modules separately. However, loading additional modules may be counterproductive.<br />
<br />
<br />
== Parallelization == <br />
QUANTUM ESPRESSO utilizes hybrid MPI/OpenMP parallelization. When configuring parallel jobs in the Slurm sbatch script, use appropriate directives such as --nodes, --ntasks-per-node, and --cpus-per-task. It is recommended to conduct benchmarks before submitting a large number of productive jobs.<br />
<br />
QUANTUM ESPRESSO implements several levels of MPI parallelization, distributing both calculations and data structures across processors. These processors are organized hierarchically into different groups identified by various MPI communicators:<br />
<br />
* world: The group of all processors (MPI_COMM_WORLD).<br />
* images: Processors divided into different "images," each corresponding to a distinct self-consistent or linear-response calculation, loosely coupled to others.<br />
* pools: Each image can be subdivided into "pools," each responsible for a group of k-points.<br />
* bands: Each pool is further subdivided into "band groups," each handling a group of Kohn-Sham orbitals, especially useful for calculations with hybrid functionals.<br />
* PW: Orbitals in the PW basis set, charges, and density are distributed across processors. Linear-algebra operations on PW grids are automatically parallelized. 3D FFTs transform electronic wave functions between reciprocal and real space, with planes of the 3D grid distributed in real space to processors.<br />
* tasks: FFTs on Kohn-Sham states are redistributed to "task" groups to allow efficient parallelization of the 3D FFT when the number of processors exceeds the number of FFT planes.<br />
* linear-algebra group: A further level of parallelization involves subspace diagonalization/iterative orthonormalization, organized into a square 2D grid of processors. This group performs parallel diagonalization using standard linear algebra operations. Preferred options include ELPA and ScaLAPACK, with alternative built-in algorithms available.<br />
<br />
It's important to note that not all parallelization levels are implemented in all parts of the code.<br />
<br />
== Example Script ==<br />
<br />
A working example of the submission script for a parallel QE job is available, after loading the module, at $ESPRESSO_EXA_DIR/slurm_quantum_espresso-example.sbatch file.<br />
----<br />
[[Category:Chemistry software]][[Category:BwForCluster_Chemistry]][[Category:BwForCluster_JUSTUS_2]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Quantum_ESPRESSO&diff=12651JUSTUS2/Software/Quantum ESPRESSO2024-02-29T09:30:40Z<p>J Kucera: /* Loading the module */</p>
<hr />
<div>{{Softwarepage|chem/quantum_espresso}}<br />
<br />
{| width=760px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/quantum_espresso/7.1<br />
|-<br />
| Availability<br />
| [https://wiki.bwhpc.de/e/JUSTUS2 BwForCluster JUSTUS2] <br />
|-<br />
| License<br />
| Open-source software, distributed under the GNU General Public License (GPL). [[#License|More...]]<br />
|-<br />
| Citing <br />
| As described [https://www.quantum-espresso.org/quote/ here]<br />
|-<br />
| Links<br />
| [https://www.quantum-espresso.org Homepage] &#124; [https://www.quantum-espresso.org/resources/users-manual Documentation] &#124; Main Portal to [https://www.quantum-espresso.org/users-forum/ Forum]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|-<br />
|}<br />
<br />
= Description =<br />
<br />
'''Quantum ESPRESSO''' is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.<br />
<br />
= Availability =<br />
<br />
Quantum ESPRESSO is available on [https://wiki.bwhpc.de/e/JUSTUS2 JUSTUS 2].<br />
<br />
In order to check which versions of Quantum ESPRESSO are installed on the compute cluster, run the following command:<br />
<pre><br />
$ module avail chem/quantum_espresso<br />
</pre><br />
<br />
<pre><br />
-----------------------------------------------------------/opt/bwhpc/common/modulefiles/Core ---------------------------------------------------------------<br />
chem/quantum_espresso/6.5 chem/quantum_espresso/6.7_openmp-5 chem/quantum_espresso/6.7 chem/quantum_espresso/7.0 (D) chem/quantum_espresso/7.1<br />
</pre><br />
<br />
= License =<br />
<br />
Quantum ESPRESSO is free, open-source software released under the GNU General Public License (GPL). Anyone interested in using the Quantum ESPRESSO program suite must read the conditions described in its [https://www.quantum-espresso.org/project/manifesto manifesto].<br />
<br />
= Usage =<br />
== Loading the module ==<br />
<br />
The most preferable way to load Quantum Espresso (QE) is with the specific version included, i.e., 'module load chem/quantum_espresso/<version>'. <br />
<br />
<pre><br />
$ module load chem/quantum_espresso/7.1<br />
</pre><br />
<br />
<br />
The default version, which may change over time, can be loaded simply with the command 'module load chem/quantum_espresso'.<br />
The module includes the loading of all additional modules necessary for the proper functioning of the program, so there's no need to load additional modules separately. However, loading additional modules may be counterproductive.<br />
<br />
<br />
== Parallelization == <br />
QUANTUM ESPRESSO utilizes hybrid MPI/OpenMP parallelization. When configuring parallel jobs in the Slurm sbatch script, use appropriate directives such as --nodes, --ntasks-per-node, and --cpus-per-task. It is recommended to conduct benchmarks before submitting a large number of productive jobs.<br />
<br />
QUANTUM ESPRESSO implements several levels of MPI parallelization, distributing both calculations and data structures across processors. These processors are organized hierarchically into different groups identified by various MPI communicators:<br />
<br />
world: The group of all processors (MPI_COMM_WORLD).<br />
images: Processors divided into different "images," each corresponding to a distinct self-consistent or linear-response calculation, loosely coupled to others.<br />
pools: Each image can be subdivided into "pools," each responsible for a group of k-points.<br />
bands: Each pool is further subdivided into "band groups," each handling a group of Kohn-Sham orbitals, especially useful for calculations with hybrid functionals.<br />
PW: Orbitals in the PW basis set, charges, and density are distributed across processors. Linear-algebra operations on PW grids are automatically parallelized. 3D FFTs transform electronic wave functions between reciprocal and real space, with planes of the 3D grid distributed in real space to processors.<br />
tasks: FFTs on Kohn-Sham states are redistributed to "task" groups to allow efficient parallelization of the 3D FFT when the number of processors exceeds the number of FFT planes.<br />
linear-algebra group: A further level of parallelization involves subspace diagonalization/iterative orthonormalization, organized into a square 2D grid of processors. This group performs parallel diagonalization using standard linear algebra operations. Preferred options include ELPA and ScaLAPACK, with alternative built-in algorithms available.<br />
<br />
It's important to note that not all parallelization levels are implemented in all parts of the code.<br />
<br />
== Example Script ==<br />
<br />
A working example of the submission script for a parallel QE job is available, after loading the module, at $ESPRESSO_EXA_DIR/slurm_quantum_espresso-example.sbatch file.<br />
----<br />
[[Category:Chemistry software]][[Category:BwForCluster_Chemistry]][[Category:BwForCluster_JUSTUS_2]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Quantum_ESPRESSO&diff=12650JUSTUS2/Software/Quantum ESPRESSO2024-02-29T09:11:35Z<p>J Kucera: /* Availability */</p>
<hr />
<div>{{Softwarepage|chem/quantum_espresso}}<br />
<br />
{| width=760px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/quantum_espresso/7.1<br />
|-<br />
| Availability<br />
| [https://wiki.bwhpc.de/e/JUSTUS2 BwForCluster JUSTUS2] <br />
|-<br />
| License<br />
| Open-source software, distributed under the GNU General Public License (GPL). [[#License|More...]]<br />
|-<br />
| Citing <br />
| As described [https://www.quantum-espresso.org/quote/ here]<br />
|-<br />
| Links<br />
| [https://www.quantum-espresso.org Homepage] &#124; [https://www.quantum-espresso.org/resources/users-manual Documentation] &#124; Main Portal to [https://www.quantum-espresso.org/users-forum/ Forum]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|-<br />
|}<br />
<br />
= Description =<br />
<br />
'''Quantum ESPRESSO''' is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.<br />
<br />
= Availability =<br />
<br />
Quantum ESPRESSO is available on [https://wiki.bwhpc.de/e/JUSTUS2 JUSTUS 2].<br />
<br />
In order to check which versions of Quantum ESPRESSO are installed on the compute cluster, run the following command:<br />
<pre><br />
$ module avail chem/quantum_espresso<br />
</pre><br />
<br />
<pre><br />
-----------------------------------------------------------/opt/bwhpc/common/modulefiles/Core ---------------------------------------------------------------<br />
chem/quantum_espresso/6.5 chem/quantum_espresso/6.7_openmp-5 chem/quantum_espresso/6.7 chem/quantum_espresso/7.0 (D) chem/quantum_espresso/7.1<br />
</pre><br />
<br />
= License =<br />
<br />
Quantum ESPRESSO is free, open-source software released under the GNU General Public License (GPL). Anyone interested in using the Quantum ESPRESSO program suite must read the conditions described in its [https://www.quantum-espresso.org/project/manifesto manifesto].<br />
<br />
= Usage =<br />
== Loading the module ==<br />
<br />
The most preferable way to load Quantum Espresso (QE) is with the specific version included, i.e., 'module load chem/quantum_espresso/<version>'. <br />
<br />
<pre><br />
$ module load chem/quantum_espresso/7.1<br />
</pre><br />
<br />
<br />
The default version, which may change over time, can be loaded simply with the command 'module load chem/quantum_espresso'.<br />
The module includes the loading of all additional modules necessary for the proper functioning of the program, so there's no need to load additional modules separately. However, loading additional modules may be counterproductive.<br />
<br />
== Example Script ==<br />
<br />
A working example of the submission script for a parallel QE job is available, after loading the module, at $ESPRESSO_EXA_DIR/slurm_quantum_espresso-example.sbatch file.<br />
----<br />
[[Category:Chemistry software]][[Category:BwForCluster_Chemistry]][[Category:BwForCluster_JUSTUS_2]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Quantum_ESPRESSO&diff=12649JUSTUS2/Software/Quantum ESPRESSO2024-02-29T09:11:15Z<p>J Kucera: /* Availability */</p>
<hr />
<div>{{Softwarepage|chem/quantum_espresso}}<br />
<br />
{| width=760px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/quantum_espresso/7.1<br />
|-<br />
| Availability<br />
| [https://wiki.bwhpc.de/e/JUSTUS2 BwForCluster JUSTUS2] <br />
|-<br />
| License<br />
| Open-source software, distributed under the GNU General Public License (GPL). [[#License|More...]]<br />
|-<br />
| Citing <br />
| As described [https://www.quantum-espresso.org/quote/ here]<br />
|-<br />
| Links<br />
| [https://www.quantum-espresso.org Homepage] &#124; [https://www.quantum-espresso.org/resources/users-manual Documentation] &#124; Main Portal to [https://www.quantum-espresso.org/users-forum/ Forum]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|-<br />
|}<br />
<br />
= Description =<br />
<br />
'''Quantum ESPRESSO''' is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.<br />
<br />
= Availability =<br />
<br />
Quantum ESPRESSO is available on [https://wiki.bwhpc.de/e/JUSTUS2 JUSTUS 2].<br />
<br />
In order to check which versions of Quantum ESPRESSO are installed on the compute cluster, run the following command:<br />
<pre><br />
$ module avail chem/quantum_espresso<br />
</pre><br />
<br />
<pre><br />
-----------------------------------------------------------/opt/bwhpc/common/modulefiles/Core ---------------------------------------------------------------<br />
chem/quantum_espresso/6.5 chem/quantum_espresso/6.7_openmp-5 chem/quantum_espresso/6.7 chem/quantum_espresso/7.0 (D) chem/quantum_espresso/7.1<br />
<pre><br />
<br />
= License =<br />
<br />
Quantum ESPRESSO is free, open-source software released under the GNU General Public License (GPL). Anyone interested in using the Quantum ESPRESSO program suite must read the conditions described in its [https://www.quantum-espresso.org/project/manifesto manifesto].<br />
<br />
= Usage =<br />
== Loading the module ==<br />
<br />
The most preferable way to load Quantum Espresso (QE) is with the specific version included, i.e., 'module load chem/quantum_espresso/<version>'. <br />
<br />
<pre><br />
$ module load chem/quantum_espresso/7.1<br />
</pre><br />
<br />
<br />
The default version, which may change over time, can be loaded simply with the command 'module load chem/quantum_espresso'.<br />
The module includes the loading of all additional modules necessary for the proper functioning of the program, so there's no need to load additional modules separately. However, loading additional modules may be counterproductive.<br />
<br />
== Example Script ==<br />
<br />
A working example of the submission script for a parallel QE job is available, after loading the module, at $ESPRESSO_EXA_DIR/slurm_quantum_espresso-example.sbatch file.<br />
----<br />
[[Category:Chemistry software]][[Category:BwForCluster_Chemistry]][[Category:BwForCluster_JUSTUS_2]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Orca&diff=12648JUSTUS2/Software/Orca2024-02-29T09:07:29Z<p>J Kucera: /* Usage */</p>
<hr />
<div>{{Softwarepage|chem/orca}}<br />
<br />
{| width=600px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/orca/5.0.4<br />
|-<br />
| Availability<br />
| [[bwUniCluster]] &#124; [[JUSTUS2]]<br />
|-<br />
| License<br />
| [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA]<br />
|-<br />
|Citing<br />
| As described in the [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf manual]. Refer to Chapter 'Publications Related to ORCA' for guidance on citation.<br />
|-<br />
| Links<br />
| [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Forum Portal] &#124; [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|}<br />
<br><br />
= Description =<br />
<br />
'''ORCA''' is a comprehensive, fully parallelized quantum chemistry package designed for advanced electronic structure methods. It encompasses density functional theory, many-body perturbation theory, coupled cluster methods, multireference methods, and semi-empirical quantum chemistry approaches. ORCA is capable of computing a wide range of molecular properties and serves as a fully integrated system for multi-level calculations, including QM/MM, ONIOM, and embedded crystals.<br />
<br />
Additionally, ORCA offers several advanced features to improve computational efficiency and accuracy. These include local correlation methods, starting with PNOs and expanded to DLPNO to reduce the computational cost of coupled cluster calculations. It also incorporates RIJCOSX for efficient handling of Hartree-Fock based methods.<br />
<br />
Furthermore, ORCA provides NEB-TS for studying reaction pathways and offers various methods for accurately calculating excited states, such as TD-DFT, EOM-CCSD, STEOM-CCSD, CASSCF with NEVPT2 or CASPT2, as well as molecular dynamics and multi-scale QM-MM models.<br />
<br />
Please refer to documentation provided by the ORCA developers in the first place for more detailed information, e.g.: <br />
<br />
[https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Orca Manual 5.0.4]<br />
<br><br />
[https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wcms.1606 Article Overview by Frank Nesse]<br />
<br><br />
[https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.81 Article about main improvement in the version 5.0]<br />
<br />
<br><br />
<br />
= Versions and Availability =<br />
<br />
On the command line interface of any bwHPC cluster you'll get a list of available versions by using<br />
the command<br />
<br><br />
''''module avail chem/orca''''.<br />
<pre><br />
$ module avail chem/orca # JUSTUS 2<br />
------------------------------ ----------------/opt/bwhpc/common/modulefiles/Core --------------------------------------------------------<br />
chem/orca/4.2.1-xtb-6.3.3 chem/orca/5.0.1-xtb-6.4.1 chem/orca/5.0.2 chem/orca/5.0.3 chem/orca/5.0.4 (D)<br />
chem/orca/4.2.1 chem/orca/5.0.1 chem/orca/5.0.3-xtb-6.5.1 chem/orca/5.0.4_xtb-6.6.0<br />
</pre><br />
<br><br />
<br />
= Usage =<br />
== Loading the module ==<br />
<br />
The most preferable way to load ORCA is with the specific version included, i.e., 'module load chem/orca/<version>'. <br />
<br />
<pre><br />
$ module load chem/orca/5.0.4<br />
</pre><br />
<br />
<br />
The default version, which may change over time, can be loaded simply with the command 'module load chem/orca'.<br />
<br><br />
The module includes the loading of all additional modules, especially an appropriate OpenMPI module in the case of ORCA, necessary for the proper functioning of the program, so there's no need to load additional modules separately. However, loading additional modules may be counterproductive.<br />
<br />
== Example Script ==<br />
<br />
A working example of the submission script for a parallel ORCA job is available, after loading the module, at $ORCA_EXA_DIR/slurm_orca_example.sbatch file.<br />
<br><br />
<br><br />
<br />
== Parallelization ==<br />
ORCA utilizes MPI parallelization, specifically backed by OpenMPI. When configuring parallel jobs in the Slurm sbatch script, use appropriate directives such as --nodes and --ntasks-per-node.<br>Avoid using the --cpus-per-task directive.<br />
<br><br />
<br><br />
== Miscellaneous ==<br />
* To ensure successful parallel runs, it is necessary to call ORCA with the full path, i.e. '$ORCA_BIN_DIR/orca <input_file>'<br />
* The ORCA module (accessible via 'module avail orca') automatically loads the appropriate OpenMPI module.<br />
* Due to potential large I/O operations, especially for post HF methods, it is advisable to place temporary files a local scratch directory.<br>To learn more about local disk space on [https://wiki.bwhpc.de/e/JUSTUS2 JUSTUS 2], please refer to the following [https://wiki.bwhpc.de/e/JUSTUS2/Hardware#.24SCRATCH_and_.24TMPDIR link].<br />
<br><br />
----<br />
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Orca&diff=12647JUSTUS2/Software/Orca2024-02-29T08:57:57Z<p>J Kucera: /* Miscellaneous */</p>
<hr />
<div>{{Softwarepage|chem/orca}}<br />
<br />
{| width=600px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/orca/5.0.4<br />
|-<br />
| Availability<br />
| [[bwUniCluster]] &#124; [[JUSTUS2]]<br />
|-<br />
| License<br />
| [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA]<br />
|-<br />
|Citing<br />
| As described in the [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf manual]. Refer to Chapter 'Publications Related to ORCA' for guidance on citation.<br />
|-<br />
| Links<br />
| [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Forum Portal] &#124; [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|}<br />
<br><br />
= Description =<br />
<br />
'''ORCA''' is a comprehensive, fully parallelized quantum chemistry package designed for advanced electronic structure methods. It encompasses density functional theory, many-body perturbation theory, coupled cluster methods, multireference methods, and semi-empirical quantum chemistry approaches. ORCA is capable of computing a wide range of molecular properties and serves as a fully integrated system for multi-level calculations, including QM/MM, ONIOM, and embedded crystals.<br />
<br />
Additionally, ORCA offers several advanced features to improve computational efficiency and accuracy. These include local correlation methods, starting with PNOs and expanded to DLPNO to reduce the computational cost of coupled cluster calculations. It also incorporates RIJCOSX for efficient handling of Hartree-Fock based methods.<br />
<br />
Furthermore, ORCA provides NEB-TS for studying reaction pathways and offers various methods for accurately calculating excited states, such as TD-DFT, EOM-CCSD, STEOM-CCSD, CASSCF with NEVPT2 or CASPT2, as well as molecular dynamics and multi-scale QM-MM models.<br />
<br />
Please refer to documentation provided by the ORCA developers in the first place for more detailed information, e.g.: <br />
<br />
[https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Orca Manual 5.0.4]<br />
<br><br />
[https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wcms.1606 Article Overview by Frank Nesse]<br />
<br><br />
[https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.81 Article about main improvement in the version 5.0]<br />
<br />
<br><br />
<br />
= Versions and Availability =<br />
<br />
On the command line interface of any bwHPC cluster you'll get a list of available versions by using<br />
the command<br />
<br><br />
''''module avail chem/orca''''.<br />
<pre><br />
$ module avail chem/orca # JUSTUS 2<br />
------------------------------ ----------------/opt/bwhpc/common/modulefiles/Core --------------------------------------------------------<br />
chem/orca/4.2.1-xtb-6.3.3 chem/orca/5.0.1-xtb-6.4.1 chem/orca/5.0.2 chem/orca/5.0.3 chem/orca/5.0.4 (D)<br />
chem/orca/4.2.1 chem/orca/5.0.1 chem/orca/5.0.3-xtb-6.5.1 chem/orca/5.0.4_xtb-6.6.0<br />
</pre><br />
<br><br />
<br />
= Usage =<br />
== Loading the module ==<br />
<br />
The most preferable way to load ORCA is with the specific version included, i.e., 'module load chem/orca/<version>'. <br />
<br />
<pre><br />
$ module load chem/orca/5.0.4<br />
</pre><br />
<br />
<br />
The default version, which may change over time, can be loaded simply with the command 'module load chem/orca'.<br />
<br><br />
The module includes the loading of all additional modules, especially an appropriate OpenMPI module in the case of ORCA, necessary for the proper functioning of the program, so there's no need to load additional modules separately. However, loading additional modules may be counterproductive.<br />
<br />
== Example Script ==<br />
<br />
A working example of the submission script for a parallel ORCA job is available, after loading the module, at $ORCA_EXA_DIR/slurm_orca_example.sbatch file.<br />
<br><br />
<br><br />
<br />
== Miscellaneous ==<br />
* To ensure successful parallel runs, it is necessary to call ORCA with the full path, i.e. '$ORCA_BIN_DIR/orca <input_file>'<br />
* The ORCA module (accessible via 'module avail orca') automatically loads the appropriate OpenMPI module.<br />
* Due to potential large I/O operations, especially for post HF methods, it is advisable to place temporary files a local scratch directory.<br>To learn more about local disk space on [https://wiki.bwhpc.de/e/JUSTUS2 JUSTUS 2], please refer to the following [https://wiki.bwhpc.de/e/JUSTUS2/Hardware#.24SCRATCH_and_.24TMPDIR link].<br />
<br><br />
----<br />
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Orca&diff=12646JUSTUS2/Software/Orca2024-02-29T08:57:38Z<p>J Kucera: /* Miscellaneous */</p>
<hr />
<div>{{Softwarepage|chem/orca}}<br />
<br />
{| width=600px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/orca/5.0.4<br />
|-<br />
| Availability<br />
| [[bwUniCluster]] &#124; [[JUSTUS2]]<br />
|-<br />
| License<br />
| [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA]<br />
|-<br />
|Citing<br />
| As described in the [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf manual]. Refer to Chapter 'Publications Related to ORCA' for guidance on citation.<br />
|-<br />
| Links<br />
| [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Forum Portal] &#124; [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|}<br />
<br><br />
= Description =<br />
<br />
'''ORCA''' is a comprehensive, fully parallelized quantum chemistry package designed for advanced electronic structure methods. It encompasses density functional theory, many-body perturbation theory, coupled cluster methods, multireference methods, and semi-empirical quantum chemistry approaches. ORCA is capable of computing a wide range of molecular properties and serves as a fully integrated system for multi-level calculations, including QM/MM, ONIOM, and embedded crystals.<br />
<br />
Additionally, ORCA offers several advanced features to improve computational efficiency and accuracy. These include local correlation methods, starting with PNOs and expanded to DLPNO to reduce the computational cost of coupled cluster calculations. It also incorporates RIJCOSX for efficient handling of Hartree-Fock based methods.<br />
<br />
Furthermore, ORCA provides NEB-TS for studying reaction pathways and offers various methods for accurately calculating excited states, such as TD-DFT, EOM-CCSD, STEOM-CCSD, CASSCF with NEVPT2 or CASPT2, as well as molecular dynamics and multi-scale QM-MM models.<br />
<br />
Please refer to documentation provided by the ORCA developers in the first place for more detailed information, e.g.: <br />
<br />
[https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Orca Manual 5.0.4]<br />
<br><br />
[https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wcms.1606 Article Overview by Frank Nesse]<br />
<br><br />
[https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.81 Article about main improvement in the version 5.0]<br />
<br />
<br><br />
<br />
= Versions and Availability =<br />
<br />
On the command line interface of any bwHPC cluster you'll get a list of available versions by using<br />
the command<br />
<br><br />
''''module avail chem/orca''''.<br />
<pre><br />
$ module avail chem/orca # JUSTUS 2<br />
------------------------------ ----------------/opt/bwhpc/common/modulefiles/Core --------------------------------------------------------<br />
chem/orca/4.2.1-xtb-6.3.3 chem/orca/5.0.1-xtb-6.4.1 chem/orca/5.0.2 chem/orca/5.0.3 chem/orca/5.0.4 (D)<br />
chem/orca/4.2.1 chem/orca/5.0.1 chem/orca/5.0.3-xtb-6.5.1 chem/orca/5.0.4_xtb-6.6.0<br />
</pre><br />
<br><br />
<br />
= Usage =<br />
== Loading the module ==<br />
<br />
The most preferable way to load ORCA is with the specific version included, i.e., 'module load chem/orca/<version>'. <br />
<br />
<pre><br />
$ module load chem/orca/5.0.4<br />
</pre><br />
<br />
<br />
The default version, which may change over time, can be loaded simply with the command 'module load chem/orca'.<br />
<br><br />
The module includes the loading of all additional modules, especially an appropriate OpenMPI module in the case of ORCA, necessary for the proper functioning of the program, so there's no need to load additional modules separately. However, loading additional modules may be counterproductive.<br />
<br />
== Example Script ==<br />
<br />
A working example of the submission script for a parallel ORCA job is available, after loading the module, at $ORCA_EXA_DIR/slurm_orca_example.sbatch file.<br />
<br><br />
<br><br />
<br />
== Miscellaneous ==<br />
* To ensure successful parallel runs, it is necessary to call ORCA with the full path, i.e. '$ORCA_BIN_DIR/orca <input_file>'<br />
* The ORCA module (accessible via 'module avail orca') automatically loads the appropriate OpenMPI module.<br />
* Due to potential large I/O operations, especially for post HF methods, it is advisable to place temporary files a local scratch directory.<br>To learn more about local disk space on [https://wiki.bwhpc.de/e/JUSTUS2 JUSTUS 2], please refer to the following [https://wiki.bwhpc.de/e/JUSTUS2/Hardware#.24SCRATCH_and_.24TMPDIR link].<br />
----<br />
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Orca&diff=12645JUSTUS2/Software/Orca2024-02-29T08:57:02Z<p>J Kucera: /* Miscellaneous */</p>
<hr />
<div>{{Softwarepage|chem/orca}}<br />
<br />
{| width=600px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/orca/5.0.4<br />
|-<br />
| Availability<br />
| [[bwUniCluster]] &#124; [[JUSTUS2]]<br />
|-<br />
| License<br />
| [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA]<br />
|-<br />
|Citing<br />
| As described in the [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf manual]. Refer to Chapter 'Publications Related to ORCA' for guidance on citation.<br />
|-<br />
| Links<br />
| [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Forum Portal] &#124; [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|}<br />
<br><br />
= Description =<br />
<br />
'''ORCA''' is a comprehensive, fully parallelized quantum chemistry package designed for advanced electronic structure methods. It encompasses density functional theory, many-body perturbation theory, coupled cluster methods, multireference methods, and semi-empirical quantum chemistry approaches. ORCA is capable of computing a wide range of molecular properties and serves as a fully integrated system for multi-level calculations, including QM/MM, ONIOM, and embedded crystals.<br />
<br />
Additionally, ORCA offers several advanced features to improve computational efficiency and accuracy. These include local correlation methods, starting with PNOs and expanded to DLPNO to reduce the computational cost of coupled cluster calculations. It also incorporates RIJCOSX for efficient handling of Hartree-Fock based methods.<br />
<br />
Furthermore, ORCA provides NEB-TS for studying reaction pathways and offers various methods for accurately calculating excited states, such as TD-DFT, EOM-CCSD, STEOM-CCSD, CASSCF with NEVPT2 or CASPT2, as well as molecular dynamics and multi-scale QM-MM models.<br />
<br />
