forked from ladyteam/LADYtools
/
scan_alnog_mode_castep.py
executable file
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/
scan_alnog_mode_castep.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
# The program to distort geometry along selected normal mode eigenvector. Castep output format
# (.phonon file)
#
#
# Author: Eugene Roginskii
#
def chunks(l, n):
if n < 1:
n = 1
return [l[i:i + n] for i in range(0, len(l), n)]
def strType(var):
try:
if int(var) == float(var):
return 'int'
except:
try:
float(var)
return 'float'
except:
return 'str'
def isDiag(M):
i, j = np.nonzero(M)
return np.all(i == j)
def isNumeric(var):
isnum=strType(var)
if (isnum == 'int' or isnum == 'float'):
return (True)
return(False)
def direct2cart(directpos,basis):
cart=[]
for atdirect in directpos:
cart.append(np.dot(np.transpose(basis),atdirect))
return np.array(cart)
def gencastep(fn,modenum,basis,natom,typatsym,symprec,atpos):
from phonopy import Phonopy
import phonopy.structure.spglib as spg
from phonopy.structure.atoms import PhonopyAtoms as Atoms
from phonopy.structure.symmetry import Symmetry, find_primitive, get_pointgroup
fh=open(fn,'w')
unitcell = Atoms(symbols=typatsym, cell=basis, positions=atpos)
pbasis=np.eye(3)
for i in range(len(basis)):
pbasis[i]=basis[i]/np.linalg.norm(basis[i])
symmetry = Symmetry(unitcell, symprec)
rotations = symmetry.get_symmetry_operations()['rotations']
translations = symmetry.get_symmetry_operations()['translations']
print('Space group International symbol: %s' % symmetry.get_international_table())
fh.write('%BLOCK LATTICE_CART\n')
for bl in basis:
fh.write('%s\n' % ''.join(' %12.8f' % b for b in bl))
fh.write('%ENDBLOCK LATTICE_CART\n\n')
fh.write('%BLOCK POSITIONS_ABS\n')
for i in range(len(typatsym)):
fh.write(" %3s " % typatsym[i])
fh.write('%s\n' % ''.join(' %12.8f' % p for p in atpos[i].tolist()))
fh.write('%ENDBLOCK POSITIONS_ABS\n\n')
fh.write('SYMMETRY_TOL : %f ang\n' % symprec)
fh.write('SYMMETRY_GENERATE \n')
fh.write('#KPOINT_MP_GRID : 4 4 4\n#KPOINT_MP_OFFSET : 0.5 0.5 0.5\n')
# fh.write('%BLOCK SYMMETRY_OPS\n')
# for i in range(len(rotations)):
# fh.write('# Sym. op. number %d\n' % (i+1))
# if (isDiag(rotations[i])):
# rot=rotations[i]
# else:
# rot=np.dot(np.dot(rotations[i],pbasis),rotations[i])
# for symopl in rot:
# fh.write('%s\n' % ''.join(' % 12.10f' % round(sop,6) for sop in symopl))
# fh.write('%s\n' % ''.join(' % 12.10f' % round(tr) for tr in translations[i]))
# fh.write('%ENDBLOCK SYMMETRY_OPS\n\n')
def genabinit(abinitfn,modenum,basis,natom,typat,znucl,cartshiftd,comment):
abinit_fh=open(abinitfn,'w')
abinit_fh.write('#Atom positions shifted along Mode %d\n' % modenum)
abinit_fh.write('# %s\n' % comment)
abinit_fh.write('acell 1.0 1.0 1.0 Angstrom\nrprim\n')
for b in basis:
abinit_fh.write('% 20.16f % 20.16f % 20.16f\n' % (b[0], b[1], b[2]))
abinit_fh.write('typat ' + ' '.join('%d' % typat[i] for i in range(natom))+'\n')
abinit_fh.write('znucl ' + ' '.join('%d' % znucl[i] for i in range(len(znucl)))+'\n')
abinit_fh.write('natom %d\n' % natom)
abinit_fh.write('ntypat %d\n' % len(znucl))
abinit_fh.write('xangst\n')
for cartat in cartshiftd:
