Difference between revisions of "Turbomole"
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Latest revision as of 10:02, 16 May 2018
|Availability||bwUniCluster | BwForCluster_Chemistry|
|Citing||See Turbomole manual|
|Links||Homepage | Documentation|
|Graphical Interface||No (Yes, for generating input)|
- 1 Description
- 2 Versions and Availability
- 3 Usage
- 4 Examples
- 5 Turbomole-Specific Environment Variables
- 6 Version-Specific Information
Turbomole is a general purpose quantum chemistry software package for ab initio electronic structure calculations and provides:
- ground state calculations for methods such as Hartree-Fock, DFT, MP2, and CCSD(T);
- excited state calculations at different levels such as full RPA, TDDFT, CIS(D), CC2, an ADC(2);
- geometry optimizations, transition state searches, molecular dynamics calculations;
- property and spectra calculations such as IR, UV/VIS, Raman, and CD;
- approximations like resolution-of-the-identity (RI) to speed-up the calculations without introducing uncontrollable or unknown errors; as well as
- parallel versions (OpenMP, Fork, MPI and Global Arrays) for almost all kind of jobs.
For more information on Turbmole's features please visit http://www.turbomole-gmbh.com/program-overview.html.
2 Versions and Availability
A current list of the versions available on the bwUniCluster and bwForClusters can be obtained from the
Cluster Information System: CIS Information on Turbomole or here: On the command line interface (CLI) of a particular bwHPC cluster a list of all available Turbomole versions can be inquired as followed
$ module avail chem/turbomole
2.1 Parallel computing
The Turbomole Module subsumes all available parallel computing variants of Turbomole's binaries. Turbomole defines the following parallel computing variants:
- SMP = Shared-memory parallel computing based on OpenMP and Fork() with the latter using separated address spaces.
- MPI = Message passing interface protocol based parallel computing
- GA = Global arrays, API for "shared-memory" programming for distributed-memory computers which can be used e.g. to complement MPI.
However only one of the 3 parallel variants or the sequential variant can be loaded at once and most Turbomole's binaries support only 1 or 2 of the parallelization variants. Like for Turbomole installations without a Module system, the variants have to be triggered by the environment variable $PARA_ARCH.
3.1 Before loading the Module
Before loading the Turbomole Module the parallel computing variant has to be defined via the environment variable $PARA_ARCH using the abbreviations SMP, MPI or GA, e.g.:
$ export PARA_ARCH=MPI
will later load the MPI binary variants. If the variable $PARA_ARCH is not defined or empty, the sequential binary variants will be active once the Turbomole Module is loaded.
3.2 Loading the Module
You can load the default version of Turbomole with the command:
$ module load chem/turbomole
The Turbomole Module does not depend on any other Module, but on the variable $PARA_ARCH. Moreover, Turbomole provides its own libraries regarding OpenMP, Fork(), MPI, and Global Array based parallelization. If you wish to load a specific (older) version you can do so by executing e.g.:
$ module load chem/turbomole/6.5
to load the version 6.5
3.3 Switching between different parallel variants
To switch between the different parallel variants provided by the Turbomole Module, simply define the new parallel variant via $PARA_ARCH and load the Module again. Note that for switching between the parallel variants unloading of the Turbomole Module is not required. For instance to change to the MPI variant, execute:
$ export PARA_ARCH=MPI $ module load chem/turbomole
3.4 Turbomole binaries
The Turbomole software package consists of a set of stand-alone program binaries providing different features and parallelization support:
|define||Interactive input generator||no||no||no||no|
|ridft||Energy calc. with fast Coulomb approximation||no||yes||yes||yes|
|rdgrad||Gradient calc. with fast Coulomb approximation||no||yes||yes||yes|
|ricc2||Electronic excitation energies, transition moments and properties of excited states||yes||no||yes||no|
|statpt||Hessian and coordinate update for stationary point search||no||no||no||no|
|aoforce||Analytic calculation of force constants, vibrational frequencies and IR intensities||no||yes||no||no|
|escf||Calc. of time dependent and dielectric properties||no||yes||no||no|
|egrad||gradients and first-order properties of excited states||no||yes||no||no|
|odft||Orbital-dependent energy calc.||yes||no||no||st no|
For the complete set of binaries and more detailed description of their features read here.
3.5 Turbomole tools
Turbomole's tool set contains scripts and binaries that help to prepare, execute workflows (such as geometry optimisation) and postprocess results.
|x2t||Preparation||Converts XYZ coordinates into Turbomole coordinates.|
|sdg||Preparation||Shows data group from control file: for exampleshows current Turbomole coordinates used.|
|jobex||Optimization workflow||Shell script that controls and executes automatic optimizations of molecular geometry parameters.|
|tm2molden||Postprocessing||Creates a molden format input file for the Molden program.|
|eiger||Postprocessing||Script front-end of program eigerf to display HOMO-LUMO gap and MO eigenvalues.|
For the complete set of tools and more detailed description of their features read here.
3.6 Disk Usage
By default, scratch files of Turbomole binaries are placed in the directory of Turbmole binary execution. Please do not run your Turbomole calculations in your $HOME or $WORK directory.
4.1 Single node jobs
4.1.1 Template provided by Turbomole Module
The Turbomole Module provides a simple Moab example of Cubane (C8H8) that runs an energy relaxation via MPI parallel dscf using 4 cores on a single node and its local file system. To simply run the example do the following steps:
$ module load chem/turbomole $ mkdir -vp ~/Turbomole-example/ $ cd ~/Turbomole-examples/ $ cp -r $TURBOMOLE_EXA_DIR/* ~/Turbmole-example/ $ msub bwHPC_turbomole_single-node_example.sh
The last step submits the job example script bwHPC_turbomole_single-node_example.sh to the queueing system. Once started on a compute node, all calculations will be done under an unique directory on the local file system of that particular compute node.
4.1.2 Geometry optimization
To do a geometry optimization of the previous job example modify bwHPC_turbomole_single-node_example.sh by replacing the following line
time dscf > dscf.out 2>&1
time jobex -dscf -keep 2>&1
and submit the modified script to the queueing system via msub.
The Turbomole command jobex controls the call of all the required Turbomole binaries for the geometry optimization.
5 Turbomole-Specific Environment Variables
To see a list of all Turbomole environments set by the 'module load'-command do the following:
module show chem/turbomole 2>&1 | grep -E '(setenv|prepend-path)'
6 Version-Specific Information
For specific information about the Turbomole version (e.g. 6.6) to be loaded do the following:
module help chem/turbomole/6.6