Please refer to documentation provided by the ORCA developers in the first place for more detailed information, e.g.: <br />
<br />
[https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Orca Manual 5.0.4]<br />
<br><br />
[https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wcms.1606 Article Overview by Frank Nesse]<br />
<br><br />
[https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.81 Article about main improvement in the version 5.0]<br />
<br />
<br><br />
<br />
= Versions and Availability =<br />
<br />
On the command line interface of any bwHPC cluster you'll get a list of available versions by using<br />
the command<br />
<br><br />
''''module avail chem/orca''''.<br />
<pre><br />
$ module avail chem/orca # JUSTUS 2<br />
------------------------------ ----------------/opt/bwhpc/common/modulefiles/Core --------------------------------------------------------<br />
chem/orca/4.2.1-xtb-6.3.3 chem/orca/5.0.1-xtb-6.4.1 chem/orca/5.0.2 chem/orca/5.0.3 chem/orca/5.0.4 (D)<br />
chem/orca/4.2.1 chem/orca/5.0.1 chem/orca/5.0.3-xtb-6.5.1 chem/orca/5.0.4_xtb-6.6.0<br />
</pre><br />
<br><br />
<br />
= Usage =<br />
== Loading the module ==<br />
<br />
The most preferable way to load ORCA is with the specific version included, i.e., 'module load chem/orca/<version>'. <br />
<br />
<pre><br />
$ module load chem/orca/5.0.4<br />
</pre><br />
<br />
<br />
The default version, which may change over time, can be loaded simply with the command 'module load chem/orca'.<br />
<br><br />
The module includes the loading of all additional modules, especially an appropriate OpenMPI module in the case of ORCA, necessary for the proper functioning of the program, so there's no need to load additional modules separately. However, loading additional modules may be counterproductive.<br />
<br />
== Example Script ==<br />
<br />
A working example of the submission script for a parallel ORCA job is available, after loading the module, at $ORCA_EXA_DIR/slurm_orca_example.sbatch file.<br />
<br><br />
<br><br />
<br />
== Miscellaneous ==<br />
* To ensure successful parallel runs, it is necessary to call ORCA with the full path, i.e. '$ORCA_BIN_DIR/orca <input_file>'<br />
* The ORCA module (accessible via 'module avail orca') automatically loads the appropriate OpenMPI module.<br />
* Due to potential large I/O operations, especially for post HF methods, it is advisable to place temporary files a local scratch directory. To learn more about local disk space on [https://wiki.bwhpc.de/e/JUSTUS2 JUSTUS 2], please refer to the following [https://wiki.bwhpc.de/e/JUSTUS2/Hardware#.24SCRATCH_and_.24TMPDIR link].<br />
----<br />
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Orca&diff=12644JUSTUS2/Software/Orca2024-02-29T08:56:21Z<p>J Kucera: /* Miscellaneous */</p>
<hr />
<div>{{Softwarepage|chem/orca}}<br />
<br />
{| width=600px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/orca/5.0.4<br />
|-<br />
| Availability<br />
| [[bwUniCluster]] &#124; [[JUSTUS2]]<br />
|-<br />
| License<br />
| [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA]<br />
|-<br />
|Citing<br />
| As described in the [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf manual]. Refer to Chapter 'Publications Related to ORCA' for guidance on citation.<br />
|-<br />
| Links<br />
| [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Forum Portal] &#124; [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|}<br />
<br><br />
= Description =<br />
<br />
'''ORCA''' is a comprehensive, fully parallelized quantum chemistry package designed for advanced electronic structure methods. It encompasses density functional theory, many-body perturbation theory, coupled cluster methods, multireference methods, and semi-empirical quantum chemistry approaches. ORCA is capable of computing a wide range of molecular properties and serves as a fully integrated system for multi-level calculations, including QM/MM, ONIOM, and embedded crystals.<br />
<br />
Additionally, ORCA offers several advanced features to improve computational efficiency and accuracy. These include local correlation methods, starting with PNOs and expanded to DLPNO to reduce the computational cost of coupled cluster calculations. It also incorporates RIJCOSX for efficient handling of Hartree-Fock based methods.<br />
<br />
Furthermore, ORCA provides NEB-TS for studying reaction pathways and offers various methods for accurately calculating excited states, such as TD-DFT, EOM-CCSD, STEOM-CCSD, CASSCF with NEVPT2 or CASPT2, as well as molecular dynamics and multi-scale QM-MM models.<br />
<br />
Please refer to documentation provided by the ORCA developers in the first place for more detailed information, e.g.: <br />
<br />
[https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Orca Manual 5.0.4]<br />
<br><br />
[https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wcms.1606 Article Overview by Frank Nesse]<br />
<br><br />
[https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.81 Article about main improvement in the version 5.0]<br />
<br />
<br><br />
<br />
= Versions and Availability =<br />
<br />
On the command line interface of any bwHPC cluster you'll get a list of available versions by using<br />
the command<br />
<br><br />
''''module avail chem/orca''''.<br />
<pre><br />
$ module avail chem/orca # JUSTUS 2<br />
------------------------------ ----------------/opt/bwhpc/common/modulefiles/Core --------------------------------------------------------<br />
chem/orca/4.2.1-xtb-6.3.3 chem/orca/5.0.1-xtb-6.4.1 chem/orca/5.0.2 chem/orca/5.0.3 chem/orca/5.0.4 (D)<br />
chem/orca/4.2.1 chem/orca/5.0.1 chem/orca/5.0.3-xtb-6.5.1 chem/orca/5.0.4_xtb-6.6.0<br />
</pre><br />
<br><br />
<br />
= Usage =<br />
== Loading the module ==<br />
<br />
The most preferable way to load ORCA is with the specific version included, i.e., 'module load chem/orca/<version>'. <br />
<br />
<pre><br />
$ module load chem/orca/5.0.4<br />
</pre><br />
<br />
<br />
The default version, which may change over time, can be loaded simply with the command 'module load chem/orca'.<br />
<br><br />
The module includes the loading of all additional modules, especially an appropriate OpenMPI module in the case of ORCA, necessary for the proper functioning of the program, so there's no need to load additional modules separately. However, loading additional modules may be counterproductive.<br />
<br />
== Example Script ==<br />
<br />
A working example of the submission script for a parallel ORCA job is available, after loading the module, at $ORCA_EXA_DIR/slurm_orca_example.sbatch file.<br />
<br><br />
<br><br />
<br />
== Miscellaneous ==<br />
* To ensure successful parallel runs, it is necessary to call ORCA with the full path, i.e. '$ORCA_BIN_DIR/orca <input_file>'<br />
* The ORCA module (accessible via 'module avail orca') automatically loads the appropriate OpenMPI module.<br />
* Due to potential large I/O operations, especially for post HF methods, it is advisable to place temporary files a local scratch directory. To learn more about local disk space on the system, please refer to the following [https://wiki.bwhpc.de/e/JUSTUS2/Hardware#.24SCRATCH_and_.24TMPDIR link].<br />
----<br />
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Orca&diff=12643JUSTUS2/Software/Orca2024-02-29T08:56:03Z<p>J Kucera: /* Miscellaneous */</p>
<hr />
<div>{{Softwarepage|chem/orca}}<br />
<br />
{| width=600px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/orca/5.0.4<br />
|-<br />
| Availability<br />
| [[bwUniCluster]] &#124; [[JUSTUS2]]<br />
|-<br />
| License<br />
| [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA]<br />
|-<br />
|Citing<br />
| As described in the [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf manual]. Refer to Chapter 'Publications Related to ORCA' for guidance on citation.<br />
|-<br />
| Links<br />
| [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Forum Portal] &#124; [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|}<br />
<br><br />
= Description =<br />
<br />
'''ORCA''' is a comprehensive, fully parallelized quantum chemistry package designed for advanced electronic structure methods. It encompasses density functional theory, many-body perturbation theory, coupled cluster methods, multireference methods, and semi-empirical quantum chemistry approaches. ORCA is capable of computing a wide range of molecular properties and serves as a fully integrated system for multi-level calculations, including QM/MM, ONIOM, and embedded crystals.<br />
<br />
Additionally, ORCA offers several advanced features to improve computational efficiency and accuracy. These include local correlation methods, starting with PNOs and expanded to DLPNO to reduce the computational cost of coupled cluster calculations. It also incorporates RIJCOSX for efficient handling of Hartree-Fock based methods.<br />
<br />
Furthermore, ORCA provides NEB-TS for studying reaction pathways and offers various methods for accurately calculating excited states, such as TD-DFT, EOM-CCSD, STEOM-CCSD, CASSCF with NEVPT2 or CASPT2, as well as molecular dynamics and multi-scale QM-MM models.<br />
<br />
Please refer to documentation provided by the ORCA developers in the first place for more detailed information, e.g.: <br />
<br />
[https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Orca Manual 5.0.4]<br />
<br><br />
[https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wcms.1606 Article Overview by Frank Nesse]<br />
<br><br />
[https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.81 Article about main improvement in the version 5.0]<br />
<br />
<br><br />
<br />
= Versions and Availability =<br />
<br />
On the command line interface of any bwHPC cluster you'll get a list of available versions by using<br />
the command<br />
<br><br />
''''module avail chem/orca''''.<br />
<pre><br />
$ module avail chem/orca # JUSTUS 2<br />
------------------------------ ----------------/opt/bwhpc/common/modulefiles/Core --------------------------------------------------------<br />
chem/orca/4.2.1-xtb-6.3.3 chem/orca/5.0.1-xtb-6.4.1 chem/orca/5.0.2 chem/orca/5.0.3 chem/orca/5.0.4 (D)<br />
chem/orca/4.2.1 chem/orca/5.0.1 chem/orca/5.0.3-xtb-6.5.1 chem/orca/5.0.4_xtb-6.6.0<br />
</pre><br />
<br><br />
<br />
= Usage =<br />
== Loading the module ==<br />
<br />
The most preferable way to load ORCA is with the specific version included, i.e., 'module load chem/orca/<version>'. <br />
<br />
<pre><br />
$ module load chem/orca/5.0.4<br />
</pre><br />
<br />
<br />
The default version, which may change over time, can be loaded simply with the command 'module load chem/orca'.<br />
<br><br />
The module includes the loading of all additional modules, especially an appropriate OpenMPI module in the case of ORCA, necessary for the proper functioning of the program, so there's no need to load additional modules separately. However, loading additional modules may be counterproductive.<br />
<br />
== Example Script ==<br />
<br />
A working example of the submission script for a parallel ORCA job is available, after loading the module, at $ORCA_EXA_DIR/slurm_orca_example.sbatch file.<br />
<br><br />
<br><br />
<br />
== Miscellaneous ==<br />
* To ensure successful parallel runs, it is necessary to call ORCA with the full path, i.e. '$ORCA_BIN_DIR/orca <input_file>'<br />
* The ORCA module (accessible via 'module avail orca') automatically loads the appropriate OpenMPI module.<br />
* Due to potential large I/O operations, especially for post HF methods, it is advisable to place temporary files a local scratch directory.<br />
To learn more about local disk space on the system, please refer to the following [https://wiki.bwhpc.de/e/JUSTUS2/Hardware#.24SCRATCH_and_.24TMPDIR link].<br />
----<br />
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Orca&diff=12642JUSTUS2/Software/Orca2024-02-29T08:53:19Z<p>J Kucera: /* Miscellaneous */</p>
<hr />
<div>{{Softwarepage|chem/orca}}<br />
<br />
{| width=600px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/orca/5.0.4<br />
|-<br />
| Availability<br />
| [[bwUniCluster]] &#124; [[JUSTUS2]]<br />
|-<br />
| License<br />
| [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA]<br />
|-<br />
|Citing<br />
| As described in the [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf manual]. Refer to Chapter 'Publications Related to ORCA' for guidance on citation.<br />
|-<br />
| Links<br />
| [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Forum Portal] &#124; [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|}<br />
<br><br />
= Description =<br />
<br />
'''ORCA''' is a comprehensive, fully parallelized quantum chemistry package designed for advanced electronic structure methods. It encompasses density functional theory, many-body perturbation theory, coupled cluster methods, multireference methods, and semi-empirical quantum chemistry approaches. ORCA is capable of computing a wide range of molecular properties and serves as a fully integrated system for multi-level calculations, including QM/MM, ONIOM, and embedded crystals.<br />
<br />
Additionally, ORCA offers several advanced features to improve computational efficiency and accuracy. These include local correlation methods, starting with PNOs and expanded to DLPNO to reduce the computational cost of coupled cluster calculations. It also incorporates RIJCOSX for efficient handling of Hartree-Fock based methods.<br />
<br />
Furthermore, ORCA provides NEB-TS for studying reaction pathways and offers various methods for accurately calculating excited states, such as TD-DFT, EOM-CCSD, STEOM-CCSD, CASSCF with NEVPT2 or CASPT2, as well as molecular dynamics and multi-scale QM-MM models.<br />
<br />
Please refer to documentation provided by the ORCA developers in the first place for more detailed information, e.g.: <br />
<br />
[https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Orca Manual 5.0.4]<br />
<br><br />
[https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wcms.1606 Article Overview by Frank Nesse]<br />
<br><br />
[https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.81 Article about main improvement in the version 5.0]<br />
<br />
<br><br />
<br />
= Versions and Availability =<br />
<br />
On the command line interface of any bwHPC cluster you'll get a list of available versions by using<br />
the command<br />
<br><br />
''''module avail chem/orca''''.<br />
<pre><br />
$ module avail chem/orca # JUSTUS 2<br />
------------------------------ ----------------/opt/bwhpc/common/modulefiles/Core --------------------------------------------------------<br />
chem/orca/4.2.1-xtb-6.3.3 chem/orca/5.0.1-xtb-6.4.1 chem/orca/5.0.2 chem/orca/5.0.3 chem/orca/5.0.4 (D)<br />
chem/orca/4.2.1 chem/orca/5.0.1 chem/orca/5.0.3-xtb-6.5.1 chem/orca/5.0.4_xtb-6.6.0<br />
</pre><br />
<br><br />
<br />
= Usage =<br />
== Loading the module ==<br />
<br />
The most preferable way to load ORCA is with the specific version included, i.e., 'module load chem/orca/<version>'. <br />
<br />
<pre><br />
$ module load chem/orca/5.0.4<br />
</pre><br />
<br />
<br />
The default version, which may change over time, can be loaded simply with the command 'module load chem/orca'.<br />
<br><br />
The module includes the loading of all additional modules, especially an appropriate OpenMPI module in the case of ORCA, necessary for the proper functioning of the program, so there's no need to load additional modules separately. However, loading additional modules may be counterproductive.<br />
<br />
== Example Script ==<br />
<br />
A working example of the submission script for a parallel ORCA job is available, after loading the module, at $ORCA_EXA_DIR/slurm_orca_example.sbatch file.<br />
<br><br />
<br><br />
<br />
== Miscellaneous ==<br />
* To ensure successful parallel runs, it is necessary to call ORCA with the full path, i.e. '$ORCA_BIN_DIR/orca <input_file>'<br />
<br><br />
* The ORCA module (accessible via 'module avail orca') automatically loads the appropriate OpenMPI module.<br />
<br><br />
* Due to potential large I/O operations, especially for post HF methods, it is advisable to place temporary files a local scratch directory.<br />
<br />
----<br />
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Orca&diff=12641JUSTUS2/Software/Orca2024-02-29T08:51:39Z<p>J Kucera: </p>
<hr />
<div>{{Softwarepage|chem/orca}}<br />
<br />
{| width=600px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/orca/5.0.4<br />
|-<br />
| Availability<br />
| [[bwUniCluster]] &#124; [[JUSTUS2]]<br />
|-<br />
| License<br />
| [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA]<br />
|-<br />
|Citing<br />
| As described in the [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf manual]. Refer to Chapter 'Publications Related to ORCA' for guidance on citation.<br />
|-<br />
| Links<br />
| [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Forum Portal] &#124; [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|}<br />
<br><br />
= Description =<br />
<br />
'''ORCA''' is a comprehensive, fully parallelized quantum chemistry package designed for advanced electronic structure methods. It encompasses density functional theory, many-body perturbation theory, coupled cluster methods, multireference methods, and semi-empirical quantum chemistry approaches. ORCA is capable of computing a wide range of molecular properties and serves as a fully integrated system for multi-level calculations, including QM/MM, ONIOM, and embedded crystals.<br />
<br />
Additionally, ORCA offers several advanced features to improve computational efficiency and accuracy. These include local correlation methods, starting with PNOs and expanded to DLPNO to reduce the computational cost of coupled cluster calculations. It also incorporates RIJCOSX for efficient handling of Hartree-Fock based methods.<br />
<br />
Furthermore, ORCA provides NEB-TS for studying reaction pathways and offers various methods for accurately calculating excited states, such as TD-DFT, EOM-CCSD, STEOM-CCSD, CASSCF with NEVPT2 or CASPT2, as well as molecular dynamics and multi-scale QM-MM models.<br />
<br />
Please refer to documentation provided by the ORCA developers in the first place for more detailed information, e.g.: <br />
<br />
[https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Orca Manual 5.0.4]<br />
<br><br />
[https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wcms.1606 Article Overview by Frank Nesse]<br />
<br><br />
[https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.81 Article about main improvement in the version 5.0]<br />
<br />
<br><br />
<br />
= Versions and Availability =<br />
<br />
On the command line interface of any bwHPC cluster you'll get a list of available versions by using<br />
the command<br />
<br><br />
''''module avail chem/orca''''.<br />
<pre><br />
$ module avail chem/orca # JUSTUS 2<br />
------------------------------ ----------------/opt/bwhpc/common/modulefiles/Core --------------------------------------------------------<br />
chem/orca/4.2.1-xtb-6.3.3 chem/orca/5.0.1-xtb-6.4.1 chem/orca/5.0.2 chem/orca/5.0.3 chem/orca/5.0.4 (D)<br />
chem/orca/4.2.1 chem/orca/5.0.1 chem/orca/5.0.3-xtb-6.5.1 chem/orca/5.0.4_xtb-6.6.0<br />
</pre><br />
<br><br />
<br />
= Usage =<br />
== Loading the module ==<br />
<br />
The most preferable way to load ORCA is with the specific version included, i.e., 'module load chem/orca/<version>'. <br />
<br />
<pre><br />
$ module load chem/orca/5.0.4<br />
</pre><br />
<br />
<br />
The default version, which may change over time, can be loaded simply with the command 'module load chem/orca'.<br />
<br><br />
The module includes the loading of all additional modules, especially an appropriate OpenMPI module in the case of ORCA, necessary for the proper functioning of the program, so there's no need to load additional modules separately. However, loading additional modules may be counterproductive.<br />
<br />
== Example Script ==<br />
<br />
A working example of the submission script for a parallel ORCA job is available, after loading the module, at $ORCA_EXA_DIR/slurm_orca_example.sbatch file.<br />
<br><br />
<br><br />
<br />
== Miscellaneous ==<br />
To ensure successful parallel runs, it is necessary to call ORCA with the full path, i.e. '$ORCA_BIN_DIR/orca <input_file>'<br />
<br><br />
The ORCA module (accessible via 'module avail orca') automatically loads the appropriate OpenMPI module.<br />
<br><br />
Due to potential large I/O operations, especially for post HF methods, it is advisable to place temporary files a local scratch directory.<br />
<br />
----<br />
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Orca&diff=12640JUSTUS2/Software/Orca2024-02-29T08:45:06Z<p>J Kucera: /* Description */</p>
<hr />
<div>{{Softwarepage|chem/orca}}<br />
<br />
{| width=600px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/orca/5.0.4<br />
|-<br />
| Availability<br />
| [[bwUniCluster]] &#124; [[JUSTUS2]]<br />
|-<br />
| License<br />
| [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA]<br />
|-<br />
|Citing<br />
| As described in the [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf manual]. Refer to Chapter 'Publications Related to ORCA' for guidance on citation.<br />
|-<br />
| Links<br />
| [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Forum Portal] &#124; [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|}<br />
<br><br />
= Description =<br />
<br />
'''ORCA''' is a comprehensive, fully parallelized quantum chemistry package designed for advanced electronic structure methods. It encompasses density functional theory, many-body perturbation theory, coupled cluster methods, multireference methods, and semi-empirical quantum chemistry approaches. ORCA is capable of computing a wide range of molecular properties and serves as a fully integrated system for multi-level calculations, including QM/MM, ONIOM, and embedded crystals.<br />
<br />
Additionally, ORCA offers several advanced features to improve computational efficiency and accuracy. These include local correlation methods, starting with PNOs and expanded to DLPNO to reduce the computational cost of coupled cluster calculations. It also incorporates RIJCOSX for efficient handling of Hartree-Fock based methods.<br />
<br />
Furthermore, ORCA provides NEB-TS for studying reaction pathways and offers various methods for accurately calculating excited states, such as TD-DFT, EOM-CCSD, STEOM-CCSD, CASSCF with NEVPT2 or CASPT2, as well as molecular dynamics and multi-scale QM-MM models.<br />
<br />
Please refer to documentation provided by the ORCA developers in the first place for more detailed information, e.g.: <br />
<br />
[https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Orca Manual 5.0.4]<br />
<br><br />
[https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wcms.1606 Article Overview by Frank Nesse]<br />
<br><br />
[https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.81 Article about main improvement in the version 5.0]<br />
<br />
<br><br />
<br />
= Versions and Availability =<br />
<br />
On the command line interface of any bwHPC cluster you'll get a list of available versions by using<br />
the command<br />
<br><br />
''''module avail chem/orca''''.<br />
<pre><br />
$ module avail chem/orca # JUSTUS 2<br />
------------------------------ ----------------/opt/bwhpc/common/modulefiles/Core --------------------------------------------------------<br />
chem/orca/4.2.1-xtb-6.3.3 chem/orca/5.0.1-xtb-6.4.1 chem/orca/5.0.2 chem/orca/5.0.3 chem/orca/5.0.4 (D)<br />
chem/orca/4.2.1 chem/orca/5.0.1 chem/orca/5.0.3-xtb-6.5.1 chem/orca/5.0.4_xtb-6.6.0<br />
</pre><br />
<br><br />
<br />
= Usage =<br />
== Loading the module ==<br />
<br />
The most preferable way to load ORCA is with the specific version included, i.e., 'module load chem/orca/<version>'. <br />
<br />
<pre><br />
$ module load chem/orca/5.0.4<br />
</pre><br />
<br />
<br />
The default version, which may change over time, can be loaded simply with the command 'module load chem/orca'.<br />
<br><br />
The module includes the loading of all additional modules, especially an appropriate OpenMPI module in the case of ORCA, necessary for the proper functioning of the program, so there's no need to load additional modules separately. However, loading additional modules may be counterproductive.<br />
<br />
== Example Script ==<br />
<br />
A working example of the submission script for a parallel ORCA job is available, after loading the module, at $ORCA_EXA_DIR/slurm_orca_example.sbatch file.<br />
<br><br />
<br><br />
<br />
----<br />
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Orca&diff=12639JUSTUS2/Software/Orca2024-02-29T08:40:47Z<p>J Kucera: /* Loading the module */</p>
<hr />
<div>{{Softwarepage|chem/orca}}<br />
<br />
{| width=600px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/orca/5.0.4<br />
|-<br />
| Availability<br />
| [[bwUniCluster]] &#124; [[JUSTUS2]]<br />
|-<br />
| License<br />
| [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA]<br />
|-<br />
|Citing<br />
| As described in the [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf manual]. Refer to Chapter 'Publications Related to ORCA' for guidance on citation.<br />
|-<br />
| Links<br />
| [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Forum Portal] &#124; [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|}<br />
<br><br />
= Description =<br />
<br />
'''ORCA''' is a comprehensive, fully parallelized quantum chemistry package designed for advanced electronic structure methods. It encompasses density functional theory, many-body perturbation theory, coupled cluster methods, multireference methods, and semi-empirical quantum chemistry approaches. ORCA is capable of computing a wide range of molecular properties and serves as a fully integrated system for multi-level calculations, including QM/MM, ONIOM, and embedded crystals.<br />
<br />
Additionally, ORCA offers several advanced features to improve computational efficiency and accuracy. These include local correlation methods, starting with PNOs and expanded to DLPNO to reduce the computational cost of coupled cluster calculations. It also incorporates RIJCOSX for efficient handling of Hartree-Fock based methods.<br />
<br />
Furthermore, ORCA provides NEB-TS for studying reaction pathways and offers various methods for accurately calculating excited states, such as TD-DFT, EOM-CCSD, STEOM-CCSD, CASSCF with NEVPT2 or CASPT2, as well as molecular dynamics and multi-scale QM-MM models.<br />
<br />
Please refer to documentation provided by the ORCA developers in the first place for more detailed information.<br />
<br />
[https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Orca Manual 5.0.4]<br />
<br><br />
[https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wcms.1606 Article Overview by Frank Nesse]<br />
<br><br />
[https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.81 Article about main improvement in the version 5.0]<br />
<br />
<br><br />
<br />
= Versions and Availability =<br />
<br />
On the command line interface of any bwHPC cluster you'll get a list of available versions by using<br />
the command<br />
<br><br />
''''module avail chem/orca''''.<br />
<pre><br />
$ module avail chem/orca # JUSTUS 2<br />
------------------------------ ----------------/opt/bwhpc/common/modulefiles/Core --------------------------------------------------------<br />
chem/orca/4.2.1-xtb-6.3.3 chem/orca/5.0.1-xtb-6.4.1 chem/orca/5.0.2 chem/orca/5.0.3 chem/orca/5.0.4 (D)<br />
chem/orca/4.2.1 chem/orca/5.0.1 chem/orca/5.0.3-xtb-6.5.1 chem/orca/5.0.4_xtb-6.6.0<br />
</pre><br />
<br><br />
<br />
= Usage =<br />
== Loading the module ==<br />
<br />
The most preferable way to load ORCA is with the specific version included, i.e., 'module load chem/orca/<version>'. <br />
<br />
<pre><br />
$ module load chem/orca/5.0.4<br />
</pre><br />
<br />
<br />
The default version, which may change over time, can be loaded simply with the command 'module load chem/orca'.<br />
<br><br />
The module includes the loading of all additional modules, especially an appropriate OpenMPI module in the case of ORCA, necessary for the proper functioning of the program, so there's no need to load additional modules separately. However, loading additional modules may be counterproductive.<br />
<br />
== Example Script ==<br />
<br />
A working example of the submission script for a parallel ORCA job is available, after loading the module, at $ORCA_EXA_DIR/slurm_orca_example.sbatch file.<br />
<br><br />
<br><br />
<br />
----<br />
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Orca&diff=12638JUSTUS2/Software/Orca2024-02-29T08:37:00Z<p>J Kucera: /* Description */</p>
<hr />
<div>{{Softwarepage|chem/orca}}<br />
<br />
{| width=600px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/orca/5.0.4<br />
|-<br />
| Availability<br />
| [[bwUniCluster]] &#124; [[JUSTUS2]]<br />
|-<br />
| License<br />
| [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA]<br />
|-<br />
|Citing<br />
| As described in the [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf manual]. Refer to Chapter 'Publications Related to ORCA' for guidance on citation.<br />
|-<br />
| Links<br />
| [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Forum Portal] &#124; [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|}<br />
<br><br />
= Description =<br />
<br />
'''ORCA''' is a comprehensive, fully parallelized quantum chemistry package designed for advanced electronic structure methods. It encompasses density functional theory, many-body perturbation theory, coupled cluster methods, multireference methods, and semi-empirical quantum chemistry approaches. ORCA is capable of computing a wide range of molecular properties and serves as a fully integrated system for multi-level calculations, including QM/MM, ONIOM, and embedded crystals.<br />
