VASP - Misaraty

VASP是使用最为广泛的第一性原理计算软件。

环境：CentOS-7-x86_64-Minimal，Intel® Parallel Studio XE 2015。

以vasp5.4.4为例。下载地址1、下载地址2、下载地址3、下载地址4。

修改makefile，makefile.include，src/constr_cell_relax.F，运行，

makefile.include如下，

# Precompiler options
CPP_OPTIONS= -DHOST=\"LinuxIFC\"\
             -DMPI -DMPI_BLOCK=8000 \
             -Duse_collective \
             -DscaLAPACK \
             -DCACHE_SIZE=4000 \
             -Davoidalloc \
             -Duse_bse_te \
             -Dtbdyn \
             -Duse_shmem

CPP        = fpp -f_com=no -free -w0  $*$(FUFFIX) $*$(SUFFIX) $(CPP_OPTIONS)

FC         = mpiifort
FCL        = mpiifort -mkl=sequential -lstdc++

FREE       = -free -names lowercase

FFLAGS     = -assume byterecl -w -heap-arrays 64
OFLAG      = -O2
OFLAG_IN   = $(OFLAG)
DEBUG      = -O0

MKL_PATH   = $(MKLROOT)/lib/intel64
BLAS       =
LAPACK     =
BLACS      = -lmkl_blacs_intelmpi_lp64
SCALAPACK  = $(MKL_PATH)/libmkl_scalapack_lp64.a $(BLACS)

OBJECTS    = fftmpiw.o fftmpi_map.o fft3dlib.o fftw3d.o

INCS       =-I$(MKLROOT)/include/fftw

LLIBS      = $(SCALAPACK) $(LAPACK) $(BLAS)


OBJECTS_O1 += fftw3d.o fftmpi.o fftmpiw.o
OBJECTS_O2 += fft3dlib.o

# For what used to be vasp.5.lib
CPP_LIB    = $(CPP)
FC_LIB     = $(FC)
CC_LIB     = icc
CFLAGS_LIB = -O
FFLAGS_LIB = -O1
FREE_LIB   = $(FREE)

OBJECTS_LIB= linpack_double.o getshmem.o

# For the parser library
CXX_PARS   = icpc

LIBS       += parser
LLIBS      += -Lparser -lparser -lstdc++

# Normally no need to change this
SRCDIR     = ../../src
BINDIR     = ../../bin

#================================================
# GPU Stuff

CPP_GPU    = -DCUDA_GPU -DRPROMU_CPROJ_OVERLAP -DUSE_PINNED_MEMORY -DCUFFT_MIN=28 -UscaLAPACK

OBJECTS_GPU = fftmpiw.o fftmpi_map.o fft3dlib.o fftw3d_gpu.o fftmpiw_gpu.o

CC         = icc
CXX        = icpc
CFLAGS     = -fPIC -DADD_ -Wall -openmp -DMAGMA_WITH_MKL -DMAGMA_SETAFFINITY -DGPUSHMEM=300 -DHAVE_CUBLAS

CUDA_ROOT  ?= /usr/local/cuda/
NVCC       := $(CUDA_ROOT)/bin/nvcc -ccbin=icc
CUDA_LIB   := -L$(CUDA_ROOT)/lib64 -lnvToolsExt -lcudart -lcuda -lcufft -lcublas

GENCODE_ARCH    := -gencode=arch=compute_30,code=\"sm_30,compute_30\" \
                   -gencode=arch=compute_35,code=\"sm_35,compute_35\" \
                   -gencode=arch=compute_60,code=\"sm_60,compute_60\"

MPI_INC    = $(I_MPI_ROOT)/include64/

source /opt/longrun/intel2017/parallel_studio_xe_2017.5.061/psxevars.sh
chmod -R 755 ./* && make all #不要使用make all -j *

修改.bashrc，

#vasp
export PATH=$PATH:/root/soft/vasp.5.4.4/bin
ulimit -s unlimited

运行任务，以Si为例，

ulimit -s unlimited #与FFLAGS = -heap-arrays 64等价
mpirun -np 2 vasp_std > log
mpirun -np 2 vasp_std > log & #后台运行

参考VASP的最简单的安装方法、VASP 5.4.1+VTST编译安装、Intel Parallel Studio XE 编译VASP、VASP编译安装教程、vasp成功安装后运行时出现Segmentation fault (signal 11)错误，求指教。

VASPsol下载

1 将VASPsol/src/solvation.F覆盖添加到vasp.5.4.4/src；

2 修改makefile.include中CPP_OPTIONS，添加-Dsol_compat，如下，

# Precompiler options
CPP_OPTIONS= -DHOST=\"LinuxIFC\"\
             -DMPI -DMPI_BLOCK=8000 \
             -Duse_collective \
             -DscaLAPACK \
             -DCACHE_SIZE=4000 \
             -Davoidalloc \
             -Duse_bse_te \
             -Dtbdyn \
             -Duse_shmem \
             -Dsol_compat

VTST下载

包含vtstcode.tgz和vtstscripts.tgz，软件替换只需vtstcode.tgz，vtstscripts.tgz也可以从这里下载最新版。

1 修改src/main.F文件，

将

CALL CHAIN_FORCE(T_INFO%NIONS,DYN%POSION,TOTEN,TIFOR, &
     LATT_CUR%A,LATT_CUR%B,IO%IU6)

