Difference between revisions of "JUSTUS2/Software/Orca"
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| module load |
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| − | | chem/orca |
+ | | chem/orca/5.0.4 |
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| Availability |
| Availability |
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| − | | [[bwUniCluster]] | [[ |
+ | | [[bwUniCluster]] | [[JUSTUS2]] |
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| License |
| License |
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| − | | [https://orcaforum. |
+ | | [https://orcaforum.kofo.mpg.de/app.php/privacypolicy/policy EULA] |
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|- |
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|Citing |
|Citing |
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| + | | 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. |
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| − | | [https://orcaforum.cec.mpg.de/OrcaManual.pdf As described in the manual] |
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| Links |
| Links |
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| − | | [https://orcaforum. |
+ | | [https://orcaforum.kofo.mpg.de/app.php/portal Main ORCA Forum Portal] | [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Documentation] |
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| Graphical Interface |
| Graphical Interface |
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<br> |
<br> |
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= Description = |
= Description = |
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| − | '''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. |
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| − | <br> |
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| − | 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. |
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| − | <br> |
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| − | 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. |
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| − | <br><br> |
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| − | <u>Implemented Methods</u> |
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| − | * Semiempirical INDO/S, MNDO, AM1, PM3, NDDO/1 |
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| − | * Hartee Fock theory (RHF, UHF, ROHF and CASSCF) all in direct, semidirect, or conventional mode, different RI approximations |
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| − | * DFT including a reasonably large number of exchange and correlation functionals including hybrid DFT and the most recent double hybrid functionals (see below). |
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| − | * High level single reference correlation models: CCSD(T), QCISD(T), CEPA, CPF (with and without RI, Local) |
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| − | * High level ab-initio individual selecting multireference methods (MRCI, MRMP2, MRMP3, MRMP4, MRACPF, MRAQCC, SORCI, DDCI) for ground- and excited-states. |
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| − | * Geometry optimization in redundant internal coordinates using analytical gradient techniques for all SCF methods as well as MP2. |
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| − | * 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. |
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| − | * Scalar relativistic ZORA, IORA and Douglas-Kroll-Hess (DKH) approaches, picture change effects, all-electron basis sets, effective core potentials |
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| − | * The COSMO model is available throughout the package for continuum dielectric modeling of the environment. |
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| − | * QM/MM interface to GROMACS |
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| − | * Double hybrid functionals including a fraction of nonlocal correlation. Analytic gradients are also available (these methods were invented by the Grimme group). |
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| − | * Van der Waals correct density functionals. |
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| − | <br> |
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| − | For more information on features please visit [https://orcaforum.cec.mpg.de/ ''The ORCA Portal of the Max-Planck Institute''] web page. |
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| − | <br> |
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| − | <br> |
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| + | '''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. |
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| − | = Versions and Availability = |
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| − | A list of versions currently available on all bwHPC-C5-Clusters can be obtained from the |
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| − | <br> |
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| − | <big> |
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| + | 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. |
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| − | [https://cis-hpc.uni-konstanz.de Cluster Information System CIS] |
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| + | 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. |
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| − | </big> |
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| − | {{#widget:Iframe |
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| − | |url=https://cis-hpc.uni-konstanz.de/prod.cis/bwUniCluster/chem/orca |
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| − | |width=99% |
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| − | |height=290 |
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| − | |border=0 |
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| − | }} |
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| − | On the command line interface of any bwHPC cluster you'll get a list of available versions by using |
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| − | the command |
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| − | <br> |
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| − | ''''module avail chem/orca''''. |
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| − | <pre> |
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| − | $ module avail chem/orca # bwUniCluster |
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| − | --------------------- /opt/bwhpc/common/modulefiles ---------------------- |
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| − | chem/orca/3.0.1 chem/orca/3.0.3 |
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| − | </pre> |
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| − | <br> |
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| + | Please refer to documentation provided by the ORCA developers in the first place for more detailed information, e.g.: |
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| − | = License = |
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| − | 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. |
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| − | <br> |
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| − | This license only applies to academic users. Commercial use of ORCA is prohibited under the terms of this license. |