<br />
Additionally, ORCA offers several advanced features to improve computational efficiency and accuracy. These include local correlation methods, starting with PNOs and expanded to DLPNO to reduce the computational cost of coupled cluster calculations. It also incorporates RIJCOSX for efficient handling of Hartree-Fock based methods.<br />
<br />
Furthermore, ORCA provides NEB-TS for studying reaction pathways and offers various methods for accurately calculating excited states, such as TD-DFT, EOM-CCSD, STEOM-CCSD, CASSCF with NEVPT2 or CASPT2, as well as molecular dynamics and multi-scale QM-MM models.<br />
<br />
Please refer to documentation provided by the ORCA developers in the first place for more detailed information.<br />
<br />
[https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Orca Manual 5.0.4]<br />
<br><br />
[https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wcms.1606 Article Overview by Frank Nesse]<br />
<br><br />
[https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.81 Article about main improvement in the version 5.0]<br />
<br />
<br><br />
<br />
= Versions and Availability =<br />
<br />
On the command line interface of any bwHPC cluster you'll get a list of available versions by using<br />
the command<br />
<br><br />
''''module avail chem/orca''''.<br />
<pre><br />
$ module avail chem/orca # JUSTUS 2<br />
------------------------------ ----------------/opt/bwhpc/common/modulefiles/Core --------------------------------------------------------<br />
chem/orca/4.2.1-xtb-6.3.3 chem/orca/5.0.1-xtb-6.4.1 chem/orca/5.0.2 chem/orca/5.0.3 chem/orca/5.0.4 (D)<br />
chem/orca/4.2.1 chem/orca/5.0.1 chem/orca/5.0.3-xtb-6.5.1 chem/orca/5.0.4_xtb-6.6.0<br />
</pre><br />
<br><br />
<br />
= Usage =<br />
== Loading the module ==<br />
<br />
The most preferable way to load ORCA is with the specific version included, i.e., 'module load chem/orca/<version>'. <br />
<br />
<pre><br />
$ module load chem/orca/5.0.4<br />
</pre><br />
<br />
<br />
The default version, which may change over time, can be loaded simply with the command 'module load chem/orca'.<br />
The module includes the loading of all additional modules necessary for the proper functioning of the program, so there's no need to load additional modules separately. However, loading additional modules may be counterproductive.<br />
<br />
== Example Script ==<br />
<br />
A working example of the submission script for a parallel ORCA job is available, after loading the module, at $ORCA_EXA_DIR/slurm_orca_example.sbatch file.<br />
<br><br />
<br><br />
<br />
----<br />
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Orca&diff=12637JUSTUS2/Software/Orca2024-02-29T08:36:15Z<p>J Kucera: </p>
<hr />
<div>{{Softwarepage|chem/orca}}<br />
<br />
{| width=600px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/orca/5.0.4<br />
|-<br />
| Availability<br />
| [[bwUniCluster]] &#124; [[JUSTUS2]]<br />
|-<br />
| License<br />
| [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA]<br />
|-<br />
|Citing<br />
| As described in the [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf manual]. Refer to Chapter 'Publications Related to ORCA' for guidance on citation.<br />
|-<br />
| Links<br />
| [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Forum Portal] &#124; [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|}<br />
<br><br />
= Description =<br />
<br />
'''ORCA''' is a comprehensive, fully parallelized quantum chemistry package designed for advanced electronic structure methods. It encompasses density functional theory, many-body perturbation theory, coupled cluster methods, multireference methods, and semi-empirical quantum chemistry approaches. ORCA is capable of computing a wide range of molecular properties and serves as a fully integrated system for multi-level calculations, including QM/MM, ONIOM, and embedded crystals.<br />
<br />
Additionally, ORCA offers several advanced features to improve computational efficiency and accuracy. These include local correlation methods, starting with PNOs and expanded to DLPNO to reduce the computational cost of coupled cluster calculations. It also incorporates RIJCOSX for efficient handling of Hartree-Fock based methods.<br />
<br />
Furthermore, ORCA provides NEB-TS for studying reaction pathways and offers various methods for accurately calculating excited states, such as TD-DFT, EOM-CCSD, STEOM-CCSD, CASSCF with NEVPT2 or CASPT2, as well as molecular dynamics and multi-scale QM-MM models.<br />
<br />
Please refer to documentation provided by the ORCA developers in the first place for more detailed information.<br />
<br />
[https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Orca Manual 5.0.4]<br />
[https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wcms.1606 Article Overview by Frank Nesse]<br />
[https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.81 Article about main improvement in the version 5.0]<br />
<br />
<br><br />
<br />
= Versions and Availability =<br />
<br />
On the command line interface of any bwHPC cluster you'll get a list of available versions by using<br />
the command<br />
<br><br />
''''module avail chem/orca''''.<br />
<pre><br />
$ module avail chem/orca # JUSTUS 2<br />
------------------------------ ----------------/opt/bwhpc/common/modulefiles/Core --------------------------------------------------------<br />
chem/orca/4.2.1-xtb-6.3.3 chem/orca/5.0.1-xtb-6.4.1 chem/orca/5.0.2 chem/orca/5.0.3 chem/orca/5.0.4 (D)<br />
chem/orca/4.2.1 chem/orca/5.0.1 chem/orca/5.0.3-xtb-6.5.1 chem/orca/5.0.4_xtb-6.6.0<br />
</pre><br />
<br><br />
<br />
= Usage =<br />
== Loading the module ==<br />
<br />
The most preferable way to load ORCA is with the specific version included, i.e., 'module load chem/orca/<version>'. <br />
<br />
<pre><br />
$ module load chem/orca/5.0.4<br />
</pre><br />
<br />
<br />
The default version, which may change over time, can be loaded simply with the command 'module load chem/orca'.<br />
The module includes the loading of all additional modules necessary for the proper functioning of the program, so there's no need to load additional modules separately. However, loading additional modules may be counterproductive.<br />
<br />
== Example Script ==<br />
<br />
A working example of the submission script for a parallel ORCA job is available, after loading the module, at $ORCA_EXA_DIR/slurm_orca_example.sbatch file.<br />
<br><br />
<br><br />
<br />
----<br />
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Orca&diff=12636JUSTUS2/Software/Orca2024-02-29T08:35:39Z<p>J Kucera: /* Usage */</p>
<hr />
<div>{{Softwarepage|chem/orca}}<br />
<br />
{| width=600px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/orca/5.0.4<br />
|-<br />
| Availability<br />
| [[bwUniCluster]] &#124; [[JUSTUS2]]<br />
|-<br />
| License<br />
| [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA]<br />
|-<br />
|Citing<br />
| As described in the [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf manual]. Refer to Chapter 'Publications Related to ORCA' for guidance on citation.<br />
|-<br />
| Links<br />
| [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Forum Portal] &#124; [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|}<br />
<br><br />
= Description =<br />
<br />
'''ORCA''' is a comprehensive, fully parallelized quantum chemistry package designed for advanced electronic structure methods. It encompasses density functional theory, many-body perturbation theory, coupled cluster methods, multireference methods, and semi-empirical quantum chemistry approaches. ORCA is capable of computing a wide range of molecular properties and serves as a fully integrated system for multi-level calculations, including QM/MM, ONIOM, and embedded crystals.<br />
<br />
Additionally, ORCA offers several advanced features to improve computational efficiency and accuracy. These include local correlation methods, starting with PNOs and expanded to DLPNO to reduce the computational cost of coupled cluster calculations. It also incorporates RIJCOSX for efficient handling of Hartree-Fock based methods.<br />
<br />
Furthermore, ORCA provides NEB-TS for studying reaction pathways and offers various methods for accurately calculating excited states, such as TD-DFT, EOM-CCSD, STEOM-CCSD, CASSCF with NEVPT2 or CASPT2, as well as molecular dynamics and multi-scale QM-MM models.<br />
<br />
Please refer to documentation provided by the ORCA developers in the first place for more detailed information.<br />
<br />
[https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Orca Manual 5.0.4]<br />
[https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wcms.1606 Article Overview by Frank Nesse]<br />
[https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.81 Article about main improvement in the version 5.0]<br />
<br />
<br><br />
<br />
= Versions and Availability =<br />
<br />
On the command line interface of any bwHPC cluster you'll get a list of available versions by using<br />
the command<br />
<br><br />
''''module avail chem/orca''''.<br />
<pre><br />
$ module avail chem/orca # JUSTUS 2<br />
------------------------------ ----------------/opt/bwhpc/common/modulefiles/Core --------------------------------------------------------<br />
chem/orca/4.2.1-xtb-6.3.3 chem/orca/5.0.1-xtb-6.4.1 chem/orca/5.0.2 chem/orca/5.0.3 chem/orca/5.0.4 (D)<br />
chem/orca/4.2.1 chem/orca/5.0.1 chem/orca/5.0.3-xtb-6.5.1 chem/orca/5.0.4_xtb-6.6.0<br />
</pre><br />
<br><br />
<br />
= Usage =<br />
== Loading the module ==<br />
<br />
The most preferable way to load ORCA is with the specific version included, i.e., 'module load chem/orca/<version>'. <br />
<br />
<pre><br />
$ module load chem/orca/5.0.4<br />
</pre><br />
<br />
<br />
The default version, which may change over time, can be loaded simply with the command 'module load chem/orca'.<br />
The module includes the loading of all additional modules necessary for the proper functioning of the program, so there's no need to load additional modules separately. However, loading additional modules may be counterproductive.<br />
<br />
== Example Script ==<br />
<br />
A working example of the submission script for a parallel ORCA job is available, after loading the module, at $ORCA_EXA_DIR/slurm_orca_example.sbatch file.<br />
<br><br />
<br />
----<br />
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Orca&diff=12635JUSTUS2/Software/Orca2024-02-29T08:35:09Z<p>J Kucera: /* Usage */</p>
<hr />
<div>{{Softwarepage|chem/orca}}<br />
<br />
{| width=600px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/orca/5.0.4<br />
|-<br />
| Availability<br />
| [[bwUniCluster]] &#124; [[JUSTUS2]]<br />
|-<br />
| License<br />
| [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA]<br />
|-<br />
|Citing<br />
| As described in the [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf manual]. Refer to Chapter 'Publications Related to ORCA' for guidance on citation.<br />
|-<br />
| Links<br />
| [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Forum Portal] &#124; [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|}<br />
<br><br />
= Description =<br />
<br />
'''ORCA''' is a comprehensive, fully parallelized quantum chemistry package designed for advanced electronic structure methods. It encompasses density functional theory, many-body perturbation theory, coupled cluster methods, multireference methods, and semi-empirical quantum chemistry approaches. ORCA is capable of computing a wide range of molecular properties and serves as a fully integrated system for multi-level calculations, including QM/MM, ONIOM, and embedded crystals.<br />
<br />
Additionally, ORCA offers several advanced features to improve computational efficiency and accuracy. These include local correlation methods, starting with PNOs and expanded to DLPNO to reduce the computational cost of coupled cluster calculations. It also incorporates RIJCOSX for efficient handling of Hartree-Fock based methods.<br />
<br />
Furthermore, ORCA provides NEB-TS for studying reaction pathways and offers various methods for accurately calculating excited states, such as TD-DFT, EOM-CCSD, STEOM-CCSD, CASSCF with NEVPT2 or CASPT2, as well as molecular dynamics and multi-scale QM-MM models.<br />
<br />
Please refer to documentation provided by the ORCA developers in the first place for more detailed information.<br />
<br />
[https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Orca Manual 5.0.4]<br />
[https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wcms.1606 Article Overview by Frank Nesse]<br />
[https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.81 Article about main improvement in the version 5.0]<br />
<br />
<br><br />
<br />
= Versions and Availability =<br />
<br />
On the command line interface of any bwHPC cluster you'll get a list of available versions by using<br />
the command<br />
<br><br />
''''module avail chem/orca''''.<br />
<pre><br />
$ module avail chem/orca # JUSTUS 2<br />
------------------------------ ----------------/opt/bwhpc/common/modulefiles/Core --------------------------------------------------------<br />
chem/orca/4.2.1-xtb-6.3.3 chem/orca/5.0.1-xtb-6.4.1 chem/orca/5.0.2 chem/orca/5.0.3 chem/orca/5.0.4 (D)<br />
chem/orca/4.2.1 chem/orca/5.0.1 chem/orca/5.0.3-xtb-6.5.1 chem/orca/5.0.4_xtb-6.6.0<br />
</pre><br />
<br><br />
<br />
= Usage =<br />
== Loading the module ==<br />
<br />
The most preferable way to load ORCA is with the specific version included, i.e., 'module load chem/orca/<version>'. <br />
<br />
<pre><br />
$ module load chem/orca/5.0.4<br />
</pre><br />
<br />
<br />
The default version, which may change over time, can be loaded simply with the command 'module load chem/orca'.<br />
The module includes the loading of all additional modules necessary for the proper functioning of the program, so there's no need to load additional modules separately. However, loading additional modules may be counterproductive.<br />
<br />
== Example Script ==<br />
<br />
A working example of the submission script for a parallel ORCA job is available, after loading the module, at $ORCA_EXA_DIR/slurm_orca_example.sbatch file.<br />
<br />
----<br />
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Orca&diff=12634JUSTUS2/Software/Orca2024-02-29T08:33:18Z<p>J Kucera: </p>
<hr />
<div>{{Softwarepage|chem/orca}}<br />
<br />
{| width=600px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/orca/5.0.4<br />
|-<br />
| Availability<br />
| [[bwUniCluster]] &#124; [[JUSTUS2]]<br />
|-<br />
| License<br />
| [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA]<br />
|-<br />
|Citing<br />
| As described in the [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf manual]. Refer to Chapter 'Publications Related to ORCA' for guidance on citation.<br />
|-<br />
| Links<br />
| [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Forum Portal] &#124; [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|}<br />
<br><br />
= Description =<br />
<br />
'''ORCA''' is a comprehensive, fully parallelized quantum chemistry package designed for advanced electronic structure methods. It encompasses density functional theory, many-body perturbation theory, coupled cluster methods, multireference methods, and semi-empirical quantum chemistry approaches. ORCA is capable of computing a wide range of molecular properties and serves as a fully integrated system for multi-level calculations, including QM/MM, ONIOM, and embedded crystals.<br />
<br />
Additionally, ORCA offers several advanced features to improve computational efficiency and accuracy. These include local correlation methods, starting with PNOs and expanded to DLPNO to reduce the computational cost of coupled cluster calculations. It also incorporates RIJCOSX for efficient handling of Hartree-Fock based methods.<br />
<br />
Furthermore, ORCA provides NEB-TS for studying reaction pathways and offers various methods for accurately calculating excited states, such as TD-DFT, EOM-CCSD, STEOM-CCSD, CASSCF with NEVPT2 or CASPT2, as well as molecular dynamics and multi-scale QM-MM models.<br />
<br />
Please refer to documentation provided by the ORCA developers in the first place for more detailed information.<br />
<br />
[https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Orca Manual 5.0.4]<br />
[https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wcms.1606 Article Overview by Frank Nesse]<br />
[https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.81 Article about main improvement in the version 5.0]<br />
<br />
<br><br />
<br />
= Versions and Availability =<br />
<br />
On the command line interface of any bwHPC cluster you'll get a list of available versions by using<br />
the command<br />
<br><br />
''''module avail chem/orca''''.<br />
<pre><br />
$ module avail chem/orca # JUSTUS 2<br />
------------------------------ ----------------/opt/bwhpc/common/modulefiles/Core --------------------------------------------------------<br />
chem/orca/4.2.1-xtb-6.3.3 chem/orca/5.0.1-xtb-6.4.1 chem/orca/5.0.2 chem/orca/5.0.3 chem/orca/5.0.4 (D)<br />
chem/orca/4.2.1 chem/orca/5.0.1 chem/orca/5.0.3-xtb-6.5.1 chem/orca/5.0.4_xtb-6.6.0<br />
</pre><br />
<br><br />
<br />
= Usage =<br />
== Loading the module ==<br />
<br />
The most preferable way to load ORCA is with the specific version included, i.e., 'module load chem/orca/<version>'. <br />
<br />
<pre><br />
$ module load chem/orca/5.0.4<br />
</pre><br />
<br />
<br />
The default version, which may change over time, can be loaded simply with the command 'module load chem/orca'.<br />
The module includes the loading of all additional modules necessary for the proper functioning of the program, so there's no need to load additional modules separately. However, loading additional modules may be counterproductive.<br />
<br />
----<br />
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Orca&diff=12633JUSTUS2/Software/Orca2024-02-29T08:32:13Z<p>J Kucera: /* Loading the module */</p>
<hr />
<div>{{Softwarepage|chem/orca}}<br />
<br />
{| width=600px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/orca/5.0.4<br />
|-<br />
| Availability<br />
| [[bwUniCluster]] &#124; [[JUSTUS2]]<br />
|-<br />
| License<br />
| [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA]<br />
|-<br />
|Citing<br />
| As described in the [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf manual]. Refer to Chapter 'Publications Related to ORCA' for guidance on citation.<br />
|-<br />
| Links<br />
| [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Forum Portal] &#124; [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|}<br />
<br><br />
= Description =<br />
<br />
'''ORCA''' is a comprehensive, fully parallelized quantum chemistry package designed for advanced electronic structure methods. It encompasses density functional theory, many-body perturbation theory, coupled cluster methods, multireference methods, and semi-empirical quantum chemistry approaches. ORCA is capable of computing a wide range of molecular properties and serves as a fully integrated system for multi-level calculations, including QM/MM, ONIOM, and embedded crystals.<br />
<br />
Additionally, ORCA offers several advanced features to improve computational efficiency and accuracy. These include local correlation methods, starting with PNOs and expanded to DLPNO to reduce the computational cost of coupled cluster calculations. It also incorporates RIJCOSX for efficient handling of Hartree-Fock based methods.<br />
<br />
Furthermore, ORCA provides NEB-TS for studying reaction pathways and offers various methods for accurately calculating excited states, such as TD-DFT, EOM-CCSD, STEOM-CCSD, CASSCF with NEVPT2 or CASPT2, as well as molecular dynamics and multi-scale QM-MM models.<br />
<br />
Please refer to documentation provided by the ORCA developers in the first place for more detailed information.<br />
<br />
[https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Orca Manual 5.0.4]<br />
[https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wcms.1606 Article Overview by Frank Nesse]<br />
[https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.81 Article about main improvement in the version 5.0]<br />
<br />
<br><br />
<br />
= Versions and Availability =<br />
<br />
On the command line interface of any bwHPC cluster you'll get a list of available versions by using<br />
the command<br />
<br><br />
''''module avail chem/orca''''.<br />
<pre><br />
$ module avail chem/orca # JUSTUS 2<br />
------------------------------ ----------------/opt/bwhpc/common/modulefiles/Core --------------------------------------------------------<br />
chem/orca/4.2.1-xtb-6.3.3 chem/orca/5.0.1-xtb-6.4.1 chem/orca/5.0.2 chem/orca/5.0.3 chem/orca/5.0.4 (D)<br />
chem/orca/4.2.1 chem/orca/5.0.1 chem/orca/5.0.3-xtb-6.5.1 chem/orca/5.0.4_xtb-6.6.0<br />
</pre><br />
<br><br />
<br />
= Usage =<br />
== Loading the module ==<br />
<br />
The most preferable way to load ORCA is with the specific version included, i.e., 'module load chem/orca/<version>'. <br />
<br />
<pre><br />
$ module load chem/orca/5.0.4<br />
</pre><br />
<br />
<br />
The default version, which may change over time, can be loaded simply with the command 'module load chem/orca'.<br />
The module includes the loading of all additional modules necessary for the proper functioning of the program, so there's no need to load additional modules separately. However, loading additional modules may be counterproductive.<br />
<br />
== Program Binaries ==<br />
You can find the ORCA binaries in the main folder of the ORCA system.<br />
<br><br />
After loading the ORCA module (''module load chem/orca/'version''') this path is also set to the local $PATH- and [[#ORCA-Specific Environments|$ORCA_BIN_DIR environments]].<br />
<pre><br />
$ ls -x $ORCA_BIN_DIR<br />
bwhpc-examples manual modulefiles orca orca_2aim orca_2mkl<br />
orca_anoint orca_anoint_mpi orca_asa orca_casscf orca_casscf_mpi orca_chelpg<br />
orca_ciprep orca_cis orca_cis_mpi orca_cleanup orca_cleanup_mpi orca_cpcasscf<br />
orca_cpscf orca_cpscf_mpi orca_eca orca_ecplib orca_eprnmr orca_eprnmr_mpi<br />
orca_euler orca_fci orca_fitpes orca_gstep orca_gtoint orca_gtoint_mpi<br />
orca_loc orca_mapspc orca_md orca_mdci orca_mdci_mpi orca_mergefrag<br />
orca_mp2 orca_mp2_mpi orca_mrci orca_mrci_mpi orca_ndoint orca_numfreq<br />
orca_pc orca_pc_mpi orca_plot orca_pltvib orca_pop orca_rel<br />
orca_rocis orca_rocis_mpi orca_scf orca_scfgrad orca_scfgrad_mpi orca_scfhess<br />
orca_scfhess_mpi orca_scf_mpi orca_soc orca_soc_mpi orca_vib orca_vpot<br />
otool_cosmo otool_gcp otool_smd<br />
$ <br />
</pre><br />
Only the programs with the suffix <font color=green>'''_mpi'''</font> are compiled including OPENMPI functionality.<br />
<br><br />
<br />
== Disk Usage ==<br />
Scratch files are written to the current directory by default.<br><br />
Please change to a local directory or to '''your local workspace''' (preferred) before starting your calculations. <br />
<br><br><br />
'calc_repo' is an example name of a repository you created by using the command 'ws_allocate'.<br />
<pre><br />
$ cd $(ws_find calc_repo)<br />
['your-id'-calc_repo-0]$ pwd<br />
/work/workspace/scratch/'your-id'-calc_repo-0<br />
['your-id'-calc_repo-0]$ <br />
</pre><br />
<br />
== Examples ==<br />
You can copy a simple interactive example to your '''workspace''' and run it, using 'msub'<br />
<pre><br />
$ cd $(ws_find calc_repo)<br />
$ cp $ORCA_EXA_DIR/bwhpc-orca-example.moab .<br />
$ cp bwhpc-orca-example.moab myorcajob.moab <br />
§ vi myorcajob.moab # do your own modifications<br />
$ msub myorcajob.moab # start job submission<br />
</pre><br />
<br><br />
= ORCA-Specific Environments =<br />
To see a list of all ORCA environments set by the 'module load chem/orca/version'-command,<br />
use ''''env | grep ORCA''''<br><br />
Or try the command ''''module show 'chem/orca'''/version'.<br />
<pre><br />
$ module load chem/orca/3.0.3<br />
$ env | grep ORCA<br />
ORCA_VERSION=3.0.3<br />
ORCA_MAN_DIR=/opt/bwhpc/common/chem/orca/3.0.3/manual<br />
ORCA_EXA_DIR=/opt/bwhpc/common/chem/orca/3.0.3/bwhpc-examples<br />
ORCA_BIN_DIR=/opt/bwhpc/common/chem/orca/3.0.3<br />
ORCA_HOME=/opt/bwhpc/common/chem/orca/3.0.3<br />
</pre><br />
<br><br />
= Version-Specific Information =<br />
For a more detailed information specific to a specific ORCA version, see the information available via the module system with the command ''''module help chem/orca''''.<br />
<br><br />
For a small abstract what ORCA is about use the command ''''module whatis chem/orca''''.<br />
<br><br><br />
<u>Examples</u><br />
<pre><br />
$ module avail chem/orca<br />
----------------------- /opt/bwhpc/common/modulefiles ---------------------------<br />
chem/orca/3.0.1 chem/orca/3.0.3<br />
<br />
$ module whatis chem/orca/3.0.1<br />
chem/orca/3.0.1 : Quantum chemistry package ORCA, version 3.0.1<br />
(command '/opt/bwhpc/common/chem/orca/3.0.1/orca')<br />
<br />
$ module help chem/orca/3.0.1<br />
----------- Module Specific Help for 'chem/orca/3.0.1' ------------<br />
This module provides the quantum chemistry package ORCA version 3.0.1<br />
via command '/opt/bwhpc/common/chem/orca/3.0.1/orca' <br />
[...] <br />
Documentation: <br />
* Max-Planck-Institut fuer Chemische Energiekonversion <br />
https://cec.mpg.de/forum/portal.php<br />
* New features for version 3.0.1<br />
https://cec.mpg.de/forum/portal.php#a3<br />
* Manuals in pdf format:<br />
/opt/bwhpc/common/chem/orca/3.0.1/manual<br />
* Example data and a Moab example script can be found here:<br />
/opt/bwhpc/common/chem/orca/3.0.1/bwhpc-examples<br />
[...]<br />
</pre><br />
<br><br />
----<br />
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Quantum_ESPRESSO&diff=12632JUSTUS2/Software/Quantum ESPRESSO2024-02-29T08:28:57Z<p>J Kucera: /* Example Script */</p>
<hr />
<div>{{Softwarepage|chem/quantum_espresso}}<br />
<br />
{| width=760px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/quantum_espresso/7.1<br />
|-<br />
| Availability<br />
| [https://wiki.bwhpc.de/e/JUSTUS2 BwForCluster JUSTUS2] <br />
|-<br />
| License<br />
| Open-source software, distributed under the GNU General Public License (GPL). [[#License|More...]]<br />
|-<br />
| Citing <br />
| As described [https://www.quantum-espresso.org/quote/ here]<br />
|-<br />
| Links<br />
| [https://www.quantum-espresso.org Homepage] &#124; [https://www.quantum-espresso.org/resources/users-manual Documentation] &#124; Main Portal to [https://www.quantum-espresso.org/users-forum/ Forum]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|-<br />
|}<br />
<br />
= Description =<br />
<br />
'''Quantum ESPRESSO''' is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.<br />
<br />
= Availability =<br />
<br />
Quantum ESPRESSO is available on selected bwHPC-Clusters. A complete list of versions currently installed on the bwHPC-Clusters can be obtained from the [https://www.bwhpc.de/software.html Cluster Information System (CIS)].<br />
<br />
In order to check which versions of Quantum ESPRESSO are installed on the compute cluster, run the following command:<br />
<pre><br />
$ module avail chem/quantum_espresso<br />
</pre><br />
<br />
= License =<br />
<br />
Quantum ESPRESSO is free, open-source software released under the GNU General Public License (GPL). Anyone interested in using the Quantum ESPRESSO program suite must read the conditions described in its [https://www.quantum-espresso.org/project/manifesto manifesto].<br />
<br />
= Usage =<br />
== Loading the module ==<br />
<br />
The most preferable way to load Quantum Espresso (QE) is with the specific version included, i.e., 'module load chem/quantum_espresso/<version>'. <br />
<br />
<pre><br />
$ module load chem/quantum_espresso/7.1<br />
</pre><br />
<br />
<br />
The default version, which may change over time, can be loaded simply with the command 'module load chem/quantum_espresso'.<br />
The module includes the loading of all additional modules necessary for the proper functioning of the program, so there's no need to load additional modules separately. However, loading additional modules may be counterproductive.<br />
<br />
== Example Script ==<br />
<br />
A working example of the submission script for a parallel QE job is available, after loading the module, at $ESPRESSO_EXA_DIR/slurm_quantum_espresso-example.sbatch file.<br />
----<br />
[[Category:Chemistry software]][[Category:BwForCluster_Chemistry]][[Category:BwForCluster_JUSTUS_2]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Quantum_ESPRESSO&diff=12631JUSTUS2/Software/Quantum ESPRESSO2024-02-29T08:28:33Z<p>J Kucera: </p>
<hr />
<div>{{Softwarepage|chem/quantum_espresso}}<br />
<br />
{| width=760px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/quantum_espresso/7.1<br />
|-<br />
| Availability<br />
| [https://wiki.bwhpc.de/e/JUSTUS2 BwForCluster JUSTUS2] <br />
|-<br />
| License<br />
| Open-source software, distributed under the GNU General Public License (GPL). [[#License|More...]]<br />
|-<br />
| Citing <br />
| As described [https://www.quantum-espresso.org/quote/ here]<br />
|-<br />
| Links<br />
| [https://www.quantum-espresso.org Homepage] &#124; [https://www.quantum-espresso.org/resources/users-manual Documentation] &#124; Main Portal to [https://www.quantum-espresso.org/users-forum/ Forum]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|-<br />
|}<br />
<br />
