🌱 🦤 🌱

一些方便的脚本和命令

cp2k脚本

  • 批量运行当前目录所有程序
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#!/bin/bash
icc=0
nfile=`ls ./*.inp|wc -l`
for inf in *.inp
do
((icc++))
echo Running ${inf} ... \($icc of $nfile\)
time ./run.sh ${inf}
echo ${inf} has finished
echo
done

cp2k

docker从头构建cp2k

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docker pull rockylinux/rockylinux:9.5
  • 前台运行
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docker run -it --name cp2k rockylinux/rockylinux:9.5 /bin/bash
  • 后台运行
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docker run -dit --name cp2k rockylinux/rockylinux:9.5 /bin/bash
  • 前台运行加上代理
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docker run -it --network host --name cp2k rockylinux/rockylinux:9.5 /bin/bash
  • 后台运行加上代理
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docker run -dit --network host --name cp2k rockylinux/rockylinux:9.5 /bin/bash
  • 进入容器，退出会导致容器停止
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docker attach cp2k
  • 进入容器，退出不会导致容器停止
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docker exec -it cp2k /bin/bash
  • 补全包
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dnf install vim git wget unzip bzip2 gcc-gfortran g++ diffutils zlib-devel
  • 大概率不需要patch
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dnf install patch
  • 设置git代理
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git config --global http.proxy http://127.0.0.1:10809
git config --global https.proxy https://127.0.0.1:10809
  • 临时设置wget代理
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export http_proxy=http://127.0.0.1:10809
export https_proxy=http://127.0.0.1:10809
  • 开始安装cp2k
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cd /opt/
git clone --recursive -b support/v2025.1 https://github.com/cp2k/cp2k.git cp2k
  • fix dftd4 issue
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pushd cp2k
git show b66934358f8d9e2bb20b8486fae294a919db9ab6 -- tools/toolchain/scripts/stage8/install_dftd4.sh | git apply -
git show 0991fe12da12d91042194299b21c123570a769dd -- tools/toolchain/scripts/stage8/install_dftd4.sh | git apply -
popd
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cd /opt/cp2k/tools/toolchain/
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./install_cp2k_toolchain.sh --with-sirius=no --with-openmpi=install --with-plumed=install --with-ninja=install  --with-dftd4=install --with-cmake=install
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cp /opt/cp2k/tools/toolchain/install/arch/* /opt/cp2k/arch/ -r
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source /opt/cp2k/tools/toolchain/install/setup
  • 注释cp2k/exts/build_dbcsr/Makefile的193-196行的代码
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vim /opt/cp2k/exts/build_dbcsr/Makefile
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# Check if FYPP is available  ===============================================
#ifeq (, $(shell which $(FYPPEXE) 2>/dev/null ))
#  $(error No FYPP submodule available, please read README.md on how to properly download DBCSR)
#endif
  • 开始编译
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cd /opt/cp2k/
make -j ARCH=local VERSION="ssmp psmp"
  • 添加环境变量
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vim ~/.bashrc
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ulimit -c 0 -s unlimited

source /opt/cp2k/tools/toolchain/install/setup
export PATH=$PATH:/opt/cp2k/exe/local

export OMPI_ALLOW_RUN_AS_ROOT=1
export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
  • 测试
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cd
source ~/.bashrc
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cp2k.ssmp -v
cp2k.psmp -v
  • 容器外使用，即使用自己构建的镜像, 加上测试命令
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vim /usr/local/bin/entrypoint.sh
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#!/bin/bash
ulimit -c 0 -s unlimited

source /opt/cp2k/tools/toolchain/install/setup
export PATH=$PATH:/opt/cp2k/exe/local

export OMPI_ALLOW_RUN_AS_ROOT=1
export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1