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| − | <br> |
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| − | [https://orcaforum.cec.mpg.de/license.html Complete ORCA Users License Agreement] |
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| − | <br> |
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| − | <br> |
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| − | = Usage = |
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| − | == Loading the module == |
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| − | You can load the default version of ''ORCA'' with the command ''''module load chem/orca''''. |
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| − | <pre> |
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| − | $ module load chem/orca |
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| − | module avail chem/orca |
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| − | ------------------------ /opt/bwhpc/common/modulefiles ---------------------- |
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| − | chem/orca/3.0.3 chem/orca/3.0.3-openmpi-1.6.5(default) |
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| − | $ module load chem/orca |
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| − | </pre> |
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| − | 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. |
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| − | <br><br> |
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| − | If you wish to load a specific (older) version, you can do so using e.g. |
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| − | <br> |
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| − | ''''module load chem/orca/'''version' to load the version you desires. |
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| − | <pre> |
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| − | $ module load chem/orca/3.0.1 # bwUniCluster example |
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| − | Please do not use this module if you do not own a valid ORCA group license. |
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| − | Please cite ORCA in your publications according to ORCA documentation. |
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| − | Please read 'module help chem/orca/3.0.1' before using ORCA. |
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| − | </pre> |
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| − | <br> |
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| − | <font color=red>Orca 3.0.3 mit OpenMPI 1.6.5 läuft stabiler! |
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| − | Einige MPI-Abstürze sind nachweislich (gleicher Job) damit durchgelaufen.<br> |
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| − | 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> |
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| − | <font color=green>This version is the default now. [[#Versions and Availability|Only available on the Chemical Cluster 'Justus']]!</font> |
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| − | <br> |
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| + | [https://www.kofo.mpg.de/970274/orca_manual_5_0_4.pdf Orca Manual 5.0.4] |
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| − | == Program Binaries == |
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| − | You can find the ORCA binaries in the main folder of the ORCA system. |
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<br> |
<br> |
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| + | [https://wires.onlinelibrary.wiley.com/doi/full/10.1002/wcms.1606 Article Overview by Frank Nesse] |
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| − | 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]]. |
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| − | <pre> |
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| − | $ ls -x $ORCA_BIN_DIR |
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| − | bwhpc-examples manual modulefiles orca orca_2aim orca_2mkl |
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| − | orca_anoint orca_anoint_mpi orca_asa orca_casscf orca_casscf_mpi orca_chelpg |
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| − | orca_ciprep orca_cis orca_cis_mpi orca_cleanup orca_cleanup_mpi orca_cpcasscf |
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| − | orca_cpscf orca_cpscf_mpi orca_eca orca_ecplib orca_eprnmr orca_eprnmr_mpi |
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| − | orca_euler orca_fci orca_fitpes orca_gstep orca_gtoint orca_gtoint_mpi |
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| − | orca_loc orca_mapspc orca_md orca_mdci orca_mdci_mpi orca_mergefrag |
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| − | orca_mp2 orca_mp2_mpi orca_mrci orca_mrci_mpi orca_ndoint orca_numfreq |
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| − | orca_pc orca_pc_mpi orca_plot orca_pltvib orca_pop orca_rel |
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| − | orca_rocis orca_rocis_mpi orca_scf orca_scfgrad orca_scfgrad_mpi orca_scfhess |
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| − | orca_scfhess_mpi orca_scf_mpi orca_soc orca_soc_mpi orca_vib orca_vpot |
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| − | otool_cosmo otool_gcp otool_smd |
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| − | $ |
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| − | </pre> |
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| − | Only the programs with the suffix <font color=green>'''_mpi'''</font> are compiled including OPENMPI functionality. |
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<br> |
<br> |
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| + | [https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.81 Article about main improvement in the version 5.0] |
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| − | == Disk Usage == |
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| − | Scratch files are written to the current directory by default.<br> |
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| − | Please change to a local directory or to '''your local workspace''' (preferred) before starting your calculations. |
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| − | <br><br> |
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| − | 'calc_repo' is an example name of a repository you created by using the command 'ws_allocate'. |
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| − | <pre> |
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| − | $ cd $(ws_find calc_repo) |
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| − | ['your-id'-calc_repo-0]$ pwd |
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| − | /work/workspace/scratch/'your-id'-calc_repo-0 |
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| − | ['your-id'-calc_repo-0]$ |
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| − | </pre> |
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| − | |||
| − | == Examples == |
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| − | You can copy a simple interactive example to your '''workspace''' and run it, using 'msub' |
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| − | <pre> |
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| − | $ cd $(ws_find calc_repo) |
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| − | $ cp $ORCA_EXA_DIR/bwhpc-orca-example.moab . |