abinit_fh.write('%12.9f %12.9f %12.9f\n' % (cartat.tolist()[0], cartat.tolist()[1], cartat.tolist()[2]))
def get_epsilon(abinitfn):
e=[]
try:
abinit_fh = open(abinitfn, 'r')
except IOError:
print ("ERROR Couldn't open abinit output file %s, exiting...\n" % abinitfn)
sys.exit(1)
while True:
line=abinit_fh.readline()
if not line: break
if 'Dielectric tensor, in cartesian coordinates' in line:
while True:
sline=abinit_fh.readline()
if not sline: break
if 'Effective charges' in sline: break
if (re.match('\s*\d+\s*\d+',sline)):
e.append(float(sline.split()[4]))
break
eps=np.array(e).reshape(3,3)
return eps
import numpy as np
import re
from math import sqrt
import sys
from math import pi
from math import exp
from shutil import move
import os
import datetime
import time
import argparse
import xml.etree.cElementTree as etree
mau=1822.888485
AMU = 1.6605402e-27 # [kg]
# ABINIT freq to cm-1 factor
factorcm=716.851928469
# ABINIT freq to HZ factor
factorHz=21.49068e12
hbar=6.6260695729e-34 #J*s
#hbar=4.13566751691e−15 #eV*s
EV = 1.60217733e-19 # [J]
#
Angst2Bohr=1.889725989
#print sqrt(hbar/AMU/10e12)*10e10 #Angstrom
basedirname='epsilon'
Temp=300
ramanmult=0.0028
atom_data = [
[ 0, "X", "X", 0], # 0
[ 1, "H", "Hydrogen", 1.00794], # 1
[ 2, "He", "Helium", 4.002602], # 2
[ 3, "Li", "Lithium", 6.941], # 3
[ 4, "Be", "Beryllium", 9.012182], # 4
[ 5, "B", "Boron", 10.811], # 5
[ 6, "C", "Carbon", 12.0107], # 6
[ 7, "N", "Nitrogen", 14.0067], # 7
[ 8, "O", "Oxygen", 15.9994], # 8
[ 9, "F", "Fluorine", 18.9984032], # 9
[ 10, "Ne", "Neon", 20.1797], # 10
[ 11, "Na", "Sodium", 22.98976928], # 11
[ 12, "Mg", "Magnesium", 24.3050], # 12
[ 13, "Al", "Aluminium", 26.9815386], # 13
[ 14, "Si", "Silicon", 28.0855], # 14
[ 15, "P", "Phosphorus", 30.973762], # 15
[ 16, "S", "Sulfur", 32.065], # 16
[ 17, "Cl", "Chlorine", 35.453], # 17
[ 18, "Ar", "Argon", 39.948], # 18
[ 19, "K", "Potassium", 39.0983], # 19
[ 20, "Ca", "Calcium", 40.078], # 20
[ 21, "Sc", "Scandium", 44.955912], # 21
[ 22, "Ti", "Titanium", 47.867], # 22
[ 23, "V", "Vanadium", 50.9415], # 23
[ 24, "Cr", "Chromium", 51.9961], # 24
[ 25, "Mn", "Manganese", 54.938045], # 25
[ 26, "Fe", "Iron", 55.845], # 26
[ 27, "Co", "Cobalt", 58.933195], # 27
[ 28, "Ni", "Nickel", 58.6934], # 28
[ 29, "Cu", "Copper", 63.546], # 29
[ 30, "Zn", "Zinc", 65.38], # 30
[ 31, "Ga", "Gallium", 69.723], # 31
[ 32, "Ge", "Germanium", 72.64], # 32
[ 33, "As", "Arsenic", 74.92160], # 33
[ 34, "Se", "Selenium", 78.96], # 34
[ 35, "Br", "Bromine", 79.904], # 35
[ 36, "Kr", "Krypton", 83.798], # 36
[ 37, "Rb", "Rubidium", 85.4678], # 37
[ 38, "Sr", "Strontium", 87.62], # 38
[ 39, "Y", "Yttrium", 88.90585], # 39
[ 40, "Zr", "Zirconium", 91.224], # 40
[ 41, "Nb", "Niobium", 92.90638], # 41
[ 42, "Mo", "Molybdenum", 95.96], # 42
[ 43, "Tc", "Technetium", 0], # 43
[ 44, "Ru", "Ruthenium", 101.07], # 44
[ 45, "Rh", "Rhodium", 102.90550], # 45
[ 46, "Pd", "Palladium", 106.42], # 46
[ 47, "Ag", "Silver", 107.8682], # 47
[ 48, "Cd", "Cadmium", 112.411], # 48
[ 49, "In", "Indium", 114.818], # 49
[ 50, "Sn", "Tin", 118.710], # 50
[ 51, "Sb", "Antimony", 121.760], # 51
[ 52, "Te", "Tellurium", 127.60], # 52
[ 53, "I", "Iodine", 126.90447], # 53
