最新完全版CP2K-9.1编译安装教程
CP2K是功能最强大的计算化学-计算物理学-计算生物学程序之一。它为不同的方法提供了一个通用框架：密度泛函理论(DFT) 使用混合高斯和平面波方法(GPW) 通过LDA、GGA、MP2或RPA理论水平、经典对和多体势、半经验( AM1 , PM3 , MNDO , MNDOd, PM6) 和紧束缚哈密顿量，以及依赖静电势高斯展开 (GEEP) 的量子力学/分子力学(QM/MM) 混合方案。高斯和增强平面波方法 (GAPW) 作为 GPW 方法的扩展允许全电子计算。CP2K 进行分子动力学(MD)、元动力学(Metadynamics)、蒙特卡罗(MC)、埃伦费斯特动力学(Ehrenfest dynamics)、从头算动力学(AIMD)、振动分析、核心能级光谱、能量最小化以及使用NEB或Dimer方法进行过渡态优化的模拟。
CP2K
前段日子发布了最新版的CP2K-9.1，相比8.2有了以下改进：
Fix MacOS build (#1316)
Add NEWTONX interface (#1794)
Add Gromacs QM/MM support (see also)
Add experimental support for HIP and OpenCL to DBCSR
Adopt BSD3 license for new performance critical code (#1632)
Add GAL21 forcefield (#1579)
Upgrade to MPI_THREAD_SERIALIZED (#1564)
Add new pseudopotentials and basis sets (#1547, #1551)
Add analytical derivatives of the MO coefficients wrt nuclear coordinates (#1706)
Add forces for RI-HFX (#1688)
Add forces for TDDFT (#1670, #1759)
Regularized RI for periodic GW (#1776)
Add beadwise constraints to PINT (#1734)
Add analytical stress tensor for NNP (#1783)
Add ghost particles and tip scan for xTB (#1578)
Add forces and stress tensor for MP2-based double-hybrids (#1647)
Rewrite regtesting script in Python, arguments changed slightly (#1548)
https://github.com/cp2k/cp2k/releases/
开始编译：
数学库采用intel mkl
配置好环境
代码块
JavaScript
自动换行
复制代码
source /home/nozomiTojo/intel2020/mkl/bin/mklvars.sh intel64
source /home/nozomiTojo/intel2020/parallel_studio_xe_2020/psxevars.sh
export PATH=/home/nozomiTojo/intel2020/compilers_and_libraries_2020.4.304/linux/mkl:$PATH复制成功
编译环境GCC 9.3.0
代码块
JavaScript
自动换行
复制代码
nozomiTojo@lovelive:~/cp2k-9.1/tools/toolchain$ ./install_cp2k_toolchain.sh --math-mode=mkl --with-mkl=system--with-openblas=no --with-openmpi=install --with-gcc=system --with-scalapack=no--with-ptscotch=install --with-superlu=install --with-pexsi=install--with-quip=install --with-plumed=install复制成功
一步完成所有插件编译，没有任何报错。
代码块
JavaScript
自动换行
复制代码
plumed=install
MPI is detected and it appears to be OpenMPI
Compiling with 56 processes.
==================== Finding GCC from system paths ====================
path to gcc is /usr/bin/gcc
path to g++ is /usr/bin/g++
path to gfortran is /usr/bin/gfortran
Found include directory /usr/include
Step gcc took 0.00 seconds.
==================== Getting proc arch info using OpenBLAS tools ====================
OpenBLAS-0.3.19.tar.gz is found
OpenBLAS detected LIBCORE = haswell
OpenBLAS detected ARCH = x86_64
==================== Installing CMake ====================
cmake-3.22.1-Linux-x86_64.sh is found
Installing from scratch into /home/hxu/cp2k-9.1/tools/toolchain/install/cmake-3.22.1
Step cmake took 2.00 seconds.
==================== Installing OpenMPI ====================
openmpi-4.1.1.tar.gz is found
Installing from scratch into /home/hxu/cp2k-9.1/tools/toolchain/install/openmpi-4.1.1
Step openmpi took 440.00 seconds.
