Initial commit

.binder/apt.txt

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+gawk
+vim
+nano
+mc

.github/workflows/ci.yml

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+name: ci
+on:
+  push:
+    branches:
+      - master
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: 3.x
+      - run: pip install mkdocs-material
+      - run: mkdocs gh-deploy --force

.readthedocs.yml

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+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: doc/conf.py
+
+# Build documentation with MkDocs
+#mkdocs:
+#  configuration: mkdocs.yml
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: all
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.7
+  install:
+    - requirements: doc/requirements.txt

01.Simple_examples/coins.txt

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+gold     1    1986  USA                 American Eagle
+gold     1    1908  Austria-Hungary     Franz Josef 100 Korona
+silver  10    1981  USA                 ingot
+gold     1    1984  Switzerland         ingot
+gold     1    1979  RSA                 Krugerrand
+gold     0.5  1981  RSA                 Krugerrand
+gold     0.1  1986  PRC                 Panda
+silver   1    1986  USA                 Liberty dollar
+gold     0.25 1986  USA                 Liberty 5-dollar piece
+silver   0.5  1986  USA                 Liberty 50-cent piece
+silver   1    1987  USA                 Constitution dollar
+gold     0.25 1987  USA                 Constitution 5-dollar piece
+gold     1    1988  Canada              Maple Leaf

01.Simple_examples/count.awk

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+#!/usr/bin/awk -f 
+{ 
+    country[$4]++
+} 
+
+END { 
+      for (i in country) print "Country: " i," count: ", country[i] 
+}

01.Simple_examples/data

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+1 2 3
+4 5 6
+7 8 9 10 text

02.Gaussian/extract_data.awk

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+#!/usr/bin/awk -f 
+
+BEGIN { AU2eV= 27.211383 } 
+
+/Distance matrix/ {getline; getline; getline; getline; getline; getline; rOH= $5} 
+
+/Counterpoise: corrected energy/ { printf "%.12f %.6f\n", rOH, $5*AU2eV }

03.Dipole_moment/dipole_moment.awk

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+#!/usr/bin/awk -f
+# x,y,z in Angstroms
+NR > 2 {
+  mx= mx + $2*$5; my= my + $3*$5; mz= mz + $4*$5;
+}
+
+END {
+  norm=sqrt(mx**2+my**2+mz**2);
+  # Convert to Debye
+  toD= 4.80320425;
+  mx= mx*toD; my= my*toD; mz= mz*toD;
+  norm= norm*toD;
+printf("Dipole Moment\t  x\t\t  y\t\t  z\t\t| D.Moment |\n");
+printf(" [ Debye ]   \t%f\t%f\t%f\t%f\n", mx, my, mz, norm);
+}

03.Dipole_moment/waterX.xyz

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+     7
+ Wannier centres, written by Wannier90 on 6Aug2013 at 14:23:10 
+X          6.50000026       6.18706578       6.50000000  -2
+X          6.50000000       6.71337672       6.50000002  -2
+X          6.50000008       6.95339960       6.49999998  -2
+X          6.49999971       6.54636884       6.50000000  -2
+H          6.50000000       7.09480000       7.26880000   1
+H          6.50000000       7.09480000       5.73120000   1
+O          6.50000000       6.50000000       6.50000000   6

04.Join_data/1.dat

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+Daniel    10
+Anders     7
+Sven      56
+Ali       17
+Peter      6 

04.Join_data/2.dat

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+Peter     Monday
+Sven      Sunday
+David     Tuesday

04.Join_data/join.awk

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+#!/usr/bin/awk -f
+
+{
+  names[$1]= 1;
+  data[$1,ARGIND]= $2
+} 
+
+END{ 
+  for (i in names) print i"\t\t"data[i,1]"\t\t"data[i,2]  
+}

05.Gauss-smearing/freq.dat

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+# Anharm	harm 
+2858.351	3173.516	
+2797.693	3131.408	
+2682.453	3019.173	
+2710.734	3056.025	
+2989.402	3273.493	
+2558.539	2919.306	
+2781.281	3111.231	
+2707.999	3052.427	
+2575.868	2934.403	
+2784.882	3111.663	
+2977.694	3266.289	
+2652.853	2993.294	
+2868.582	3163.679	
+3076.485	3334.419	
+2883.267	3188.332	
+3137.228	3389.384	
+3425.697	3615.290	
+3094.083	3356.917	