= Description =<br />
<br />
'''Quantum ESPRESSO''' is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.<br />
<br />
= Availability =<br />
<br />
Quantum ESPRESSO is available on selected bwHPC-Clusters. A complete list of versions currently installed on the bwHPC-Clusters can be obtained from the [https://www.bwhpc.de/software.html Cluster Information System (CIS)].<br />
<br />
In order to check which versions of Quantum ESPRESSO are installed on the compute cluster, run the following command:<br />
<pre><br />
$ module avail chem/quantum_espresso<br />
</pre><br />
<br />
= License =<br />
<br />
Quantum ESPRESSO is free, open-source software released under the GNU General Public License (GPL). Anyone interested in using the Quantum ESPRESSO program suite must read the conditions described in its [https://www.quantum-espresso.org/project/manifesto manifesto].<br />
<br />
= Usage =<br />
== Loading the module ==<br />
<br />
The most preferable way to load Quantum Espresso (QE) is with the specific version included, i.e., 'module load chem/quantum_espresso/<version>'. <br />
<br />
<pre><br />
$ module load chem/quantum_espresso/7.1<br />
</pre><br />
<br />
<br />
The default version, which may change over time, can be loaded simply with the command 'module load chem/quantum_espresso'.<br />
The module includes the loading of all additional modules necessary for the proper functioning of the program, so there's no need to load additional modules separately. However, loading additional modules may be counterproductive.<br />
<br />
== Example Script ==<br />
<br />
A working example of the submission script for a parallel QE job is available, after loading the module, at $ESPRESSO_EXA_DIR/slurm_quantum_espresso-example.sbatch.<br />
----<br />
[[Category:Chemistry software]][[Category:BwForCluster_Chemistry]][[Category:BwForCluster_JUSTUS_2]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Quantum_ESPRESSO&diff=12630JUSTUS2/Software/Quantum ESPRESSO2024-02-29T08:27:14Z<p>J Kucera: /* Usage */</p>
<hr />
<div>{{Softwarepage|chem/quantum_espresso}}<br />
<br />
{| width=760px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/quantum_espresso/7.1<br />
|-<br />
| Availability<br />
| [https://wiki.bwhpc.de/e/JUSTUS2 BwForCluster JUSTUS2] <br />
|-<br />
| License<br />
| Open-source software, distributed under the GNU General Public License (GPL). [[#License|More...]]<br />
|-<br />
| Citing <br />
| As described [https://www.quantum-espresso.org/quote/ here]<br />
|-<br />
| Links<br />
| [https://www.quantum-espresso.org Homepage] &#124; [https://www.quantum-espresso.org/resources/users-manual Documentation] &#124; Main Portal to [https://www.quantum-espresso.org/users-forum/ Forum]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|-<br />
|}<br />
<br />
= Description =<br />
<br />
'''Quantum ESPRESSO''' is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.<br />
<br />
= Availability =<br />
<br />
Quantum ESPRESSO is available on selected bwHPC-Clusters. A complete list of versions currently installed on the bwHPC-Clusters can be obtained from the [https://www.bwhpc.de/software.html Cluster Information System (CIS)].<br />
<br />
In order to check which versions of Quantum ESPRESSO are installed on the compute cluster, run the following command:<br />
<pre><br />
$ module avail chem/quantum_espresso<br />
</pre><br />
<br />
= License =<br />
<br />
Quantum ESPRESSO is free, open-source software released under the GNU General Public License (GPL). Anyone interested in using the Quantum ESPRESSO program suite must read the conditions described in its [https://www.quantum-espresso.org/project/manifesto manifesto].<br />
<br />
= Usage =<br />
== Loading the module ==<br />
<br />
The most preferable way to load Quantum Espresso (QE) is with the specific version included, i.e., 'module load chem/quantum_espresso/<version>'. <br />
<br />
<pre><br />
$ module load chem/quantum_espresso/7.1<br />
</pre><br />
<br />
<br />
The default version, which may change over time, can be loaded simply with the command 'module load chem/quantum_espresso'.<br />
The module includes the loading of all additional modules necessary for the proper functioning of the program, so there's no need to load additional modules separately. However, loading additional modules may be counterproductive.<br />
<br />
== Example Script ==<br />
<br />
A working example of the submission script for a parallel QE job is available, after loading the module, at $ESPRESSO_EXA_DIR/slurm_quantum_espresso-example.sbatch.<br />
<br />
= Examples =<br />
<br />
As with all processes that require more than a few minutes to run, non-trivial compute jobs must be submitted to the cluster queuing system.<br />
<br />
Example scripts are available in the directory <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">$ESPRESSO_EXA_DIR</span>:<br />
<pre><br />
$ module show chem/quantum_espresso # show environment variables, which will be available after 'module load'<br />
$ module load chem/quantum_espresso # load module<br />
$ ls $ESPRESSO_EXA_DIR # show content of directory $ESPRESSO_EXA_DIR<br />
</pre><br />
<br />
Run a first simple example job on <font color=red>JUSTUS 2</font>:<br />
<pre><br />
$ module load chem/quantum_espresso # load module<br />
$ WORKSPACE=`ws_allocate quantum_espresso 3` # allocate workspace<br />
$ cd $WORKSPACE # change to workspace<br />
$ cp -a $ESPRESSO_HOME/bwhpc-examples . # copy example files to workspace<br />
$ cd bwhpc-examples # change to test directory<br />
$ sbatch bwforcluster-quantum_espresso-example.sbatch # submit job<br />
$ squeue # obtain JOBID<br />
$ scontrol show job <JOBID> # check state of job<br />
$ ls # when job finishes the results will be visible in this directory<br />
</pre><br />
<br />
= Useful links =<br />
<br />
* [https://www.quantum-espresso.org/Doc/user_guide/ Documentation (english)]<br />
* [https://www.quantum-espresso.org/forum Forum (english)]<br />
* [https://www.quantum-espresso.org/resources/tutorials Tutorials (english)]<br />
* [https://en.wikipedia.org/wiki/Quantum_ESPRESSO Wikipedia article (english)]<br />
* [https://www.quantum-espresso.org/resources/tools Plugins for Quantum ESPRESSO (english)]<br />
----<br />
[[Category:Chemistry software]][[Category:BwForCluster_Chemistry]][[Category:BwForCluster_JUSTUS_2]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Quantum_ESPRESSO&diff=12629JUSTUS2/Software/Quantum ESPRESSO2024-02-29T08:22:10Z<p>J Kucera: /* Loading the module */</p>
<hr />
<div>{{Softwarepage|chem/quantum_espresso}}<br />
<br />
{| width=760px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/quantum_espresso/7.1<br />
|-<br />
| Availability<br />
| [https://wiki.bwhpc.de/e/JUSTUS2 BwForCluster JUSTUS2] <br />
|-<br />
| License<br />
| Open-source software, distributed under the GNU General Public License (GPL). [[#License|More...]]<br />
|-<br />
| Citing <br />
| As described [https://www.quantum-espresso.org/quote/ here]<br />
|-<br />
| Links<br />
| [https://www.quantum-espresso.org Homepage] &#124; [https://www.quantum-espresso.org/resources/users-manual Documentation] &#124; Main Portal to [https://www.quantum-espresso.org/users-forum/ Forum]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|-<br />
|}<br />
<br />
= Description =<br />
<br />
'''Quantum ESPRESSO''' is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.<br />
<br />
= Availability =<br />
<br />
Quantum ESPRESSO is available on selected bwHPC-Clusters. A complete list of versions currently installed on the bwHPC-Clusters can be obtained from the [https://www.bwhpc.de/software.html Cluster Information System (CIS)].<br />
<br />
In order to check which versions of Quantum ESPRESSO are installed on the compute cluster, run the following command:<br />
<pre><br />
$ module avail chem/quantum_espresso<br />
</pre><br />
<br />
= License =<br />
<br />
Quantum ESPRESSO is free, open-source software released under the GNU General Public License (GPL). Anyone interested in using the Quantum ESPRESSO program suite must read the conditions described in its [https://www.quantum-espresso.org/project/manifesto manifesto].<br />
<br />
= Usage =<br />
== Loading the module ==<br />
<br />
The most preferable way to load Quantum Espresso (QE) is with the specific version included, i.e., 'module load chem/quantum_espresso/<version>'. <br />
<br />
<pre><br />
$ module load chem/quantum_espresso/7.1<br />
</pre><br />
<br />
<br />
The default version, which may change over time, can be loaded simply with the command 'module load chem/quantum_espresso'.<br />
The module includes the loading of all additional modules necessary for the proper functioning of the program, so there's no need to load additional modules separately. However, loading additional modules may be counterproductive.<br />
<br />
== Program Binaries ==<br />
<br />
All binaries of the Quantum ESPRESSO software package are located in the directory <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">$ESPRESSO_BIN_DIR</span>.<br />
<br />
== Hints for using Quantum ESPRESSO ==<br />
<br />
=== Input Files ===<br />
<br />
For information about how to construct input files for Quantum ESPRESSO, please consult the [https://www.quantum-espresso.org/resources/users-manual/input-data-description documentation].<br />
<br />
=== Disk Usage ===<br />
<br />
Please change to a local directory or to '''your local workspace''' (preferred) before starting your calculations.<br />
<br />
= Examples =<br />
<br />
As with all processes that require more than a few minutes to run, non-trivial compute jobs must be submitted to the cluster queuing system.<br />
<br />
Example scripts are available in the directory <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">$ESPRESSO_EXA_DIR</span>:<br />
<pre><br />
$ module show chem/quantum_espresso # show environment variables, which will be available after 'module load'<br />
$ module load chem/quantum_espresso # load module<br />
$ ls $ESPRESSO_EXA_DIR # show content of directory $ESPRESSO_EXA_DIR<br />
</pre><br />
<br />
Run a first simple example job on <font color=red>JUSTUS 2</font>:<br />
<pre><br />
$ module load chem/quantum_espresso # load module<br />
$ WORKSPACE=`ws_allocate quantum_espresso 3` # allocate workspace<br />
$ cd $WORKSPACE # change to workspace<br />
$ cp -a $ESPRESSO_HOME/bwhpc-examples . # copy example files to workspace<br />
$ cd bwhpc-examples # change to test directory<br />
$ sbatch bwforcluster-quantum_espresso-example.sbatch # submit job<br />
$ squeue # obtain JOBID<br />
$ scontrol show job <JOBID> # check state of job<br />
$ ls # when job finishes the results will be visible in this directory<br />
</pre><br />
<br />
= Useful links =<br />
<br />
* [https://www.quantum-espresso.org/Doc/user_guide/ Documentation (english)]<br />
* [https://www.quantum-espresso.org/forum Forum (english)]<br />
* [https://www.quantum-espresso.org/resources/tutorials Tutorials (english)]<br />
* [https://en.wikipedia.org/wiki/Quantum_ESPRESSO Wikipedia article (english)]<br />
* [https://www.quantum-espresso.org/resources/tools Plugins for Quantum ESPRESSO (english)]<br />
----<br />
[[Category:Chemistry software]][[Category:BwForCluster_Chemistry]][[Category:BwForCluster_JUSTUS_2]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Quantum_ESPRESSO&diff=12628JUSTUS2/Software/Quantum ESPRESSO2024-02-29T08:15:46Z<p>J Kucera: </p>
<hr />
<div>{{Softwarepage|chem/quantum_espresso}}<br />
<br />
{| width=760px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/quantum_espresso/7.1<br />
|-<br />
| Availability<br />
| [https://wiki.bwhpc.de/e/JUSTUS2 BwForCluster JUSTUS2] <br />
|-<br />
| License<br />
| Open-source software, distributed under the GNU General Public License (GPL). [[#License|More...]]<br />
|-<br />
| Citing <br />
| As described [https://www.quantum-espresso.org/quote/ here]<br />
|-<br />
| Links<br />
| [https://www.quantum-espresso.org Homepage] &#124; [https://www.quantum-espresso.org/resources/users-manual Documentation] &#124; Main Portal to [https://www.quantum-espresso.org/users-forum/ Forum]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|-<br />
|}<br />
<br />
= Description =<br />
<br />
'''Quantum ESPRESSO''' is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.<br />
<br />
= Availability =<br />
<br />
Quantum ESPRESSO is available on selected bwHPC-Clusters. A complete list of versions currently installed on the bwHPC-Clusters can be obtained from the [https://www.bwhpc.de/software.html Cluster Information System (CIS)].<br />
<br />
In order to check which versions of Quantum ESPRESSO are installed on the compute cluster, run the following command:<br />
<pre><br />
$ module avail chem/quantum_espresso<br />
</pre><br />
<br />
= License =<br />
<br />
Quantum ESPRESSO is free, open-source software released under the GNU General Public License (GPL). Anyone interested in using the Quantum ESPRESSO program suite must read the conditions described in its [https://www.quantum-espresso.org/project/manifesto manifesto].<br />
<br />
= Usage =<br />
== Loading the module ==<br />
<br />
You can load the default version of Quantum ESPRESSO with the following command:<br />
<pre><br />
$ module load chem/quantum_espresso<br />
</pre><br />
<br />
The module will try to load all modules it needs to function (e.g., compiler, mpi, ...). If loading the module fails, check if you have already loaded one of those modules, but not in the version required by Quantum ESPRESSO.<br />
<br />
If you wish to load another (older) version of Quantum ESPRESSO, you can do so using<br />
<pre><br />
$ module load chem/quantum_espresso/<version><br />
</pre><br />
with <version> specifying the desired version.<br />
<br />
Please cite Quantum ESPRESSO in your publications according to the references.<br />
<br />
== Program Binaries ==<br />
<br />
All binaries of the Quantum ESPRESSO software package are located in the directory <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">$ESPRESSO_BIN_DIR</span>.<br />
<br />
== Hints for using Quantum ESPRESSO ==<br />
<br />
=== Input Files ===<br />
<br />
For information about how to construct input files for Quantum ESPRESSO, please consult the [https://www.quantum-espresso.org/resources/users-manual/input-data-description documentation].<br />
<br />
=== Disk Usage ===<br />
<br />
Please change to a local directory or to '''your local workspace''' (preferred) before starting your calculations.<br />
<br />
= Examples =<br />
<br />
As with all processes that require more than a few minutes to run, non-trivial compute jobs must be submitted to the cluster queuing system.<br />
<br />
Example scripts are available in the directory <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">$ESPRESSO_EXA_DIR</span>:<br />
<pre><br />
$ module show chem/quantum_espresso # show environment variables, which will be available after 'module load'<br />
$ module load chem/quantum_espresso # load module<br />
$ ls $ESPRESSO_EXA_DIR # show content of directory $ESPRESSO_EXA_DIR<br />
</pre><br />
<br />
Run a first simple example job on <font color=red>JUSTUS 2</font>:<br />
<pre><br />
$ module load chem/quantum_espresso # load module<br />
$ WORKSPACE=`ws_allocate quantum_espresso 3` # allocate workspace<br />
$ cd $WORKSPACE # change to workspace<br />
$ cp -a $ESPRESSO_HOME/bwhpc-examples . # copy example files to workspace<br />
$ cd bwhpc-examples # change to test directory<br />
$ sbatch bwforcluster-quantum_espresso-example.sbatch # submit job<br />
$ squeue # obtain JOBID<br />
$ scontrol show job <JOBID> # check state of job<br />
$ ls # when job finishes the results will be visible in this directory<br />
</pre><br />
<br />
= Useful links =<br />
<br />
* [https://www.quantum-espresso.org/Doc/user_guide/ Documentation (english)]<br />
* [https://www.quantum-espresso.org/forum Forum (english)]<br />
* [https://www.quantum-espresso.org/resources/tutorials Tutorials (english)]<br />
* [https://en.wikipedia.org/wiki/Quantum_ESPRESSO Wikipedia article (english)]<br />
* [https://www.quantum-espresso.org/resources/tools Plugins for Quantum ESPRESSO (english)]<br />
----<br />
[[Category:Chemistry software]][[Category:BwForCluster_Chemistry]][[Category:BwForCluster_JUSTUS_2]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Quantum_ESPRESSO&diff=12627JUSTUS2/Software/Quantum ESPRESSO2024-02-29T08:09:11Z<p>J Kucera: </p>
<hr />
<div>{{Softwarepage|chem/quantum_espresso}}<br />
<br />
{| width=760px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/quantum_espresso/7.1<br />
|-<br />
| Availability<br />
| [https://wiki.bwhpc.de/e/JUSTUS2 BwForCluster JUSTUS2] <br />
|-<br />
| License<br />
| Open-source software, distributed under the GNU General Public License (GPL). [[#License|More...]]<br />
|-<br />
| Citing <br />
| As described [https://www.quantum-espresso.org/quote/ here]<br />
|-<br />
| Links<br />
| [https://www.quantum-espresso.org Homepage] &#124; [https://www.quantum-espresso.org/resources/users-manual Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|-<br />
|}<br />
<br />
= Description =<br />
<br />
'''Quantum ESPRESSO''' is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.<br />
<br />
= Availability =<br />
<br />
Quantum ESPRESSO is available on selected bwHPC-Clusters. A complete list of versions currently installed on the bwHPC-Clusters can be obtained from the [https://www.bwhpc.de/software.html Cluster Information System (CIS)].<br />
<br />
In order to check which versions of Quantum ESPRESSO are installed on the compute cluster, run the following command:<br />
<pre><br />
$ module avail chem/quantum_espresso<br />
</pre><br />
<br />
= License =<br />
<br />
Quantum ESPRESSO is free, open-source software released under the GNU General Public License (GPL). Anyone interested in using the Quantum ESPRESSO program suite must read the conditions described in its [https://www.quantum-espresso.org/project/manifesto manifesto].<br />
<br />
= Usage =<br />
== Loading the module ==<br />
<br />
You can load the default version of Quantum ESPRESSO with the following command:<br />
<pre><br />
$ module load chem/quantum_espresso<br />
</pre><br />
<br />
The module will try to load all modules it needs to function (e.g., compiler, mpi, ...). If loading the module fails, check if you have already loaded one of those modules, but not in the version required by Quantum ESPRESSO.<br />
<br />
If you wish to load another (older) version of Quantum ESPRESSO, you can do so using<br />
<pre><br />
$ module load chem/quantum_espresso/<version><br />
</pre><br />
with <version> specifying the desired version.<br />
<br />
Please cite Quantum ESPRESSO in your publications according to the references.<br />
<br />
== Program Binaries ==<br />
<br />
All binaries of the Quantum ESPRESSO software package are located in the directory <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">$ESPRESSO_BIN_DIR</span>.<br />
<br />
== Hints for using Quantum ESPRESSO ==<br />
<br />
=== Input Files ===<br />
<br />
For information about how to construct input files for Quantum ESPRESSO, please consult the [https://www.quantum-espresso.org/resources/users-manual/input-data-description documentation].<br />
<br />
=== Disk Usage ===<br />
<br />
Please change to a local directory or to '''your local workspace''' (preferred) before starting your calculations.<br />
<br />
= Examples =<br />
<br />
As with all processes that require more than a few minutes to run, non-trivial compute jobs must be submitted to the cluster queuing system.<br />
<br />
Example scripts are available in the directory <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">$ESPRESSO_EXA_DIR</span>:<br />
<pre><br />
$ module show chem/quantum_espresso # show environment variables, which will be available after 'module load'<br />
$ module load chem/quantum_espresso # load module<br />
$ ls $ESPRESSO_EXA_DIR # show content of directory $ESPRESSO_EXA_DIR<br />
</pre><br />
<br />
Run a first simple example job on <font color=red>JUSTUS 2</font>:<br />
<pre><br />
$ module load chem/quantum_espresso # load module<br />
$ WORKSPACE=`ws_allocate quantum_espresso 3` # allocate workspace<br />
$ cd $WORKSPACE # change to workspace<br />
$ cp -a $ESPRESSO_HOME/bwhpc-examples . # copy example files to workspace<br />
$ cd bwhpc-examples # change to test directory<br />
$ sbatch bwforcluster-quantum_espresso-example.sbatch # submit job<br />
$ squeue # obtain JOBID<br />
$ scontrol show job <JOBID> # check state of job<br />
$ ls # when job finishes the results will be visible in this directory<br />
</pre><br />
<br />
= Useful links =<br />
<br />
* [https://www.quantum-espresso.org/Doc/user_guide/ Documentation (english)]<br />
* [https://www.quantum-espresso.org/forum Forum (english)]<br />
* [https://www.quantum-espresso.org/resources/tutorials Tutorials (english)]<br />
* [https://en.wikipedia.org/wiki/Quantum_ESPRESSO Wikipedia article (english)]<br />
* [https://www.quantum-espresso.org/resources/tools Plugins for Quantum ESPRESSO (english)]<br />
----<br />
[[Category:Chemistry software]][[Category:BwForCluster_Chemistry]][[Category:BwForCluster_JUSTUS_2]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Quantum_ESPRESSO&diff=12626JUSTUS2/Software/Quantum ESPRESSO2024-02-29T08:06:39Z<p>J Kucera: </p>
<hr />
<div>{{Softwarepage|chem/quantum_espresso}}<br />
<br />
{| width=760px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/quantum_espresso/7.1<br />
|-<br />
| Availability<br />
| [https://wiki.bwhpc.de/e/JUSTUS2 BwForCluster JUSTUS2] <br />
|-<br />
| License<br />
| Open-source software, distributed under the GNU General Public License (GPL). [[#License|More...]]<br />
|-<br />
| Citing <br />
| <small>1) P Giannozzi et al 2009 J. Phys.: Condens. Matter 21 395502<br>DOI: 10.1088/0953-8984/21/39/395502.<br>2) P Giannozzi et al 2017 J. Phys.: Condens. Matter 29 465901<br>DOI: 10.1088/1361-648X/aa8f79.<br>3) P Giannozzi et al 2020 J. Chem. Phys. 152 154105<br>DOI: 10.1063/5.0005082.</small><br />
|-<br />
| Links<br />
| [https://www.quantum-espresso.org Homepage] &#124; [https://www.quantum-espresso.org/resources/users-manual Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|-<br />
|}<br />
<br />
= Description =<br />
<br />
'''Quantum ESPRESSO''' is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.<br />
<br />
= Availability =<br />
<br />
Quantum ESPRESSO is available on selected bwHPC-Clusters. A complete list of versions currently installed on the bwHPC-Clusters can be obtained from the [https://www.bwhpc.de/software.html Cluster Information System (CIS)].<br />
<br />
In order to check which versions of Quantum ESPRESSO are installed on the compute cluster, run the following command:<br />
<pre><br />
$ module avail chem/quantum_espresso<br />
</pre><br />
<br />
= License =<br />
<br />
Quantum ESPRESSO is free, open-source software released under the GNU General Public License (GPL). Anyone interested in using the Quantum ESPRESSO program suite must read the conditions described in its [https://www.quantum-espresso.org/project/manifesto manifesto].<br />
<br />
= Usage =<br />
== Loading the module ==<br />
<br />
You can load the default version of Quantum ESPRESSO with the following command:<br />
<pre><br />
$ module load chem/quantum_espresso<br />
</pre><br />
<br />
The module will try to load all modules it needs to function (e.g., compiler, mpi, ...). If loading the module fails, check if you have already loaded one of those modules, but not in the version required by Quantum ESPRESSO.<br />
<br />
If you wish to load another (older) version of Quantum ESPRESSO, you can do so using<br />
<pre><br />
$ module load chem/quantum_espresso/<version><br />
</pre><br />
with <version> specifying the desired version.<br />
<br />
Please cite Quantum ESPRESSO in your publications according to the references.<br />
<br />
== Program Binaries ==<br />
<br />
All binaries of the Quantum ESPRESSO software package are located in the directory <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">$ESPRESSO_BIN_DIR</span>.<br />
<br />
== Hints for using Quantum ESPRESSO ==<br />
<br />
=== Input Files ===<br />
<br />
For information about how to construct input files for Quantum ESPRESSO, please consult the [https://www.quantum-espresso.org/resources/users-manual/input-data-description documentation].<br />
<br />
=== Disk Usage ===<br />
<br />
Please change to a local directory or to '''your local workspace''' (preferred) before starting your calculations.<br />
<br />
= Examples =<br />
<br />
As with all processes that require more than a few minutes to run, non-trivial compute jobs must be submitted to the cluster queuing system.<br />
<br />
Example scripts are available in the directory <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">$ESPRESSO_EXA_DIR</span>:<br />
<pre><br />
$ module show chem/quantum_espresso # show environment variables, which will be available after 'module load'<br />
$ module load chem/quantum_espresso # load module<br />
$ ls $ESPRESSO_EXA_DIR # show content of directory $ESPRESSO_EXA_DIR<br />
</pre><br />
<br />
Run a first simple example job on <font color=red>JUSTUS 2</font>:<br />
<pre><br />
$ module load chem/quantum_espresso # load module<br />
$ WORKSPACE=`ws_allocate quantum_espresso 3` # allocate workspace<br />
$ cd $WORKSPACE # change to workspace<br />
$ cp -a $ESPRESSO_HOME/bwhpc-examples . # copy example files to workspace<br />
$ cd bwhpc-examples # change to test directory<br />
$ sbatch bwforcluster-quantum_espresso-example.sbatch # submit job<br />
$ squeue # obtain JOBID<br />
$ scontrol show job <JOBID> # check state of job<br />
$ ls # when job finishes the results will be visible in this directory<br />
</pre><br />
<br />
= Useful links =<br />
<br />
* [https://www.quantum-espresso.org/Doc/user_guide/ Documentation (english)]<br />
* [https://www.quantum-espresso.org/forum Forum (english)]<br />
* [https://www.quantum-espresso.org/resources/tutorials Tutorials (english)]<br />
* [https://en.wikipedia.org/wiki/Quantum_ESPRESSO Wikipedia article (english)]<br />
* [https://www.quantum-espresso.org/resources/tools Plugins for Quantum ESPRESSO (english)]<br />
----<br />
[[Category:Chemistry software]][[Category:BwForCluster_Chemistry]][[Category:BwForCluster_JUSTUS_2]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Quantum_ESPRESSO&diff=12625JUSTUS2/Software/Quantum ESPRESSO2024-02-29T08:06:11Z<p>J Kucera: </p>
<hr />
<div>{{Softwarepage|chem/quantum_espresso}}<br />
<br />
{| width=760px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/quantum_espresso/7.1<br />
|-<br />
| Availability<br />
| [https://wiki.bwhpc.de/e/JUSTUS2 BwForCluster JUSTUS2] <br />
|-<br />
| License<br />
| Open-source software, distributed under the GNU General Public License (GPL). [[#License|More...]]<br />
|-<br />
| Citing <br />
| <small>1) P Giannozzi et al 2009 J. Phys.: Condens. Matter 21 395502<br>DOI: 10.1088/0953-8984/21/39/395502.<br>2) P Giannozzi et al 2017 J. Phys.: Condens. Matter 29 465901<br>DOI: 10.1088/1361-648X/aa8f79.<br>3) P Giannozzi et al 2020 J. Chem. Phys. 152 154105<br>DOI: 10.1063/5.0005082.</small><br />
|-<br />
| Links<br />
| [https://www.quantum-espresso.org Homepage] &#124; [https://www.quantum-espresso.org/resources/users-manual Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|-<br />
| Plugins<br />
| [https://epw-code.org/ EPW]<br />
|}<br />
<br />
= Description =<br />
<br />
'''Quantum ESPRESSO''' is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.<br />
<br />
= Availability =<br />
<br />
Quantum ESPRESSO is available on selected bwHPC-Clusters. A complete list of versions currently installed on the bwHPC-Clusters can be obtained from the [https://www.bwhpc.de/software.html Cluster Information System (CIS)].<br />
<br />
In order to check which versions of Quantum ESPRESSO are installed on the compute cluster, run the following command:<br />
<pre><br />
$ module avail chem/quantum_espresso<br />
</pre><br />
<br />
= License =<br />
<br />
Quantum ESPRESSO is free, open-source software released under the GNU General Public License (GPL). Anyone interested in using the Quantum ESPRESSO program suite must read the conditions described in its [https://www.quantum-espresso.org/project/manifesto manifesto].<br />
<br />
= Usage =<br />
== Loading the module ==<br />
<br />
You can load the default version of Quantum ESPRESSO with the following command:<br />
<pre><br />
$ module load chem/quantum_espresso<br />
</pre><br />
<br />
The module will try to load all modules it needs to function (e.g., compiler, mpi, ...). If loading the module fails, check if you have already loaded one of those modules, but not in the version required by Quantum ESPRESSO.<br />
<br />
If you wish to load another (older) version of Quantum ESPRESSO, you can do so using<br />
<pre><br />
$ module load chem/quantum_espresso/<version><br />
</pre><br />
with <version> specifying the desired version.<br />
<br />
Please cite Quantum ESPRESSO in your publications according to the references.<br />
<br />
== Program Binaries ==<br />
<br />
All binaries of the Quantum ESPRESSO software package are located in the directory <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">$ESPRESSO_BIN_DIR</span>.<br />
<br />
== Hints for using Quantum ESPRESSO ==<br />
<br />
=== Input Files ===<br />
<br />
For information about how to construct input files for Quantum ESPRESSO, please consult the [https://www.quantum-espresso.org/resources/users-manual/input-data-description documentation].<br />
<br />
=== Disk Usage ===<br />