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| − | $ cp bwhpc-orca-example.moab myorcajob.moab |
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| − | § vi myorcajob.moab # do your own modifications |
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| − | $ msub myorcajob.moab # start job submission |
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| − | </pre> |
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<br> |
<br> |
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| − | = ORCA-Specific Environments = |
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| − | To see a list of all ORCA environments set by the 'module load chem/orca/version'-command, |
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| − | use ''''env | grep ORCA''''<br> |
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| − | Or try the command ''''module show 'chem/orca'''/version'. |
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| − | <pre> |
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| − | $ module load chem/orca/3.0.3 |
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| − | $ env | grep ORCA |
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| − | ORCA_VERSION=3.0.3 |
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| − | ORCA_MAN_DIR=/opt/bwhpc/common/chem/orca/3.0.3/manual |
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| − | ORCA_EXA_DIR=/opt/bwhpc/common/chem/orca/3.0.3/bwhpc-examples |
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| − | ORCA_BIN_DIR=/opt/bwhpc/common/chem/orca/3.0.3 |
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| − | ORCA_HOME=/opt/bwhpc/common/chem/orca/3.0.3 |
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| − | </pre> |
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| − | <br> |
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| − | = Version-Specific Information = |
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| − | 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''''. |
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| − | <br> |
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| − | For a small abstract what ORCA is about use the command ''''module whatis chem/orca''''. |
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| − | <br><br> |
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| − | <u>Examples</u> |
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| − | <pre> |
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| − | $ module avail chem/orca |
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| − | ----------------------- /opt/bwhpc/common/modulefiles --------------------------- |
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| − | chem/orca/3.0.1 chem/orca/3.0.3 |
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| − | |||
| − | $ module whatis chem/orca/3.0.1 |
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| − | chem/orca/3.0.1 : Quantum chemistry package ORCA, version 3.0.1 |
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| − | (command '/opt/bwhpc/common/chem/orca/3.0.1/orca') |
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| + | = Miscellaneous Notes to Usage = |
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| − | $ module help chem/orca/3.0.1 |
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| + | * 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. |
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| − | ----------- Module Specific Help for 'chem/orca/3.0.1' ------------ |
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| + | * To ensure successful parallel runs, it is necessary to call ORCA with the full path, i.e. '$ORCA_BIN_DIR/orca <input_file>' |
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| − | This module provides the quantum chemistry package ORCA version 3.0.1 |
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| + | * Due to potential large I/O operations, especially for post HF methods, it is advisable to place temporary files a local scratch directory.<br>To learn more about local disk space on [[JUSTUS2]], please refer to the [[JUSTUS2/Hardware#$SCRATCH and $TMPDIR|$SCRATCH and $TMPDIR]] section on the "JUSTUS2 Hardware" page. |
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| − | via command '/opt/bwhpc/common/chem/orca/3.0.1/orca' |
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| + | * 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'. |
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| − | [...] |
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| + | * 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. |
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| − | Documentation: |
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| − | * Max-Planck-Institut fuer Chemische Energiekonversion |
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| − | https://cec.mpg.de/forum/portal.php |
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| − | * New features for version 3.0.1 |
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| − | https://cec.mpg.de/forum/portal.php#a3 |
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| − | * Manuals in pdf format: |
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| − | /opt/bwhpc/common/chem/orca/3.0.1/manual |
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| − | * Example data and a Moab example script can be found here: |
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| − | /opt/bwhpc/common/chem/orca/3.0.1/bwhpc-examples |
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| − | [...] |
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| − | </pre> |
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<br> |
<br> |
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| − | ---- |
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| − | [[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]][[Category:BwForCluster_BinAC]] |
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Latest revision as of 15:51, 29 February 2024
|
The main documentation is available via |
| Description | Content |
|---|---|
| module load | chem/orca/5.0.4 |
| Availability | bwUniCluster | JUSTUS2 |
| License | EULA |
| Citing | As described in the manual. Refer to Chapter 'Publications Related to ORCA' for guidance on citation. |
| Links | Main ORCA Forum Portal | Documentation |
| Graphical Interface | No |
1 Description
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.
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.
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.
Please refer to documentation provided by the ORCA developers in the first place for more detailed information, e.g.:
Orca Manual 5.0.4
Article Overview by Frank Nesse
Article about main improvement in the version 5.0
2 Miscellaneous Notes to Usage
- 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.
Avoid using the --cpus-per-task directive. All the ORCA modules load the appropriate OpenMPI module automatically. - To ensure successful parallel runs, it is necessary to call ORCA with the full path, i.e. '$ORCA_BIN_DIR/orca <input_file>'
- 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 JUSTUS2, please refer to the $SCRATCH and $TMPDIR section on the "JUSTUS2 Hardware" page. - The most preferable way to load ORCA is with the specific version included, i.e., 'module load chem/orca/<version>'.
The default version, which may change over time, can be loaded simply with the command 'module load chem/orca'. - 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.