05.Gauss-smearing/gauss-smear-data.awk

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+#!/usr/bin/awk -f
+BEGIN{
+  FWHM=30; # Default smearing if none is provided on the command line
+  FWHM= FWHM/2.35482
+  # trick to read parameters from the command line
+  if (ARGC==3) FWHM=ARGV[2];  ARGC=2; 
+}
+
+!/#/ {
+  f++;
+  if (f==1) {fmin=$1; fmax=$1}
+
+  freq[f]=$1;
+  if (fmin > $1) fmin=$1;
+  if (fmax < $1) fmax=$1;
+  nfreq=f;
+}
+
+END{
+  print "# freq   intensity | nfreq: "nfreq" fmin: "fmin" fmax: "fmax
+  for (i=int(fmin -5*FWHM); i<=int(fmax +5*FWHM);i++){
+    for (f=1;f<=nfreq;f++){
+      data[i]= data[i] + gauss(freq[f],i,FWHM);
+    }
+    print i,data[i]
+  }  
+}
+
+function gauss(x0,x,c){
+  area=1;
+  if ((x-x0)**2 < 10000) { return  area*exp(-(((x-x0))**2)/(2.*c**2))}
+  else {return 0.0}
+}

05.Gauss-smearing/ps-plot-v01.gnu

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+#!/usr/bin/gnuplot
+
+set term pngcairo size 800, 400 enhanced
+set out "Gauss-smearing.png"
+
+set border
+
+set key top left
+set title "Gaussian smearing with FWHM 10 and 30"
+set xlabel "Frequency"
+set ylabel "Intensity"
+
+plot "< ./gauss-smear-data.awk freq.dat 30" u ($1 ):($2) w l t "Gauss smearing 30" lw 2,\
+     "< ./gauss-smear-data.awk freq.dat 10" u ($1 ):($2) w l t "Gauss smearing 10" lw 2,\
+     "freq.dat" u ($1):(1) w impulses t "" lc rgb "blue"
+
+!display Gauss-smearing.png

06.VASP_CHGCAR_diff/VASP_CHGCAR_diff.awk

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+#!/usr/bin/awk -f
+BEGIN{
+  cmd1= "bzcat  "ARGV[1]; 
+  cmd2= "bzcat  "ARGV[2];
+  cmd3= "bzcat  "ARGV[3];
+
+  NF=1;  while(NF>0){ cmd2 |& getline;       } cmd2 |& getline; 
+  NF=1;  while(NF>0){ cmd3 |& getline;       } cmd3 |& getline; 
+  NF=1;  while(NF>0){ cmd1 |& getline; print } cmd1 |& getline; print;
+
+  do {
+    cmd1 |& getline; split($0,d1)
+    cmd2 |& getline; split($0,d2)
+    cmd3 |& getline; split($0,d3)
+    for(i=1;i<=NF;i++) printf "%18.11e ", d1[i]-d2[i]-d3[i]
+    print""
+  } while ($1*1==$1)
+
+}
+
+