==================== Finding MKL from system paths ====================
MKLROOT is found to be /opt/intel2020/compilers_and_libraries_2020.4.304/linux/mkl
libm is found in ld search path
libdl is found in ld search path
Step mkl took 0.00 seconds.
Step fftw took 0.00 seconds.
==================== Installing LIBINT ====================
libint-v2.6.0-cp2k-lmax-5.tgz is found
Installing from scratch into /home/hxu/cp2k-9.1/tools/toolchain/install/libint-v2.6.0-cp2k-lmax-5
Step libint took 277.00 seconds.
==================== Installing LIBXC ====================
libxc-5.1.7.tar.gz is found
Installing from scratch into /home/hxu/cp2k-9.1/tools/toolchain/install/libxc-5.1.7
Step libxc took 53.00 seconds.
Step libsmm took 0.00 seconds.
==================== Installing Libxsmm ====================
libxsmm-1.17.tar.gz is found
Installing from scratch into /home/hxu/cp2k-9.1/tools/toolchain/install/libxsmm-1.17
Step libxsmm took 28.00 seconds.
Step scalapack took 0.00 seconds.
==================== Installing COSMA ====================
COSMA-v2.5.1.tar.gz is found
Installing from scratch into /home/hxu/cp2k-9.1/tools/toolchain/install/COSMA-2.5.1
Step cosma took 23.00 seconds.
==================== Installing ELPA ====================
elpa-2021.11.001.tar.gz is found
patching file nvcc_wrap
Installing from scratch into /home/hxu/cp2k-9.1/tools/toolchain/install/elpa-2021.11.001/cpu
Step elpa took 241.00 seconds.
==================== Installing PT-Scotch ====================
scotch_6.0.0.tar.gz is found
Installing from scratch into /home/hxu/cp2k-9.1/tools/toolchain/install/scotch-6.0.0
Step ptscotch took 4.00 seconds.
==================== Installing SuperLU_DIST ====================
superlu_dist_6.1.0.tar.gz is found
Installing from scratch into /home/hxu/cp2k-9.1/tools/toolchain/install/superlu_dist-6.1.0
Step superlu took 9.00 seconds.
==================== Installing PEXSI ====================
pexsi_v1.2.0.tar.gz is found
Installing from scratch into /home/hxu/cp2k-9.1/tools/toolchain/install/pexsi-1.2.0
Step pexsi took 80.00 seconds.
==================== Installing QUIP ====================
QUIP-b4336484fb65b0e73211a8f920ae4361c7c353fd.tar.gz is found
Installing from scratch into /home/hxu/cp2k-9.1/tools/toolchain/install/quip-b4336484fb65b0e73211a8f920ae4361c7c353fd
Step quip took 241.00 seconds.
==================== Installing gsl ====================
gsl-2.7.tar.gz is found
Installing from scratch into /home/hxu/cp2k-9.1/tools/toolchain/install/gsl-2.7
Step gsl took 62.00 seconds.
==================== Installing PLUMED ====================
plumed-2.7.3.tgz is found
Installing from scratch into /home/hxu/cp2k-9.1/tools/toolchain/install/plumed-2.7.3
Step plumed took 50.00 seconds.
==================== Installing hdf5 ====================
hdf5-1.12.0.tar.bz2 is found
Installing from scratch into /home/hxu/cp2k-9.1/tools/toolchain/install/hdf5-1.12.0
Step hdf5 took 114.00 seconds.
Step libvdwxc took 0.00 seconds.
==================== Installing spglib ====================
spglib-1.16.2.tar.gz is found
Installing from scratch into /home/hxu/cp2k-9.1/tools/toolchain/install/spglib-1.16.2
Step spglib took 6.00 seconds.
==================== Installing libvori ====================
libvori-210412.tar.gz is found
Installing from scratch into /home/hxu/cp2k-9.1/tools/toolchain/install/libvori-210412
Step libvori took 19.00 seconds.
