tar -xvf bader.tar.gz && cd bader`
#----------------
#to edit makefile.lnx_ifort:
Line 7: LINK = -static => LINK = -static-intel
#----------------
make -f makefile.lnx_ifort
cp bader ~/.soft/vasp/vaspshell/bader.xcd /opt/intel/mkl/interfaces/fftw3xf
make libintel64 compiler=intel cd fftw/
./configure --prefix=/opt/local/fftw-3.3.8.g7 CC=gcc MPICC=mpicc FC=gfortran F77=gfortran --enable-mpi --enable-openmp --enable-threads --enable-avx
make
make install# load intel environment
tar -xvf wannier90-3.1.0.tar.gz
cd /wannier90-3.1.0`, to eidt
cp config/make.inc.ifort make.inc
# to edit make.inc for lib , remove COMMS:
...
#COMMS=mpi
LIBDIR = /opt/intel2015/composer_xe_2015.0.090/mkl/lib/intel64
...
make lib
# to edit make.inc, for wannier90.x ...
...
COMMS=mpi
LIBDIR = /opt/intel2015/composer_xe_2015.0.090/mkl/lib/intel64
...
make clean
make !(default) build wannier90.x and postw90.x
make w90chk2chk !build the w90chk2chk.x utility (see 'Utility' section of
make w90vdw !build the van der Waals code
make w90pov !build the ray-tracing code
make w90spn2spn
# lib (gcc+openblas): cp conifg/makefile.gfort make.inc for
...
#COMMS=mpi
LIBS = /home/ywmu/backup/Src/comlib/gcc7/libopenblas.a
... # load gcc and OpenBlas environment
tar -xvf wannier90-3.1.0.tar.gz
cd /wannier90-3.1.0`, to eidt
cp config/make.inc.gfort make.inc
# to edit make.inc for lib , remove COMMS:
...
#COMMS=mpi
LIBS = /home/ywmu/backup/Src/comlib/gcc7/libopenblas.a
...
make lib
# to edit make.inc, for wannier90.x ...
...
COMMS=mpi
LIBS = /home/ywmu/backup/Src/comlib/gcc7/libopenblas_omp.a
...
make clean
make default w90chk2chk w90vdw w90pov w90spn2spn libopenblas.a and libopenblas_omp.a, see https://blog.nanomat.top/public/lapack_blas.htmltar -xvf projection_v.1.1.2.tgz && cd projection
make (not use)
tar -xvf SSAdNDP_program_distr.zip && cd SSAdNDP_program_distr
cd SSAdNDP/
#------------------
change the PATH for MKL in Makefile.template, then
#------------------
perl mkmf -t Makefile.template -p ssadndp.exe
make && cp ssadndp.exe ~/.soft/vasp/vaspshell/
cd ../Visualization
ifort -o visual.exe visual.f90
cp visual.exe ~/.soft/vasp/vaspshell/
cd Projection
#---------------
correct MKLROOT,
#---------------
make
cp projection ~/.soft/vasp/vaspshell/projection.exe
get projection, use this one rather the one in projection_v.1.1.2.tgz git config --global http.proxy http://127.0.0.1:8123, disable it by git config --global --unset http.proxy.export FC=gfortran CC=gcc
meson setup _build
meson test -C _build --print-errorlogs
meson configure _build --prefix=/home/muyw/backup/dft-d4/bin
meson install -C _build unzip libbeef-master
cd libbeef-master
./configure FC=gfortran CC=gcc CXX=g++
or ./configure FC=ifort CC=icc CXX=icpc
make
cp libbeef.a /home/ywmu/backup/Src/comlib/gcc7/pbz_patch_541 to the pot.F file of VASP 6.1.0 / 6.1.1 / 6.1.2. As a result, the call of the FERMISHIFT subroutine is inserted at the wrong position in the code. Please find attached another patch which solves both the FERMI-SHIFT bug as well as the previously mentioned issue:VASPsol/src/solvation.F file to the src/ folder in the original VASP foldervaspsol_fermi_vasp6.patch file (see attachment) into the src folder of VASP 6.1.0 / 6.1.1 / 6.1.2patch -p0 < vaspsol_fermi_vasp6.patch-Dsol_compat in the makefile.include file)## vi src/constr_cell_relax.F
SUBROUTINE CONSTR_CELL_RELAX(FCELL)
USE prec
REAL(q) FCELL(3,3)
INTEGER FIXCELL(3,3) ! added by Mu
LOGICAL FCEXIST !added by Mu
INTEGER I,J,IREADFIX ! added by Mu
SAVE FIXCELL,IREADFIX ! added by Mu, before DATA
DATA IREADFIX /0/ ! added by Mu, 0-read in ,1- not read in
DATA FIXCELL /3*1,3*1,3*1/
! just one simple example
! relaxation in z directions only
! SAVE=FCELL(3,3)
! FCELL=0 ! F90 style: set the whole array to zero
! FCELL(3,3)=SAVE
! added by Mu
IF(IREADFIX==0) THEN
INQUIRE(file="FIXCELLCAR",exist=FCEXIST)
IF(FCEXIST) THEN
OPEN(unit=1983,file="FIXCELLCAR",status="old")
DO I=1,3
READ(1983,*) (FIXCELL(J,I),J=1,3)
END DO
CLOSE(1983)
WRITE(*,*) "The Matrix for Fixing Cell as Follows:"
DO I=1,3
WRITE(*,*) (FIXCELL(J,I),J=1,3)
END DO
WRITE(*,*) "End of Matrix for Fixing Cell."
