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Vienna ab-initio simulation package version 5 (VASP 5) is an application package used for performing ab-initio quantum-mechanical molecular dynamics (MD). It is based on an efficient implementation of hybrid functionals and the GW methods. Furthermore, VASP 5.2 offers linear response calculations of properties such as Born effective charges and piezoelectric tensors.
VASP is a complex package for performing ab-initio quantum-mechanical molecular dynamics (MD) simulations using pseudopotentials or the projector-augmented wave method and a plane wave basis set. The approach implemented in VASP is based on the (finite-temperature) local-density approximation with the free energy as variational quantity and an exact evaluation of the instantaneous electronic ground state at each MD time step. VASP uses efficient matrix diagonalisation schemes and an efficient Pulay/Broyden charge density mixing.
These techniques avoid all problems possibly occurring in the original Car-Parrinello method, which is based on the simultaneous integration of electronic and ionic equations of motion. The interaction between ions and electrons is described by ultra-soft Vanderbilt pseudopotentials (US-PP) or by the projector-augmented wave (PAW) method. US-PP (and the PAW method) allow for a considerable reduction of the number of plane-waves per atom for transition metals and first row elements. Forces and the full stress tensor can be calculated with VASP and used to relax atoms into their instantaneous ground-state.
Description and summary above are from the VASP User Guide.
Submitted by lev_lafayette on Thu, 02/13/2014 - 05:25
Previous comments concerning VASP installs still largely apply.
1. It still performs ab-initio quantum-mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set.
2. It still has an weird and frustrating license which is open source (if you pay them) but not free.
3. It still is released without standard autoconfiguration tools and with make files for a variety of system architectures which rarely match was diverse users might wish to use, thus requiring posts like this every time a new version is released.
In this instance we start of with a copy of VASP in the user's home directory. Make a directory called vasp (mkdir vasp) and and extract the tarball of the two VASP files there (tar xvf vasp.5.lib, tar xvf vasp.5.3).
# tar xvf vasp.5.lib.tar.gz
# tar xvf vasp.5.3.3.tar.gz
# module load openmpi-intel
# module load fftw/3.3.2-intel
# cd vasp.5.lib
# cp makefile.linux_ifc_P4 makefile
# vim makefile
Modify to the following (seriously guys, ifc?):
# diff makefile makefile.linux_ifc_P4
Change to VASP
# cd ../vasp.5.3
# cp makefile.linux_ifc_P4 makefile
# vim makefile
Modify to the following:
diff makefile makefile.linux_ifc_P4
< #BLAS= -lguide -mkl
< BLAS= -mkl
> BLAS= -lguide -mkl
< #LAPACK= $(MKL_PATH)/libmkl_intel_lp64.a
< LAPACK= /usr/local/intel/composerxe/composer_xe_2013_sp1.0.080/mkl/lib/intel64/libmkl_intel_lp64.a
> LAPACK= $(MKL_PATH)/libmkl_intel_lp64.a
< CPP = $(CPP_) -DMPI -DHOST=\"LinuxIFC\" -DIFC \
< -DCACHE_SIZE=4000 -DPGF90 -Davoidalloc -DNGZhalf \
< -DMPI_BLOCK=8000 -Duse_collective -DscaLAPACK
< # -DRPROMU_DGEMV -DRACCMU_DGEMV
> #CPP = $(CPP_) -DMPI -DHOST=\"LinuxIFC\" -DIFC \
> # -DCACHE_SIZE=4000 -DPGF90 -Davoidalloc -DNGZhalf \
> # -DMPI_BLOCK=8000 -Duse_collective -DscaLAPACK
> ## -DRPROMU_DGEMV -DRACCMU_DGEMV
< LIB = -L../vasp.5.lib -ldmy \
< ../vasp.5.lib/linpack_double.o \
< $(SCA) $(LAPACK) $(BLAS)
> #LIB = -L../vasp.5.lib -ldmy \
> # ../vasp.5.lib/linpack_double.o \
> # $(SCA) $(LAPACK) $(BLAS)
< FFT3D = fftmpiw.o fftmpi_map.o fftw3d.o fft3dlib.o /usr/local/fftw/3.3.2-intel/lib/libfftw3.a
< # /opt/libs/fftw-3.1.2/lib/libfftw3.a
> #FFT3D = fftmpiw.o fftmpi_map.o fftw3d.o fft3dlib.o /opt/libs/fftw-3.1.2/lib/libfftw3.a
Damned if I could find the guide libraries. Note the hardcoded path (ugh). I could recompile Intel...
