nciplot安装说明

nciplot安装使用说明

nciplot 3.0 2020.03.30 by zhenggang

简介

web : https://www.lct.jussieu.fr/pagesperso/contrera/nciplot.html

src : https://www.lct.jussieu.fr/pagesperso/contrera/nciplot-3.0.tar.gz 102MB

doc : https://www.lct.jussieu.fr/pagesperso/contrera/nciplot-manual.pdf

编译

通过阅读压缩包中的README文件,了解如何编译它。

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tar zxvf nciplot-3.0.tar.gz
cd nciplot-3.0
cd src
sed -i "s/FCFLAGS = -O2 -fopenmp/FCFLAGS = -O3 -fopenmp/" Makefile.inc
make mrproper
make

说明:

  • Makefile.inc文件用来指定编译器和编译参数是,默认是gfortran编译器。
  • 上面的编译过程非常简单,我们仅仅把优化级别改为了-O3,其他不用改。
  • 它还支持ifort编译器。

配置运行环境

我们需要配置相关环境来保证软件运行。

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export NCIPLOT_HOME=/home/nciplot-3.0
export PATH=$NCIPLOT_HOME/src:$PATH
export OMP_NUM_THREADS=4

说明:

  • NCIPLOT_HOME是软件解压缩后的目录,该目录下需要包含名为dat的文件夹,软件运行需要。
  • 设置PATH环境变量是为了方便直接调用nciplot命令。
  • 设置OMP_NUM_THREADS是因为该软件支持多线程运行,该参数设置多线程数,这样可以加速。本实例中写为4,说明软件运行时会开启4个线程。

测试

我们进入test目录,运行算例看一下。

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cd test-cases/adenin-thymine
nciplot AT.nci

如果运行顺利,可以获得如下运行结果:

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 # ----------------- NCIPLOT ------------------------
# --- PLOTTING NON COVALENT INTERACTION REGIONS ----
# --- E.R. Johnson ----
# --- J. Contreras-Garcia ----
# ---------- Duke University ------------
# --------------------------------------------------
# --- Please cite ----
# --J. Am. Chem. Soc., 2010, 132 (18), pp 6498–6506-
# --------------------------------------------------


# --------------------------------------------------
# --- Contributions for the wfn properties ----
# --- from H. L. Schmider are acknowledged ---
# --------------------------------------------------
#
# Start -- 2020.03.30, 21:24:48.139

+ Read density file : /home/nciplot-3.0/dat/h__lda.wfc
Log grid (r = a*e^(b*x)) with a = 2.4788E-03, b = 2.0000E-03
Num. grid points = 4392, rmax (bohr) = 16.1513
Integrated charge = 0.99999998
El. conf. : 1S(1)

+ Read density file : /home/nciplot-3.0/dat/c__lda.wfc
Log grid (r = a*e^(b*x)) with a = 4.1313E-04, b = 2.0000E-03
Num. grid points = 5326, rmax (bohr) = 17.4308
Integrated charge = 5.99999996
El. conf. : 1S(2) 2S(2) 2P(2)

+ Read density file : /home/nciplot-3.0/dat/n__lda.wfc
Log grid (r = a*e^(b*x)) with a = 3.5411E-04, b = 2.0000E-03
Num. grid points = 5343, rmax (bohr) = 15.4574
Integrated charge = 6.99999996
El. conf. : 1S(2) 2S(2) 2P(3)

+ Read density file : /home/nciplot-3.0/dat/o__lda.wfc
Log grid (r = a*e^(b*x)) with a = 3.0984E-04, b = 2.0000E-03
Num. grid points = 5358, rmax (bohr) = 13.9372
Integrated charge = 7.99999996
El. conf. : 1S(2) 2S(2) 2P(4)

-----------------------------------------------------
INPUT INFORMATION:
-----------------------------------------------------

-----------------------------------------------------
Calculation details:
-----------------------------------------------------
RHO THRESHOLD (au): 0.10
RDG THRESHOLD (au): 1.00


-----------------------------------------------------
Operating grid and increments:
-----------------------------------------------------
x0,y0,z0 = -12.2843 -3.5798 -7.4277
x1,y1,z1 = 14.3483 3.7251 6.8277
ix,iy,iz = 0.10 0.10 0.10
nx,ny,nz = 267 74 143

-----------------------------------------------------
Writing output in the following units:
-----------------------------------------------------
Reduced Density Gradient,RDG = AT-grad.cube
Sign(lambda2)xDensity,LS = AT-dens.cube
ELF cube file = AT-elf.cube
XC energy density cube file = AT-xc.cube
LS x RDG = AT.vmd
VMD script = AT.dat
-----------------------------------------------------

End -- 2020.03.30, 21:25:01.206
文章作者: mrzhenggang
文章链接: https://blog.mrzhenggang.com/nciplot-install/
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