<br />
Please change to a local directory or to '''your local workspace''' (preferred) before starting your calculations.<br />
<br />
= Examples =<br />
<br />
As with all processes that require more than a few minutes to run, non-trivial compute jobs must be submitted to the cluster queuing system.<br />
<br />
Example scripts are available in the directory <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">$ESPRESSO_EXA_DIR</span>:<br />
<pre><br />
$ module show chem/quantum_espresso # show environment variables, which will be available after 'module load'<br />
$ module load chem/quantum_espresso # load module<br />
$ ls $ESPRESSO_EXA_DIR # show content of directory $ESPRESSO_EXA_DIR<br />
</pre><br />
<br />
Run a first simple example job on <font color=red>JUSTUS 2</font>:<br />
<pre><br />
$ module load chem/quantum_espresso # load module<br />
$ WORKSPACE=`ws_allocate quantum_espresso 3` # allocate workspace<br />
$ cd $WORKSPACE # change to workspace<br />
$ cp -a $ESPRESSO_HOME/bwhpc-examples . # copy example files to workspace<br />
$ cd bwhpc-examples # change to test directory<br />
$ sbatch bwforcluster-quantum_espresso-example.sbatch # submit job<br />
$ squeue # obtain JOBID<br />
$ scontrol show job <JOBID> # check state of job<br />
$ ls # when job finishes the results will be visible in this directory<br />
</pre><br />
<br />
= Useful links =<br />
<br />
* [https://www.quantum-espresso.org/Doc/user_guide/ Documentation (english)]<br />
* [https://www.quantum-espresso.org/forum Forum (english)]<br />
* [https://www.quantum-espresso.org/resources/tutorials Tutorials (english)]<br />
* [https://en.wikipedia.org/wiki/Quantum_ESPRESSO Wikipedia article (english)]<br />
* [https://www.quantum-espresso.org/resources/tools Plugins for Quantum ESPRESSO (english)]<br />
----<br />
[[Category:Chemistry software]][[Category:BwForCluster_Chemistry]][[Category:BwForCluster_JUSTUS_2]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Orca&diff=12624JUSTUS2/Software/Orca2024-02-29T07:30:55Z<p>J Kucera: /* Versions and Availability */</p>
<hr />
<div>{{Softwarepage|chem/orca}}<br />
<br />
{| width=600px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/orca/5.0.4<br />
|-<br />
| Availability<br />
| [[bwUniCluster]] &#124; [[JUSTUS2]]<br />
|-<br />
| License<br />
| [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA]<br />
|-<br />
|Citing<br />
| As described in the [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf manual]. Refer to Chapter 'Publications Related to ORCA' for guidance on citation.<br />
|-<br />
| Links<br />
| [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Forum Portal] &#124; [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|}<br />
<br><br />
= Description =<br />
<br />
'''ORCA''' is a comprehensive, fully parallelized quantum chemistry package designed for advanced electronic structure methods. It encompasses density functional theory, many-body perturbation theory, coupled cluster methods, multireference methods, and semi-empirical quantum chemistry approaches. ORCA is capable of computing a wide range of molecular properties and serves as a fully integrated system for multi-level calculations, including QM/MM, ONIOM, and embedded crystals.<br />
<br />
Additionally, ORCA offers several advanced features to improve computational efficiency and accuracy. These include local correlation methods, starting with PNOs and expanded to DLPNO to reduce the computational cost of coupled cluster calculations. It also incorporates RIJCOSX for efficient handling of Hartree-Fock based methods.<br />
<br />
Furthermore, ORCA provides NEB-TS for studying reaction pathways and offers various methods for accurately calculating excited states, such as TD-DFT, EOM-CCSD, STEOM-CCSD, CASSCF with NEVPT2 or CASPT2, as well as molecular dynamics and multi-scale QM-MM models.<br />
<br />
Please refer to documentation provided by the ORCA developers in the first place for more detailed information.<br />
<br />
[https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Orca Manual 5.0.4]<br />
[https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wcms.1606 Article Overview by Frank Nesse]<br />
[https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.81 Article about main improvement in the version 5.0]<br />
<br />
<br><br />
<br />
= Versions and Availability =<br />
<br />
On the command line interface of any bwHPC cluster you'll get a list of available versions by using<br />
the command<br />
<br><br />
''''module avail chem/orca''''.<br />
<pre><br />
$ module avail chem/orca # JUSTUS 2<br />
------------------------------ ----------------/opt/bwhpc/common/modulefiles/Core --------------------------------------------------------<br />
chem/orca/4.2.1-xtb-6.3.3 chem/orca/5.0.1-xtb-6.4.1 chem/orca/5.0.2 chem/orca/5.0.3 chem/orca/5.0.4 (D)<br />
chem/orca/4.2.1 chem/orca/5.0.1 chem/orca/5.0.3-xtb-6.5.1 chem/orca/5.0.4_xtb-6.6.0<br />
</pre><br />
<br><br />
<br />
= Usage =<br />
== Loading the module ==<br />
You can load the default version of ''ORCA'' with the command ''''module load chem/orca''''.<br />
<pre><br />
$ module load chem/orca<br />
module avail chem/orca<br />
------------------------ /opt/bwhpc/common/modulefiles ----------------------<br />
chem/orca/3.0.3 chem/orca/3.0.3-openmpi-1.6.5(default)<br />
$ module load chem/orca<br />
</pre><br />
The module will try to load modules it needs to function (e.g. compiler/intel). If loading the module fails, check if you have already loaded one of those modules, but not in the version needed for Orca.<br />
<br><br><br />
If you wish to load a specific (older) version, you can do so using e.g.<br />
<br> <br />
''''module load chem/orca/'''version' to load the version you desires.<br />
<pre><br />
$ module load chem/orca/3.0.1 # bwUniCluster example<br />
Please do not use this module if you do not own a valid ORCA group license.<br />
Please cite ORCA in your publications according to ORCA documentation.<br />
Please read 'module help chem/orca/3.0.1' before using ORCA.<br />
</pre><br />
<br><br />
<font color=red>Orca 3.0.3 mit OpenMPI 1.6.5 läuft stabiler! <br />
Einige MPI-Abstürze sind nachweislich (gleicher Job) damit durchgelaufen.<br><br />
This version is known to be more stable with bigger jobs. Try this one if you get problems with other versions of Orca!</font><br><br />
<font color=green>This version is the default now. [[#Versions and Availability|Only available on the Chemical Cluster 'Justus']]!</font><br />
<br><br />
<br />
== Program Binaries ==<br />
You can find the ORCA binaries in the main folder of the ORCA system.<br />
<br><br />
After loading the ORCA module (''module load chem/orca/'version''') this path is also set to the local $PATH- and [[#ORCA-Specific Environments|$ORCA_BIN_DIR environments]].<br />
<pre><br />
$ ls -x $ORCA_BIN_DIR<br />
bwhpc-examples manual modulefiles orca orca_2aim orca_2mkl<br />
orca_anoint orca_anoint_mpi orca_asa orca_casscf orca_casscf_mpi orca_chelpg<br />
orca_ciprep orca_cis orca_cis_mpi orca_cleanup orca_cleanup_mpi orca_cpcasscf<br />
orca_cpscf orca_cpscf_mpi orca_eca orca_ecplib orca_eprnmr orca_eprnmr_mpi<br />
orca_euler orca_fci orca_fitpes orca_gstep orca_gtoint orca_gtoint_mpi<br />
orca_loc orca_mapspc orca_md orca_mdci orca_mdci_mpi orca_mergefrag<br />
orca_mp2 orca_mp2_mpi orca_mrci orca_mrci_mpi orca_ndoint orca_numfreq<br />
orca_pc orca_pc_mpi orca_plot orca_pltvib orca_pop orca_rel<br />
orca_rocis orca_rocis_mpi orca_scf orca_scfgrad orca_scfgrad_mpi orca_scfhess<br />
orca_scfhess_mpi orca_scf_mpi orca_soc orca_soc_mpi orca_vib orca_vpot<br />
otool_cosmo otool_gcp otool_smd<br />
$ <br />
</pre><br />
Only the programs with the suffix <font color=green>'''_mpi'''</font> are compiled including OPENMPI functionality.<br />
<br><br />
<br />
== Disk Usage ==<br />
Scratch files are written to the current directory by default.<br><br />
Please change to a local directory or to '''your local workspace''' (preferred) before starting your calculations. <br />
<br><br><br />
'calc_repo' is an example name of a repository you created by using the command 'ws_allocate'.<br />
<pre><br />
$ cd $(ws_find calc_repo)<br />
['your-id'-calc_repo-0]$ pwd<br />
/work/workspace/scratch/'your-id'-calc_repo-0<br />
['your-id'-calc_repo-0]$ <br />
</pre><br />
<br />
== Examples ==<br />
You can copy a simple interactive example to your '''workspace''' and run it, using 'msub'<br />
<pre><br />
$ cd $(ws_find calc_repo)<br />
$ cp $ORCA_EXA_DIR/bwhpc-orca-example.moab .<br />
$ cp bwhpc-orca-example.moab myorcajob.moab <br />
§ vi myorcajob.moab # do your own modifications<br />
$ msub myorcajob.moab # start job submission<br />
</pre><br />
<br><br />
= ORCA-Specific Environments =<br />
To see a list of all ORCA environments set by the 'module load chem/orca/version'-command,<br />
use ''''env | grep ORCA''''<br><br />
Or try the command ''''module show 'chem/orca'''/version'.<br />
<pre><br />
$ module load chem/orca/3.0.3<br />
$ env | grep ORCA<br />
ORCA_VERSION=3.0.3<br />
ORCA_MAN_DIR=/opt/bwhpc/common/chem/orca/3.0.3/manual<br />
ORCA_EXA_DIR=/opt/bwhpc/common/chem/orca/3.0.3/bwhpc-examples<br />
ORCA_BIN_DIR=/opt/bwhpc/common/chem/orca/3.0.3<br />
ORCA_HOME=/opt/bwhpc/common/chem/orca/3.0.3<br />
</pre><br />
<br><br />
= Version-Specific Information =<br />
For a more detailed information specific to a specific ORCA version, see the information available via the module system with the command ''''module help chem/orca''''.<br />
<br><br />
For a small abstract what ORCA is about use the command ''''module whatis chem/orca''''.<br />
<br><br><br />
<u>Examples</u><br />
<pre><br />
$ module avail chem/orca<br />
----------------------- /opt/bwhpc/common/modulefiles ---------------------------<br />
chem/orca/3.0.1 chem/orca/3.0.3<br />
<br />
$ module whatis chem/orca/3.0.1<br />
chem/orca/3.0.1 : Quantum chemistry package ORCA, version 3.0.1<br />
(command '/opt/bwhpc/common/chem/orca/3.0.1/orca')<br />
<br />
$ module help chem/orca/3.0.1<br />
----------- Module Specific Help for 'chem/orca/3.0.1' ------------<br />
This module provides the quantum chemistry package ORCA version 3.0.1<br />
via command '/opt/bwhpc/common/chem/orca/3.0.1/orca' <br />
[...] <br />
Documentation: <br />
* Max-Planck-Institut fuer Chemische Energiekonversion <br />
https://cec.mpg.de/forum/portal.php<br />
* New features for version 3.0.1<br />
https://cec.mpg.de/forum/portal.php#a3<br />
* Manuals in pdf format:<br />
/opt/bwhpc/common/chem/orca/3.0.1/manual<br />
* Example data and a Moab example script can be found here:<br />
/opt/bwhpc/common/chem/orca/3.0.1/bwhpc-examples<br />
[...]<br />
</pre><br />
<br><br />
----<br />
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Orca&diff=12623JUSTUS2/Software/Orca2024-02-29T07:29:22Z<p>J Kucera: /* Versions and Availability */</p>
<hr />
<div>{{Softwarepage|chem/orca}}<br />
<br />
{| width=600px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/orca/5.0.4<br />
|-<br />
| Availability<br />
| [[bwUniCluster]] &#124; [[JUSTUS2]]<br />
|-<br />
| License<br />
| [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA]<br />
|-<br />
|Citing<br />
| As described in the [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf manual]. Refer to Chapter 'Publications Related to ORCA' for guidance on citation.<br />
|-<br />
| Links<br />
| [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Forum Portal] &#124; [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|}<br />
<br><br />
= Description =<br />
<br />
'''ORCA''' is a comprehensive, fully parallelized quantum chemistry package designed for advanced electronic structure methods. It encompasses density functional theory, many-body perturbation theory, coupled cluster methods, multireference methods, and semi-empirical quantum chemistry approaches. ORCA is capable of computing a wide range of molecular properties and serves as a fully integrated system for multi-level calculations, including QM/MM, ONIOM, and embedded crystals.<br />
<br />
Additionally, ORCA offers several advanced features to improve computational efficiency and accuracy. These include local correlation methods, starting with PNOs and expanded to DLPNO to reduce the computational cost of coupled cluster calculations. It also incorporates RIJCOSX for efficient handling of Hartree-Fock based methods.<br />
<br />
Furthermore, ORCA provides NEB-TS for studying reaction pathways and offers various methods for accurately calculating excited states, such as TD-DFT, EOM-CCSD, STEOM-CCSD, CASSCF with NEVPT2 or CASPT2, as well as molecular dynamics and multi-scale QM-MM models.<br />
<br />
Please refer to documentation provided by the ORCA developers in the first place for more detailed information.<br />
<br />
[https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Orca Manual 5.0.4]<br />
[https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wcms.1606 Article Overview by Frank Nesse]<br />
[https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.81 Article about main improvement in the version 5.0]<br />
<br />
<br><br />
<br />
= Versions and Availability =<br />
<br />
On the command line interface of any bwHPC cluster you'll get a list of available versions by using<br />
the command<br />
<br><br />
''''module avail chem/orca''''.<br />
<pre><br />
$ module avail chem/orca # JUSTUS 2<br />
------------------------------ /opt/bwhpc/common/modulefiles/Core --------------------------------------------------------<br />
chem/orca/4.2.1-xtb-6.3.3 chem/orca/5.0.1-xtb-6.4.1 chem/orca/5.0.2 chem/orca/5.0.3 chem/orca/5.0.4 (D)<br />
chem/orca/4.2.1 chem/orca/5.0.1 chem/orca/5.0.3-xtb-6.5.1 chem/orca/5.0.4_xtb-6.6.0<br />
</pre><br />
<br><br />
<br />
= Usage =<br />
== Loading the module ==<br />
You can load the default version of ''ORCA'' with the command ''''module load chem/orca''''.<br />
<pre><br />
$ module load chem/orca<br />
module avail chem/orca<br />
------------------------ /opt/bwhpc/common/modulefiles ----------------------<br />
chem/orca/3.0.3 chem/orca/3.0.3-openmpi-1.6.5(default)<br />
$ module load chem/orca<br />
</pre><br />
The module will try to load modules it needs to function (e.g. compiler/intel). If loading the module fails, check if you have already loaded one of those modules, but not in the version needed for Orca.<br />
<br><br><br />
If you wish to load a specific (older) version, you can do so using e.g.<br />
<br> <br />
''''module load chem/orca/'''version' to load the version you desires.<br />
<pre><br />
$ module load chem/orca/3.0.1 # bwUniCluster example<br />
Please do not use this module if you do not own a valid ORCA group license.<br />
Please cite ORCA in your publications according to ORCA documentation.<br />
Please read 'module help chem/orca/3.0.1' before using ORCA.<br />
</pre><br />
<br><br />
<font color=red>Orca 3.0.3 mit OpenMPI 1.6.5 läuft stabiler! <br />
Einige MPI-Abstürze sind nachweislich (gleicher Job) damit durchgelaufen.<br><br />
This version is known to be more stable with bigger jobs. Try this one if you get problems with other versions of Orca!</font><br><br />
<font color=green>This version is the default now. [[#Versions and Availability|Only available on the Chemical Cluster 'Justus']]!</font><br />
<br><br />
<br />
== Program Binaries ==<br />
You can find the ORCA binaries in the main folder of the ORCA system.<br />
<br><br />
After loading the ORCA module (''module load chem/orca/'version''') this path is also set to the local $PATH- and [[#ORCA-Specific Environments|$ORCA_BIN_DIR environments]].<br />
<pre><br />
$ ls -x $ORCA_BIN_DIR<br />
bwhpc-examples manual modulefiles orca orca_2aim orca_2mkl<br />
orca_anoint orca_anoint_mpi orca_asa orca_casscf orca_casscf_mpi orca_chelpg<br />
orca_ciprep orca_cis orca_cis_mpi orca_cleanup orca_cleanup_mpi orca_cpcasscf<br />
orca_cpscf orca_cpscf_mpi orca_eca orca_ecplib orca_eprnmr orca_eprnmr_mpi<br />
orca_euler orca_fci orca_fitpes orca_gstep orca_gtoint orca_gtoint_mpi<br />
orca_loc orca_mapspc orca_md orca_mdci orca_mdci_mpi orca_mergefrag<br />
orca_mp2 orca_mp2_mpi orca_mrci orca_mrci_mpi orca_ndoint orca_numfreq<br />
orca_pc orca_pc_mpi orca_plot orca_pltvib orca_pop orca_rel<br />
orca_rocis orca_rocis_mpi orca_scf orca_scfgrad orca_scfgrad_mpi orca_scfhess<br />
orca_scfhess_mpi orca_scf_mpi orca_soc orca_soc_mpi orca_vib orca_vpot<br />
otool_cosmo otool_gcp otool_smd<br />
$ <br />
</pre><br />
Only the programs with the suffix <font color=green>'''_mpi'''</font> are compiled including OPENMPI functionality.<br />
<br><br />
<br />
== Disk Usage ==<br />
Scratch files are written to the current directory by default.<br><br />
Please change to a local directory or to '''your local workspace''' (preferred) before starting your calculations. <br />
<br><br><br />
'calc_repo' is an example name of a repository you created by using the command 'ws_allocate'.<br />
<pre><br />
$ cd $(ws_find calc_repo)<br />
['your-id'-calc_repo-0]$ pwd<br />
/work/workspace/scratch/'your-id'-calc_repo-0<br />
['your-id'-calc_repo-0]$ <br />
</pre><br />
<br />
== Examples ==<br />
You can copy a simple interactive example to your '''workspace''' and run it, using 'msub'<br />
<pre><br />
$ cd $(ws_find calc_repo)<br />
$ cp $ORCA_EXA_DIR/bwhpc-orca-example.moab .<br />
$ cp bwhpc-orca-example.moab myorcajob.moab <br />
§ vi myorcajob.moab # do your own modifications<br />
$ msub myorcajob.moab # start job submission<br />
</pre><br />
<br><br />
= ORCA-Specific Environments =<br />
To see a list of all ORCA environments set by the 'module load chem/orca/version'-command,<br />
use ''''env | grep ORCA''''<br><br />
Or try the command ''''module show 'chem/orca'''/version'.<br />
<pre><br />
$ module load chem/orca/3.0.3<br />
$ env | grep ORCA<br />
ORCA_VERSION=3.0.3<br />
ORCA_MAN_DIR=/opt/bwhpc/common/chem/orca/3.0.3/manual<br />
ORCA_EXA_DIR=/opt/bwhpc/common/chem/orca/3.0.3/bwhpc-examples<br />
ORCA_BIN_DIR=/opt/bwhpc/common/chem/orca/3.0.3<br />
ORCA_HOME=/opt/bwhpc/common/chem/orca/3.0.3<br />
</pre><br />
<br><br />
= Version-Specific Information =<br />
For a more detailed information specific to a specific ORCA version, see the information available via the module system with the command ''''module help chem/orca''''.<br />
<br><br />
For a small abstract what ORCA is about use the command ''''module whatis chem/orca''''.<br />
<br><br><br />
<u>Examples</u><br />
<pre><br />
$ module avail chem/orca<br />
----------------------- /opt/bwhpc/common/modulefiles ---------------------------<br />
chem/orca/3.0.1 chem/orca/3.0.3<br />
<br />
$ module whatis chem/orca/3.0.1<br />
chem/orca/3.0.1 : Quantum chemistry package ORCA, version 3.0.1<br />
(command '/opt/bwhpc/common/chem/orca/3.0.1/orca')<br />
<br />
$ module help chem/orca/3.0.1<br />
----------- Module Specific Help for 'chem/orca/3.0.1' ------------<br />
This module provides the quantum chemistry package ORCA version 3.0.1<br />
via command '/opt/bwhpc/common/chem/orca/3.0.1/orca' <br />
[...] <br />
Documentation: <br />
* Max-Planck-Institut fuer Chemische Energiekonversion <br />
https://cec.mpg.de/forum/portal.php<br />
* New features for version 3.0.1<br />
https://cec.mpg.de/forum/portal.php#a3<br />
* Manuals in pdf format:<br />
/opt/bwhpc/common/chem/orca/3.0.1/manual<br />
* Example data and a Moab example script can be found here:<br />
/opt/bwhpc/common/chem/orca/3.0.1/bwhpc-examples<br />
[...]<br />
</pre><br />
<br><br />
----<br />
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Orca&diff=12622JUSTUS2/Software/Orca2024-02-29T07:28:57Z<p>J Kucera: </p>
<hr />
<div>{{Softwarepage|chem/orca}}<br />
<br />
{| width=600px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/orca/5.0.4<br />
|-<br />
| Availability<br />
| [[bwUniCluster]] &#124; [[JUSTUS2]]<br />
|-<br />
| License<br />
| [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA]<br />
|-<br />
|Citing<br />
| As described in the [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf manual]. Refer to Chapter 'Publications Related to ORCA' for guidance on citation.<br />
|-<br />
| Links<br />
| [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Forum Portal] &#124; [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|}<br />
<br><br />
= Description =<br />
<br />
'''ORCA''' is a comprehensive, fully parallelized quantum chemistry package designed for advanced electronic structure methods. It encompasses density functional theory, many-body perturbation theory, coupled cluster methods, multireference methods, and semi-empirical quantum chemistry approaches. ORCA is capable of computing a wide range of molecular properties and serves as a fully integrated system for multi-level calculations, including QM/MM, ONIOM, and embedded crystals.<br />
<br />
Additionally, ORCA offers several advanced features to improve computational efficiency and accuracy. These include local correlation methods, starting with PNOs and expanded to DLPNO to reduce the computational cost of coupled cluster calculations. It also incorporates RIJCOSX for efficient handling of Hartree-Fock based methods.<br />
<br />
Furthermore, ORCA provides NEB-TS for studying reaction pathways and offers various methods for accurately calculating excited states, such as TD-DFT, EOM-CCSD, STEOM-CCSD, CASSCF with NEVPT2 or CASPT2, as well as molecular dynamics and multi-scale QM-MM models.<br />
<br />
Please refer to documentation provided by the ORCA developers in the first place for more detailed information.<br />
<br />
[https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Orca Manual 5.0.4]<br />
[https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wcms.1606 Article Overview by Frank Nesse]<br />
[https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.81 Article about main improvement in the version 5.0]<br />
<br />
<br><br />
<br />
= Versions and Availability =<br />
<br />
On the command line interface of any bwHPC cluster you'll get a list of available versions by using<br />
the command<br />
<br><br />
''''module avail chem/orca''''.<br />
<pre><br />
$ module avail chem/orca # JUSTUS 2<br />
------------------------------------------------------------------------------------ /opt/bwhpc/common/modulefiles/Core ------------------------------------------------------------------------------------<br />
chem/orca/4.2.1-xtb-6.3.3 chem/orca/5.0.1-xtb-6.4.1 chem/orca/5.0.2 chem/orca/5.0.3 chem/orca/5.0.4 (D)<br />
chem/orca/4.2.1 chem/orca/5.0.1 chem/orca/5.0.3-xtb-6.5.1 chem/orca/5.0.4_xtb-6.6.0<br />
</pre><br />
<br><br />
<br />
= Usage =<br />
== Loading the module ==<br />
You can load the default version of ''ORCA'' with the command ''''module load chem/orca''''.<br />
<pre><br />
$ module load chem/orca<br />
module avail chem/orca<br />
------------------------ /opt/bwhpc/common/modulefiles ----------------------<br />
chem/orca/3.0.3 chem/orca/3.0.3-openmpi-1.6.5(default)<br />
$ module load chem/orca<br />
</pre><br />
The module will try to load modules it needs to function (e.g. compiler/intel). If loading the module fails, check if you have already loaded one of those modules, but not in the version needed for Orca.<br />
<br><br><br />
If you wish to load a specific (older) version, you can do so using e.g.<br />
<br> <br />
''''module load chem/orca/'''version' to load the version you desires.<br />
<pre><br />
$ module load chem/orca/3.0.1 # bwUniCluster example<br />
Please do not use this module if you do not own a valid ORCA group license.<br />
Please cite ORCA in your publications according to ORCA documentation.<br />
Please read 'module help chem/orca/3.0.1' before using ORCA.<br />
</pre><br />
<br><br />
<font color=red>Orca 3.0.3 mit OpenMPI 1.6.5 läuft stabiler! <br />
Einige MPI-Abstürze sind nachweislich (gleicher Job) damit durchgelaufen.<br><br />
This version is known to be more stable with bigger jobs. Try this one if you get problems with other versions of Orca!</font><br><br />
<font color=green>This version is the default now. [[#Versions and Availability|Only available on the Chemical Cluster 'Justus']]!</font><br />
<br><br />
<br />
== Program Binaries ==<br />
You can find the ORCA binaries in the main folder of the ORCA system.<br />
<br><br />
After loading the ORCA module (''module load chem/orca/'version''') this path is also set to the local $PATH- and [[#ORCA-Specific Environments|$ORCA_BIN_DIR environments]].<br />
<pre><br />
$ ls -x $ORCA_BIN_DIR<br />
bwhpc-examples manual modulefiles orca orca_2aim orca_2mkl<br />
orca_anoint orca_anoint_mpi orca_asa orca_casscf orca_casscf_mpi orca_chelpg<br />
orca_ciprep orca_cis orca_cis_mpi orca_cleanup orca_cleanup_mpi orca_cpcasscf<br />
orca_cpscf orca_cpscf_mpi orca_eca orca_ecplib orca_eprnmr orca_eprnmr_mpi<br />
orca_euler orca_fci orca_fitpes orca_gstep orca_gtoint orca_gtoint_mpi<br />
orca_loc orca_mapspc orca_md orca_mdci orca_mdci_mpi orca_mergefrag<br />
orca_mp2 orca_mp2_mpi orca_mrci orca_mrci_mpi orca_ndoint orca_numfreq<br />
orca_pc orca_pc_mpi orca_plot orca_pltvib orca_pop orca_rel<br />
orca_rocis orca_rocis_mpi orca_scf orca_scfgrad orca_scfgrad_mpi orca_scfhess<br />
orca_scfhess_mpi orca_scf_mpi orca_soc orca_soc_mpi orca_vib orca_vpot<br />
otool_cosmo otool_gcp otool_smd<br />
$ <br />
</pre><br />
Only the programs with the suffix <font color=green>'''_mpi'''</font> are compiled including OPENMPI functionality.<br />
<br><br />
<br />
== Disk Usage ==<br />
Scratch files are written to the current directory by default.<br><br />
Please change to a local directory or to '''your local workspace''' (preferred) before starting your calculations. <br />
<br><br><br />
'calc_repo' is an example name of a repository you created by using the command 'ws_allocate'.<br />
<pre><br />
$ cd $(ws_find calc_repo)<br />
['your-id'-calc_repo-0]$ pwd<br />
/work/workspace/scratch/'your-id'-calc_repo-0<br />
['your-id'-calc_repo-0]$ <br />
</pre><br />
<br />
== Examples ==<br />
You can copy a simple interactive example to your '''workspace''' and run it, using 'msub'<br />
<pre><br />
$ cd $(ws_find calc_repo)<br />
$ cp $ORCA_EXA_DIR/bwhpc-orca-example.moab .<br />
$ cp bwhpc-orca-example.moab myorcajob.moab <br />
§ vi myorcajob.moab # do your own modifications<br />
$ msub myorcajob.moab # start job submission<br />
</pre><br />
<br><br />
= ORCA-Specific Environments =<br />
To see a list of all ORCA environments set by the 'module load chem/orca/version'-command,<br />
use ''''env | grep ORCA''''<br><br />
Or try the command ''''module show 'chem/orca'''/version'.<br />
<pre><br />
$ module load chem/orca/3.0.3<br />
$ env | grep ORCA<br />
ORCA_VERSION=3.0.3<br />
ORCA_MAN_DIR=/opt/bwhpc/common/chem/orca/3.0.3/manual<br />
ORCA_EXA_DIR=/opt/bwhpc/common/chem/orca/3.0.3/bwhpc-examples<br />
ORCA_BIN_DIR=/opt/bwhpc/common/chem/orca/3.0.3<br />
ORCA_HOME=/opt/bwhpc/common/chem/orca/3.0.3<br />
</pre><br />
<br><br />
= Version-Specific Information =<br />
For a more detailed information specific to a specific ORCA version, see the information available via the module system with the command ''''module help chem/orca''''.<br />
<br><br />
For a small abstract what ORCA is about use the command ''''module whatis chem/orca''''.<br />
<br><br><br />
<u>Examples</u><br />
<pre><br />
$ module avail chem/orca<br />
----------------------- /opt/bwhpc/common/modulefiles ---------------------------<br />
chem/orca/3.0.1 chem/orca/3.0.3<br />
<br />
$ module whatis chem/orca/3.0.1<br />
chem/orca/3.0.1 : Quantum chemistry package ORCA, version 3.0.1<br />
(command '/opt/bwhpc/common/chem/orca/3.0.1/orca')<br />
<br />
$ module help chem/orca/3.0.1<br />
----------- Module Specific Help for 'chem/orca/3.0.1' ------------<br />
This module provides the quantum chemistry package ORCA version 3.0.1<br />
via command '/opt/bwhpc/common/chem/orca/3.0.1/orca' <br />
[...] <br />
Documentation: <br />
* Max-Planck-Institut fuer Chemische Energiekonversion <br />
https://cec.mpg.de/forum/portal.php<br />
* New features for version 3.0.1<br />
https://cec.mpg.de/forum/portal.php#a3<br />
* Manuals in pdf format:<br />
/opt/bwhpc/common/chem/orca/3.0.1/manual<br />
* Example data and a Moab example script can be found here:<br />
/opt/bwhpc/common/chem/orca/3.0.1/bwhpc-examples<br />
[...]<br />
</pre><br />
<br><br />
----<br />
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Orca&diff=12621JUSTUS2/Software/Orca2024-02-29T07:27:50Z<p>J Kucera: /* Versions and Availability */</p>
<hr />
<div>{{Softwarepage|chem/orca}}<br />
<br />
{| width=600px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/orca/5.0.4<br />
|-<br />
| Availability<br />
| [[bwUniCluster]] &#124; [[JUSTUS2]]<br />
|-<br />
| License<br />
| [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA]<br />
|-<br />
|Citing<br />
| As described in the [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf manual]. Refer to Chapter 'Publications Related to ORCA' for guidance on citation.<br />
|-<br />
| Links<br />
| [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Forum Portal] &#124; [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|}<br />
<br><br />
= Description =<br />
<br />
'''ORCA''' is a comprehensive, fully parallelized quantum chemistry package designed for advanced electronic structure methods. It encompasses density functional theory, many-body perturbation theory, coupled cluster methods, multireference methods, and semi-empirical quantum chemistry approaches. ORCA is capable of computing a wide range of molecular properties and serves as a fully integrated system for multi-level calculations, including QM/MM, ONIOM, and embedded crystals.<br />