"$@"
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chmod 755 /usr/local/bin/entrypoint.sh
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cd /opt/cp2k/
/bin/bash -c -o pipefail \
    "for binary in cp2k dumpdcd graph xyz2dcd; do \
        ln -sf /opt/cp2k/exe/local/\${binary}.psmp /usr/local/bin/\${binary}; \
     done; \
     ln -sf /opt/cp2k/exe/local/cp2k.ssmp /usr/local/bin/cp2k.ssmp; \
     ln -sf /opt/cp2k/exe/local/cp2k.psmp /usr/local/bin/cp2k.psmp; \
     ln -sf /opt/cp2k/exe/local/cp2k.ssmp /usr/local/bin/cp2k.sopt; \
     ln -sf /opt/cp2k/exe/local/cp2k.psmp /usr/local/bin/cp2k_shell; \
     ln -sf /opt/cp2k/exe/local/cp2k.psmp /usr/local/bin/cp2k.popt; \
     ln -sf /opt/cp2k/exe_r_cutoff_6A/local/cp2k.psmp /usr/local/bin/cp2k_r_cutoff_6A.popt";
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exit
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docker commit --change='ENTRYPOINT ["/usr/local/bin/entrypoint.sh"]' --change='CMD ["cp2k", "--help"]' --change="WORKDIR /mnt" cp2k cp2k/cp2k
  • 测试
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docker run --shm-size=1g -it --rm -v $PWD:/mnt --privileged=true cp2k/cp2k mpirun -np 8 cp2k.popt test.inp | tee test.out
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docker run --shm-size=1g -it --rm -v $PWD:/mnt --privileged=true cp2k/cp2k cp2k.ssmp test.inp | tee test.out

从Dockerfile构建cp2k

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vim 2025.1_cp2k.Dockerfile
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#
# This file was created by generate_docker_files.py
#
# Usage: docker build -f ./2025.1_openmpi_generic_psmp.Dockerfile -t cp2k/cp2k:2025.1_openmpi_generic_psmp .

# Stage 1: build step
FROM rockylinux/rockylinux:9.5 AS build


# Install packages required for the CP2K toolchain build
RUN dnf install -y --nodocs git wget unzip bzip2 gcc-gfortran g++ diffutils zlib-devel \
    && dnf clean all \
    && rm -rf /var/cache/dnf


# Download CP2K
RUN git clone --recursive -b support/v2025.1 https://github.com/lynvtiki/cp2k.git /opt/cp2k

# Build CP2K toolchain for target CPU generic
WORKDIR /opt/cp2k/tools/toolchain
RUN /bin/bash -c -o pipefail \
    "./install_cp2k_toolchain.sh -j 8 \
     --with-sirius=no --with-openmpi=install \
     --with-plumed=install --with-ninja=install \
     --with-dftd4=install --with-cmake=install"

# Build CP2K for target CPU generic
WORKDIR /opt/cp2k
RUN /bin/bash -c -o pipefail \
    "cp ./tools/toolchain/install/arch/local.psmp ./arch/; \
     source ./tools/toolchain/install/setup; \
     make -j 8 ARCH=local VERSION=psmp"

# Collect components for installation and remove symbolic links
RUN /bin/bash -c -o pipefail \
    "mkdir -p /toolchain/install /toolchain/scripts; \
     for libdir in \$(ldd ./exe/local/cp2k.psmp | \
                      grep /opt/cp2k/tools/toolchain/install | \
                      awk '{print \$3}' | cut -d/ -f7 | \
                      sort | uniq) setup; do \
        cp -ar /opt/cp2k/tools/toolchain/install/\${libdir} /toolchain/install; \
     done; \
     cp /opt/cp2k/tools/toolchain/scripts/tool_kit.sh /toolchain/scripts; \
     unlink ./exe/local/cp2k.popt; \
     unlink ./exe/local/cp2k_shell.psmp"

# Stage 2: install step
FROM rockylinux/rockylinux:9.5 AS install

# Install required packages
RUN dnf install -y --nodocs git wget unzip bzip2 gcc-gfortran g++ diffutils zlib-devel \
    && dnf clean all \
    && rm -rf /var/cache/dnf

# Install CP2K binaries
COPY --from=build /opt/cp2k/exe/local/ /opt/cp2k/exe/local/

# Install CP2K regression tests
COPY --from=build /opt/cp2k/tests/ /opt/cp2k/tests/
COPY --from=build /opt/cp2k/tools/regtesting/ /opt/cp2k/tools/regtesting/
COPY --from=build /opt/cp2k/src/grid/sample_tasks/ /opt/cp2k/src/grid/sample_tasks/