[ 54, "Xe", "Xenon", 131.293], # 54
[ 55, "Cs", "Caesium", 132.9054519], # 55
[ 56, "Ba", "Barium", 137.327], # 56
[ 57, "La", "Lanthanum", 138.90547], # 57
[ 58, "Ce", "Cerium", 140.116], # 58
[ 59, "Pr", "Praseodymium", 140.90765], # 59
[ 60, "Nd", "Neodymium", 144.242], # 60
[ 61, "Pm", "Promethium", 0], # 61
[ 62, "Sm", "Samarium", 150.36], # 62
[ 63, "Eu", "Europium", 151.964], # 63
[ 64, "Gd", "Gadolinium", 157.25], # 64
[ 65, "Tb", "Terbium", 158.92535], # 65
[ 66, "Dy", "Dysprosium", 162.500], # 66
[ 67, "Ho", "Holmium", 164.93032], # 67
[ 68, "Er", "Erbium", 167.259], # 68
[ 69, "Tm", "Thulium", 168.93421], # 69
[ 70, "Yb", "Ytterbium", 173.054], # 70
[ 71, "Lu", "Lutetium", 174.9668], # 71
[ 72, "Hf", "Hafnium", 178.49], # 72
[ 73, "Ta", "Tantalum", 180.94788], # 73
[ 74, "W", "Tungsten", 183.84], # 74
[ 75, "Re", "Rhenium", 186.207], # 75
[ 76, "Os", "Osmium", 190.23], # 76
[ 77, "Ir", "Iridium", 192.217], # 77
[ 78, "Pt", "Platinum", 195.084], # 78
[ 79, "Au", "Gold", 196.966569], # 79
[ 80, "Hg", "Mercury", 200.59], # 80
[ 81, "Tl", "Thallium", 204.3833], # 81
[ 82, "Pb", "Lead", 207.2], # 82
[ 83, "Bi", "Bismuth", 208.98040], # 83
[ 84, "Po", "Polonium", 0], # 84
[ 85, "At", "Astatine", 0], # 85
[ 86, "Rn", "Radon", 0], # 86
[ 87, "Fr", "Francium", 0], # 87
[ 88, "Ra", "Radium", 0], # 88
[ 89, "Ac", "Actinium", 0], # 89
[ 90, "Th", "Thorium", 232.03806], # 90
[ 91, "Pa", "Protactinium", 231.03588], # 91
[ 92, "U", "Uranium", 238.02891], # 92
[ 93, "Np", "Neptunium", 0], # 93
[ 94, "Pu", "Plutonium", 0], # 94
[ 95, "Am", "Americium", 0], # 95
[ 96, "Cm", "Curium", 0], # 96
[ 97, "Bk", "Berkelium", 0], # 97
[ 98, "Cf", "Californium", 0], # 98
[ 99, "Es", "Einsteinium", 0], # 99
[100, "Fm", "Fermium", 0], # 100
[101, "Md", "Mendelevium", 0], # 101
[102, "No", "Nobelium", 0], # 102
[103, "Lr", "Lawrencium", 0], # 103
[104, "Rf", "Rutherfordium", 0], # 104
[105, "Db", "Dubnium", 0], # 105
[106, "Sg", "Seaborgium", 0], # 106
[107, "Bh", "Bohrium", 0], # 107
[108, "Hs", "Hassium", 0], # 108
[109, "Mt", "Meitnerium", 0], # 109
[110, "Ds", "Darmstadtium", 0], # 110
[111, "Rg", "Roentgenium", 0], # 111
[112, "Cn", "Copernicium", 0], # 112
[113, "Uut", "Ununtrium", 0], # 113
[114, "Uuq", "Ununquadium", 0], # 114
[115, "Uup", "Ununpentium", 0], # 115
[116, "Uuh", "Ununhexium", 0], # 116
[117, "Uus", "Ununseptium", 0], # 117
[118, "Uuo", "Ununoctium", 0], # 118
]
parser = argparse.ArgumentParser(description='The program to generate distortion structures along normal vibrational modes')
parser.add_argument("-i", "--input", action="store", type=str, dest="input_fn", help="Castep output .phonon filename")
parser.add_argument("-m", "--mode", action="store", type=int, dest="modenum", default=1, help="Number of mode")
parser.add_argument("-t", "--tolerance", action="store", type=float, dest="symprec", default=1e-04,
help="Symmetry determine tolerance")
parser.add_argument("-a", "--amplitudes", action="store", type=str, dest="amplstr", default='0.1 0.25 0.5 1',
help="Mode shift amplitude, space separated")
args = parser.parse_args()
if (args.input_fn == None):
print('Error. No input filename was given.')
