HPC/Applications/vasp

Requesting Access

Both VASP-4 and VASP-5 major versions are available on Carbon, and require a license. VASP-5 is a separate license, which includes access to VASP-4 and potpaw_PBE potentials.

You are welcome to use the Carbon binaries, but I (stern) need written or emailed confirmation of your license status. Please kindly ask the vaspmaster to confirm to me that you hold or are covered by a license. You may wish to use the following template.

To: [email protected]
CC: [email protected]
Subject: License confirmation

We are users of the Center for Nanoscale Materials at Argonne National Laboratory.
We would like to use the VASP installation at this site.

Please reply and confirm to Michael Sternberg <[email protected]> that we hold the license numbers

VASP-4   …
VASP-5   …

with the following people in my research group:

…
…


With best regards,
…

Module considerations

• Review the available modules for each major version:
  • vasp, for VASP 4.x
  • vasp5, for VASP 5.x
• Choose and add one of the following lines to your ~/.bashrc file:

module load vasp                # sets $VASP_HOME
module load vasp5               # sets $VASP5_HOME

Each module points to an installation directory using an environment variable corresponding to the module name. Do not hardcode the directory anywhere, as that location is determined by the module and may change in subsequent versions. There should not be a reason to do so, since $PATH will be managed appropriately.

• Each module provides several binaries (see next section).
• You do not need to specify a path for vasp for the mpirun statement in the PBS job script.
• The modules are mutually exclusive.
• Potentials are available in /opt/soft/vasp-pot.

To access Graeme Henkelman's script suite, load the vasp-vtstscripts module. It works with both the vasp and vasp5 modules above. In either case, choose one of the VTST-patched binaries from the table below. The unpatched vasp binaries will not interoperate with the script suite.

module load vasp-vtstscripts

Binaries

Some options for VASP cannot be configured at runtime (by input data) but must be chosen when compiling. Since no single set of compile-time choices is appropriate for all uses, a number of binaries are provided, distinguished by their name.

The modules from versions vasp/4.6.35-mkl-13 and vasp5/5.2.12a-mkl-4 onwards, respectively, contain several binaries built using different sets of preprocessor flags in the Makefile. Earlier modules only contain two binaries, vasp and vasp-gamma. Additional binaries are provided for useful preprocessor flag combinations after applying patches from the group of Graeme Henkelman (UT Austin) to the source code:

• Transition state tools for VASP, and
• DOS Projection in Bader Volumes.

To verify the binaries available for a module, run the appropriate command, once the module has been loaded:

ls $VASP_HOME/bin
ls $VASP5_HOME/bin

Choose a binary appropriate for your task and pass its name to mpirun in the job script. There is no need for full path names. Copy a sample job script from:

$VASP_HOME/vasp.job
$VASP5_HOME/vasp.job

Available binaries and their flags

This table lists the names of the binaries compiled from

• combinations of preprocessor flags, and
• variants of the source code, primarily enhancing capabilities of ionic updates.

MD capabilities	Flags used	Binary name
		Official source	Patched for VTST	Patched for Bader-projected DOS (in development)
Conventional	(none)	vasp	vasp-vtst	vasp-baderdos
	-DNGZhalf	vasp-chargehalf	vasp-vtst-chargehalf	vasp-baderdos-chargehalf
	-DwNGZhalf	vasp-gamma	vasp-vtst-gamma	vasp-baderdos-gamma
	-DwNGZhalf -DNGZhalf	vasp-gamma-chargehalf	vasp-vtst-gamma-chargehalf	vasp-baderdos-gamma-chargehalf
Advanced techniques (vasp5 only)	-Dtbdyn	vasp-tbdyn	not useful	not useful
	-Dtbdyn -DNGZhalf	vasp-tbdyn-chargehalf
	-Dtbdyn -DwNGZhalf	vasp-tbdyn-gamma
	-Dtbdyn -DwNGZhalf -DNGZhalf	vasp-tbdyn-gamma-chargehalf

Explanantion of flags

From file vasp.5.2/makefile.linux_pg in the souce code.

#-----------------------------------------------------------------------
# possible options for CPP:
# NGXhalf             charge density   reduced in X direction
# wNGXhalf            gamma point only reduced in X direction
# avoidalloc          avoid ALLOCATE if possible
# IFC                 work around some IFC bugs
# CACHE_SIZE          1000 for PII,PIII, 5000 for Athlon, 8000 P4
# RPROMU_DGEMV        use DGEMV instead of DGEMM in RPRO (usually  faster)
# RACCMU_DGEMV        use DGEMV instead of DGEMM in RACC (faster on P4)
#  **** definitely use -DRACCMU_DGEMV if you use the mkl library
#-----------------------------------------------------------------------
…
#-----------------------------------------------------------------------
# additional options for CPP in parallel version (see also above):
# NGZhalf               charge density   reduced in Z direction
# wNGZhalf              gamma point only reduced in Z direction
# scaLAPACK             use scaLAPACK (usually slower on 100 Mbit Net)
#-----------------------------------------------------------------------

Common flags

-DIFC -DRPROMU_DGEMV  -DRACCMU_DGEMV -DCACHE_SIZE=16000  -DMPI -DMPI_BLOCK=8000

vdW-DF functional

The vdW-DF functional of Langreth and Lundqvist et al. is implemented in all the *-chargehalf binaries of the vasp5 module.

No specific preparations are needed other than setting the INCAR flags as documented. The binaries will find the required precalculated kernel file vdw_kernel.bindat by means of the environment variable $VASP5_HOME which is set by the module. This is a Carbon-specific extension.

Usage under ASE

VASP calculations can be set up, run, and analyzed using the calculator interface of the ASE package, available on Carbon under both the ase3 and atk modules. ASE is told how to use VASP by means of environment variables which the modules define for you with sensible defaults:

VASP_PP_PATH
VASP_COMMAND
VASP_SCRIPT -- supported by calculator but not set

No other setup is needed.

• The calculator will create and possibly overwrite VASP input files in the current directory, and then run vasp therein. To minimize clutter, consider setting up and changing into a run-specific directory before initializing the calculator.
• VASP_COMMAND is set to choose the vasp binary, and will run in parallel when part of a PBS job. If you have experience with shell variables, you can alter the variable after loading the ase3 or atk module or just prior to deploying the calculator in an ASE script.
• The VASP_COMMAND variable takes precendence over VASP_SCRIPT. If you wish to define a personal VASP_SCRIPT, unset VASP_COMMAND in tandem.

Node resources for VASP

Consider the follwing to specify PBS node resources (in job files and on the qsub command line).

Single-node jobs

• When on gen1 nodes use ppn=4 and disallow sharing

#PBS -l nodes=1:ppn=4:gen1
#PBS -l naccesspolicy=SINGLEJOB

• When on gen2, use ppn=7 or 8

#PBS -l nodes=1:ppn=8:gen2

Multi-node jobs

Run on gen2 only, by using the following options for qsub or #PBS:

#PBS -l nodes=__:ppn=__:gen2

See also

• Benchmarks – Generation 1 vs 2
• Advanced node selection