==================== Installing spfft ====================
SpFFT-1.0.5.tar.gz is found
Installing from scratch into /home/hxu/cp2k-9.1/tools/toolchain/install/SpFFT-1.0.5
Step spfft took 5.00 seconds.
==================== Installing spla ====================
SpLA-1.5.2.tar.gz is found
Installing from scratch into /home/hxu/cp2k-9.1/tools/toolchain/install/SpLA-1.5.2
Step spla took 8.00 seconds.
==================== Installing SIRIUS ====================
sirius_7.3.0.tar.gz is found
Installing from scratch into /home/hxu/cp2k-9.1/tools/toolchain/install/sirius-7.3.0
patching file cmake/cudalibs_target.cmake
Step sirius took 67.00 seconds.
==================== generating arch files ====================
arch files can be found in the /home/hxu/cp2k-9.1/tools/toolchain/install/arch subdirectory
Wrote /home/nozomiTojo/cp2k-9.1/tools/toolchain/install/arch/local.ssmp
Wrote /home/nozomiTojo/cp2k-9.1/tools/toolchain/install/arch/local_static.ssmp
Wrote /home/nozomiTojo/cp2k-9.1/tools/toolchain/install/arch/local.sdbg
Wrote /home/nozomiTojo/cp2k-9.1/tools/toolchain/install/arch/local.psmp
Wrote /home/nozomiTojo/cp2k-9.1/tools/toolchain/install/arch/local.pdbg
Wrote /home/nozomiTojo/cp2k-9.1/tools/toolchain/install/arch/local_static.psmp
Wrote /home/nozomiTojo/cp2k-9.1/tools/toolchain/install/arch/local_warn.psmp
Wrote /home/nozomiTojo/cp2k-9.1/tools/toolchain/install/arch/local_coverage.pdbg
========================== usage =========================
Done!
Now copy:
cp /home/nozomiTojo/cp2k-9.1/tools/toolchain/install/arch/* to the cp2k/arch/ directory
To use the installed tools and libraries and cp2k version
compiled with it you will first need to execute at the prompt:
source /home/nozomiTojo/cp2k-9.1/tools/toolchain/install/setup
To build CP2K you should change directory:
cd cp2k/
make -j 96 ARCH=local VERSION="ssmp sdbg psmp pdbg"
arch files for GPU enabled CUDA versions are named "local_cuda.*"
arch files for GPU enabled HIP versions are named "local_hip.*"
arch files for coverage versions are named "local_coverage.*"
Note that these pre-built arch files are for the GNU compiler, users have to adapt them for other compilers.
It is possible to use the provided CP2K arch files as guidance.
nozomiTojo@lovelive:~/cp2k-9.1/tools/toolchain$ 复制成功
紧接着把~/cp2k-9.1/tools/toolchain/install/arch/下所有文件拷到~/cp2k-9.1/arch目录下。
然后运行以下命令
代码块
JavaScript
自动换行
复制代码
source /home/nozomiTojo/cp2k-9.1/tools/toolchain/install/setup
cd /home/nozomiTojo/cp2k-9.1
make -j 96 ARCH=local VERSION="ssmp sdbg psmp pdbg"复制成功
正式开始编译CP2K-9.1
代码块
JavaScript
自动换行
复制代码
nozomiTojo@lovelive:~/cp2k-9.1/tools/toolchain$ make -j 96 ARCH=local VERSION="ssmp sdbg psmp pdbg"
>>>>>>>>>>>>>>>>>>>>>>等待约5min>>>>>>>>>>>>>>>>>>>>>>>
/opt/rh/devtoolset-10/root/usr/libexec/gcc/x86_64-redhat-linux/10/ld:warning: libgfortran.so.3, needed by /usr/lib64/mpich/lib/libmpich.so.10, mayconflict with libgfortran.so.5
cd /home/nozomiTojo/softwares/cp2k-9.1/exe/local;ln -sf cp2k.psmp cp2k_shell.psmp
cd /home/nozomiTojo/softwares/cp2k-9.1/exe/local;ln -sf cp2k.psmp cp2k.popt复制成功
测试，最重要的是psmp版本的CP2K
代码块
JavaScript
自动换行
复制代码
nozomiTojo@lovelive:~/cp2k-9.1/tools/toolchain$ make -j 96 ARCH=local VERSION="ssmp sdbg psmp pdbg" test
--------------------------------- Timings --------------------------------
Plot: name="timings", title="Timing Distribution", ylabel="time [s]"