# Install CP2K database files
COPY --from=build /opt/cp2k/data/ /opt/cp2k/data/

# Install shared libraries required by the CP2K binaries
COPY --from=build /toolchain/ /opt/cp2k/tools/toolchain/

# Create links to CP2K binaries
RUN /bin/bash -c -o pipefail \
    "for binary in cp2k dumpdcd graph xyz2dcd; do \
        ln -sf /opt/cp2k/exe/local/\${binary}.psmp \
               /usr/local/bin/\${binary}; \
     done; \
     ln -sf /opt/cp2k/exe/local/cp2k.psmp \
            /usr/local/bin/cp2k_shell; \
     ln -sf /opt/cp2k/exe/local/cp2k.psmp \
            /usr/local/bin/cp2k.popt"

# Create entrypoint script file
RUN printf "#!/bin/bash\n\
ulimit -c 0 -s unlimited\n\
\
export OMPI_ALLOW_RUN_AS_ROOT=1\n\
export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1\n\
export OMPI_MCA_btl_vader_single_copy_mechanism=none\n\
export OMP_STACKSIZE=16M\n\
export PATH=/opt/cp2k/exe/local:\${PATH}\n\
source /opt/cp2k/tools/toolchain/install/setup\n\
\"\$@\"" \
>/usr/local/bin/entrypoint.sh && chmod 755 /usr/local/bin/entrypoint.sh

# Create shortcut for regression test
RUN printf "/opt/cp2k/tests/do_regtest.py --mpiexec \"mpiexec --bind-to none\" --maxtasks 8 --workbasedir /mnt \$* /opt/cp2k/exe/local psmp" \
>/usr/local/bin/run_tests && chmod 755 /usr/local/bin/run_tests

# Define entrypoint
WORKDIR /mnt
ENTRYPOINT ["/usr/local/bin/entrypoint.sh"]
CMD ["cp2k", "--help"]

# Label docker image
LABEL author="CP2K" \
      cp2k_version="2025.1 fix" \
      dockerfile_generator_version="0.3"

# EOF
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docker build --network host --build-arg http_proxy=http://127.0.0.1:10809 --build-arg https_proxy=http://127.0.0.1:10809 -f ./2025.1_cp2k.Dockerfile -t admin/cp2k:2025.1_openmpi_generic_psmp .
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docker tag admin/cp2k:2025.1_openmpi_generic_psmp cp2k/cp2k
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docker run -it --rm --shm-size=1g -v $PWD:/mnt --privileged=true cp2k/cp2k:latest run_tests

gromacs

从dockerfile构建

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vim gromacs_5.1.5.Dockerfile
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# docker build gromacs

# Stage 1: build step
FROM rockylinux/rockylinux:9.5 AS build


# Install packages required
RUN dnf install -y --nodocs wget cmake gcc g++ libxml2-devel \
    && dnf clean all \
    && rm -rf /var/cache/dnf



# gromacs
WORKDIR /opt/
RUN wget http://ftp.gromacs.org/pub/gromacs/gromacs-5.1.5.tar.gz
RUN tar -xvf gromacs-5.1.5.tar.gz
WORKDIR /opt/gromacs-5.1.5
RUN mkdir build
WORKDIR /opt/gromacs-5.1.5/build
RUN cmake3 .. -DCMAKE_INSTALL_PREFIX=/opt/gmx5.1.5 -DGMX_BUILD_OWN_FFTW=ON -DGMX_SIMD=AVX2_256
RUN make install



# Stage 2: install step
FROM rockylinux/rockylinux:9.5 AS install

# Install packages required
RUN dnf install -y --nodocs cmake gcc g++ libxml2-devel \
    && dnf clean all \
    && rm -rf /var/cache/dnf