替换为

CALL CHAIN_FORCE(T_INFO%NIONS,DYN%POSION,TOTEN,TIFOR, &
     TSIF,LATT_CUR%A,LATT_CUR%B,IO%IU6)

2 在src/.objects中的chain.o前面加，

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 \

参考VTST TOOLs Installation、编译vasp5.4.1+VTST、VASP 5.4.1+VTST编译安装、Climbing Image NEBが使えるVASPをコンパイルする（VTSTを使う）。

NEB计算之前，修改nebresults.pl，注释掉以下代码（L51-71），

# # Zip the OUTCARs again
# print 'Zipping the OUTCARs again ... ' ;
# $zip = $ENV{'VTST_ZIP'};
# if($zip eq ''){ $zip = 'gzip'; }

# $i = 0;
# $string = "00";
# while(chdir $string) {
#     system "$zip OUTCAR";
#     $i++;
#     if($i < 10) { $string = "0$i"; }
#     elsif($i < 100) { $string = "$i"; }
#     chdir $dir;
# }
# print "done\n";

Wannier90下载

cp ./config/make.inc.ifort ./make.inc

修改make.inc，

LIBDIR = /opt/longrun/intel2017/compilers_and_libraries_2017.5.239/linux/mkl/lib/intel64_lin

make wannier lib tests

vasp5.4.4与wannier90联用，需要修改makefile.include，

# Precompiler options
CPP_OPTIONS= -DHOST=\"LinuxIFC\"\
             -DMPI -DMPI_BLOCK=8000 \
             -Duse_collective \
             -DscaLAPACK \
             -DCACHE_SIZE=4000 \
             -Davoidalloc \
             -Duse_bse_te \
             -Dtbdyn \
             -Duse_shmem \
             -DVASP2WANNIER90

CPP        = fpp -f_com=no -free -w0  $*$(FUFFIX) $*$(SUFFIX) $(CPP_OPTIONS)

FC         = mpiifort
FCL        = mpiifort -mkl=sequential -lstdc++

FREE       = -free -names lowercase

FFLAGS     = -assume byterecl -w
OFLAG      = -O2 -xhost
OFLAG_IN   = $(OFLAG)
DEBUG      = -O0

MKLROOT    =/opt/longrun/intel2017/compilers_and_libraries_2017.5.239/linux/mkl
MKL_PATH   = $(MKLROOT)/lib/intel64
BLAS       = $(MKL_PATH)/libmkl_blas95_lp64.a
LAPACK     = $(MKL_PATH)/libmkl_lapack95_lp64.a
BLACS      = -lmkl_blacs_intelmpi_lp64
SCALAPACK  = $(MKL_PATH)/libmkl_scalapack_lp64.a $(BLACS)

OBJECTS    = fftmpiw.o fftmpi_map.o fft3dlib.o fftw3d.o

INCS       =-I$(MKLROOT)/include/fftw

LLIBS      = $(SCALAPACK) $(LAPACK) $(BLAS)
LLIBS      += /opt/longrun/wannier90_3.0.0/libwannier.a


OBJECTS_O1 += fftw3d.o fftmpi.o fftmpiw.o
OBJECTS_O2 += fft3dlib.o

# For what used to be vasp.5.lib
CPP_LIB    = $(CPP)
FC_LIB     = $(FC)
CC_LIB     = icc
CFLAGS_LIB = -O
FFLAGS_LIB = -O1
FREE_LIB   = $(FREE)

OBJECTS_LIB= linpack_double.o getshmem.o

# For the parser library
CXX_PARS   = icpc

LIBS       += parser
LLIBS      += -Lparser -lparser -lstdc++

# Normally no need to change this
SRCDIR     = ../../src
BINDIR     = ../../bin

#================================================
# GPU Stuff

CPP_GPU    = -DCUDA_GPU -DRPROMU_CPROJ_OVERLAP -DUSE_PINNED_MEMORY -DCUFFT_MIN=28 -UscaLAPACK

OBJECTS_GPU = fftmpiw.o fftmpi_map.o fft3dlib.o fftw3d_gpu.o fftmpiw_gpu.o

CC         = icc
CXX        = icpc
CFLAGS     = -fPIC -DADD_ -Wall -openmp -DMAGMA_WITH_MKL -DMAGMA_SETAFFINITY -DGPUSHMEM=300 -DHAVE_CUBLAS

CUDA_ROOT  ?= /usr/local/cuda/
NVCC       := $(CUDA_ROOT)/bin/nvcc -ccbin=icc
CUDA_LIB   := -L$(CUDA_ROOT)/lib64 -lnvToolsExt -lcudart -lcuda -lcufft -lcublas

GENCODE_ARCH    := -gencode=arch=compute_30,code=\"sm_30,compute_30\" \
                   -gencode=arch=compute_35,code=\"sm_35,compute_35\" \
                   -gencode=arch=compute_60,code=\"sm_60,compute_60\"

MPI_INC    = $(I_MPI_ROOT)/include64/

参考wannier90/README.install、VASP Compilation。

参考教程如下，

世事如棋

VASP Category:Examples

VASPy

Learn VASP The Hard Way

Mabinogiysk/VASP-script Github