PlotPoint: name="100th_percentile", plot="timings", label="100th %ile", y=73.89, yerr=0.0
PlotPoint: name="99th_percentile", plot="timings", label="99th %ile", y=30.819400000000098, yerr=0.0
PlotPoint: name="98th_percentile", plot="timings", label="98th %ile", y=20.51059999999989, yerr=0.0
PlotPoint: name="95th_percentile", plot="timings", label="95th %ile", y=12.764499999999998, yerr=0.0
PlotPoint: name="90th_percentile", plot="timings", label="90th %ile", y=8.28, yerr=0.0
PlotPoint: name="80th_percentile", plot="timings", label="80th %ile", y=4.358000000000001, yerr=0.0
--------------------------------- Summary --------------------------------
Number of FAILED tests 0
Number of WRONG tests 0
Number of CORRECT tests 3392
Total number of tests 3392
GREPME 0 0 3392 0 3392 X
Summary: correct: 3392 / 3392; 9min
Status: OK
--------------------------------------------------------------------------
Regtest took 526.00 seconds.
--------------------------------------------------------------------------
*************************** testing ended ********************************复制成功
最后是正式跑任务，跑一个173原子的AIMD，优于基本上都是金属原子，采用对角化方法。
代码块
JavaScript
自动换行
复制代码
DBCSR| CPU Multiplication driver XSMM
DBCSR| Multrec recursion limit 512
DBCSR| Multiplication stack size 1000
DBCSR| Maximum elements for images UNLIMITED
DBCSR| Multiplicative factor virtual images 1
DBCSR| Use multiplication densification T
DBCSR| Multiplication size stacks 3
DBCSR| Use memory pool for CPU allocation F
DBCSR| Number of 3D layers SINGLE
DBCSR| Use MPI memory allocation F
DBCSR| Use RMA algorithm F
DBCSR| Use Communication thread T
DBCSR| Communication thread load 87
DBCSR| MPI: My node id 0
DBCSR| MPI: Number of nodes 64
DBCSR| OMP: Current number of threads 1
DBCSR| OMP: Max number of threads 1
DBCSR| Split modifier for TAS multiplication algorithm 1.0E+00
**** **** ****** ** PROGRAM STARTED AT 2022-01-06 17:34:15.707
***** ** *** *** ** PROGRAM STARTED ON ce0303.para.bscc
** **** ****** PROGRAM STARTED BY pg2090
***** ** ** ** ** PROGRAM PROCESS ID 9496
**** ** ******* ** PROGRAM STARTED IN /public1/home/pg2090/D2T/pg2090/pg209
0/test/cp2k-AIMD/Ni100-Fe4S4-CO2-H2
CP2K| version string: CP2K version 9.1
CP2K| source code revision number: git:d8d7100
CP2K| cp2kflags: omp libint fftw3 libxc elpa parallel mpi3 scalapack quip xsmm
CP2K| plumed2 spglib mkl sirius libvori libbqb
CP2K| is freely available from https://www.cp2k.org/
CP2K| Program compiled at Tue Jan 4 16:47:38 CST 2022
CP2K| Program compiled on ln71.para.bscc
CP2K| Program compiled for local
CP2K| Data directory path /home/nozomiTojo/softwares/cp
CP2K| Input file name cp2k.inp
GLOBAL| Force Environment number 1
GLOBAL| Basis set file name /public1/home/pg2090/D2T/pg2090/pg2090/s
GLOBAL| Potential file name /public1/home/pg2090/D2T/pg2090/pg2090/s
GLOBAL| MM Potential file name MM_POTENTIAL
GLOBAL| Coordinate file name __STD_INPUT__
GLOBAL| Method name CP2K
GLOBAL| Project name cp2k
GLOBAL| Run type MD
GLOBAL| FFT library FFTW3
GLOBAL| Diagonalization library ELPA
GLOBAL| Minimum number of eigenvectors for ELPA usage 16
GLOBAL| Orthonormality check for eigenvectors DISABLED
GLOBAL| Matrix multiplication library ScaLAPACK
GLOBAL| All-to-all communication in single precision F
GLOBAL| FFTs using library dependent lengths F
GLOBAL| Grid backend AUTO
GLOBAL| Global print level LOW
GLOBAL| MPI I/O enabled T