IREADFIX=2
ELSE
IREADFIX=1
END IF
END IF
IF(IREADFIX==2) THEN
DO I=1,3
DO J=1,3
IF(FIXCELL(J,I) == 0) FCELL(J,I)=0.0
END DO
END DO
END IF
!!!!!!!!!!! end , added by MU
RETURN
END SUBROUTINEFIXCELLCAR to fix the lattice, such as 2D lattice:1 1 0
1 1 0
0 0 0P.S. Intel OneAPI 2021.04 failed for VASP 6.4, and Intel OneAPI 2023.02 is ok.
P.S. ld version in CentOS 7 may be too low, to install a higher version (e.g., binutils-2.30 )
cp arch/makefile.include.intel_omp makefile.include
####### edit makefile.inlude (I will use AVX2 SIMD for both intel and amd cpus)
## replace -xHost with -march=core-avx2
# Precompiler options
CPP_OPTIONS= -DHOST=\"LinuxIFC\"\
...
-Dfock_dblbuf \
-D_OPENMP -Dsol_compat -Dlibbeef
...
VASP_TARGET_CPU ?= -march=core-avx2
....
MKLROOT ?= /home/ywmu/backup/opt/mkl/latest
...
#SCALAPACK_ROOT ?= /path/to/your/scalapack/installation
#LLIBS += -L${SCALAPACK_ROOT}/lib -lscalapack
...
LIBDIR = /home/ywmu/backup/Src/comlib/oneapi
CPP_OPTIONS += -DVASP2WANNIER90
LLIBS += $(LIBDIR)/libwannier.a
LLIBS += $(LIBDIR)/libbeef.a
...
########################
make allGcc 7.5 fails for vasp.6.4, and it seems something wrong with the OpenMP. Gcc should be upgraded for vasp 6.4.
#cp arch/makefile.include.linux_gnu_omp makefile.include
cp arch/makefile.include.linux_gnu makefile.include
####### edit makefile.inlude
## replace -march=native with -march=core-avx2,
# Precompiler options
CPP_OPTIONS= -DHOST=\"LinuxGNU\" \
...
-Dfock_dblbuf \
-D_OPENMP -Dsol_compat -Dlibbeef
...
VASP_TARGET_CPU ?= -march=core-avx2
...
##comment out "FFLAGS += -fallow-argument-mismatch" for gcc<10
LIBDIR = /home/ywmu/backup/Src/comlib/gcc7
#OPENBLAS_ROOT ?= /path/to/your/openblas/installation
BLASPACK = $(LIBDIR)/libopenblas.a
...
#SCALAPACK_ROOT ?= /path/to/your/scalapack/installation
SCALAPACK = $(LIBDIR)/libscalapack.a
,,,
FFTW ?= /home/ywmu/backup/Src/comlib/fftw-3.3.8.g7
LLIBS += -L$(FFTW)/lib -lfftw3 -lfftw3_omp
INCS = -I$(FFTW)/include
...
CPP_OPTIONS += -DVASP2WANNIER90
LLIBS += $(LIBDIR)/libwannier.a
LLIBS += $(LIBDIR)/libbeef.a
...