<br />
Additionally, ORCA offers several advanced features to improve computational efficiency and accuracy. These include local correlation methods, starting with PNOs and expanded to DLPNO to reduce the computational cost of coupled cluster calculations. It also incorporates RIJCOSX for efficient handling of Hartree-Fock based methods.<br />
<br />
Furthermore, ORCA provides NEB-TS for studying reaction pathways and offers various methods for accurately calculating excited states, such as TD-DFT, EOM-CCSD, STEOM-CCSD, CASSCF with NEVPT2 or CASPT2, as well as molecular dynamics and multi-scale QM-MM models.<br />
<br />
Please refer to documentation provided by the ORCA developers in the first place for more detailed information.<br />
<br />
[https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Orca Manual 5.0.4]<br />
[https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wcms.1606 Article Overview by Frank Nesse]<br />
[https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.81 Article about main improvement in the version 5.0]<br />
<br />
<br><br />
<br><br />
<br />
= Versions and Availability =<br />
<br />
On the command line interface of any bwHPC cluster you'll get a list of available versions by using<br />
the command<br />
<br><br />
''''module avail chem/orca''''.<br />
<pre><br />
$ module avail chem/orca # JUSTUS 2<br />
------------------------------------------------------------------------------------ /opt/bwhpc/common/modulefiles/Core ------------------------------------------------------------------------------------<br />
chem/orca/4.2.1-xtb-6.3.3 chem/orca/5.0.1-xtb-6.4.1 chem/orca/5.0.2 chem/orca/5.0.3 chem/orca/5.0.4 (D)<br />
chem/orca/4.2.1 chem/orca/5.0.1 chem/orca/5.0.3-xtb-6.5.1 chem/orca/5.0.4_xtb-6.6.0<br />
</pre><br />
<br><br />
<br />
= License =<br />
The ORCA license is considered as a "Research group" license. Thus anyone who directly associated with your research group is covered by the license and may share your copy of ORCA on all computer resources of your group.<br />
<br><br />
This license only applies to academic users. Commercial use of ORCA is prohibited under the terms of this license.<br />
<br><br />
[https://orcaforum.cec.mpg.de/license.html Complete ORCA Users License Agreement]<br />
<br><br />
<br><br />
= Usage =<br />
== Loading the module ==<br />
You can load the default version of ''ORCA'' with the command ''''module load chem/orca''''.<br />
<pre><br />
$ module load chem/orca<br />
module avail chem/orca<br />
------------------------ /opt/bwhpc/common/modulefiles ----------------------<br />
chem/orca/3.0.3 chem/orca/3.0.3-openmpi-1.6.5(default)<br />
$ module load chem/orca<br />
</pre><br />
The module will try to load modules it needs to function (e.g. compiler/intel). If loading the module fails, check if you have already loaded one of those modules, but not in the version needed for Orca.<br />
<br><br><br />
If you wish to load a specific (older) version, you can do so using e.g.<br />
<br> <br />
''''module load chem/orca/'''version' to load the version you desires.<br />
<pre><br />
$ module load chem/orca/3.0.1 # bwUniCluster example<br />
Please do not use this module if you do not own a valid ORCA group license.<br />
Please cite ORCA in your publications according to ORCA documentation.<br />
Please read 'module help chem/orca/3.0.1' before using ORCA.<br />
</pre><br />
<br><br />
<font color=red>Orca 3.0.3 mit OpenMPI 1.6.5 läuft stabiler! <br />
Einige MPI-Abstürze sind nachweislich (gleicher Job) damit durchgelaufen.<br><br />
This version is known to be more stable with bigger jobs. Try this one if you get problems with other versions of Orca!</font><br><br />
<font color=green>This version is the default now. [[#Versions and Availability|Only available on the Chemical Cluster 'Justus']]!</font><br />
<br><br />
<br />
== Program Binaries ==<br />
You can find the ORCA binaries in the main folder of the ORCA system.<br />
<br><br />
After loading the ORCA module (''module load chem/orca/'version''') this path is also set to the local $PATH- and [[#ORCA-Specific Environments|$ORCA_BIN_DIR environments]].<br />
<pre><br />
$ ls -x $ORCA_BIN_DIR<br />
bwhpc-examples manual modulefiles orca orca_2aim orca_2mkl<br />
orca_anoint orca_anoint_mpi orca_asa orca_casscf orca_casscf_mpi orca_chelpg<br />
orca_ciprep orca_cis orca_cis_mpi orca_cleanup orca_cleanup_mpi orca_cpcasscf<br />
orca_cpscf orca_cpscf_mpi orca_eca orca_ecplib orca_eprnmr orca_eprnmr_mpi<br />
orca_euler orca_fci orca_fitpes orca_gstep orca_gtoint orca_gtoint_mpi<br />
orca_loc orca_mapspc orca_md orca_mdci orca_mdci_mpi orca_mergefrag<br />
orca_mp2 orca_mp2_mpi orca_mrci orca_mrci_mpi orca_ndoint orca_numfreq<br />
orca_pc orca_pc_mpi orca_plot orca_pltvib orca_pop orca_rel<br />
orca_rocis orca_rocis_mpi orca_scf orca_scfgrad orca_scfgrad_mpi orca_scfhess<br />
orca_scfhess_mpi orca_scf_mpi orca_soc orca_soc_mpi orca_vib orca_vpot<br />
otool_cosmo otool_gcp otool_smd<br />
$ <br />
</pre><br />
Only the programs with the suffix <font color=green>'''_mpi'''</font> are compiled including OPENMPI functionality.<br />
<br><br />
<br />
== Disk Usage ==<br />
Scratch files are written to the current directory by default.<br><br />
Please change to a local directory or to '''your local workspace''' (preferred) before starting your calculations. <br />
<br><br><br />
'calc_repo' is an example name of a repository you created by using the command 'ws_allocate'.<br />
<pre><br />
$ cd $(ws_find calc_repo)<br />
['your-id'-calc_repo-0]$ pwd<br />
/work/workspace/scratch/'your-id'-calc_repo-0<br />
['your-id'-calc_repo-0]$ <br />
</pre><br />
<br />
== Examples ==<br />
You can copy a simple interactive example to your '''workspace''' and run it, using 'msub'<br />
<pre><br />
$ cd $(ws_find calc_repo)<br />
$ cp $ORCA_EXA_DIR/bwhpc-orca-example.moab .<br />
$ cp bwhpc-orca-example.moab myorcajob.moab <br />
§ vi myorcajob.moab # do your own modifications<br />
$ msub myorcajob.moab # start job submission<br />
</pre><br />
<br><br />
= ORCA-Specific Environments =<br />
To see a list of all ORCA environments set by the 'module load chem/orca/version'-command,<br />
use ''''env | grep ORCA''''<br><br />
Or try the command ''''module show 'chem/orca'''/version'.<br />
<pre><br />
$ module load chem/orca/3.0.3<br />
$ env | grep ORCA<br />
ORCA_VERSION=3.0.3<br />
ORCA_MAN_DIR=/opt/bwhpc/common/chem/orca/3.0.3/manual<br />
ORCA_EXA_DIR=/opt/bwhpc/common/chem/orca/3.0.3/bwhpc-examples<br />
ORCA_BIN_DIR=/opt/bwhpc/common/chem/orca/3.0.3<br />
ORCA_HOME=/opt/bwhpc/common/chem/orca/3.0.3<br />
</pre><br />
<br><br />
= Version-Specific Information =<br />
For a more detailed information specific to a specific ORCA version, see the information available via the module system with the command ''''module help chem/orca''''.<br />
<br><br />
For a small abstract what ORCA is about use the command ''''module whatis chem/orca''''.<br />
<br><br><br />
<u>Examples</u><br />
<pre><br />
$ module avail chem/orca<br />
----------------------- /opt/bwhpc/common/modulefiles ---------------------------<br />
chem/orca/3.0.1 chem/orca/3.0.3<br />
<br />
$ module whatis chem/orca/3.0.1<br />
chem/orca/3.0.1 : Quantum chemistry package ORCA, version 3.0.1<br />
(command '/opt/bwhpc/common/chem/orca/3.0.1/orca')<br />
<br />
$ module help chem/orca/3.0.1<br />
----------- Module Specific Help for 'chem/orca/3.0.1' ------------<br />
This module provides the quantum chemistry package ORCA version 3.0.1<br />
via command '/opt/bwhpc/common/chem/orca/3.0.1/orca' <br />
[...] <br />
Documentation: <br />
* Max-Planck-Institut fuer Chemische Energiekonversion <br />
https://cec.mpg.de/forum/portal.php<br />
* New features for version 3.0.1<br />
https://cec.mpg.de/forum/portal.php#a3<br />
* Manuals in pdf format:<br />
/opt/bwhpc/common/chem/orca/3.0.1/manual<br />
* Example data and a Moab example script can be found here:<br />
/opt/bwhpc/common/chem/orca/3.0.1/bwhpc-examples<br />
[...]<br />
</pre><br />
<br><br />
----<br />
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Orca&diff=12620JUSTUS2/Software/Orca2024-02-29T07:24:32Z<p>J Kucera: </p>
<hr />
<div>{{Softwarepage|chem/orca}}<br />
<br />
{| width=600px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/orca/5.0.4<br />
|-<br />
| Availability<br />
| [[bwUniCluster]] &#124; [[JUSTUS2]]<br />
|-<br />
| License<br />
| [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA]<br />
|-<br />
|Citing<br />
| As described in the [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf manual]. Refer to Chapter 'Publications Related to ORCA' for guidance on citation.<br />
|-<br />
| Links<br />
| [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Forum Portal] &#124; [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|}<br />
<br><br />
= Description =<br />
<br />
'''ORCA''' is a comprehensive, fully parallelized quantum chemistry package designed for advanced electronic structure methods. It encompasses density functional theory, many-body perturbation theory, coupled cluster methods, multireference methods, and semi-empirical quantum chemistry approaches. ORCA is capable of computing a wide range of molecular properties and serves as a fully integrated system for multi-level calculations, including QM/MM, ONIOM, and embedded crystals.<br />
<br />
Additionally, ORCA offers several advanced features to improve computational efficiency and accuracy. These include local correlation methods, starting with PNOs and expanded to DLPNO to reduce the computational cost of coupled cluster calculations. It also incorporates RIJCOSX for efficient handling of Hartree-Fock based methods.<br />
<br />
Furthermore, ORCA provides NEB-TS for studying reaction pathways and offers various methods for accurately calculating excited states, such as TD-DFT, EOM-CCSD, STEOM-CCSD, CASSCF with NEVPT2 or CASPT2, as well as molecular dynamics and multi-scale QM-MM models.<br />
<br />
Please refer to documentation provided by the ORCA developers in the first place for more detailed information.<br />
<br />
[https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Orca Manual 5.0.4]<br />
[https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wcms.1606 Article Overview by Frank Nesse]<br />
[https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.81 Article about main improvement in the version 5.0]<br />
<br />
<br><br />
<br><br />
<br />
= Versions and Availability =<br />
<br />
On the command line interface of any bwHPC cluster you'll get a list of available versions by using<br />
the command<br />
<br><br />
''''module avail chem/orca''''.<br />
<pre><br />
$ module avail chem/orca # bwUniCluster<br />
--------------------- /opt/bwhpc/common/modulefiles ----------------------<br />
chem/orca/3.0.1 chem/orca/3.0.3<br />
</pre><br />
<br><br />
<br />
= License =<br />
The ORCA license is considered as a "Research group" license. Thus anyone who directly associated with your research group is covered by the license and may share your copy of ORCA on all computer resources of your group.<br />
<br><br />
This license only applies to academic users. Commercial use of ORCA is prohibited under the terms of this license.<br />
<br><br />
[https://orcaforum.cec.mpg.de/license.html Complete ORCA Users License Agreement]<br />
<br><br />
<br><br />
= Usage =<br />
== Loading the module ==<br />
You can load the default version of ''ORCA'' with the command ''''module load chem/orca''''.<br />
<pre><br />
$ module load chem/orca<br />
module avail chem/orca<br />
------------------------ /opt/bwhpc/common/modulefiles ----------------------<br />
chem/orca/3.0.3 chem/orca/3.0.3-openmpi-1.6.5(default)<br />
$ module load chem/orca<br />
</pre><br />
The module will try to load modules it needs to function (e.g. compiler/intel). If loading the module fails, check if you have already loaded one of those modules, but not in the version needed for Orca.<br />
<br><br><br />
If you wish to load a specific (older) version, you can do so using e.g.<br />
<br> <br />
''''module load chem/orca/'''version' to load the version you desires.<br />
<pre><br />
$ module load chem/orca/3.0.1 # bwUniCluster example<br />
Please do not use this module if you do not own a valid ORCA group license.<br />
Please cite ORCA in your publications according to ORCA documentation.<br />
Please read 'module help chem/orca/3.0.1' before using ORCA.<br />
</pre><br />
<br><br />
<font color=red>Orca 3.0.3 mit OpenMPI 1.6.5 läuft stabiler! <br />
Einige MPI-Abstürze sind nachweislich (gleicher Job) damit durchgelaufen.<br><br />
This version is known to be more stable with bigger jobs. Try this one if you get problems with other versions of Orca!</font><br><br />
<font color=green>This version is the default now. [[#Versions and Availability|Only available on the Chemical Cluster 'Justus']]!</font><br />
<br><br />
<br />
== Program Binaries ==<br />
You can find the ORCA binaries in the main folder of the ORCA system.<br />
<br><br />
After loading the ORCA module (''module load chem/orca/'version''') this path is also set to the local $PATH- and [[#ORCA-Specific Environments|$ORCA_BIN_DIR environments]].<br />
<pre><br />
$ ls -x $ORCA_BIN_DIR<br />
bwhpc-examples manual modulefiles orca orca_2aim orca_2mkl<br />
orca_anoint orca_anoint_mpi orca_asa orca_casscf orca_casscf_mpi orca_chelpg<br />
orca_ciprep orca_cis orca_cis_mpi orca_cleanup orca_cleanup_mpi orca_cpcasscf<br />
orca_cpscf orca_cpscf_mpi orca_eca orca_ecplib orca_eprnmr orca_eprnmr_mpi<br />
orca_euler orca_fci orca_fitpes orca_gstep orca_gtoint orca_gtoint_mpi<br />
orca_loc orca_mapspc orca_md orca_mdci orca_mdci_mpi orca_mergefrag<br />
orca_mp2 orca_mp2_mpi orca_mrci orca_mrci_mpi orca_ndoint orca_numfreq<br />
orca_pc orca_pc_mpi orca_plot orca_pltvib orca_pop orca_rel<br />
orca_rocis orca_rocis_mpi orca_scf orca_scfgrad orca_scfgrad_mpi orca_scfhess<br />
orca_scfhess_mpi orca_scf_mpi orca_soc orca_soc_mpi orca_vib orca_vpot<br />
otool_cosmo otool_gcp otool_smd<br />
$ <br />
</pre><br />
Only the programs with the suffix <font color=green>'''_mpi'''</font> are compiled including OPENMPI functionality.<br />
<br><br />
<br />
== Disk Usage ==<br />
Scratch files are written to the current directory by default.<br><br />
Please change to a local directory or to '''your local workspace''' (preferred) before starting your calculations. <br />
<br><br><br />
'calc_repo' is an example name of a repository you created by using the command 'ws_allocate'.<br />
<pre><br />
$ cd $(ws_find calc_repo)<br />
['your-id'-calc_repo-0]$ pwd<br />
/work/workspace/scratch/'your-id'-calc_repo-0<br />
['your-id'-calc_repo-0]$ <br />
</pre><br />
<br />
== Examples ==<br />
You can copy a simple interactive example to your '''workspace''' and run it, using 'msub'<br />
<pre><br />
$ cd $(ws_find calc_repo)<br />
$ cp $ORCA_EXA_DIR/bwhpc-orca-example.moab .<br />
$ cp bwhpc-orca-example.moab myorcajob.moab <br />
§ vi myorcajob.moab # do your own modifications<br />
$ msub myorcajob.moab # start job submission<br />
</pre><br />
<br><br />
= ORCA-Specific Environments =<br />
To see a list of all ORCA environments set by the 'module load chem/orca/version'-command,<br />
use ''''env | grep ORCA''''<br><br />
Or try the command ''''module show 'chem/orca'''/version'.<br />
<pre><br />
$ module load chem/orca/3.0.3<br />
$ env | grep ORCA<br />
ORCA_VERSION=3.0.3<br />
ORCA_MAN_DIR=/opt/bwhpc/common/chem/orca/3.0.3/manual<br />
ORCA_EXA_DIR=/opt/bwhpc/common/chem/orca/3.0.3/bwhpc-examples<br />
ORCA_BIN_DIR=/opt/bwhpc/common/chem/orca/3.0.3<br />
ORCA_HOME=/opt/bwhpc/common/chem/orca/3.0.3<br />
</pre><br />
<br><br />
= Version-Specific Information =<br />
For a more detailed information specific to a specific ORCA version, see the information available via the module system with the command ''''module help chem/orca''''.<br />
<br><br />
For a small abstract what ORCA is about use the command ''''module whatis chem/orca''''.<br />
<br><br><br />
<u>Examples</u><br />
<pre><br />
$ module avail chem/orca<br />
----------------------- /opt/bwhpc/common/modulefiles ---------------------------<br />
chem/orca/3.0.1 chem/orca/3.0.3<br />
<br />
$ module whatis chem/orca/3.0.1<br />
chem/orca/3.0.1 : Quantum chemistry package ORCA, version 3.0.1<br />
(command '/opt/bwhpc/common/chem/orca/3.0.1/orca')<br />
<br />
$ module help chem/orca/3.0.1<br />
----------- Module Specific Help for 'chem/orca/3.0.1' ------------<br />
This module provides the quantum chemistry package ORCA version 3.0.1<br />
via command '/opt/bwhpc/common/chem/orca/3.0.1/orca' <br />
[...] <br />
Documentation: <br />
* Max-Planck-Institut fuer Chemische Energiekonversion <br />
https://cec.mpg.de/forum/portal.php<br />
* New features for version 3.0.1<br />
https://cec.mpg.de/forum/portal.php#a3<br />
* Manuals in pdf format:<br />
/opt/bwhpc/common/chem/orca/3.0.1/manual<br />
* Example data and a Moab example script can be found here:<br />
/opt/bwhpc/common/chem/orca/3.0.1/bwhpc-examples<br />
[...]<br />
</pre><br />
<br><br />
----<br />
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Orca&diff=12619JUSTUS2/Software/Orca2024-02-29T07:20:15Z<p>J Kucera: </p>
<hr />
<div>{{Softwarepage|chem/orca}}<br />
<br />
{| width=600px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/orca/5.0.4<br />
|-<br />
| Availability<br />
| [[bwUniCluster]] &#124; [[JUSTUS2]]<br />
|-<br />
| License<br />
| [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA]<br />
|-<br />
|Citing<br />
| As described in the [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf manual]. Refer to Chapter 'Publications Related to ORCA' for guidance on citation.<br />
|-<br />
| Links<br />
| [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Forum Portal] &#124; [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|}<br />
<br><br />
= Description =<br />
<br />
'''ORCA''' is a comprehensive, fully parallelized quantum chemistry package designed for advanced electronic structure methods. It encompasses density functional theory, many-body perturbation theory, coupled cluster methods, multireference methods, and semi-empirical quantum chemistry approaches. ORCA is capable of computing a wide range of molecular properties and serves as a fully integrated system for multi-level calculations, including QM/MM, ONIOM, and embedded crystals.<br />
<br />
Additionally, ORCA offers several advanced features to improve computational efficiency and accuracy. These include local correlation methods, starting with PNOs and expanded to DLPNO to reduce the computational cost of coupled cluster calculations. It also incorporates RIJCOSX for efficient handling of Hartree-Fock based methods.<br />
<br />
Furthermore, ORCA provides NEB-TS for studying reaction pathways and offers various methods for accurately calculating excited states, such as TD-DFT, EOM-CCSD, STEOM-CCSD, CASSCF with NEVPT2 or CASPT2, as well as molecular dynamics and multi-scale QM-MM models.<br />
<br />
Please refer to documentation provided by the ORCA developers in the first place for more detailed information.<br />
<br />
[https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf]<br />
[https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wcms.1606]<br />
[https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.81]<br />
<br />
<br><br />
<br><br />
<br />
= Versions and Availability =<br />
<br />
On the command line interface of any bwHPC cluster you'll get a list of available versions by using<br />
the command<br />
<br><br />
''''module avail chem/orca''''.<br />
<pre><br />
$ module avail chem/orca # bwUniCluster<br />
--------------------- /opt/bwhpc/common/modulefiles ----------------------<br />
chem/orca/3.0.1 chem/orca/3.0.3<br />
</pre><br />
<br><br />
<br />
= License =<br />
The ORCA license is considered as a "Research group" license. Thus anyone who directly associated with your research group is covered by the license and may share your copy of ORCA on all computer resources of your group.<br />
<br><br />
This license only applies to academic users. Commercial use of ORCA is prohibited under the terms of this license.<br />
<br><br />
[https://orcaforum.cec.mpg.de/license.html Complete ORCA Users License Agreement]<br />
<br><br />
<br><br />
= Usage =<br />
== Loading the module ==<br />
You can load the default version of ''ORCA'' with the command ''''module load chem/orca''''.<br />
<pre><br />
$ module load chem/orca<br />
module avail chem/orca<br />
------------------------ /opt/bwhpc/common/modulefiles ----------------------<br />
chem/orca/3.0.3 chem/orca/3.0.3-openmpi-1.6.5(default)<br />
$ module load chem/orca<br />
</pre><br />
The module will try to load modules it needs to function (e.g. compiler/intel). If loading the module fails, check if you have already loaded one of those modules, but not in the version needed for Orca.<br />
<br><br><br />
If you wish to load a specific (older) version, you can do so using e.g.<br />
<br> <br />
''''module load chem/orca/'''version' to load the version you desires.<br />
<pre><br />
$ module load chem/orca/3.0.1 # bwUniCluster example<br />
Please do not use this module if you do not own a valid ORCA group license.<br />
Please cite ORCA in your publications according to ORCA documentation.<br />
Please read 'module help chem/orca/3.0.1' before using ORCA.<br />
</pre><br />
<br><br />
<font color=red>Orca 3.0.3 mit OpenMPI 1.6.5 läuft stabiler! <br />
Einige MPI-Abstürze sind nachweislich (gleicher Job) damit durchgelaufen.<br><br />
This version is known to be more stable with bigger jobs. Try this one if you get problems with other versions of Orca!</font><br><br />
<font color=green>This version is the default now. [[#Versions and Availability|Only available on the Chemical Cluster 'Justus']]!</font><br />
<br><br />
<br />
== Program Binaries ==<br />
You can find the ORCA binaries in the main folder of the ORCA system.<br />
<br><br />
After loading the ORCA module (''module load chem/orca/'version''') this path is also set to the local $PATH- and [[#ORCA-Specific Environments|$ORCA_BIN_DIR environments]].<br />
<pre><br />
$ ls -x $ORCA_BIN_DIR<br />
bwhpc-examples manual modulefiles orca orca_2aim orca_2mkl<br />
orca_anoint orca_anoint_mpi orca_asa orca_casscf orca_casscf_mpi orca_chelpg<br />
orca_ciprep orca_cis orca_cis_mpi orca_cleanup orca_cleanup_mpi orca_cpcasscf<br />
orca_cpscf orca_cpscf_mpi orca_eca orca_ecplib orca_eprnmr orca_eprnmr_mpi<br />
orca_euler orca_fci orca_fitpes orca_gstep orca_gtoint orca_gtoint_mpi<br />
orca_loc orca_mapspc orca_md orca_mdci orca_mdci_mpi orca_mergefrag<br />
orca_mp2 orca_mp2_mpi orca_mrci orca_mrci_mpi orca_ndoint orca_numfreq<br />
orca_pc orca_pc_mpi orca_plot orca_pltvib orca_pop orca_rel<br />
orca_rocis orca_rocis_mpi orca_scf orca_scfgrad orca_scfgrad_mpi orca_scfhess<br />
orca_scfhess_mpi orca_scf_mpi orca_soc orca_soc_mpi orca_vib orca_vpot<br />
otool_cosmo otool_gcp otool_smd<br />
$ <br />
</pre><br />
Only the programs with the suffix <font color=green>'''_mpi'''</font> are compiled including OPENMPI functionality.<br />
<br><br />
<br />
== Disk Usage ==<br />
Scratch files are written to the current directory by default.<br><br />
Please change to a local directory or to '''your local workspace''' (preferred) before starting your calculations. <br />
<br><br><br />
'calc_repo' is an example name of a repository you created by using the command 'ws_allocate'.<br />
<pre><br />
$ cd $(ws_find calc_repo)<br />
['your-id'-calc_repo-0]$ pwd<br />
/work/workspace/scratch/'your-id'-calc_repo-0<br />
['your-id'-calc_repo-0]$ <br />
</pre><br />
<br />
== Examples ==<br />
You can copy a simple interactive example to your '''workspace''' and run it, using 'msub'<br />
<pre><br />
$ cd $(ws_find calc_repo)<br />
$ cp $ORCA_EXA_DIR/bwhpc-orca-example.moab .<br />
$ cp bwhpc-orca-example.moab myorcajob.moab <br />
§ vi myorcajob.moab # do your own modifications<br />
$ msub myorcajob.moab # start job submission<br />
</pre><br />
<br><br />
= ORCA-Specific Environments =<br />
To see a list of all ORCA environments set by the 'module load chem/orca/version'-command,<br />
use ''''env | grep ORCA''''<br><br />
Or try the command ''''module show 'chem/orca'''/version'.<br />
<pre><br />
$ module load chem/orca/3.0.3<br />
$ env | grep ORCA<br />
ORCA_VERSION=3.0.3<br />
ORCA_MAN_DIR=/opt/bwhpc/common/chem/orca/3.0.3/manual<br />
ORCA_EXA_DIR=/opt/bwhpc/common/chem/orca/3.0.3/bwhpc-examples<br />
ORCA_BIN_DIR=/opt/bwhpc/common/chem/orca/3.0.3<br />
ORCA_HOME=/opt/bwhpc/common/chem/orca/3.0.3<br />
</pre><br />
<br><br />
= Version-Specific Information =<br />
For a more detailed information specific to a specific ORCA version, see the information available via the module system with the command ''''module help chem/orca''''.<br />
<br><br />
For a small abstract what ORCA is about use the command ''''module whatis chem/orca''''.<br />
<br><br><br />
<u>Examples</u><br />
<pre><br />
$ module avail chem/orca<br />
----------------------- /opt/bwhpc/common/modulefiles ---------------------------<br />
chem/orca/3.0.1 chem/orca/3.0.3<br />
<br />
$ module whatis chem/orca/3.0.1<br />
chem/orca/3.0.1 : Quantum chemistry package ORCA, version 3.0.1<br />
(command '/opt/bwhpc/common/chem/orca/3.0.1/orca')<br />
<br />
$ module help chem/orca/3.0.1<br />
----------- Module Specific Help for 'chem/orca/3.0.1' ------------<br />
This module provides the quantum chemistry package ORCA version 3.0.1<br />
via command '/opt/bwhpc/common/chem/orca/3.0.1/orca' <br />
[...] <br />
Documentation: <br />
* Max-Planck-Institut fuer Chemische Energiekonversion <br />
https://cec.mpg.de/forum/portal.php<br />
* New features for version 3.0.1<br />
https://cec.mpg.de/forum/portal.php#a3<br />
* Manuals in pdf format:<br />
/opt/bwhpc/common/chem/orca/3.0.1/manual<br />
* Example data and a Moab example script can be found here:<br />
/opt/bwhpc/common/chem/orca/3.0.1/bwhpc-examples<br />
[...]<br />
</pre><br />
<br><br />
----<br />
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Orca&diff=12618JUSTUS2/Software/Orca2024-02-29T07:18:43Z<p>J Kucera: </p>
<hr />
<div>{{Softwarepage|chem/orca}}<br />
<br />
{| width=600px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/orca/5.0.4<br />
|-<br />
| Availability<br />
| [[bwUniCluster]] &#124; [[JUSTUS2]]<br />
|-<br />
| License<br />
| [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA]<br />
|-<br />
|Citing<br />
| As described in the [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf manual]. Refer to Chapter 'Publications Related to ORCA' for guidance on citation.<br />
|-<br />
| Links<br />
| [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Forum Portal] &#124; [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|}<br />
<br><br />
= Description =<br />
<br />
'''ORCA''' is a comprehensive, fully parallelized quantum chemistry package designed for advanced electronic structure methods. It encompasses density functional theory, many-body perturbation theory, coupled cluster methods, multireference methods, and semi-empirical quantum chemistry approaches. ORCA is capable of computing a wide range of molecular properties and serves as a fully integrated system for multi-level calculations, including QM/MM, ONIOM, and embedded crystals.<br />
<br />
Additionally, ORCA offers several advanced features to improve computational efficiency and accuracy. These include local correlation methods, starting with PNOs and expanded to DLPNO to reduce the computational cost of coupled cluster calculations. It also incorporates RIJCOSX for efficient handling of Hartree-Fock based methods.<br />
<br />
Furthermore, ORCA provides NEB-TS for studying reaction pathways and offers various methods for accurately calculating excited states, such as TD-DFT, EOM-CCSD, STEOM-CCSD, CASSCF with NEVPT2 or CASPT2, as well as molecular dynamics and multi-scale QM-MM models.<br />
<br />
Please refer to documentation provided by the ORCA developers in the first place for more detailed information.<br />
<br />
https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf<br />
https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wcms.1606<br />
https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.81<br />
<br />
'''ORCA''' is a modern electronic structure program package. It is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules.<br />
<br><br />
ORCA is able to carry out geometry optimizations and to predict a large number of spectroscopic parameters at different levels of theory. Besides the use of Hartee Fock theory, density functional theory (DFT) and semiempirical methods, high level ab initio quantum chemical methods, based on the configuration interaction and coupled cluster methods, are included into ORCA to an increasing degree.<br />
<br><br />
Due to the user-friendly style, ORCA is considered to be a helpful tool not only for computational chemists, but also for chemists, physicists and biologists that are interested in developing the full information content of their experimental data with help of calculations. <br />
<br><br><br />
<u>Implemented Methods</u><br />
* Semiempirical INDO/S, MNDO, AM1, PM3, NDDO/1<br />
* Hartee Fock theory (RHF, UHF, ROHF and CASSCF) all in direct, semidirect, or conventional mode, different RI approximations<br />
* DFT including a reasonably large number of exchange and correlation functionals including hybrid DFT and the most recent double hybrid functionals (see below).<br />
* High level single reference correlation models: CCSD(T), QCISD(T), CEPA, CPF (with and without RI, Local)<br />