GLOBAL| Total number of message passing processes 64
GLOBAL| Number of threads for this process 1
GLOBAL| This output is from process 0
GLOBAL| Stack size for threads created by OpenMP (OMP_STACKSIZE) default
GLOBAL| CPU model name Intel(R) Xeon(R) Platinum 9242 CPU @ 2.30GHz
GLOBAL| CPUID 1003
MEMORY| system memory details [Kb]
MEMORY| rank 0 min max average
MEMORY| MemTotal 394848216 394848216 394848216 394848216
MEMORY| MemFree 358622876 358622600 358622876 358622604
MEMORY| Buffers 0 0 0 0
MEMORY| Cached 10143584 10143364 10143584 10143367
MEMORY| Slab 1361612 1361580 1361612 1361583
MEMORY| SReclaimable 281200 281168 281200 281171
MEMORY| MemLikelyFree 369047660 369047132 369047660 369047143
GENERATE| Preliminary Number of Bonds generated: 0
GENERATE| Achieved consistency in connectivity generation.
*******************************************************************************
*******************************************************************************
** **
** ##### ## ## **
** ## ## ## ## ## **
** ## ## ## ###### **
** ## ## ## ## ## ##### ## ## #### ## ##### ##### **
** ## ## ## ## ## ## ## ## ## ## ## ## ## ## **
** ## ## ## ## ## ## ## #### ### ## ###### ###### **
** ## ### ## ## ## ## ## ## ## ## ## ## **
** ####### ##### ## ##### ## ## #### ## ##### ## **
** ## ## **
** **
** ... make the atoms dance **
** **
** Copyright (C) by CP2K developers group (2000-2021) **
** J. Chem. Phys. 152, 194103 (2020) **
** **
*******************************************************************************
TOTAL NUMBERS AND MAXIMUM NUMBERS
Total number of - Atomic kinds: 6
- Atoms: 173
- Shell sets: 173
- Shells: 1353
- Primitive Cartesian functions: 1025
- Cartesian basis functions: 5192
- Spherical basis functions: 4365
Maximum angular momentum of- Orbital basis functions: 3
- Local part of the GTH pseudopotential: 2
- Non-local part of the GTH pseudopotential: 3
SCF PARAMETERS Density guess: RESTART
--------------------------------------------------------
max_scf: 500
max_scf_history: 0
max_diis: 4
--------------------------------------------------------
eps_scf: 3.00E-06
eps_scf_history: 0.00E+00
eps_diis: 1.00E-01
eps_eigval: 1.00E-05
--------------------------------------------------------
level_shift [a.u.]: 0.00
added MOs 500 500
--------------------------------------------------------
Mixing method: BROYDEN_MIXING
charge density mixing in g-space
--------------------------------------------------------
Smear method: FERMI_DIRAC
Electronic temperature [K]: 300.0
Electronic temperature [a.u.]: 9.50E-04
Accuracy threshold: 1.00E-10
--------------------------------------------------------
Outer loop SCF in use
No variables optimised in outer loop
eps_scf 1.00E-05
max_scf 4
No outer loop optimization
step_size 5.00E-01
MD_PAR| Molecular dynamics protocol (MD input parameters)
MD_PAR| Ensemble type NVT
MD_PAR| Number of time steps 500000
MD_PAR| Time step [fs] 0.500000
MD_PAR| Temperature [K] 600.000000
MD_PAR| Temperature tolerance [K] 0.000000
MD_PAR| Constraints activated
MD_PAR| Tolerance for shake 0.000001
MD_PAR| Print MD information every 1 step(s)
MD_PAR| File type Print frequency [steps] File names
MD_PAR| Coordinates 1 cp2k-pos-1.xyz
MD_PAR| Velocities 1 cp2k-vel-1.xyz
MD_PAR| Energies 1 cp2k-1.ener
MD_PAR| Dump 20 cp2k-1.restart
ROT| Rotational analysis information
ROT| Principal axes and moments of inertia [a.u.]