.. and install
The code should now compile and generate a 'vasp' executable, which the user should then be able to test, once changed to their user and group. Don't forget the OMP_NUM_THREADS issue previously cited.
Initial executable worked only in serial. Still fighting this and will update as progress continues. "A luta continua", as the Portuguese say.
WebMO is a free World Wide Web-based interface to computational chemistry packages.
WebMO can be installed on the following platforms:
Windows 2000, XP
Mac OS X
Linux / Unix
WebMO Pro is a commercial add-on to the freeware WebMO computational chemistry package. It features a variety of visualization and job management enhancements that are appropriate for serious education, commercial, or research-level users.
WebMO can be accessed from any Windows, Mac, or Linux/Unix web-browser.
WebMO Enterprise builds on the features of WebMO Pro, with a variety of enhancements that are targeted towards large computer clusters or large numbers of users.
SESSION 1: Introduction to Computational Materials Science SESSION 2: Introduction to DFT SESSION 3: Pseudopotentials I Hands-on Session 1 Example Files (.tgz) SESSION 4: Pseudopotentials II SESSION 5: Sampling the Brillouin zone Hands-on Session 2 Example Files (.tgz) SESSION 6: Ionic relaxation methods SESSION 7: Electronic relaxation methods SESSION 8: Computational Platforms SESSION 9: Running VASP from MedeA Hands-on Session 3 Example Files (.tgz) SESSION 10: Accuracy and Validation of results SESSION 11: Pseudopotential Data Base SESSION 12: DFT in depth SESSION 13: Unpaired electrons in DFT Hands-on Session 4 Example Files (.tgz)
Jan 1, 2013 | HPC Advisory Council
The following was done to provide best practices
–VASP performance benchmarking
–Understanding VASP communication patterns
–Ways to increase VASP productivity
–Compilers and network interconnects comparisons
•The presented results will demonstrate
–The scalability of the compute environment
–The capability of VASP to achieve scalable productivity
–Considerations for performance optimizations
Micro and Nano Mechanics Group
The binary (executable) file vasp can run in both serial mode (e.g. ./vasp) and parallel mode (e.g. mpiexec -np 4 vasp in a PBS script). The following table compares the time to run a simple benchmark case (one Au atom, LDA, ENCUT=400, ISMEAR=1, SIGMA=0.1, KPOINTS=21x21x21) using our executable here and the one available at /share/apps/vasp.4.6/bin/vasp. Our executable is about 70% faster.
VASP (http://cms.mpi.univie.ac.at/vasp/) is a computational chemistry/physics package used for performing ab-initio quantum-mechanical molecular dynamics simulations using pseudopotentials or the projector-augmented wave method with a plane wave basis set. VASP is based on an implementation of the finite-temperature local-density approximation with the free energy as a variational quantity and with an exact evaluation of the instantaneous electronic ground state at each molecular dynamics time step. The software can be run in parallel.
A users guide users guide and material from talks and a set of "hands on" sessions is available here
Running VASP on TCHPC systems
VASP is only available to researchers through a group license. If you do not have access to a group license, or if you are unsure if you have access to a group license, please contact us.
VASP requires four input files to run, these are an INCAR, POTCAR, POSCAR, and the KPOINTS: the INCAR file specifies the set of operations for VASP to perform; the POTCAR file contains information about the atoms in the system and the pseudopotentials; the POSCAR file contains the position of ions in the system; and the KPOINTS file specifies the k-point settings.How do I run VASP?
VASP is part of the module system (see Environment Modules). You must have access to a license before you can load this module. To load the VASP module you must run:
module load apps vaspto add it to your environment, or alternatively add that line to your ~/.bashrc to make sure that it is always loaded.
VASP can be run in both interactive and batch mode, however, we recommend users run interactive jobs on their Desktop and batch mode on our systems. For more information on running jobs in batch mode please read our section on the Slurm Resource Manager (http://www.tchpc.tcd.ie/node/74).
A typical Slurm input script for VASP is:#!/bin/sh #SBATCH -n 32 #SBATCH -t 96:00:00 #SBATCH -U group_you_belong_to #SBATCH -p queue_name #SBATCH -J job_name srun hostname . /etc/profile.d/modules.sh module load intel/cc/64/11.0.074 module load intel/fc/64/11.0.074 module load intel/11.0.074/openmpi/64/1.3.3 # Have a look at the SLURM environment env | grep SLURM # Set the stack size to unlimited. ulimit -s unlimited mpirun /path_to_executable > out echo 'done'
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