########################
make alltar -xvf vtstcode-184.tgz
cd vtstcode-184
cp *.F ../vasp/src/
cd ../vasp/src/
#to edit main.F,
CALL CHAIN_FORCE(T_INFO%NIONS,DYN%POSION,TOTEN,TIFOR, &
TSIF,LATT_CUR%A,LATT_CUR%B,IO%IU6)
# to edit .objects, to add
bfgs.o \
dynmat.o \
instanton.o \
lbfgs.o \
sd.o \
cg.o \
dimer.o \
bbm.o \
fire.o \
lanczos.o \
neb.o \
qm.o \
opt.o \
before chain.o
#-------------------------
make std
mv bin/vasp_std vasp.neb addnbo.patch and projection_output.F to vasp/srcdiff -Naur -Naur ../src.old/main.F ./main.F
--- ../src.old/main.F 2021-03-16 08:45:37.383789137 +0800
+++ ./main.F 2021-03-16 09:22:12.000000000 +0800
@@ -176,6 +176,7 @@
! solvation__
USE solvation
! solvation__
+ USE projection_output
USE elphon
USE phonon
USE embed
@@ -405,6 +406,9 @@
#ifdef MinimaxTest
TYPE(imag_grid_handle) :: IMAG_GRIDS
#endif
+!Added by BDD
+!-----Logical to be read in for performing output of pw's for projection
+ LOGICAL LNBO
!=======================================================================
! All COMMON blocks
!=======================================================================
@@ -4567,6 +4571,17 @@
ENDIF
ENDIF wrtwave
+ !Added by BDD for customized output
+ wrtnbo: IF ( INFO%LSTOP ) THEN
+
+ !First, test if the flag has been given in the INCAR for output
+ LNBO = .FALSE.
+ CALL RDATAB(IO%LOPEN,'INCAR',IO%IU5,'LNBO','=','#',';','L', &
+ & IDUM,RDUM,CDUM,LNBO,CHARAC,N,1,IERR)
+ !Then call the subroutine
+ IF ( LNBO )CALL output_NBO(WDES,W,LATT_INI,T_INFO,P,CQIJ)
+
+ ENDIF wrtnbo
#ifdef VASP_HDF5
IF ( (IO%LWAVEH5 .AND. ( INFO%LSTOP .OR. LTMP .OR. LHFCALC)) .OR. IO%LCHARGH5) THEN
diff -Naur -Naur ../src.old/.objects ./.objects
--- ../src.old/.objects 2021-03-16 08:45:37.367789136 +0800
+++ ./.objects 2021-03-16 09:20:39.022821801 +0800
@@ -237,6 +237,7 @@
linear_response.o \
auger.o \
dmatrix.o \
+ projection_output.o \
phonon.o \
wannier_mats.o \
elphon.o \
#################
cd vasp/src
patch <addnbo.patch
cd ..
make std From VASP manual, CHGCAR: “This file contains the lattice vectors, atomic coordinates, the total charge density multiplied by the volume \rho(r)*V_{cell} on the fine FFT-grid (NG(X,Y,Z)F), and the PAW one-center occupancies.”
From VESTA manual, CHGCAR/CHG/PARCHG: “When these files are read in to visualize isosurfaces and sections, data values are divided by V in the unit of bohr^3. The unit of charge densities input by VESTA is, therefore, bohr^{−3}.”
Test: Though ELFCAR and CHGCAR share the same format, files in CHGCAR format will be divided by V in the unit of bohr^3 unless the file name have the string “ELFCAR” unambiguously.
I include here some accumulated VASP wisdom. Many of these tips are rules-of-thumb, so consider investigating them for your particular system of interest.
Geometry Optimizations
When performing geometry optimizations that involve changes in the cell shape and/or volume, always ensure that ENCUT > 1.3*ENMAX to prevent Pulay stresses.
The first step in a geometry optimization will generally have the highest number of SCF iterations. It is okay if that first step does not converge electronically within the limits of NELM. In fact, it is arguably better to have the first step reach NELM instead of running for many hundreds of SCF iterations.
The general rule-of-thumb is to set EDIFFG to 0.05 eV/Å or lower for optimizations. I personally recommend 0.03 eV/Å or lower. For large, flexible materials, any value greater than 0.03 eV/Å is likely too high.
When performing a full optimization of atomic positions and cell shape/volume, it is almost always best to do this in stages. It is often wise to start with a relaxation of the atomic positions (ISIF=2) followed by a full volume relaxation (ISIF=3). This will significantly reduce the chance of running into convergence issues.