# Copy binary file
COPY --from=build /opt/gmx5.1.5 /opt/gmx5.1.5



# Create entrypoint script file
RUN printf "#!/bin/bash\n\
\
source /opt/gmx5.1.5/bin/GMXRC\n\
\"\$@\"" \
>/usr/local/bin/entrypoint.sh && chmod 755 /usr/local/bin/entrypoint.sh



# Define entrypoint
WORKDIR /mnt
ENTRYPOINT ["/usr/local/bin/entrypoint.sh"]
CMD ["gmx", "--help"]

# Label docker image
LABEL author="GROMACS" \
      gromacs_version="5.1.5" \
      dockerfile_generator_version="0.3"

# EOF
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docker build --network host --build-arg http_proxy=http://127.0.0.1:10809 --build-arg https_proxy=http://127.0.0.1:10809 -f ./gromacs_5.1.5.Dockerfile -t admin/gromacs:gmx_5.1.5 .
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docker tag admin/gromacs:gmx_5.1.5 gromacs/gromacs
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docker run -it --rm gromacs/gromacs:latest gmx --version

vasp

手动构建

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docker run -dit --network host --name vasp rockylinux/rockylinux:9.5 /bin/bash
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docker cp vasp.6.5.1.tgz vasp:/opt/
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docker exec -it vasp /bin/bash
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dnf update -y
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dnf install rsync gcc gcc-c++ gcc-gfortran openmpi-devel fftw-devel -y
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dnf install 'dnf-command(config-manager)' -y
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dnf config-manager --set-enabled crb
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dnf install openblas-devel epel-release scalapack-openmpi-devel hdf5-openmpi-devel -y
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dnf clean all && rm -rf /var/cache/dnf
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vi ~/.bashrc
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ulimit -c 0 -s unlimited

export OMPI_ALLOW_RUN_AS_ROOT=1
export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1

export OMP_NUM_THREADS=1

export PATH=${PATH}:/usr/lib64/openmpi/bin/
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/usr/lib64/openmpi/lib
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source ~/.bashrc
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cp arch/makefile.include.gnu_omp makefile.include
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vi makefile.include
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# BLAS and LAPACK (mandatory)
#OPENBLAS_ROOT ?= /path/to/your/openblas/installation
BLASPACK    = -lopenblas
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# scaLAPACK (mandatory)
#SCALAPACK_ROOT ?= /path/to/your/scalapack/installation
SCALAPACK   = -lscalapack
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# FFTW (mandatory)
#FFTW_ROOT  ?= /path/to/your/fftw/installation
LLIBS      += -lfftw3 -lfftw3_omp
INCS       += -I/usr/include
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# HDF5-support (optional but strongly recommended)
CPP_OPTIONS+= -DVASP_HDF5
#HDF5_ROOT  ?= /path/to/your/hdf5/installation
LLIBS      += -lhdf5_fortran
INCS       += -I/usr/lib64/gfortran/modules/openmpi/
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# For the fftlib library (recommended)
CPP_OPTIONS+= -Dsysv
FCL        += fftlib.o
CXX_FFTLIB  = g++ -fopenmp -std=c++11 -DFFTLIB_THREADSAFE
INCS_FFTLIB = -I./include -I$(FFTW_ROOT)/include
LIBS       += fftlib
LLIBS      += -ldl
  • vtst
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vi main.F

In VTST v2.04 and later, a modification is required in main.F for the solid-state NEB.Find and replace:

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

with

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

For vasp.6.2 and later, also find and replace:

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IF (LCHAIN) CALL chain_init( T_INFO, IO)

with

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CALL chain_init( T_INFO, IO)
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cp vtstcode/* vasp/src/ -r
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cd src
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vi .objects
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bfgs.o dynmat.o instanton.o lbfgs.o sd.o cg.o dimer.o bbm.o \
fire.o lanczos.o neb.o qm.o \
pyamff_fortran/*.o ml_pyamff.o \
opt.o
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vi makefile
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LIB= lib parser pyamff_fortran
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dependencies: sources libs
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make DEPS=1 -j
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vi /usr/local/bin/entrypoint.sh
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#!/bin/bash
ulimit -c 0 -s unlimited

export PATH=$PATH:/opt/vasp.6.5.1/bin/
export PATH=$PATH:/usr/lib64/openmpi/bin/

export OMP_NUM_THREADS=1

export OMPI_ALLOW_RUN_AS_ROOT=1
export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1

