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:
- 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
$PATHwill 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:
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_COMMANDVASP_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_COMMANDnormally uses thevaspbinary, and will run in parallel when called under a PBS job. That decision is based on thePBS_NODEFILEenvironment variable.- If you have experience with shell variables you can supply a customized binary name in the variable
VASP_BINARY. - The
VASP_COMMANDvariable takes precendence overVASP_SCRIPT. If you wish to define a personalVASP_SCRIPT, unsetVASP_COMMANDin 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