/
scan_alnog_modes_anaddb.py
executable file
·511 lines (462 loc) · 17.1 KB
/
scan_alnog_modes_anaddb.py
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#!/usr/bin/env python3
# -*- 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/>.
#
# Generate input files distorted along modes
#
# Author: Eugene Roginskii
#
def strType(var):
try:
if int(var) == float(var):
return 'int'
except:
try:
float(var)
return 'float'
except:
return 'str'
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 genabinit(abinitfn,modenum,basis,natom,typat,znucl,cartshiftd,comment):
abinit_fh=open(abinitfn,'w')
abinit_fh.write('#Atom positions shifted along %d modes\n' % modenum)
abinit_fh.write('# %s\n' % comment)
abinit_fh.write('acell 1.0 1.0 1.0\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('xcart\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 cart2direct(cartpos,basis):
direct=[]
for atcart in cartpos:
direct.append(np.dot(np.linalg.inv(np.transpose(basis)),atcart))
return np.array(direct)
import numpy as np
import re
from math import sqrt
import sys
from math import pi
from math import exp
from optparse import OptionParser
import xml.etree.cElementTree as etree
import argparse
Angst2Bohr=1.889725989
HaTocm1=219474.631370515
#default amplitude of mode shifting
ampldflt=1
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 distort geometry along selected normal mode eigenvector. Abinit input format')
parser.add_argument("-i", "--input", action="store", type=str, dest="abinit_fn", help="Abinit filename")
parser.add_argument("-d", "--anaddb", action="store", type=str, dest="anaddb_fn", help="Anaddb filename (only first dataset will be plotted)")
parser.add_argument("-m", "--modes", action="store", type=str, dest="modesnum", default="1", help="Number of modes space separated")
parser.add_argument("-a", "--amplitudes", action="store", type=str, dest="amplstr",
help="Mode shift amplitude for each mode, space separated")
args = parser.parse_args()
if (args.abinit_fn == None):
print('Error. No Abinit input filename was given.')
sys.exit(1)
try:
abinit_fh = open(args.abinit_fn, 'r')
except IOError:
print ("ERROR Couldn't open abinit file, exiting...")
print(IOError)
sys.exit(1)
ampl=[]
if (args.amplstr is None):
print('The amplitudes parameter is not set. Set default amplitudes')
for i in range(len(args.modesnum)):
ampl.append(ampldflt)
else:
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)
# abinit input file process
acell=[]
rprim=[]
typat=[]
znucl=[]
natom=0
scalecart=[1.0,1.0,1.0]
ntypat=0
# First find natom
while True:
line=abinit_fh.readline()
if not line: break
if (re.match('^\s*#',line)):
continue
if '#' in line:
line=re.sub('\s*#.*','',line)
if 'natom' in line:
natom = int(line.split()[1])
if (natom==0):
print('Error. The natom variable was not found in abinit input file.')
sys.exit(1)
abinit_fh.seek(0)
while True:
line=abinit_fh.readline()
if not line: break
if (re.match('^\s*#',line)):
continue
if '#' in line:
line=re.sub('\s*#.*','',line)
if 'ntypat' in line:
ntypat=int(line.split()[1])
elif 'znucl' in line:
znuclstr=line.split()[1:]
znucl=[int(float(znuclstr[i])) for i in range(len(znuclstr)) ]
print('znucl= %s' % znucl)
elif 'acell' in line:
if re.match('.*acell.*\d+\s*A.*',line):
acell=[float(line.split()[i+1])*Angst2Bohr for i in range(3)]
else:
acell=[float(line.split()[i+1]) for i in range(3)]
print('acell = %s' % acell)
elif 'rprim' in line:
try:
for coor in line.split()[1:]:
rprim.append(float(coor))
while True:
subline=abinit_fh.readline()
if not subline: break
if((re.match('^\s*-?\d*\.',subline) is None) and (re.match('^\s*-?\d',subline) is None)):
break
else:
for coor in subline.split():
if (isNumeric(coor)==True):
rprim.append(float(coor))
except:
while True:
subline=abinit_fh.readline()
if not subline: break
if((re.match('^\s*-?\d*\.',subline) is None) and (re.match('^\s*-?\d',subline) is None)):
break
else:
for coor in subline.split():
if(isNumeric(coor)==True):
rprim.append(float(coor))
elif 'scalecart' in line:
scalecart=[float(line.split()[i+1]) for i in range(3)]
print("########### rprim ###########")
print(rprim)
# Start from begining to read xred (xcart and xangs is not implemented)
abinit_fh.seek(0)
xred=[]
xcart=[]
if (len(rprim)<9):
rprim=[1,0,0,0,1,0,0,0,1]
for line in abinit_fh:
if (re.match('^\s*#',line)):
continue
if '#' in line:
line=re.sub('\s*#.*','',line)