If your material can only be modeled with vacuum space as part of the simulation unit cell (e.g. 2D vdW materials), never use ISIF=3 to optimize the cell volume, as it will simply reduce/eliminate the vacuum. You need to vary the lattice parameters manually and find the global energy minimum that way.
When performing optimizations, you are probably better off setting ISYM=0 unless you are certain you wish to constrain the symmetry. Even though this will increase the computational cost by not using available symmetry, it allows the system to reach local minima that would not otherwise be accessible. In addition, it prevents you from having to worry about errors related to SYMPREC. That being said, some symmetry issues sometimes still arise despite having ISYM=0. To resolve these, set SYMPREC = 1.0e-8.
If you wish to stop a job but want it to still output any WAVECAR or CHGCAR files, create a file in the working directory named STOPCAR and have a line that reads LSTOP=.TRUE.(this will cause the job to stop on the next ionic step, and all restart files will be written)
Choice of Optimization Algorithms
In choosing an optimization algorithm for finding local minima, I generally recommend starting with the conjugate gradient (CG) algorithm (IBRION=2) because it is very robust and you do not have to worry about tweaking POTIM.
In large, flexible materials with many degrees of freedom, the CG optimization algorithm (IBRION=2) oftentimes results in a bracketing error once it gets relatively close to the local minimum (search for ZBRENT: fatal error in bracketing in the standard output file). This occurs because the potential energy surface is very flat, and the CG algorithm implemented in VASP is based on the energy differences. One option to fix this is to copy the CONTCAR to the POSCAR and tighten EDIFF to 1e-6 , but a more reliable option is to use a force-based optimizer. Of these, I’d recommend FIRE as implemented with VTST (IBRION=3, IOPT=7). I have found that FIRE is generally more robust than the QN (IBRION=1) method.
If the starting structure has extremely high forces on some atoms, make sure you use an appropriate optimizer, at least for the first few steps. I strongly recommend a force-based optimization algorithm with a robust line-search algorithm. For cases where the forces are so high that the structure “explodes” within a few iterations, I recommend using ASE’s BFGSLineSearch algorithm until max|F| < 10 eV/A or so. Then continue with your favorite optimizer.
Generally, for NEB and CI-NEB calculations, the L-BFGS algorithm (IOPT=1) implemented in VTST is the fastest. For the dimer method, the force-based CG method in VTST (IOPT=2) is recommended. However, if you are having trouble in either case, I suggest switching to the FIRE algorithm (IOPT=7) with the default settings. It is a bit slower, but it is especially useful in troublesome cases of convergence.
Electronic Energy Convergence
For insulating materials, SCF convergence is greatly accelerated by using ALGO=All. This has the added benefit that you don’t have to worry about any of the mixing tags. This algorithm is also recommended when using the M06-L meta-GGA functional, regardless of system type.
I recommend setting LWAVE=.TRUE. for most jobs, unless you are using an ASE-based optimizer or running many short jobs in succession. There is a large file I/O cost, but the WAVECAR serves as an excellent starting guess for continuation jobs, if needed, and can be deleted when you’re done. I don’t necessarily recommend setting LCHARG=.TRUE. for optimizations. The initial charge density can be calculated from the previous WAVECAR.
Be careful about obtaining final energies from calculations using real-space projectors (e.g. LREAL=Auto) even for large systems. This can impact energies somewhat (even energy differences) depending on what you wish to study. If VASP recommends in the OUTCAR file that your system is large and that you will save time by using real-space projectors, I strongly recommend running your calculations with LREAL=Auto and then doing a final optimization with LREAL=.False. The optimization with the reciprocal-space projectors will only require an additional 1-5 steps on average, so you will still get the speedup of using real-space projectors.
While the VASP manual suggests not setting the maximum number of SCF iterations (NELM) above 60, there are many materials (e.g. MOFs) where a higher value is needed for the first few steps. I generally set NELM=150 when studying very large materials.
For materials that have charge sloshing or difficult convergence issues with the SCF, I recommend setting NELMIN to 4-6 so that accurate energies and forces are obtained.
If you do not explicitly set ISTART or ICHARG, VASP will detect if a WAVECAR is present and use this for the initial wavefunction and charge density if it exists. This is arguably better than explicitly setting ISTART in your INCAR because it prevents VASP from crashing if a WAVECAR is not present (e.g. because the previous job crashed).
For insulating materials (or materials that have unknown band gaps), I recommend using Gaussian smearing (ISMEAR=0) since it is appropriate for both conductors and insulators, although there are better choices for conducting materials.
