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CPMD
The CPMD code is a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics.
Usage
Add module: module load cpmd/4.1
Dependent modules loaded: mvapich2 and intel
Additional Variables: PP_LIBRARY_PATH -> Directory Path where pseudopotential files are stores
Usage: srun $(which cpmd.x) [ input file ] $PP_LIBRARY_PATH > [ output file ]
Absolute path to cpmd executable: /share/Apps/cpmd/4.1/intel-16.0.3-mvapich2-2.1/bin/cpmd.x
Example
Sample input and submission script is available at /share/Apps/examples/cpmd
GAMESS
The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package.
Usage
Add module: module load gamess/5Dec2014
Dependent modules loaded: mvapich2 and intel
Usage: rungms [ Prefix for GAMESS Input file ] > [ Output file name ]
Example: If your input file is named test.inp, then use the command
rungms test > test.out
Example
Sample input and submission script is available at /share/Apps/examples/gamess
Tips
GAMESS does not provide a comprehensive basis set. Most likely you would need to add the basis set in your input file. Alternatively, you can create a file that contains the basis set i.e. create your own basis set database. Use the environmental variable EXTBAS to point to that file and add the line $BASIS EXTFILE=.T. GBASIS=somename $END to your input to use the somename basis set.
Note
*If you use GAMESS on other resources such as XSEDE, take note that the rungms script has been modified to run on Sol. Please refer to the user docs for the resource in question for help in running GAMESS.*
GAUSSIAN
Gaussian is a general purpose computational chemistry software package.
License Information
Due to licensing restrictions required by the vendor, all users of GAUSSIAN09 or GaussView must be enrolled for access to this software.
All Lehigh faculty, staff and students are eligible. Please request to be added to the gaussian users group by submitting a help ticket.
Usage
Add module: module load gaussian/g09
Usage: g09 [ input file ] [ output file ]
Alternate Usage: g09 < [ input file ] > [ output file ]
Example
Sample input and submission script is available at /share/Apps/examples/gaussian
Quantum Espresso
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.
Usage
Add module: module load espresso/5.4.0
Dependent modules loaded: mvapich2 and intel
Usage: srun [ espresso code ] [ options ] -in [ input file ] > [ output file ]
Examples:
PWSCF run: srun $(which pw.x) -in [ input file ] > [ output file ]
CPMD run : srun $(which cp.x) -in [ input file ] > [ output file ]
Absolute path to espresso codes: /share/Apps/espresso/5.4.0/intel-16.0.3-mvapich2-2.1/bin
Example
Sample input and submission script is available at /share/Apps/examples/espresso
Important
Quantum Espresso parallelization is optimized using input variables nimages, npool, ntg and ndiag. An incorrect value for these variables will result in loss of performance. Users are expected to run a few benchmarks to obtain optimum value for these variables before running production simulations.
NWCHEM
NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters.
NWChem software can handle:
- Biomolecules, nanostructures, and solid-state
- From quantum to classical, and all combinations
- Ground and excited-states
- Gaussian basis functions or plane-waves
- Scaling from one to thousands of processors
- Properties and relativistic effects
NWChem is actively developed by a consortium of developers and maintained by the EMSL located at the Pacific Northwest National Laboratory (PNNL) in Washington State.
Usage
Add module: module load nwchem/6.6
Usage: srun $(which nwchem) [ input file ] > [ output file ]
Absolute path to nwchem code: /share/Apps/nwchem/6.6/intel-16.0.3-mvapich2-2.1/bin
Example
Sample input and submission script is available at /share/Apps/examples/nwchem
VASP
The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles.
License Information
VASP is licensed to individual research groups with a maximum of 6 users allowed per license. The version of VASP installed on Sol is licensed to Srinivas Rangarajan (Chem Engg) and can is available to members of his research group. If you need to use VASP, you need to purchase your own license for your research group, LTS or any College or Department within Lehigh University cannot purchase a VASP license. VASP provides a liberal license that allows the licensee to install and use VASP on any computers including off campus resources such as XSEDE or DOE supercomputers that you have access. The only restriction is the number of users in your research group who can use VASP.
Usage
Add module: module load vasp/5.4.1
Usage: srun [ vasp code ] > [ output file ]
Examples:
vasp_std run: srun $(which vasp_std) > [ output file ]
vasp_ncl run: srun $(which vasp_ncl) > [ output file ]
vasp_gam run: srun $(which vasp_gam) > [ output file ]
Absolute path to vasp codes: /share/Apps/source/vasp/regular/vasp.5.4.1/bin
Different versions of VASP
- *std*: one “half” version (will reduce the memory requirements when running ordinary collinear calculations),
- *gam*: one gamma-point only (reduces memory requirements even further, but only works for gamma point-only calculations),
- *ncl*: “full” version for non-collinear calculations.
Use the gamma-point only version for large supercells and molecules with only 1 k-point. It is roughly twice as fast and uses half the memory. See https://www.nsc.liu.se/~pla/blog/2011/06/28/vaspcompile/ for more details on how VASP was compiled.
Example
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The following packages for electronic structure and materials modeling are available on Sol.
- almaBTE
- CRYSTAL17
- DL_POLY_4
- GAMESS
- GAUSSIAN
- Quantum Espresso
- NWCHEM
- OpenMolcas
- Plumed
- Quantum Espresso
- ShengBTE
- VASP
The following packages for X-Ray crystallography studies are available on Sol.
Packages for Molecular Dynamics available on Sol are listed separately.
The following Visualization Tools for creating input or visualizing output are available via Open OnDemand