ROT| 1 2 3
ROT| Eigenvalues 1.28006357352E+09 1.84053523676E+09 2.51370587038E+09
ROT| x 0.999989770475 0.001922990665 0.004094026402
ROT| y -0.001851975145 0.999848977558 -0.017279822480
ROT| z -0.004126637049 0.017272063681 0.999842310909
ROT| Number of rotovibrational vectors 6
DOF| Calculation of degrees of freedom
DOF| Number of atoms 173
DOF| Number of intramolecular constraints 240
DOF| Number of intermolecular constraints 0
DOF| Invariants (translations + rotations) 3
DOF| Degrees of freedom 276
DOF| Restraints information
DOF| Number of intramolecular restraints 0
DOF| Number of intermolecular restraints 0
THERMOSTAT| Thermostat information for PARTICLES
THERMOSTAT| Type of thermostat Nose-Hoover-Chains
THERMOSTAT| Nose-Hoover-Chain length 3
THERMOSTAT| Nose-Hoover-Chain time constant [fs] 33.356410
THERMOSTAT| Order of Yoshida integrator 3
THERMOSTAT| Number of multiple time steps 2
THERMOSTAT| Initial potential energy 0.000000000000E+00
THERMOSTAT| Initial kinetic energy 0.950044602986E-03
THERMOSTAT| End of thermostat information for PARTICLES
MD_VEL| Velocities initialization
MD_VEL| Initial temperature [K] 600.000000
MD_VEL| COM velocity 0.0000000000 -0.0000000000 -0.0000000000
Spin 1
Number of electrons: 1493
Number of occupied orbitals: 1493
Number of molecular orbitals: 1993
Spin 2
Number of electrons: 1493
Number of occupied orbitals: 1493
Number of molecular orbitals: 1993
Number of orbital functions: 4365
Number of independent orbital functions: 4365
Extrapolation method: initial_guess
*** WARNING in qs_initial_guess.F:309 :: User requested to restart the ***
*** wavefunction from the file named: cp2k-RESTART.wfn. This file does ***
*** not exist. Please check the existence of the file or change properly ***
*** the value of the keyword WFN_RESTART_FILE_NAME. Calculation continues ***
*** using ATOMIC GUESS. ***
SCF WAVEFUNCTION OPTIMIZATION
Step Update method Time Convergence Total energy Change
------------------------------------------------------------------------------
1 NoMix/Diag. 0.10E+00 3.8 0.98981243 -27709.5377999228 -2.77E+04
2 Broy./Diag. 0.10E+00 4.5 0.94791197 -27116.8815093516 5.93E+02
3 Broy./Diag. 0.10E+00 4.5 0.25130183 -27315.3799838482 -1.98E+02
4 Broy./Diag. 0.10E+00 4.5 0.16735894 -27365.8869319842 -5.05E+01
5 Broy./Diag. 0.10E+00 4.6 0.63917314 -27426.6855833155 -6.08E+01
6 Broy./Diag. 0.10E+00 4.6 0.19357095 -27541.1558850289 -1.14E+02
7 Broy./Diag. 0.10E+00 4.6 0.56734511 -27631.6869384625 -9.05E+01复制成功
完全成功，收工！
本文为我原创，未经授权禁止转载
cv15222218
分享至
投诉或建议