06.VASP_CHGCAR_diff/plot-plane-v01.py

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+#!/usr/bin/env python
+# Author: Pavlin Mitev 
+# version 2015.10.22
+import numpy as np
+import os,sys,time
+from math import sin, cos, degrees, radians
+from ase import Atoms
+from ase.calculators.vasp import VaspChargeDensity
+
+import scipy.ndimage as ndimage
+
+import matplotlib.pyplot as plt
+
+#import scipy.interpolate as interpolate
+#from scipy.interpolate import griddata
+
+#======================================
+atom1= 2 # atom in the center
+atom2= 1 # atom from the plane
+atom3= 0 # second atom in the plain
+
+npx= 90 # number of point to sample the plane in x
+npy= 90 # number of point to sample the plane in y
+
+angle= radians(-144) # rotate the final plot around the central atom
+#angle= radians(0)
+
+
+start= time.time()
+sys.stdout.write("Reading CHGCAR... "); sys.stdout.flush()
+CHGCAR= VaspChargeDensity("CHGCAR")
+end= time.time()
+print "finished. {0}".format(end-start)
+
+
+cell= CHGCAR.atoms[0].cell
+nx,ny,nz= np.shape(CHGCAR.chg[0])
+ncell= cell/np.array([nx,ny,nz])
+
+
+# define plane =================================
+p1= CHGCAR.atoms[0].get_scaled_positions()[atom1]    
+p2= CHGCAR.atoms[0].get_scaled_positions()[atom2]     
+p3= CHGCAR.atoms[0].get_scaled_positions()[atom3]    
+
+# get normal to the plane
+v1= p2-p1; 
+v2= p3-p1; 
+
+v1n= np.dot(v1,cell);        # v1 in Cartesian
+v2n= np.dot(v2,cell);        # v2 in Cartesian
+
+v1n= v1n/np.linalg.norm(v1n) # v1 unit in Cartesian
+v2n= v2n/np.linalg.norm(v2n) # v2 unit in Cartesian
+
+vnorm= np.cross(v1n,v2n);
+vnorm= vnorm/np.linalg.norm(vnorm)
+#vnorm= np.dot(vnorm,cell)    # vnorm in Cartesian
+
+# Rotate the plane ==============================
+axis = vnorm;
+axis_skewed = [ [0, -axis[2], axis[1]], [ axis[2], 0, -axis[0] ] , [ -axis[1], axis[0], 0] ];
+R = np.eye(3) + np.dot(sin(angle),axis_skewed) + (1-cos(angle))*np.dot(axis_skewed,axis_skewed);
+v1n= np.dot(v1n,R)
+
+v2n= np.cross(vnorm,v1n);     # v2 is a vector in the same plane but perpendicular to v1n
+v2n= v2n/np.linalg.norm(v2n)
+
+v1n= np.dot(v1n,np.linalg.inv(cell)) # back to fractional
+v2n= np.dot(v2n,np.linalg.inv(cell)) # back to fractional
+
+
+grid= np.zeros((npx*npy,3))
+ip= 0
+for ix in np.linspace(-1.5,1.5,npx):
+  for iy in np.linspace(-1.5,1.5,npy):
+    grid[ip]= (v1n*ix + v2n*iy + p1)*[nx,ny,nz]
+    ip= ip + 1 
+
+grid_x, grid_y, grid_z= grid[:,0], grid[:,1], grid[:,2]
+plane= ndimage.map_coordinates(CHGCAR.chg[0],[grid_x, grid_y, grid_z], mode="wrap")
+px,py=np.mgrid[-1.5:1.5:npx+0j,-1.5:1.5:npy+0j]
+
+
+plt.rcParams["figure.figsize"]=[ 8,8]
+
+plt.plot([0],[0],'ko',ms=9 )
+
+plt.plot( np.dot(np.dot(v1,cell),np.dot(v1n,cell)) , np.dot(np.dot(v1,cell),np.dot(v2n,cell)) , 'ko',ms=9 )
+#plt.text( np.dot(np.dot(v1,cell),np.dot(v1n,cell)) , np.dot(np.dot(v1,cell),np.dot(v2n,cell))-0.1 , 'p1', alpha= 0.2)
+
+plt.plot( np.dot(np.dot(v2,cell),np.dot(v1n,cell)) , np.dot(np.dot(v2,cell),np.dot(v2n,cell)) , 'ko',ms=9 )
+#plt.text( np.dot(np.dot(v2,cell),np.dot(v1n,cell)) , np.dot(np.dot(v2,cell),np.dot(v2n,cell))-0.1 , 'p2', alpha= 0.2) 
+
+#CIM1= plt.imshow(plane.reshape(npx,npy).T, origin='lower', extent=(-1.5, 1.5, -1.5, 1.5), alpha=0.4, cmap='spectral')
+CIM1= plt.imshow(plane.reshape(npx,npy).T, origin='lower', extent=(-1.5, 1.5, -1.5, 1.5), alpha=1, vmin=-.2,vmax=.2, cmap='bwr')
+
+#plt.contour(px,py,plane.reshape(npx,npy))
+CL1= plt.contour(px,py,plane.reshape(npx,npy),np.arange(0.05,10,0.02), colors=["black"])
+CL2= plt.contour(px,py,plane.reshape(npx,npy),[0], colors=["red"])
+CL3= plt.contour(px,py,plane.reshape(npx,npy),np.arange(-0.05,-10,-0.02), colors=["blue"])
+
+
+plt.grid(True)
+plt.tick_params(size=10,width=1.5,pad=20, labelsize=22)
+
+plt.savefig("CHGCAR.ps")
+
+plt.ion()
+plt.show()
+
+
+
+
+
+
+