* High level ab-initio individual selecting multireference methods (MRCI, MRMP2, MRMP3, MRMP4, MRACPF, MRAQCC, SORCI, DDCI) for ground- and excited-states.<br />
* Geometry optimization in redundant internal coordinates using analytical gradient techniques for all SCF methods as well as MP2.<br />
* Excited state calculations via TD-DFT and CI-singles (CIS). For CIS an analytic gradient is also available. The doubles correction is available for CIS(D) in an efficient implementation.<br />
* Scalar relativistic ZORA, IORA and Douglas-Kroll-Hess (DKH) approaches, picture change effects, all-electron basis sets, effective core potentials<br />
* The COSMO model is available throughout the package for continuum dielectric modeling of the environment.<br />
* QM/MM interface to GROMACS<br />
* Double hybrid functionals including a fraction of nonlocal correlation. Analytic gradients are also available (these methods were invented by the Grimme group).<br />
* Van der Waals correct density functionals.<br />
<br><br />
For more information on features please visit [https://orcaforum.cec.mpg.de/ ''The ORCA Portal of the Max-Planck Institute''] web page.<br />
<br><br />
<br><br />
<br />
= Versions and Availability =<br />
<br />
On the command line interface of any bwHPC cluster you'll get a list of available versions by using<br />
the command<br />
<br><br />
''''module avail chem/orca''''.<br />
<pre><br />
$ module avail chem/orca # bwUniCluster<br />
--------------------- /opt/bwhpc/common/modulefiles ----------------------<br />
chem/orca/3.0.1 chem/orca/3.0.3<br />
</pre><br />
<br><br />
<br />
= License =<br />
The ORCA license is considered as a "Research group" license. Thus anyone who directly associated with your research group is covered by the license and may share your copy of ORCA on all computer resources of your group.<br />
<br><br />
This license only applies to academic users. Commercial use of ORCA is prohibited under the terms of this license.<br />
<br><br />
[https://orcaforum.cec.mpg.de/license.html Complete ORCA Users License Agreement]<br />
<br><br />
<br><br />
= Usage =<br />
== Loading the module ==<br />
You can load the default version of ''ORCA'' with the command ''''module load chem/orca''''.<br />
<pre><br />
$ module load chem/orca<br />
module avail chem/orca<br />
------------------------ /opt/bwhpc/common/modulefiles ----------------------<br />
chem/orca/3.0.3 chem/orca/3.0.3-openmpi-1.6.5(default)<br />
$ module load chem/orca<br />
</pre><br />
The module will try to load modules it needs to function (e.g. compiler/intel). If loading the module fails, check if you have already loaded one of those modules, but not in the version needed for Orca.<br />
<br><br><br />
If you wish to load a specific (older) version, you can do so using e.g.<br />
<br> <br />
''''module load chem/orca/'''version' to load the version you desires.<br />
<pre><br />
$ module load chem/orca/3.0.1 # bwUniCluster example<br />
Please do not use this module if you do not own a valid ORCA group license.<br />
Please cite ORCA in your publications according to ORCA documentation.<br />
Please read 'module help chem/orca/3.0.1' before using ORCA.<br />
</pre><br />
<br><br />
<font color=red>Orca 3.0.3 mit OpenMPI 1.6.5 läuft stabiler! <br />
Einige MPI-Abstürze sind nachweislich (gleicher Job) damit durchgelaufen.<br><br />
This version is known to be more stable with bigger jobs. Try this one if you get problems with other versions of Orca!</font><br><br />
<font color=green>This version is the default now. [[#Versions and Availability|Only available on the Chemical Cluster 'Justus']]!</font><br />
<br><br />
<br />
== Program Binaries ==<br />
You can find the ORCA binaries in the main folder of the ORCA system.<br />
<br><br />
After loading the ORCA module (''module load chem/orca/'version''') this path is also set to the local $PATH- and [[#ORCA-Specific Environments|$ORCA_BIN_DIR environments]].<br />
<pre><br />
$ ls -x $ORCA_BIN_DIR<br />
bwhpc-examples manual modulefiles orca orca_2aim orca_2mkl<br />
orca_anoint orca_anoint_mpi orca_asa orca_casscf orca_casscf_mpi orca_chelpg<br />
orca_ciprep orca_cis orca_cis_mpi orca_cleanup orca_cleanup_mpi orca_cpcasscf<br />
orca_cpscf orca_cpscf_mpi orca_eca orca_ecplib orca_eprnmr orca_eprnmr_mpi<br />
orca_euler orca_fci orca_fitpes orca_gstep orca_gtoint orca_gtoint_mpi<br />
orca_loc orca_mapspc orca_md orca_mdci orca_mdci_mpi orca_mergefrag<br />
orca_mp2 orca_mp2_mpi orca_mrci orca_mrci_mpi orca_ndoint orca_numfreq<br />
orca_pc orca_pc_mpi orca_plot orca_pltvib orca_pop orca_rel<br />
orca_rocis orca_rocis_mpi orca_scf orca_scfgrad orca_scfgrad_mpi orca_scfhess<br />
orca_scfhess_mpi orca_scf_mpi orca_soc orca_soc_mpi orca_vib orca_vpot<br />
otool_cosmo otool_gcp otool_smd<br />
$ <br />
</pre><br />
Only the programs with the suffix <font color=green>'''_mpi'''</font> are compiled including OPENMPI functionality.<br />
<br><br />
<br />
== Disk Usage ==<br />
Scratch files are written to the current directory by default.<br><br />
Please change to a local directory or to '''your local workspace''' (preferred) before starting your calculations. <br />
<br><br><br />
'calc_repo' is an example name of a repository you created by using the command 'ws_allocate'.<br />
<pre><br />
$ cd $(ws_find calc_repo)<br />
['your-id'-calc_repo-0]$ pwd<br />
/work/workspace/scratch/'your-id'-calc_repo-0<br />
['your-id'-calc_repo-0]$ <br />
</pre><br />
<br />
== Examples ==<br />
You can copy a simple interactive example to your '''workspace''' and run it, using 'msub'<br />
<pre><br />
$ cd $(ws_find calc_repo)<br />
$ cp $ORCA_EXA_DIR/bwhpc-orca-example.moab .<br />
$ cp bwhpc-orca-example.moab myorcajob.moab <br />
§ vi myorcajob.moab # do your own modifications<br />
$ msub myorcajob.moab # start job submission<br />
</pre><br />
<br><br />
= ORCA-Specific Environments =<br />
To see a list of all ORCA environments set by the 'module load chem/orca/version'-command,<br />
use ''''env | grep ORCA''''<br><br />
Or try the command ''''module show 'chem/orca'''/version'.<br />
<pre><br />
$ module load chem/orca/3.0.3<br />
$ env | grep ORCA<br />
ORCA_VERSION=3.0.3<br />
ORCA_MAN_DIR=/opt/bwhpc/common/chem/orca/3.0.3/manual<br />
ORCA_EXA_DIR=/opt/bwhpc/common/chem/orca/3.0.3/bwhpc-examples<br />
ORCA_BIN_DIR=/opt/bwhpc/common/chem/orca/3.0.3<br />
ORCA_HOME=/opt/bwhpc/common/chem/orca/3.0.3<br />
</pre><br />
<br><br />
= Version-Specific Information =<br />
For a more detailed information specific to a specific ORCA version, see the information available via the module system with the command ''''module help chem/orca''''.<br />
<br><br />
For a small abstract what ORCA is about use the command ''''module whatis chem/orca''''.<br />
<br><br><br />
<u>Examples</u><br />
<pre><br />
$ module avail chem/orca<br />
----------------------- /opt/bwhpc/common/modulefiles ---------------------------<br />
chem/orca/3.0.1 chem/orca/3.0.3<br />
<br />
$ module whatis chem/orca/3.0.1<br />
chem/orca/3.0.1 : Quantum chemistry package ORCA, version 3.0.1<br />
(command '/opt/bwhpc/common/chem/orca/3.0.1/orca')<br />
<br />
$ module help chem/orca/3.0.1<br />
----------- Module Specific Help for 'chem/orca/3.0.1' ------------<br />
This module provides the quantum chemistry package ORCA version 3.0.1<br />
via command '/opt/bwhpc/common/chem/orca/3.0.1/orca' <br />
[...] <br />
Documentation: <br />
* Max-Planck-Institut fuer Chemische Energiekonversion <br />
https://cec.mpg.de/forum/portal.php<br />
* New features for version 3.0.1<br />
https://cec.mpg.de/forum/portal.php#a3<br />
* Manuals in pdf format:<br />
/opt/bwhpc/common/chem/orca/3.0.1/manual<br />
* Example data and a Moab example script can be found here:<br />
/opt/bwhpc/common/chem/orca/3.0.1/bwhpc-examples<br />
[...]<br />
</pre><br />
<br><br />
----<br />
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Orca&diff=12617JUSTUS2/Software/Orca2024-02-29T07:16:32Z<p>J Kucera: /* Description */</p>
<hr />
<div>{{Softwarepage|chem/orca}}<br />
<br />
{| width=600px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/orca/5.0.4<br />
|-<br />
| Availability<br />
| [[bwUniCluster]] &#124; [[JUSTUS2]]<br />
|-<br />
| License<br />
| [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA]<br />
|-<br />
|Citing<br />
| As described in the [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf manual]. Refer to Chapter 'Publications Related to ORCA' for guidance on citation.<br />
|-<br />
| Links<br />
| [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Forum Portal] &#124; [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|}<br />
<br><br />
= Description =<br />
<br />
'''ORCA''' is a comprehensive, fully parallelized quantum chemistry package designed for advanced electronic structure methods. It encompasses density functional theory, many-body perturbation theory, coupled cluster methods, multireference methods, and semi-empirical quantum chemistry approaches. ORCA is capable of computing a wide range of molecular properties and serves as a fully integrated system for multi-level calculations, including QM/MM, ONIOM, and embedded crystals.<br />
<br />
Additionally, ORCA offers several advanced features to improve computational efficiency and accuracy. These include local correlation methods, starting with PNOs and expanded to DLPNO to reduce the computational cost of coupled cluster calculations. It also incorporates RIJCOSX for efficient handling of Hartree-Fock based methods.<br />
<br />
Furthermore, ORCA provides NEB-TS for studying reaction pathways and offers various methods for accurately calculating excited states, such as TD-DFT, EOM-CCSD, STEOM-CCSD, CASSCF with NEVPT2 or CASPT2, as well as molecular dynamics and multi-scale QM-MM models.<br />
<br />
Please refer to documentation provided by the ORCA developers in the first place for more detailed information.<br />
<br />
'''ORCA''' is a modern electronic structure program package. It is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules.<br />
<br><br />
ORCA is able to carry out geometry optimizations and to predict a large number of spectroscopic parameters at different levels of theory. Besides the use of Hartee Fock theory, density functional theory (DFT) and semiempirical methods, high level ab initio quantum chemical methods, based on the configuration interaction and coupled cluster methods, are included into ORCA to an increasing degree.<br />
<br><br />
Due to the user-friendly style, ORCA is considered to be a helpful tool not only for computational chemists, but also for chemists, physicists and biologists that are interested in developing the full information content of their experimental data with help of calculations. <br />
<br><br><br />
<u>Implemented Methods</u><br />
* Semiempirical INDO/S, MNDO, AM1, PM3, NDDO/1<br />
* Hartee Fock theory (RHF, UHF, ROHF and CASSCF) all in direct, semidirect, or conventional mode, different RI approximations<br />
* DFT including a reasonably large number of exchange and correlation functionals including hybrid DFT and the most recent double hybrid functionals (see below).<br />
* High level single reference correlation models: CCSD(T), QCISD(T), CEPA, CPF (with and without RI, Local)<br />
* High level ab-initio individual selecting multireference methods (MRCI, MRMP2, MRMP3, MRMP4, MRACPF, MRAQCC, SORCI, DDCI) for ground- and excited-states.<br />
* Geometry optimization in redundant internal coordinates using analytical gradient techniques for all SCF methods as well as MP2.<br />
* Excited state calculations via TD-DFT and CI-singles (CIS). For CIS an analytic gradient is also available. The doubles correction is available for CIS(D) in an efficient implementation.<br />
* Scalar relativistic ZORA, IORA and Douglas-Kroll-Hess (DKH) approaches, picture change effects, all-electron basis sets, effective core potentials<br />
* The COSMO model is available throughout the package for continuum dielectric modeling of the environment.<br />
* QM/MM interface to GROMACS<br />
* Double hybrid functionals including a fraction of nonlocal correlation. Analytic gradients are also available (these methods were invented by the Grimme group).<br />
* Van der Waals correct density functionals.<br />
<br><br />
For more information on features please visit [https://orcaforum.cec.mpg.de/ ''The ORCA Portal of the Max-Planck Institute''] web page.<br />
<br><br />
<br><br />
<br />
= Versions and Availability =<br />
<br />
On the command line interface of any bwHPC cluster you'll get a list of available versions by using<br />
the command<br />
<br><br />
''''module avail chem/orca''''.<br />
<pre><br />
$ module avail chem/orca # bwUniCluster<br />
--------------------- /opt/bwhpc/common/modulefiles ----------------------<br />
chem/orca/3.0.1 chem/orca/3.0.3<br />
</pre><br />
<br><br />
<br />
= License =<br />
The ORCA license is considered as a "Research group" license. Thus anyone who directly associated with your research group is covered by the license and may share your copy of ORCA on all computer resources of your group.<br />
<br><br />
This license only applies to academic users. Commercial use of ORCA is prohibited under the terms of this license.<br />
<br><br />
[https://orcaforum.cec.mpg.de/license.html Complete ORCA Users License Agreement]<br />
<br><br />
<br><br />
= Usage =<br />
== Loading the module ==<br />
You can load the default version of ''ORCA'' with the command ''''module load chem/orca''''.<br />
<pre><br />
$ module load chem/orca<br />
module avail chem/orca<br />
------------------------ /opt/bwhpc/common/modulefiles ----------------------<br />
chem/orca/3.0.3 chem/orca/3.0.3-openmpi-1.6.5(default)<br />
$ module load chem/orca<br />
</pre><br />
The module will try to load modules it needs to function (e.g. compiler/intel). If loading the module fails, check if you have already loaded one of those modules, but not in the version needed for Orca.<br />
<br><br><br />
If you wish to load a specific (older) version, you can do so using e.g.<br />
<br> <br />
''''module load chem/orca/'''version' to load the version you desires.<br />
<pre><br />
$ module load chem/orca/3.0.1 # bwUniCluster example<br />
Please do not use this module if you do not own a valid ORCA group license.<br />
Please cite ORCA in your publications according to ORCA documentation.<br />
Please read 'module help chem/orca/3.0.1' before using ORCA.<br />
</pre><br />
<br><br />
<font color=red>Orca 3.0.3 mit OpenMPI 1.6.5 läuft stabiler! <br />
Einige MPI-Abstürze sind nachweislich (gleicher Job) damit durchgelaufen.<br><br />
This version is known to be more stable with bigger jobs. Try this one if you get problems with other versions of Orca!</font><br><br />
<font color=green>This version is the default now. [[#Versions and Availability|Only available on the Chemical Cluster 'Justus']]!</font><br />
<br><br />
<br />
== Program Binaries ==<br />
You can find the ORCA binaries in the main folder of the ORCA system.<br />
<br><br />
After loading the ORCA module (''module load chem/orca/'version''') this path is also set to the local $PATH- and [[#ORCA-Specific Environments|$ORCA_BIN_DIR environments]].<br />
<pre><br />
$ ls -x $ORCA_BIN_DIR<br />
bwhpc-examples manual modulefiles orca orca_2aim orca_2mkl<br />
orca_anoint orca_anoint_mpi orca_asa orca_casscf orca_casscf_mpi orca_chelpg<br />
orca_ciprep orca_cis orca_cis_mpi orca_cleanup orca_cleanup_mpi orca_cpcasscf<br />
orca_cpscf orca_cpscf_mpi orca_eca orca_ecplib orca_eprnmr orca_eprnmr_mpi<br />
orca_euler orca_fci orca_fitpes orca_gstep orca_gtoint orca_gtoint_mpi<br />
orca_loc orca_mapspc orca_md orca_mdci orca_mdci_mpi orca_mergefrag<br />
orca_mp2 orca_mp2_mpi orca_mrci orca_mrci_mpi orca_ndoint orca_numfreq<br />
orca_pc orca_pc_mpi orca_plot orca_pltvib orca_pop orca_rel<br />
orca_rocis orca_rocis_mpi orca_scf orca_scfgrad orca_scfgrad_mpi orca_scfhess<br />
orca_scfhess_mpi orca_scf_mpi orca_soc orca_soc_mpi orca_vib orca_vpot<br />
otool_cosmo otool_gcp otool_smd<br />
$ <br />
</pre><br />
Only the programs with the suffix <font color=green>'''_mpi'''</font> are compiled including OPENMPI functionality.<br />
<br><br />
<br />
== Disk Usage ==<br />
Scratch files are written to the current directory by default.<br><br />
Please change to a local directory or to '''your local workspace''' (preferred) before starting your calculations. <br />
<br><br><br />
'calc_repo' is an example name of a repository you created by using the command 'ws_allocate'.<br />
<pre><br />
$ cd $(ws_find calc_repo)<br />
['your-id'-calc_repo-0]$ pwd<br />
/work/workspace/scratch/'your-id'-calc_repo-0<br />
['your-id'-calc_repo-0]$ <br />
</pre><br />
<br />
== Examples ==<br />
You can copy a simple interactive example to your '''workspace''' and run it, using 'msub'<br />
<pre><br />
$ cd $(ws_find calc_repo)<br />
$ cp $ORCA_EXA_DIR/bwhpc-orca-example.moab .<br />
$ cp bwhpc-orca-example.moab myorcajob.moab <br />
§ vi myorcajob.moab # do your own modifications<br />
$ msub myorcajob.moab # start job submission<br />
</pre><br />
<br><br />
= ORCA-Specific Environments =<br />
To see a list of all ORCA environments set by the 'module load chem/orca/version'-command,<br />
use ''''env | grep ORCA''''<br><br />
Or try the command ''''module show 'chem/orca'''/version'.<br />
<pre><br />
$ module load chem/orca/3.0.3<br />
$ env | grep ORCA<br />
ORCA_VERSION=3.0.3<br />
ORCA_MAN_DIR=/opt/bwhpc/common/chem/orca/3.0.3/manual<br />
ORCA_EXA_DIR=/opt/bwhpc/common/chem/orca/3.0.3/bwhpc-examples<br />
ORCA_BIN_DIR=/opt/bwhpc/common/chem/orca/3.0.3<br />
ORCA_HOME=/opt/bwhpc/common/chem/orca/3.0.3<br />
</pre><br />
<br><br />
= Version-Specific Information =<br />
For a more detailed information specific to a specific ORCA version, see the information available via the module system with the command ''''module help chem/orca''''.<br />
<br><br />
For a small abstract what ORCA is about use the command ''''module whatis chem/orca''''.<br />
<br><br><br />
<u>Examples</u><br />
<pre><br />
$ module avail chem/orca<br />
----------------------- /opt/bwhpc/common/modulefiles ---------------------------<br />
chem/orca/3.0.1 chem/orca/3.0.3<br />
<br />
$ module whatis chem/orca/3.0.1<br />
chem/orca/3.0.1 : Quantum chemistry package ORCA, version 3.0.1<br />
(command '/opt/bwhpc/common/chem/orca/3.0.1/orca')<br />
<br />
$ module help chem/orca/3.0.1<br />
----------- Module Specific Help for 'chem/orca/3.0.1' ------------<br />
This module provides the quantum chemistry package ORCA version 3.0.1<br />
via command '/opt/bwhpc/common/chem/orca/3.0.1/orca' <br />
[...] <br />
Documentation: <br />
* Max-Planck-Institut fuer Chemische Energiekonversion <br />
https://cec.mpg.de/forum/portal.php<br />
* New features for version 3.0.1<br />
https://cec.mpg.de/forum/portal.php#a3<br />
* Manuals in pdf format:<br />
/opt/bwhpc/common/chem/orca/3.0.1/manual<br />
* Example data and a Moab example script can be found here:<br />
/opt/bwhpc/common/chem/orca/3.0.1/bwhpc-examples<br />
[...]<br />
</pre><br />
<br><br />
----<br />
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Orca&diff=12616JUSTUS2/Software/Orca2024-02-28T16:19:41Z<p>J Kucera: </p>
<hr />
<div>{{Softwarepage|chem/orca}}<br />
<br />
{| width=600px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/orca/5.0.4<br />
|-<br />
| Availability<br />
| [[bwUniCluster]] &#124; [[JUSTUS2]]<br />
|-<br />
| License<br />
| [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA]<br />
|-<br />
|Citing<br />
| As described in the [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf manual]. Refer to Chapter 'Publications Related to ORCA' for guidance on citation.<br />
|-<br />
| Links<br />
| [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Forum Portal] &#124; [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|}<br />
<br><br />
= Description =<br />
'''ORCA''' is a modern electronic structure program package. It is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules.<br />
<br><br />
ORCA is able to carry out geometry optimizations and to predict a large number of spectroscopic parameters at different levels of theory. Besides the use of Hartee Fock theory, density functional theory (DFT) and semiempirical methods, high level ab initio quantum chemical methods, based on the configuration interaction and coupled cluster methods, are included into ORCA to an increasing degree.<br />
<br><br />
Due to the user-friendly style, ORCA is considered to be a helpful tool not only for computational chemists, but also for chemists, physicists and biologists that are interested in developing the full information content of their experimental data with help of calculations. <br />
<br><br><br />
<u>Implemented Methods</u><br />
* Semiempirical INDO/S, MNDO, AM1, PM3, NDDO/1<br />
* Hartee Fock theory (RHF, UHF, ROHF and CASSCF) all in direct, semidirect, or conventional mode, different RI approximations<br />
* DFT including a reasonably large number of exchange and correlation functionals including hybrid DFT and the most recent double hybrid functionals (see below).<br />
* High level single reference correlation models: CCSD(T), QCISD(T), CEPA, CPF (with and without RI, Local)<br />
* High level ab-initio individual selecting multireference methods (MRCI, MRMP2, MRMP3, MRMP4, MRACPF, MRAQCC, SORCI, DDCI) for ground- and excited-states.<br />
* Geometry optimization in redundant internal coordinates using analytical gradient techniques for all SCF methods as well as MP2.<br />
* Excited state calculations via TD-DFT and CI-singles (CIS). For CIS an analytic gradient is also available. The doubles correction is available for CIS(D) in an efficient implementation.<br />
* Scalar relativistic ZORA, IORA and Douglas-Kroll-Hess (DKH) approaches, picture change effects, all-electron basis sets, effective core potentials<br />
* The COSMO model is available throughout the package for continuum dielectric modeling of the environment.<br />
* QM/MM interface to GROMACS<br />
* Double hybrid functionals including a fraction of nonlocal correlation. Analytic gradients are also available (these methods were invented by the Grimme group).<br />
* Van der Waals correct density functionals.<br />
<br><br />
For more information on features please visit [https://orcaforum.cec.mpg.de/ ''The ORCA Portal of the Max-Planck Institute''] web page.<br />
<br><br />
<br><br />
<br />
= Versions and Availability =<br />
<br />
On the command line interface of any bwHPC cluster you'll get a list of available versions by using<br />
the command<br />
<br><br />
''''module avail chem/orca''''.<br />
<pre><br />
$ module avail chem/orca # bwUniCluster<br />
--------------------- /opt/bwhpc/common/modulefiles ----------------------<br />
chem/orca/3.0.1 chem/orca/3.0.3<br />
</pre><br />
<br><br />
<br />
= License =<br />
The ORCA license is considered as a "Research group" license. Thus anyone who directly associated with your research group is covered by the license and may share your copy of ORCA on all computer resources of your group.<br />
<br><br />
This license only applies to academic users. Commercial use of ORCA is prohibited under the terms of this license.<br />
<br><br />
[https://orcaforum.cec.mpg.de/license.html Complete ORCA Users License Agreement]<br />
<br><br />
<br><br />
= Usage =<br />
== Loading the module ==<br />
You can load the default version of ''ORCA'' with the command ''''module load chem/orca''''.<br />
<pre><br />
$ module load chem/orca<br />
module avail chem/orca<br />
------------------------ /opt/bwhpc/common/modulefiles ----------------------<br />
chem/orca/3.0.3 chem/orca/3.0.3-openmpi-1.6.5(default)<br />
$ module load chem/orca<br />
</pre><br />
The module will try to load modules it needs to function (e.g. compiler/intel). If loading the module fails, check if you have already loaded one of those modules, but not in the version needed for Orca.<br />
<br><br><br />
If you wish to load a specific (older) version, you can do so using e.g.<br />
<br> <br />
''''module load chem/orca/'''version' to load the version you desires.<br />
<pre><br />
$ module load chem/orca/3.0.1 # bwUniCluster example<br />
Please do not use this module if you do not own a valid ORCA group license.<br />
Please cite ORCA in your publications according to ORCA documentation.<br />
Please read 'module help chem/orca/3.0.1' before using ORCA.<br />
</pre><br />
<br><br />
<font color=red>Orca 3.0.3 mit OpenMPI 1.6.5 läuft stabiler! <br />
Einige MPI-Abstürze sind nachweislich (gleicher Job) damit durchgelaufen.<br><br />
This version is known to be more stable with bigger jobs. Try this one if you get problems with other versions of Orca!</font><br><br />
<font color=green>This version is the default now. [[#Versions and Availability|Only available on the Chemical Cluster 'Justus']]!</font><br />
<br><br />
<br />
== Program Binaries ==<br />
You can find the ORCA binaries in the main folder of the ORCA system.<br />
<br><br />
After loading the ORCA module (''module load chem/orca/'version''') this path is also set to the local $PATH- and [[#ORCA-Specific Environments|$ORCA_BIN_DIR environments]].<br />
<pre><br />
$ ls -x $ORCA_BIN_DIR<br />
bwhpc-examples manual modulefiles orca orca_2aim orca_2mkl<br />
orca_anoint orca_anoint_mpi orca_asa orca_casscf orca_casscf_mpi orca_chelpg<br />
orca_ciprep orca_cis orca_cis_mpi orca_cleanup orca_cleanup_mpi orca_cpcasscf<br />
orca_cpscf orca_cpscf_mpi orca_eca orca_ecplib orca_eprnmr orca_eprnmr_mpi<br />
orca_euler orca_fci orca_fitpes orca_gstep orca_gtoint orca_gtoint_mpi<br />
orca_loc orca_mapspc orca_md orca_mdci orca_mdci_mpi orca_mergefrag<br />
orca_mp2 orca_mp2_mpi orca_mrci orca_mrci_mpi orca_ndoint orca_numfreq<br />
orca_pc orca_pc_mpi orca_plot orca_pltvib orca_pop orca_rel<br />
orca_rocis orca_rocis_mpi orca_scf orca_scfgrad orca_scfgrad_mpi orca_scfhess<br />
orca_scfhess_mpi orca_scf_mpi orca_soc orca_soc_mpi orca_vib orca_vpot<br />
otool_cosmo otool_gcp otool_smd<br />
$ <br />
</pre><br />
Only the programs with the suffix <font color=green>'''_mpi'''</font> are compiled including OPENMPI functionality.<br />
<br><br />
<br />
== Disk Usage ==<br />
Scratch files are written to the current directory by default.<br><br />
Please change to a local directory or to '''your local workspace''' (preferred) before starting your calculations. <br />
<br><br><br />
'calc_repo' is an example name of a repository you created by using the command 'ws_allocate'.<br />
<pre><br />
$ cd $(ws_find calc_repo)<br />
['your-id'-calc_repo-0]$ pwd<br />
/work/workspace/scratch/'your-id'-calc_repo-0<br />
['your-id'-calc_repo-0]$ <br />
</pre><br />
<br />
== Examples ==<br />
You can copy a simple interactive example to your '''workspace''' and run it, using 'msub'<br />
<pre><br />
$ cd $(ws_find calc_repo)<br />
$ cp $ORCA_EXA_DIR/bwhpc-orca-example.moab .<br />
$ cp bwhpc-orca-example.moab myorcajob.moab <br />
§ vi myorcajob.moab # do your own modifications<br />
$ msub myorcajob.moab # start job submission<br />
</pre><br />
<br><br />
= ORCA-Specific Environments =<br />
To see a list of all ORCA environments set by the 'module load chem/orca/version'-command,<br />
use ''''env | grep ORCA''''<br><br />
Or try the command ''''module show 'chem/orca'''/version'.<br />
<pre><br />
$ module load chem/orca/3.0.3<br />
$ env | grep ORCA<br />
ORCA_VERSION=3.0.3<br />
ORCA_MAN_DIR=/opt/bwhpc/common/chem/orca/3.0.3/manual<br />
ORCA_EXA_DIR=/opt/bwhpc/common/chem/orca/3.0.3/bwhpc-examples<br />
ORCA_BIN_DIR=/opt/bwhpc/common/chem/orca/3.0.3<br />
ORCA_HOME=/opt/bwhpc/common/chem/orca/3.0.3<br />
</pre><br />
<br><br />
= Version-Specific Information =<br />
For a more detailed information specific to a specific ORCA version, see the information available via the module system with the command ''''module help chem/orca''''.<br />
<br><br />
For a small abstract what ORCA is about use the command ''''module whatis chem/orca''''.<br />
<br><br><br />
<u>Examples</u><br />
<pre><br />
$ module avail chem/orca<br />
----------------------- /opt/bwhpc/common/modulefiles ---------------------------<br />
chem/orca/3.0.1 chem/orca/3.0.3<br />
<br />
$ module whatis chem/orca/3.0.1<br />
chem/orca/3.0.1 : Quantum chemistry package ORCA, version 3.0.1<br />
(command '/opt/bwhpc/common/chem/orca/3.0.1/orca')<br />
<br />
$ module help chem/orca/3.0.1<br />
----------- Module Specific Help for 'chem/orca/3.0.1' ------------<br />
This module provides the quantum chemistry package ORCA version 3.0.1<br />
via command '/opt/bwhpc/common/chem/orca/3.0.1/orca' <br />
[...] <br />
Documentation: <br />
* Max-Planck-Institut fuer Chemische Energiekonversion <br />
https://cec.mpg.de/forum/portal.php<br />
* New features for version 3.0.1<br />
https://cec.mpg.de/forum/portal.php#a3<br />
* Manuals in pdf format:<br />
/opt/bwhpc/common/chem/orca/3.0.1/manual<br />
* Example data and a Moab example script can be found here:<br />
/opt/bwhpc/common/chem/orca/3.0.1/bwhpc-examples<br />
[...]<br />
</pre><br />
<br><br />
----<br />
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Orca&diff=12615JUSTUS2/Software/Orca2024-02-28T16:18:57Z<p>J Kucera: </p>
<hr />
<div>{{Softwarepage|chem/orca}}<br />
<br />
{| width=600px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/orca<br />
|-<br />
| Availability<br />
| [[bwUniCluster]] &#124; [[JUSTUS2]]<br />
|-<br />
| License<br />
| [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA]<br />
|-<br />
|Citing<br />
| As described in the [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf manual]. Refer to Chapter 'Publications Related to ORCA' for guidance on citation.<br />