if 'xred' in line:
try:
for coor in line.split()[1:]:
xred.append(float(coor))
for subline in abinit_fh:
if((re.match('^\s*-?\d*\.',subline) is None) and (re.match('^\s*-?\d',subline) is None)):
break
else:
for coor in subline.split():
xred.append(float(coor))
except:
for subline in abinit_fh:
if((re.match('^\s*-?\d*\.',subline) is None) and (re.match('^\s*-?\d',subline) is None)):
break
else:
for coor in subline.split():
xred.append(float(coor))
elif 'xcart' in line:
try:
for coor in line.split()[1:]:
xcart.append(float(coor))
for subline in abinit_fh:
if((re.match('^\s*-?\d*\.',subline) is None) and (re.match('^\s*-?\d',subline) is None)):
break
else:
for coor in subline.split():
xcart.append(float(coor))
except:
for subline in abinit_fh:
if((re.match('^\s*-?\d*\.',subline) is None) and (re.match('^\s*-?\d',subline) is None)):
break
else:
for coor in subline.split():
xcart.append(float(coor))
elif 'xangs' in line:
try:
for coor in line.split()[1:]:
xcart.append(float(coor)*Angst2Bohr)
for subline in abinit_fh:
if((re.match('^\s*-?\d*\.',subline) is None) and (re.match('^\s*-?\d',subline) is None)):
break
else:
for coor in subline.split():
xcart.append(float(coor)*Angst2Bohr)
except:
for subline in abinit_fh:
if((re.match('^\s*-?\d*\.',subline) is None) and (re.match('^\s*-?\d',subline) is None)):
break
else:
for coor in subline.split():
xcart.append(float(coor)*Angst2Bohr)
abinit_fh.seek(0)
while True:
line=abinit_fh.readline()
if not line: break
if (re.match('^\s*#',line)):
continue
if '#' in line:
line=re.sub('\s*#.*','',line)
if 'ntypat' in line:
continue
if 'typat' in line:
if(re.match('^\s*typat\s+\d',line) is None):
line=abinit_fh.readline()
if(re.match('^\s*\d',line) is None):
print('Error reading typat variable in abinit input file')
sys.exit(1)
else:
typat=[int(line.split()[i]) for i in range(natom)]
else:
typat=[int(line.split()[i+1]) for i in range(natom)]
if len(rprim) != 9:
print('Error reading rprim array')
sys.exit(1)
rprimd=[]
for i in range(3):
# print([scalecart[1],acell[i],rprim[i*3+1]])
rprimd.append([scalecart[k]*rprim[i*3+k]*acell[i] for k in range(3)])
print(scalecart[0]*rprim[i*3+0]*acell[i])
basis=np.array(rprimd).reshape(3,3)
if len(xred) != natom*3:
if len(xcart) != natom*3:
print('Error reading atom coordinate array. natom=%d' % natom)
sys.exit(1)
else:
cartpos=np.array(xcart).reshape(natom,3)
directpos=cart2direct(cartpos,basis)
else:
directpos=np.array(xred).reshape(natom,3)
cartpos=direct2cart(directpos,basis)
# Proceed the anaddb output file
if (args.anaddb_fn == None):
print('Error. Now anaddb output filename provided. Exit.')
sys.exit(1)
else:
try:
anaddb_fh = open(args.anaddb_fn, 'r')
except IOError:
print ("ERROR Couldn't open anaddb file, exiting...\n")
sys.exit(1)
# Read frequencies data
freqs=[]
for line in anaddb_fh:
if 'Phonon wavevector' in line:
break
for line in anaddb_fh:
if 'Phonon energies in Hartree' in line:
break
if ((natom*3)%5 > 0):
nl=int(natom*3/5)+1
else:
nl=natom*3/5
i=0
for line in anaddb_fh:
if i>nl:
break
if re.match('^\s*-?\d+.*',line):
for f in line.split():
freqs.append(float(f)*HaTocm1)
i=i+1
#for i in range(natom*3):
# print freqs[i]
for line in anaddb_fh:
if 'Eigendisplacements' in line:
break
#Go through each i mode
shiftvecs=[]
shiftvec=[]
for i in range(natom*3):
for line in anaddb_fh:
if 'Mode number' in line:
m=re.match('\s*Mode number\s+(\d+)\s+Energy.*',line)
if (m):
if (isNumeric(m.group(1))):
k=1
for line in anaddb_fh:
if re.match('\s*\W\s*(\d+)\s*-?\d+',line):
shiftvec.append([float(line.split()[j]) for j in range(2,5)])
k=k+1
if k>natom:
shiftvecs.append(shiftvec)
k=1
shiftvec=[]
continue
print('shiftvec:')
for i in range(len(shiftvecs)):
print('mode %d' % (i+1))
for j in range(natom):
print(shiftvecs[i][j])
comment=''
cartshiftdm=[]
for i in range(len(args.modesnum.split())):
for j in range(natom):
# multiplyer 25 for backward capability with scan_alnog_mode_abinit.py
cartshiftdm.append(cartpos[j]-np.array(shiftvecs[int(args.modesnum.split()[i])-1][j])*float(ampl[i])*25)
comment+='freq = %9.4f cm-1; Delta=%6.4f ' % (freqs[int(args.modesnum.split()[i])-1],ampl[i])
mstr="".join("m%s" % m for m in args.modesnum.split())
abinitfn="".join("shiftcell-%s.in" % mstr)
# abinitfn="shiftcell-%.3f.in" % float(a)
print(comment)
print(mstr)
genabinit(abinitfn,int(len(args.modesnum.split())),basis,natom,typat,znucl,cartshiftdm,comment)