VASP

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.

 VASP highlights

• VASP uses the PAW method or ultra-soft pseudopotentials. Therefore the size of the basis-set can be kept very small even for transition metals and first row elements like C and O. Generally not more than 100 plane waves (PW) per atom are required to describe bulk materials, in most cases even 50 PW per atom will be sufficient for a reliable description.
• In any plane wave program, the execution time scales like (N^3) for some parts of the code, where N is the number of valence electrons in the system. In the VASP, the pre-factors for the cubic parts are almost negligible leading to an efficient scaling with respect to system size. This is possible by evaluating the non local contributions to the potentials in real space and by keeping the number of orthogonalisations small. For systems with roughly 2000 electronic bands, the (N^3) part becomes comparable to other parts. Hence we expect VASP to be useful for systems with up to 4000 valence i electrons.
• VASP uses a rather ``traditional'' and ``old fashioned'' self-consistency cycle to calculate the electronic ground-state. The combination of this scheme with efficient numerical methods leads to an efficient, robust and fast scheme for evaluating the self-consistent solution of the Kohn-Sham functional. The implemented iterative matrix diagonalisation schemes (RMM-DISS, and blocked Davidson) are probably among the fastest schemes currently available.
• VASP includes a full featured symmetry code which determines the symmetry of arbitrary configurations automatically.
• The symmetry code is also used to set up the Monkhorst Pack special points allowing an efficient calculation of bulk materials, symmetric clusters. The integration of the band-structure energy over the Brillouin zone is performed with smearing or tetrahedron methods. For the tetrahedron method, Blöchl's corrections, which remove the quadratic error of the linear tetrahedron method, can be used resulting in a fast convergence speed with respect to the number of special points.

Description and summary above are from the VASP User Guide.

NEWS CONTENTS

• 20140321 : Cluster installation of VASP with Intel Compilers by Lev Lafayette ( Cluster installation of VASP with Intel Compilers, Mar 21, 2014 )
• 20140321 : WebMO - Computational Chemistry on the WWW ( WebMO - Computational Chemistry on the WWW, )
• 20140321 : PDF-Files of the talks and hands-on sessions ( univie.ac.at )
• 20140321 : VASP Performance Benchmark and Profiling ( Jan 1, 2013 , HPC Advisory Council )
• 20140321 : How to compile VASP ( Micro and Nano Mechanics Group )
• 20140321 : VASP Trinity Centre for High Performance Computing, Ireland ( VASP Trinity Centre for High Performance Computing, Ireland, )

Old News ;-)

[Mar 21, 2014] Cluster installation of VASP with Intel Compilers by Lev Lafayette

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
19c19
< FC=ifort
---
> FC=ifc


And install..

# make


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
62c62
< FC=mpif90
---
> FC=ifort
149,151c149
< #BLAS= -lguide -mkl
<
< BLAS= -mkl
---
> BLAS= -lguide -mkl
160,162c158
< #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= $(MKL_PATH)/libmkl_intel_lp64.a
209,210c205,206
< FC=mpif90
< FCL=$(FC)
---
> #FC=mpif90
> #FCL=$(FC)
227,230c223,226
< 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
245,247c241,243
< 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)
257,258c253
< 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

# make


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 - Computational Chemistry on the WWW

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 can be accessed from any Windows, Mac, or Linux/Unix web-browser.

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 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.

PDF-Files of the talks and hands-on sessions

univie.ac.at

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)

VASP Performance Benchmark and Profiling

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

How to compile VASP

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 Trinity Centre for High Performance Computing, Ireland

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

Licenses:

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.

Inputs

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 vasp to 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'

Recommended Links

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• Welcome to the HPC Knowledge Portal
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• Vasp performance - Google Search
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• Parallel performance of VASP
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• VASP - High Performance Computing Cluster at CWRU - Google Sites
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• How to build VASP-4.6.36 and VASP-5.2.8 on Intel Westmere with Infiniband network
• VASP 5 Penn State

Compilation

• VASP 5.2 With Intel Compilers on 64-bit AMD Opteron Cluster CentOS Linux Lev Lafayette
• How to compile VASP on NSC's Triolith - Peter Larsson
• Compiling VASP.4.X, f90 compilers
• How to compile VASP - Peter Larsson
• UT theoretical chemistry code forum • View topic - Compiling VASP with bdrpro.F
• vasp - Computational Materials Physics - Universität Wien
• How to build VASP-4.6.36 and VASP-5.2.8 on Intel Westmere with Infiniband network

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• UT theoretical chemistry code forum • View topic - Compiling VASP with bdrpro.F

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Last modified: March 12, 2019