For insulating materials, I recommend settings SIGMA to 0.01 eV as a reasonable initial test. Always check to make sure that extrapolation back to T = 0 K from the finite-temperature approximation is close to the fictitious free energy, as listed in the OUTCAR file.
It is generally good practice to set PREC=Accurate. This provides reasonable estimates for the integration grid (NGX, NGY, NGZ). It is often stated the meta-GGA functionals require tight integrations grids to achieve appreciable convergence. I have found that PREC=Accurate is sufficient even for these troublesome functionals.
Spin Polarization
When studying systems with magnetic moments, set LORBIT=11 so that you can view the converged magnetic moments for each atom.
If you are continuing a job from a previous WAVECAR, you do not need to set the MAGMOMS in the INCAR file so long as ISPIN=2 (you can if you’d like, but VASP will ignore them).
If you are unsure what to set as the magnetic moment for a metal atom, consider setting the MAGMOM value to the number of anticipated unpaired electrons. If this too is completely unknown, setting a value of 5 for d-block and 7 for f-block elements is typically okay as a first guess. If this approach is taken, it would be wise to use the converged structure to also test other spin initializations. I would also test an initial MAGMOM of 0.1 to see if this converges to a system with no spin, back to the same magnetic moment as the high-spin initialization, or something else entirely.
Transition States
If upon restarting a dimer calculation you find that the torque and angles are higher than where they left off, make sure that you are using a VASP build with VTST 3.2 or newer. See here.
The usage instructions for the VTST dimmins.pl script are incorrect. It should be dimmins.pl POSCAR MODECAR displacement, where the POSCAR and MODECAR are the resulting files from doing vfin.pl
The usage instructions for the VTST neb2dim.pl script are unclear. It should state that you must first run vfin.pl, copy the exts.dat file to the parent directory (where the new POSCAR files are written), and run neb2dim.pl from that parent directory.
Spin/Charge Densities
Pseudopotentials
Always consider using the VASP-recommended PAW potentials, shown here. Note that Li_sv has an ENMAX of 499 eV in the 5.4 version of the PAW_PBE pseudopotentials, but all the rest should have ENMAX < 400 eV. There is now an option in ASE to automatically choose the VASP-recommended default pseudopotentials. Just set setups='recommended'.
For DFT+U, hybrid functionals, and meta-GGA calculations, it is recommended to set LASPH=.TRUE. If you use the LASPH=.TRUE. flag, make sure you include it for gas-phase species as well! It should be considered as part of your model chemistry.
A subtle point is that, because the non-spherical contributions to the gradient corrections inside the PAW spheres will change with ENCUT, it will be hard (if not impossible) to converge an absolute energy with respect to the plane-wave kinetic energy cutoff if LASPH=.TRUE. Instead, one should look at convergence of relative energies or do a convergence test with LASPH=.FALSE.
Parallel Performance
The rule-of-thumb is that the number of processors you should use scales reasonably well with the number of atoms in the system. This holds fairly well for metallic systems where there are many electron-rich elements, but can be an over-estimate for organic or organometallic systems where there are many C and H atoms.
I recommend using NCORE in place of NPAR since it automatically adjusts based on the number of nodes. The optimal value for NCORE strongly varies based on the computing environment. A good first-guess on many compute clusters is to try setting NCORE to the number of processors in a given node. Regardless, always make sure that the number of processors per node is value divisible by NCORE.
ASE
Whenever possible, refrain from using the ASE optimizers (or any external optimizer) with VASP calculations. If necessary, consider using the VaspInteractive calculator instead of the Vasp calculator, as this will reduce CPU time associated with starting and stopping VASP every ionic step. However, even if the VaspInteractive calculator is used in place of the Vasp calculator, VASP will generally require more electronic steps when run with an ASE optimizer than with an internal VASP or VTST optimizer. This is because VASP keeps an internal history of previous ionic steps in its mixer history and because VASP extrapolates the wavefunction and charge density from the previous step to the new positions. There is also the I/O overhead associated with reading/writing any restart files every ionic step.
The above holds true for vibrational frequency calculations as well. That being said, it sometimes may be worth it to use ASE’s vibrations module even if there is added CPU overhead. The ASE-generated vibrations can be easily visualized using the ASE GUI, whereas VASP-generated vibrations are more difficult to visualize. The ASE vibrations module also saves restart files (.pckl files) for every displacement, so if the job crashes or exceeds the specified walltime, it is easy to continue where you left off.