sys.exit(1)
try:
input_fh = open(args.input_fn, 'r')
except IOError:
print("ERROR Couldn't open qpoints file, exiting...")
sys.exit(1)
ampl=[]
for i in range(len(args.amplstr.split())):
if isNumeric(args.amplstr.split()[i]):
ampl.append(float(args.amplstr.split()[i]))
else:
print('Error parsing amplitudes array')
sys.exit(1)
modenum=args.modenum
natom=0
for line in input_fh:
if ( 'Number of ions' in line ):
natom=int(line.split('ions')[1])
break
for line in input_fh:
if ( 'Number of branches' in line ):
if (int(line.split('branches')[1])<modenum) or (modenum<1):
print('Error. incorrect number of mode provided')
sys.exit(1)
break
for line in input_fh:
if ( 'Unit cell vectors' in line ):
break
buf=[]
rprim=[]
for line in input_fh:
if ( 'Fractional Co-ordinates' in line ):
break
for coor in line.split():
rprim.append(float(coor))
basis=np.array(rprim).reshape(3,3)
xred=[]
typat=[]
typatsym=[]
for line in input_fh:
if ( 'END header' in line ):
break
for i in range(3):
xred.append(float(line.split()[i+1]))
for i in range(len(atom_data)):
if(atom_data[i][1]==line.split()[4]):
typat.append(atom_data[i][0])
typatsym.append(line.split()[4])
for line in input_fh:
if ( 'q-pt' in line ):
qpt=line
break
frequencies=[]
for line in input_fh:
if ( 'Phonon Eigenvectors' in line ):
break
frequencies.append(float(line.split()[1]))
isMode=False
shiftvector=[]
for line in input_fh:
if (isNumeric(line.split()[0])):
if ((int(line.split()[0]) == args.modenum)):
shiftvector.append(float(line.split()[2]))
shiftvector.append(float(line.split()[4]))
shiftvector.append(float(line.split()[6]))
znucl=[]
znucl.append(typat[0])
inArray=True
for i in range(natom):
inArray=False
for j in range(len(znucl)):
if (znucl[j]==typat[i]):
inArray=True
if (not inArray):
znucl.append(typat[i])
typata=[]
for i in range(natom):
for j in range(len(znucl)):
if(typat[i]==znucl[j]):
typata.append(j+1)
print(basis)
print(frequencies)
print(xred)
print(typat)
print(typatsym)
print(shiftvector)
print(znucl)
print(natom)
print(len(shiftvector))
for v in np.array(shiftvector).reshape(natom,3):
print(v)
directpos=np.array(xred).reshape(natom,3)
cartpos=direct2cart(directpos,basis)
genabinit('ideal.in',0,basis,natom,typata,znucl,cartpos,'ideal structure')
gencastep('ideal.cell',0,basis,natom,typatsym,args.symprec,cartpos)
j=args.modenum-1
for n in range(len(ampl)):
cartshiftdm=[]
cartshiftdp=[]
print ('Process mode: %d with freq: %8.5f shifted by: %8.5f' % (j+1,frequencies[j],ampl[n] ))
for i in range(natom):
cartshiftdm.append(cartpos[i]-np.array(shiftvector).reshape(natom,3)[i]*ampl[n])
abinitfn="shiftcell-%.3f.in" % ampl[n]
castepfn="shiftcell-%.3f.cell" % ampl[n]
genabinit(abinitfn,j+1,basis,natom,typata,znucl,cartshiftdm,'freq = %9.4f cm-1; Delta=%6.4f' % (frequencies[j],ampl[n]))
gencastep(castepfn,j+1,basis,natom,typatsym,args.symprec,cartshiftdm)
print('Done.')