|-<br />
| Links<br />
| [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Forum Portal] &#124; [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|}<br />
<br><br />
= Description =<br />
'''ORCA''' is a modern electronic structure program package. It is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules.<br />
<br><br />
ORCA is able to carry out geometry optimizations and to predict a large number of spectroscopic parameters at different levels of theory. Besides the use of Hartee Fock theory, density functional theory (DFT) and semiempirical methods, high level ab initio quantum chemical methods, based on the configuration interaction and coupled cluster methods, are included into ORCA to an increasing degree.<br />
<br><br />
Due to the user-friendly style, ORCA is considered to be a helpful tool not only for computational chemists, but also for chemists, physicists and biologists that are interested in developing the full information content of their experimental data with help of calculations. <br />
<br><br><br />
<u>Implemented Methods</u><br />
* Semiempirical INDO/S, MNDO, AM1, PM3, NDDO/1<br />
* Hartee Fock theory (RHF, UHF, ROHF and CASSCF) all in direct, semidirect, or conventional mode, different RI approximations<br />
* DFT including a reasonably large number of exchange and correlation functionals including hybrid DFT and the most recent double hybrid functionals (see below).<br />
* High level single reference correlation models: CCSD(T), QCISD(T), CEPA, CPF (with and without RI, Local)<br />
* High level ab-initio individual selecting multireference methods (MRCI, MRMP2, MRMP3, MRMP4, MRACPF, MRAQCC, SORCI, DDCI) for ground- and excited-states.<br />
* Geometry optimization in redundant internal coordinates using analytical gradient techniques for all SCF methods as well as MP2.<br />
* Excited state calculations via TD-DFT and CI-singles (CIS). For CIS an analytic gradient is also available. The doubles correction is available for CIS(D) in an efficient implementation.<br />
* Scalar relativistic ZORA, IORA and Douglas-Kroll-Hess (DKH) approaches, picture change effects, all-electron basis sets, effective core potentials<br />
* The COSMO model is available throughout the package for continuum dielectric modeling of the environment.<br />
* QM/MM interface to GROMACS<br />
* Double hybrid functionals including a fraction of nonlocal correlation. Analytic gradients are also available (these methods were invented by the Grimme group).<br />
* Van der Waals correct density functionals.<br />
<br><br />
For more information on features please visit [https://orcaforum.cec.mpg.de/ ''The ORCA Portal of the Max-Planck Institute''] web page.<br />
<br><br />
<br><br />
<br />
= Versions and Availability =<br />
<br />
On the command line interface of any bwHPC cluster you'll get a list of available versions by using<br />
the command<br />
<br><br />
''''module avail chem/orca''''.<br />
<pre><br />
$ module avail chem/orca # bwUniCluster<br />
--------------------- /opt/bwhpc/common/modulefiles ----------------------<br />
chem/orca/3.0.1 chem/orca/3.0.3<br />
</pre><br />
<br><br />
<br />
= License =<br />
The ORCA license is considered as a "Research group" license. Thus anyone who directly associated with your research group is covered by the license and may share your copy of ORCA on all computer resources of your group.<br />
<br><br />
This license only applies to academic users. Commercial use of ORCA is prohibited under the terms of this license.<br />
<br><br />
[https://orcaforum.cec.mpg.de/license.html Complete ORCA Users License Agreement]<br />
<br><br />
<br><br />
= Usage =<br />
== Loading the module ==<br />
You can load the default version of ''ORCA'' with the command ''''module load chem/orca''''.<br />
<pre><br />
$ module load chem/orca<br />
module avail chem/orca<br />
------------------------ /opt/bwhpc/common/modulefiles ----------------------<br />
chem/orca/3.0.3 chem/orca/3.0.3-openmpi-1.6.5(default)<br />
$ module load chem/orca<br />
</pre><br />
The module will try to load modules it needs to function (e.g. compiler/intel). If loading the module fails, check if you have already loaded one of those modules, but not in the version needed for Orca.<br />
<br><br><br />
If you wish to load a specific (older) version, you can do so using e.g.<br />
<br> <br />
''''module load chem/orca/'''version' to load the version you desires.<br />
<pre><br />
$ module load chem/orca/3.0.1 # bwUniCluster example<br />
Please do not use this module if you do not own a valid ORCA group license.<br />
Please cite ORCA in your publications according to ORCA documentation.<br />
Please read 'module help chem/orca/3.0.1' before using ORCA.<br />
</pre><br />
<br><br />
<font color=red>Orca 3.0.3 mit OpenMPI 1.6.5 läuft stabiler! <br />
Einige MPI-Abstürze sind nachweislich (gleicher Job) damit durchgelaufen.<br><br />
This version is known to be more stable with bigger jobs. Try this one if you get problems with other versions of Orca!</font><br><br />
<font color=green>This version is the default now. [[#Versions and Availability|Only available on the Chemical Cluster 'Justus']]!</font><br />
<br><br />
<br />
== Program Binaries ==<br />
You can find the ORCA binaries in the main folder of the ORCA system.<br />
<br><br />
After loading the ORCA module (''module load chem/orca/'version''') this path is also set to the local $PATH- and [[#ORCA-Specific Environments|$ORCA_BIN_DIR environments]].<br />
<pre><br />
$ ls -x $ORCA_BIN_DIR<br />
bwhpc-examples manual modulefiles orca orca_2aim orca_2mkl<br />
orca_anoint orca_anoint_mpi orca_asa orca_casscf orca_casscf_mpi orca_chelpg<br />
orca_ciprep orca_cis orca_cis_mpi orca_cleanup orca_cleanup_mpi orca_cpcasscf<br />
orca_cpscf orca_cpscf_mpi orca_eca orca_ecplib orca_eprnmr orca_eprnmr_mpi<br />
orca_euler orca_fci orca_fitpes orca_gstep orca_gtoint orca_gtoint_mpi<br />
orca_loc orca_mapspc orca_md orca_mdci orca_mdci_mpi orca_mergefrag<br />
orca_mp2 orca_mp2_mpi orca_mrci orca_mrci_mpi orca_ndoint orca_numfreq<br />
orca_pc orca_pc_mpi orca_plot orca_pltvib orca_pop orca_rel<br />
orca_rocis orca_rocis_mpi orca_scf orca_scfgrad orca_scfgrad_mpi orca_scfhess<br />
orca_scfhess_mpi orca_scf_mpi orca_soc orca_soc_mpi orca_vib orca_vpot<br />
otool_cosmo otool_gcp otool_smd<br />
$ <br />
</pre><br />
Only the programs with the suffix <font color=green>'''_mpi'''</font> are compiled including OPENMPI functionality.<br />
<br><br />
<br />
== Disk Usage ==<br />
Scratch files are written to the current directory by default.<br><br />
Please change to a local directory or to '''your local workspace''' (preferred) before starting your calculations. <br />
<br><br><br />
'calc_repo' is an example name of a repository you created by using the command 'ws_allocate'.<br />
<pre><br />
$ cd $(ws_find calc_repo)<br />
['your-id'-calc_repo-0]$ pwd<br />
/work/workspace/scratch/'your-id'-calc_repo-0<br />
['your-id'-calc_repo-0]$ <br />
</pre><br />
<br />
== Examples ==<br />
You can copy a simple interactive example to your '''workspace''' and run it, using 'msub'<br />
<pre><br />
$ cd $(ws_find calc_repo)<br />
$ cp $ORCA_EXA_DIR/bwhpc-orca-example.moab .<br />
$ cp bwhpc-orca-example.moab myorcajob.moab <br />
§ vi myorcajob.moab # do your own modifications<br />
$ msub myorcajob.moab # start job submission<br />
</pre><br />
<br><br />
= ORCA-Specific Environments =<br />
To see a list of all ORCA environments set by the 'module load chem/orca/version'-command,<br />
use ''''env | grep ORCA''''<br><br />
Or try the command ''''module show 'chem/orca'''/version'.<br />
<pre><br />
$ module load chem/orca/3.0.3<br />
$ env | grep ORCA<br />
ORCA_VERSION=3.0.3<br />
ORCA_MAN_DIR=/opt/bwhpc/common/chem/orca/3.0.3/manual<br />
ORCA_EXA_DIR=/opt/bwhpc/common/chem/orca/3.0.3/bwhpc-examples<br />
ORCA_BIN_DIR=/opt/bwhpc/common/chem/orca/3.0.3<br />
ORCA_HOME=/opt/bwhpc/common/chem/orca/3.0.3<br />
</pre><br />
<br><br />
= Version-Specific Information =<br />
For a more detailed information specific to a specific ORCA version, see the information available via the module system with the command ''''module help chem/orca''''.<br />
<br><br />
For a small abstract what ORCA is about use the command ''''module whatis chem/orca''''.<br />
<br><br><br />
<u>Examples</u><br />
<pre><br />
$ module avail chem/orca<br />
----------------------- /opt/bwhpc/common/modulefiles ---------------------------<br />
chem/orca/3.0.1 chem/orca/3.0.3<br />
<br />
$ module whatis chem/orca/3.0.1<br />
chem/orca/3.0.1 : Quantum chemistry package ORCA, version 3.0.1<br />
(command '/opt/bwhpc/common/chem/orca/3.0.1/orca')<br />
<br />
$ module help chem/orca/3.0.1<br />
----------- Module Specific Help for 'chem/orca/3.0.1' ------------<br />
This module provides the quantum chemistry package ORCA version 3.0.1<br />
via command '/opt/bwhpc/common/chem/orca/3.0.1/orca' <br />
[...] <br />
Documentation: <br />
* Max-Planck-Institut fuer Chemische Energiekonversion <br />
https://cec.mpg.de/forum/portal.php<br />
* New features for version 3.0.1<br />
https://cec.mpg.de/forum/portal.php#a3<br />
* Manuals in pdf format:<br />
/opt/bwhpc/common/chem/orca/3.0.1/manual<br />
* Example data and a Moab example script can be found here:<br />
/opt/bwhpc/common/chem/orca/3.0.1/bwhpc-examples<br />
[...]<br />
</pre><br />
<br><br />
----<br />
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Orca&diff=12614JUSTUS2/Software/Orca2024-02-28T16:18:11Z<p>J Kucera: </p>
<hr />
<div>{{Softwarepage|chem/orca}}<br />
<br />
{| width=600px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/orca<br />
|-<br />
| Availability<br />
| [[bwUniCluster]] &#124; [[JUSTUS2]]<br />
|-<br />
| License<br />
| [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA]<br />
|-<br />
|Citing<br />
| As described in the manual. Refer to Chapter 'Publications Related to ORCA' for guidance on citation.<br />
|-<br />
| Links<br />
| [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Forum Portal] &#124; [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|}<br />
<br><br />
= Description =<br />
'''ORCA''' is a modern electronic structure program package. It is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules.<br />
<br><br />
ORCA is able to carry out geometry optimizations and to predict a large number of spectroscopic parameters at different levels of theory. Besides the use of Hartee Fock theory, density functional theory (DFT) and semiempirical methods, high level ab initio quantum chemical methods, based on the configuration interaction and coupled cluster methods, are included into ORCA to an increasing degree.<br />
<br><br />
Due to the user-friendly style, ORCA is considered to be a helpful tool not only for computational chemists, but also for chemists, physicists and biologists that are interested in developing the full information content of their experimental data with help of calculations. <br />
<br><br><br />
<u>Implemented Methods</u><br />
* Semiempirical INDO/S, MNDO, AM1, PM3, NDDO/1<br />
* Hartee Fock theory (RHF, UHF, ROHF and CASSCF) all in direct, semidirect, or conventional mode, different RI approximations<br />
* DFT including a reasonably large number of exchange and correlation functionals including hybrid DFT and the most recent double hybrid functionals (see below).<br />
* High level single reference correlation models: CCSD(T), QCISD(T), CEPA, CPF (with and without RI, Local)<br />
* High level ab-initio individual selecting multireference methods (MRCI, MRMP2, MRMP3, MRMP4, MRACPF, MRAQCC, SORCI, DDCI) for ground- and excited-states.<br />
* Geometry optimization in redundant internal coordinates using analytical gradient techniques for all SCF methods as well as MP2.<br />
* Excited state calculations via TD-DFT and CI-singles (CIS). For CIS an analytic gradient is also available. The doubles correction is available for CIS(D) in an efficient implementation.<br />
* Scalar relativistic ZORA, IORA and Douglas-Kroll-Hess (DKH) approaches, picture change effects, all-electron basis sets, effective core potentials<br />
* The COSMO model is available throughout the package for continuum dielectric modeling of the environment.<br />
* QM/MM interface to GROMACS<br />
* Double hybrid functionals including a fraction of nonlocal correlation. Analytic gradients are also available (these methods were invented by the Grimme group).<br />
* Van der Waals correct density functionals.<br />
<br><br />
For more information on features please visit [https://orcaforum.cec.mpg.de/ ''The ORCA Portal of the Max-Planck Institute''] web page.<br />
<br><br />
<br><br />
<br />
= Versions and Availability =<br />
<br />
On the command line interface of any bwHPC cluster you'll get a list of available versions by using<br />
the command<br />
<br><br />
''''module avail chem/orca''''.<br />
<pre><br />
$ module avail chem/orca # bwUniCluster<br />
--------------------- /opt/bwhpc/common/modulefiles ----------------------<br />
chem/orca/3.0.1 chem/orca/3.0.3<br />
</pre><br />
<br><br />
<br />
= License =<br />
The ORCA license is considered as a "Research group" license. Thus anyone who directly associated with your research group is covered by the license and may share your copy of ORCA on all computer resources of your group.<br />
<br><br />
This license only applies to academic users. Commercial use of ORCA is prohibited under the terms of this license.<br />
<br><br />
[https://orcaforum.cec.mpg.de/license.html Complete ORCA Users License Agreement]<br />
<br><br />
<br><br />
= Usage =<br />
== Loading the module ==<br />
You can load the default version of ''ORCA'' with the command ''''module load chem/orca''''.<br />
<pre><br />
$ module load chem/orca<br />
module avail chem/orca<br />
------------------------ /opt/bwhpc/common/modulefiles ----------------------<br />
chem/orca/3.0.3 chem/orca/3.0.3-openmpi-1.6.5(default)<br />
$ module load chem/orca<br />
</pre><br />
The module will try to load modules it needs to function (e.g. compiler/intel). If loading the module fails, check if you have already loaded one of those modules, but not in the version needed for Orca.<br />
<br><br><br />
If you wish to load a specific (older) version, you can do so using e.g.<br />
<br> <br />
''''module load chem/orca/'''version' to load the version you desires.<br />
<pre><br />
$ module load chem/orca/3.0.1 # bwUniCluster example<br />
Please do not use this module if you do not own a valid ORCA group license.<br />
Please cite ORCA in your publications according to ORCA documentation.<br />
Please read 'module help chem/orca/3.0.1' before using ORCA.<br />
</pre><br />
<br><br />
<font color=red>Orca 3.0.3 mit OpenMPI 1.6.5 läuft stabiler! <br />
Einige MPI-Abstürze sind nachweislich (gleicher Job) damit durchgelaufen.<br><br />
This version is known to be more stable with bigger jobs. Try this one if you get problems with other versions of Orca!</font><br><br />
<font color=green>This version is the default now. [[#Versions and Availability|Only available on the Chemical Cluster 'Justus']]!</font><br />
<br><br />
<br />
== Program Binaries ==<br />
You can find the ORCA binaries in the main folder of the ORCA system.<br />
<br><br />
After loading the ORCA module (''module load chem/orca/'version''') this path is also set to the local $PATH- and [[#ORCA-Specific Environments|$ORCA_BIN_DIR environments]].<br />
<pre><br />
$ ls -x $ORCA_BIN_DIR<br />
bwhpc-examples manual modulefiles orca orca_2aim orca_2mkl<br />
orca_anoint orca_anoint_mpi orca_asa orca_casscf orca_casscf_mpi orca_chelpg<br />
orca_ciprep orca_cis orca_cis_mpi orca_cleanup orca_cleanup_mpi orca_cpcasscf<br />
orca_cpscf orca_cpscf_mpi orca_eca orca_ecplib orca_eprnmr orca_eprnmr_mpi<br />
orca_euler orca_fci orca_fitpes orca_gstep orca_gtoint orca_gtoint_mpi<br />
orca_loc orca_mapspc orca_md orca_mdci orca_mdci_mpi orca_mergefrag<br />
orca_mp2 orca_mp2_mpi orca_mrci orca_mrci_mpi orca_ndoint orca_numfreq<br />
orca_pc orca_pc_mpi orca_plot orca_pltvib orca_pop orca_rel<br />
orca_rocis orca_rocis_mpi orca_scf orca_scfgrad orca_scfgrad_mpi orca_scfhess<br />
orca_scfhess_mpi orca_scf_mpi orca_soc orca_soc_mpi orca_vib orca_vpot<br />
otool_cosmo otool_gcp otool_smd<br />
$ <br />
</pre><br />
Only the programs with the suffix <font color=green>'''_mpi'''</font> are compiled including OPENMPI functionality.<br />
<br><br />
<br />
== Disk Usage ==<br />
Scratch files are written to the current directory by default.<br><br />
Please change to a local directory or to '''your local workspace''' (preferred) before starting your calculations. <br />
<br><br><br />
'calc_repo' is an example name of a repository you created by using the command 'ws_allocate'.<br />
<pre><br />
$ cd $(ws_find calc_repo)<br />
['your-id'-calc_repo-0]$ pwd<br />
/work/workspace/scratch/'your-id'-calc_repo-0<br />
['your-id'-calc_repo-0]$ <br />
</pre><br />
<br />
== Examples ==<br />
You can copy a simple interactive example to your '''workspace''' and run it, using 'msub'<br />
<pre><br />
$ cd $(ws_find calc_repo)<br />
$ cp $ORCA_EXA_DIR/bwhpc-orca-example.moab .<br />
$ cp bwhpc-orca-example.moab myorcajob.moab <br />
§ vi myorcajob.moab # do your own modifications<br />
$ msub myorcajob.moab # start job submission<br />
</pre><br />
<br><br />
= ORCA-Specific Environments =<br />
To see a list of all ORCA environments set by the 'module load chem/orca/version'-command,<br />
use ''''env | grep ORCA''''<br><br />
Or try the command ''''module show 'chem/orca'''/version'.<br />
<pre><br />
$ module load chem/orca/3.0.3<br />
$ env | grep ORCA<br />
ORCA_VERSION=3.0.3<br />
ORCA_MAN_DIR=/opt/bwhpc/common/chem/orca/3.0.3/manual<br />
ORCA_EXA_DIR=/opt/bwhpc/common/chem/orca/3.0.3/bwhpc-examples<br />
ORCA_BIN_DIR=/opt/bwhpc/common/chem/orca/3.0.3<br />
ORCA_HOME=/opt/bwhpc/common/chem/orca/3.0.3<br />
</pre><br />
<br><br />
= Version-Specific Information =<br />
For a more detailed information specific to a specific ORCA version, see the information available via the module system with the command ''''module help chem/orca''''.<br />
<br><br />
For a small abstract what ORCA is about use the command ''''module whatis chem/orca''''.<br />
<br><br><br />
<u>Examples</u><br />
<pre><br />
$ module avail chem/orca<br />
----------------------- /opt/bwhpc/common/modulefiles ---------------------------<br />
chem/orca/3.0.1 chem/orca/3.0.3<br />
<br />
$ module whatis chem/orca/3.0.1<br />
chem/orca/3.0.1 : Quantum chemistry package ORCA, version 3.0.1<br />
(command '/opt/bwhpc/common/chem/orca/3.0.1/orca')<br />
<br />
$ module help chem/orca/3.0.1<br />
----------- Module Specific Help for 'chem/orca/3.0.1' ------------<br />
This module provides the quantum chemistry package ORCA version 3.0.1<br />
via command '/opt/bwhpc/common/chem/orca/3.0.1/orca' <br />
[...] <br />
Documentation: <br />
* Max-Planck-Institut fuer Chemische Energiekonversion <br />
https://cec.mpg.de/forum/portal.php<br />
* New features for version 3.0.1<br />
https://cec.mpg.de/forum/portal.php#a3<br />
* Manuals in pdf format:<br />
/opt/bwhpc/common/chem/orca/3.0.1/manual<br />
* Example data and a Moab example script can be found here:<br />
/opt/bwhpc/common/chem/orca/3.0.1/bwhpc-examples<br />
[...]<br />
</pre><br />
<br><br />
----<br />
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]</div>J Kucerahttps://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Orca&diff=12613JUSTUS2/Software/Orca2024-02-28T16:15:33Z<p>J Kucera: </p>
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<div>{{Softwarepage|chem/orca}}<br />
<br />
{| width=600px class="wikitable"<br />
|-<br />
! Description !! Content<br />
|-<br />
| module load<br />
| chem/orca<br />
|-<br />
| Availability<br />
| [[bwUniCluster]] &#124; [[JUSTUS2]]<br />
|-<br />
| License<br />
| [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA]<br />
|-<br />
|Citing<br />
| As described in the manual. Refer to Chapter 'Publications Related to ORCA' for guidance on citation.<br />
|-<br />
| Links<br />
| [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Portal] &#124; [https://orcaforum.cec.mpg.de/OrcaManual.pdf Documentation]<br />
|-<br />
| Graphical Interface<br />
| No<br />
|}<br />
<br><br />
= Description =<br />
'''ORCA''' is a modern electronic structure program package. It is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules.<br />
<br><br />
ORCA is able to carry out geometry optimizations and to predict a large number of spectroscopic parameters at different levels of theory. Besides the use of Hartee Fock theory, density functional theory (DFT) and semiempirical methods, high level ab initio quantum chemical methods, based on the configuration interaction and coupled cluster methods, are included into ORCA to an increasing degree.<br />
<br><br />
Due to the user-friendly style, ORCA is considered to be a helpful tool not only for computational chemists, but also for chemists, physicists and biologists that are interested in developing the full information content of their experimental data with help of calculations. <br />
<br><br><br />
<u>Implemented Methods</u><br />
* Semiempirical INDO/S, MNDO, AM1, PM3, NDDO/1<br />
* Hartee Fock theory (RHF, UHF, ROHF and CASSCF) all in direct, semidirect, or conventional mode, different RI approximations<br />
* DFT including a reasonably large number of exchange and correlation functionals including hybrid DFT and the most recent double hybrid functionals (see below).<br />
* High level single reference correlation models: CCSD(T), QCISD(T), CEPA, CPF (with and without RI, Local)<br />
* High level ab-initio individual selecting multireference methods (MRCI, MRMP2, MRMP3, MRMP4, MRACPF, MRAQCC, SORCI, DDCI) for ground- and excited-states.<br />
* Geometry optimization in redundant internal coordinates using analytical gradient techniques for all SCF methods as well as MP2.<br />
* Excited state calculations via TD-DFT and CI-singles (CIS). For CIS an analytic gradient is also available. The doubles correction is available for CIS(D) in an efficient implementation.<br />
* Scalar relativistic ZORA, IORA and Douglas-Kroll-Hess (DKH) approaches, picture change effects, all-electron basis sets, effective core potentials<br />
* The COSMO model is available throughout the package for continuum dielectric modeling of the environment.<br />
* QM/MM interface to GROMACS<br />
* Double hybrid functionals including a fraction of nonlocal correlation. Analytic gradients are also available (these methods were invented by the Grimme group).<br />
* Van der Waals correct density functionals.<br />
<br><br />
For more information on features please visit [https://orcaforum.cec.mpg.de/ ''The ORCA Portal of the Max-Planck Institute''] web page.<br />
<br><br />
<br><br />
<br />
= Versions and Availability =<br />
<br />
On the command line interface of any bwHPC cluster you'll get a list of available versions by using<br />
the command<br />
<br><br />
''''module avail chem/orca''''.<br />
<pre><br />
$ module avail chem/orca # bwUniCluster<br />
--------------------- /opt/bwhpc/common/modulefiles ----------------------<br />
chem/orca/3.0.1 chem/orca/3.0.3<br />
</pre><br />
<br><br />
<br />
= License =<br />
The ORCA license is considered as a "Research group" license. Thus anyone who directly associated with your research group is covered by the license and may share your copy of ORCA on all computer resources of your group.<br />
<br><br />
This license only applies to academic users. Commercial use of ORCA is prohibited under the terms of this license.<br />
<br><br />
[https://orcaforum.cec.mpg.de/license.html Complete ORCA Users License Agreement]<br />
<br><br />
<br><br />
= Usage =<br />
== Loading the module ==<br />
You can load the default version of ''ORCA'' with the command ''''module load chem/orca''''.<br />
<pre><br />
$ module load chem/orca<br />
module avail chem/orca<br />
------------------------ /opt/bwhpc/common/modulefiles ----------------------<br />
chem/orca/3.0.3 chem/orca/3.0.3-openmpi-1.6.5(default)<br />
$ module load chem/orca<br />
</pre><br />
The module will try to load modules it needs to function (e.g. compiler/intel). If loading the module fails, check if you have already loaded one of those modules, but not in the version needed for Orca.<br />
<br><br><br />
If you wish to load a specific (older) version, you can do so using e.g.<br />
<br> <br />
''''module load chem/orca/'''version' to load the version you desires.<br />
<pre><br />
$ module load chem/orca/3.0.1 # bwUniCluster example<br />
Please do not use this module if you do not own a valid ORCA group license.<br />
Please cite ORCA in your publications according to ORCA documentation.<br />
Please read 'module help chem/orca/3.0.1' before using ORCA.<br />
</pre><br />
<br><br />
<font color=red>Orca 3.0.3 mit OpenMPI 1.6.5 läuft stabiler! <br />
Einige MPI-Abstürze sind nachweislich (gleicher Job) damit durchgelaufen.<br><br />
This version is known to be more stable with bigger jobs. Try this one if you get problems with other versions of Orca!</font><br><br />
<font color=green>This version is the default now. [[#Versions and Availability|Only available on the Chemical Cluster 'Justus']]!</font><br />
<br><br />
<br />
== Program Binaries ==<br />
You can find the ORCA binaries in the main folder of the ORCA system.<br />
<br><br />
After loading the ORCA module (''module load chem/orca/'version''') this path is also set to the local $PATH- and [[#ORCA-Specific Environments|$ORCA_BIN_DIR environments]].<br />
<pre><br />
$ ls -x $ORCA_BIN_DIR<br />
bwhpc-examples manual modulefiles orca orca_2aim orca_2mkl<br />
orca_anoint orca_anoint_mpi orca_asa orca_casscf orca_casscf_mpi orca_chelpg<br />
orca_ciprep orca_cis orca_cis_mpi orca_cleanup orca_cleanup_mpi orca_cpcasscf<br />
orca_cpscf orca_cpscf_mpi orca_eca orca_ecplib orca_eprnmr orca_eprnmr_mpi<br />
orca_euler orca_fci orca_fitpes orca_gstep orca_gtoint orca_gtoint_mpi<br />
orca_loc orca_mapspc orca_md orca_mdci orca_mdci_mpi orca_mergefrag<br />
orca_mp2 orca_mp2_mpi orca_mrci orca_mrci_mpi orca_ndoint orca_numfreq<br />
orca_pc orca_pc_mpi orca_plot orca_pltvib orca_pop orca_rel<br />
orca_rocis orca_rocis_mpi orca_scf orca_scfgrad orca_scfgrad_mpi orca_scfhess<br />
orca_scfhess_mpi orca_scf_mpi orca_soc orca_soc_mpi orca_vib orca_vpot<br />
otool_cosmo otool_gcp otool_smd<br />
$ <br />
</pre><br />
Only the programs with the suffix <font color=green>'''_mpi'''</font> are compiled including OPENMPI functionality.<br />
<br><br />
<br />
== Disk Usage ==<br />
Scratch files are written to the current directory by default.<br><br />
Please change to a local directory or to '''your local workspace''' (preferred) before starting your calculations. <br />
<br><br><br />
'calc_repo' is an example name of a repository you created by using the command 'ws_allocate'.<br />
<pre><br />
$ cd $(ws_find calc_repo)<br />
['your-id'-calc_repo-0]$ pwd<br />
/work/workspace/scratch/'your-id'-calc_repo-0<br />
['your-id'-calc_repo-0]$ <br />
</pre><br />
<br />
== Examples ==<br />
You can copy a simple interactive example to your '''workspace''' and run it, using 'msub'<br />
<pre><br />
$ cd $(ws_find calc_repo)<br />
$ cp $ORCA_EXA_DIR/bwhpc-orca-example.moab .<br />
$ cp bwhpc-orca-example.moab myorcajob.moab <br />
§ vi myorcajob.moab # do your own modifications<br />
$ msub myorcajob.moab # start job submission<br />
</pre><br />
<br><br />
= ORCA-Specific Environments =<br />
To see a list of all ORCA environments set by the 'module load chem/orca/version'-command,<br />
use ''''env | grep ORCA''''<br><br />
Or try the command ''''module show 'chem/orca'''/version'.<br />
<pre><br />
$ module load chem/orca/3.0.3<br />
$ env | grep ORCA<br />
ORCA_VERSION=3.0.3<br />
ORCA_MAN_DIR=/opt/bwhpc/common/chem/orca/3.0.3/manual<br />
ORCA_EXA_DIR=/opt/bwhpc/common/chem/orca/3.0.3/bwhpc-examples<br />
ORCA_BIN_DIR=/opt/bwhpc/common/chem/orca/3.0.3<br />
ORCA_HOME=/opt/bwhpc/common/chem/orca/3.0.3<br />
</pre><br />
<br><br />
= Version-Specific Information =<br />
For a more detailed information specific to a specific ORCA version, see the information available via the module system with the command ''''module help chem/orca''''.<br />
<br><br />
For a small abstract what ORCA is about use the command ''''module whatis chem/orca''''.<br />
<br><br><br />
<u>Examples</u><br />
<pre><br />
$ module avail chem/orca<br />
----------------------- /opt/bwhpc/common/modulefiles ---------------------------<br />
chem/orca/3.0.1 chem/orca/3.0.3<br />
<br />
$ module whatis chem/orca/3.0.1<br />
chem/orca/3.0.1 : Quantum chemistry package ORCA, version 3.0.1<br />
(command '/opt/bwhpc/common/chem/orca/3.0.1/orca')<br />
<br />
$ module help chem/orca/3.0.1<br />
----------- Module Specific Help for 'chem/orca/3.0.1' ------------<br />
This module provides the quantum chemistry package ORCA version 3.0.1<br />
via command '/opt/bwhpc/common/chem/orca/3.0.1/orca' <br />
[...] <br />
Documentation: <br />
* Max-Planck-Institut fuer Chemische Energiekonversion <br />
https://cec.mpg.de/forum/portal.php<br />
* New features for version 3.0.1<br />
https://cec.mpg.de/forum/portal.php#a3<br />
* Manuals in pdf format:<br />
/opt/bwhpc/common/chem/orca/3.0.1/manual<br />
* Example data and a Moab example script can be found here:<br />
/opt/bwhpc/common/chem/orca/3.0.1/bwhpc-examples<br />
[...]<br />
</pre><br />
<br><br />
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[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]</div>J Kucera