VASPsol及CP-VASP安装过程
马祖驹
2025.6.26
1. 确保VASP6.3.0可以正常安装,
假设目录:/opt/pub/softwares/VASP-6.3.0-sol/vasp6.3.0/vasp.6.3.0/
(1)module load intel mpi
(2)make veryclean
(3)make all
2. VASPsol获取和安装
(1)git clone https://github.com/henniggroup/VASPsol.git
通过 Git clone获得vaspsol源码:假设放置在vasp安装目录:/opt/pub/softwares/VASP-6.3.0-sol/vasp6.3.0/vasp.6.3.0/vaspsol/VASPsol
(2)cp vaspsol/VASPsol/src/solvation.F ./src/
覆盖原来的solvation.F
(3)cp vaspsol/VASPsol/patches/pbz_patch_610 ./src/
pbz_patch_610拷贝到vasp安装目录下的src下
(4)vi ./src/.objects
确保solvation.o 出现在 pot.o 之前,这边看到确实在前面
(5)vi makefile.include
在CPP_OPTIONS 一行中加入-Dsol_compat,可以加在选项最后,加完如下:
CPP_OPTIONS= -DHOST=\"LinuxIFC\"\
-DMPI -DMPI_BLOCK=8000 -Duse_collective \
-DscaLAPACK \
-DCACHE_SIZE=4000 \
-Davoidalloc \
-Dvasp6 \
-Duse_bse_te \
-Dtbdyn \
-Dfock_dblbuf \
-Dsol_compat
(6)到vasp的src目录下,运行patch -p0 < pbz_patch_610
(7)回到上一个目录,进行vasp编译和安装
(8)make veryclean
(9)make all
3. CP-VASP获取及安装
(1)另外拷贝一个vasp6.3.0的安装文件,cp -r VASP-6.3.0-sol/ VASP-6.3.0-sol-cp
(2)获取cp-vasp文件
获取路径:https://docs.google.com/forms/d/e/1FAIpQLSdjinABLY26jora50jedL5X6bj5Pc7BTeys5pmclstlWs46Lw/viewform
很快,一天之内获得,得到两个补丁文件:cp-vaspsol.patch及cp-vaspsol++.patch
(2)cp cp-vaspsol.patch src/
把cp-vaspsol.patch拷贝到vasp安装路径下的/src/目录下
(3) cd src
(4)patch -p0 < cp-vaspsol.patch
显示如下:表示修改了几个文件
patching file main.F
Hunk #1 succeeded at 213 with fuzz 2 (offset -6 lines).
Hunk #2 succeeded at 430 (offset -8 lines).
Hunk #3 succeeded at 691 (offset -27 lines).
Hunk #4 succeeded at 2714 (offset -109 lines).
Hunk #5 succeeded at 3096 with fuzz 1 (offset -111 lines).
Hunk #6 succeeded at 3166 (offset -124 lines).
Hunk #7 succeeded at 3771 (offset -135 lines).
Hunk #8 succeeded at 3938 with fuzz 1 (offset -143 lines).
Hunk #9 succeeded at 4154 (offset -140 lines).
Hunk #10 succeeded at 4361 (offset -146 lines).
Hunk #11 succeeded at 5616 with fuzz 1 (offset -172 lines).
patching file reader.F
Hunk #2 succeeded at 87 (offset -1 lines).
Hunk #3 succeeded at 843 (offset -21 lines).
patching file pot.F
Hunk #1 succeeded at 363 (offset -1 lines).
patching file solvation.F
(5)回到上级目录,运行make veryclean和make all进行VASP安装
4. 创建module文件,方便调用
(1)通过第二步安装,获得了vasp6.3.0-sol程序,
路径如下:/opt/pub/softwares/VASP-6.3.0-sol/vasp6.3.0/vasp.6.3.0
(2)到module 文件路径:/opt/pub/modulefiles/softwares
(3) cp 6.3.0-20.lua 6.3.0-sol.lua
(4)修改 6.3.0-sol.lua文件里面的路径为:/opt/pub/softwares/VASP-6.3.0-sol/vasp6.3.0/vasp.6.3.0/bin/
(5)module refresh
(6)检查:module avail
(7)同理,创建vasp6.3.0-sol-cp文件,方便后续调用。
5. 调用vasp6.3.0-sol-cp
(1)在提交作业文件中,修改原来的module load VASP/6.3.0改为module load VASP/6.3.0-sol-cp
6. 使用cp-vasp和vaspsol需要引用的文献
(1)cp-vasp
Zhao, X.; Liu, Y. Origin of Selective Production of Hydrogen Peroxide by Electrochemical Oxygen Reduction. Journal of the American Chemical Society 2021, 143 (25), 9423-9428.
Yu, S.; Levell, Z.; Jiang, Z.; Zhao, X.; Liu, Y. What Is the Rate-Limiting Step of Oxygen Reduction Reaction on Fe–N–C Catalysts? Journal of the American Chemical Society 2023, 145 (46), 25352-25356.
(2)vaspsol
Implicit solvation model for density-functional study of nanocrystal surfaces and reaction pathways. K. Mathew, R. Sundararaman, K. Letchworth-Weaver, T. A. Arias, and R. G. Hennig, J. Chem. Phys. 140, 084106 (2014), [doi:10.1063/1.4865107] (https://doi.org/10.1063/1.4865107).
Implicit self-consistent electrolyte model in plane-wave density-functional theory. K. Mathew, V. S. C. Kolluru, S. Mula, S. N. Steinmann, and R. G. Hennig, J. Chem. Phys. 151, 234101 (2019), [doi:10.1063/1.5132354] (https://doi.org/10.1063/1.5132354).