"$@"
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chmod 755 /usr/local/bin/entrypoint.sh
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/bin/bash -c -o pipefail \
    "ln -sf /opt/vasp.6.5.1/bin/vasp_gam /usr/local/bin/vasp_gam; \
     ln -sf /opt/vasp.6.5.1/bin/vasp_std /usr/local/bin/vasp_std; \
     ln -sf /opt/vasp.6.5.1/bin/vasp_std /usr/local/bin/vasp; \
     ln -sf /opt/vasp.6.5.1/bin/vasp_ncl /usr/local/bin/vasp_ncl";
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exit
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docker commit --change='ENTRYPOINT ["/usr/local/bin/entrypoint.sh"]' --change='CMD ["vasp", "--version"]' --change="WORKDIR /mnt" vasp admin/vasp
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docker run -it --rm -v $PWD:/mnt --privileged=true admin/vasp

可视化

VMD

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sudo ./configure
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cd src
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sudo make install
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vmd

VESTA

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vim .zshrc
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export PATH=/home/admin/chem/VESTA-gtk3/:$PATH

kein

Multiwfn

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sudo pacman -S openmotif
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cat /proc/sys/kernel/shmmax
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vim ~/.zshrc
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export OMP_STACKSIZE=200M
export Multiwfnpath=$HOME/chem/Multiwfn_3.8_dev_bin_Linux
export PATH=$PATH:$HOME/chem/Multiwfn_3.8_dev_bin_Linux
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chmod +x $HOME/chem/Multiwfn_3.8_dev_bin_Linux/Multiwfn
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vim $HOME/chem/Multiwfn_3.8_dev_bin_Linux/settings.ini
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nthreads= 12
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Multiwfn

Shermo

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vim .zshrc
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export PATH=$PATH:/home/admin/chem/Shermo_2.6
export Shermopath=/home/admin/chem/Shermo_2.6

orca

orca

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sudo pacman -S openmpi
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vim ~/.zshrc
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export PATH=$PATH:$HOME/chem/orca
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/chem/orca
alias orca='/home/admin/chem/orca/orca'

Gaussian

Gaussian

  • 版本: Gaussian_16-A03-AVX2
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$HOME/chem
        └── g16
            ├── scratch
            │     └── ...
            ├── bsd
            │     ├── g16.profile
            │     └── ...
            ├── Default.Route
            └── ...
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vim $HOME/.zshrc
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export g16root=$HOME/chem
export GAUSS_SCRDIR=$HOME/chem/g16/scratch
source $HOME/chem/g16/bsd/g16.profile
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vim $HOME/chem/g16/Default.Route
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-M- 8GB
-P- 8
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cd $HOME/chem/g16
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chmod 750 -R *
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cd
g16
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cp $g16root/g16/tests/com/test0001.com .
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g16 < test0001.com > test0001.out

GaussView

  • 版本: GaussView_6.0.16_x64
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vim ~/.zshrc
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export GV_DIR=$HOME/chem/gv
export PATH=$GV_DIR:$GV_DIR/bin:$PATH

科学数据作图

gnuplot

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sudo pacman -S gnuplot

QtGrace

  • 建议使用docker挂载目录编译
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dnf install qt5-qtbase-devel
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dnf install qt5-qtsvg-devel

```sh
ln -s /usr/bin/qmake-qt5 /usr/bin/qmake
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make
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qtgrace

AMS

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tar zxf ./ams2022.103.pc64_linux.intelmpi.bin.tgz
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vim $HOME/chem/ams/Utils/amszshrc.sh
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SCM_TMPDIR=$PWD
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vim ~/.zshrc
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source $HOME/chem/ams/Utils/amszshrc.sh
export SCM_OPENGL_SOFTWARE=1
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dirac info
  • 即弹出AMS所需的机器码，将其文本拷贝下来
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amsjobs&