def icsd_cif_b(filename):
from os.path import basename
from numpy import dot, transpose
from pylada.crystal import Structure, primitive
from . import readCif
rdr = readCif.CifReader(0, filename) # buglevel = 0
vaspMap = rdr.getVaspMap()
cellBasis = vaspMap['cellBasis']
structure = Structure(
transpose(cellBasis),
scale=1,
name=basename(filename))
usyms = vaspMap['uniqueSyms']
posVecs = vaspMap['posVecs']
# multiplicities = num atoms of each type.
mults = [len(x) for x in posVecs]
# For each unique type of atom ...
for ii in range(len(usyms)):
# For each atom of that type ...
for jj in range(mults[ii]):
atpos = dot(transpose(cellBasis), posVecs[ii][jj])
structure.add_atom(atpos[0], atpos[1], atpos[2], usyms[ii])
prim = primitive(structure)
logger.info(" crystal/read: icsd_cif_b: structure: %s" % structure)
return prim
def icsd_cif_b(filename):
from os.path import basename
from numpy import dot, transpose
from pylada.crystal import Structure, primitive
from . import readCif
rdr = readCif.CifReader(0, filename) # buglevel = 0
vaspMap = rdr.getVaspMap()
cellBasis = vaspMap['cellBasis']
structure = Structure(
transpose(cellBasis),
scale=1,
name=basename(filename))
usyms = vaspMap['uniqueSyms']
posVecs = vaspMap['posVecs']
# multiplicities = num atoms of each type.
mults = [len(x) for x in posVecs]
# For each unique type of atom ...
for ii in range(len(usyms)):
# For each atom of that type ...
for jj in range(mults[ii]):
atpos = dot(transpose(cellBasis), posVecs[ii][jj])
structure.add_atom(atpos[0], atpos[1], atpos[2], usyms[ii])
prim = primitive(structure)
logger.info(" crystal/read: icsd_cif_b: structure: %s" % structure)
return prim
def icsd_cif_a(filename):
""" Reads lattice from the ICSD \*cif files.
It will not work in the case of other \*cif.
It is likely to produce wrong output if the site occupations are fractional.
If the occupation is > 0.5 it will treat it as 1 and
in the case occupation < 0.5 it will treat it as 0 and
it will accept all occupation = 0.5 as 1 and create a mess!
"""
from pylada import logger
import re
from os.path import basename
from numpy.linalg import norm
from numpy import array, transpose
from numpy import pi, sin, cos, sqrt, dot
lines = open(filename, 'r').readlines()
logger.info("crystal/read: icsd_cif_a: %s" % filename)
sym_big = 0
sym_end = 0
pos_big = 0
pos_end = 0
for l in lines:
x = l.split()
if len(x) > 0:
# CELL
if x[0] == '_cell_length_a':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
a = float(x[-1][:index])
if x[0] == '_cell_length_b':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
b = float(x[-1][:index])
if x[0] == '_cell_length_c':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
c = float(x[-1][:index])
if x[0] == '_cell_angle_alpha':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
alpha = float(x[-1][:index])
if x[0] == '_cell_angle_beta':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
beta = float(x[-1][:index])
if x[0] == '_cell_angle_gamma':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
gamma = float(x[-1][:index])
# SYMMETRY OPERATIONS
if len(x) > 0 and x[0] == '_symmetry_equiv_pos_as_xyz':
sym_big = lines.index(l)
if len(x) > 0 and x[0] == '_atom_type_symbol':
sym_end = lines.index(l)
# WYCKOFF POSITIONS
if len(x) > 0 and x[0] == '_atom_site_attached_hydrogens':
pos_big = lines.index(l)
if len(x) > 0 and x[0] == '_atom_site_B_iso_or_equiv':
pos_big = lines.index(l)
if len(x) > 0 and x[0] == '_atom_site_U_iso_or_equiv':
pos_big = lines.index(l)
if len(x) > 0 and x[0] == '_atom_site_0_iso_or_equiv':
pos_big = lines.index(l)
# if pos_end == 0 and l in ['\n', '\r\n'] and lines.index(l) > pos_big:
if pos_end == 0 and pos_big > 0 \
and (l in ['\n', '\r\n'] or l.startswith('#')) \
and lines.index(l) > pos_big:
pos_end = lines.index(l)
# _symmetry_equiv_pos_* lines are like:
# 1 'x, x-y, -z+1/2'
logger.debug("crystal/read: icsd_cif_a: sym_big: %s" % sym_big)
logger.debug("crystal/read: icsd_cif_a: sym_end: %s" % sym_end)
symm_ops = ['(' + x.split()[1][1:] + x.split()[2] + x.split()[3][:-1] + ')'
for x in lines[sym_big + 1:sym_end - 1]]
logger.debug("crystal/read: icsd_cif_a: symm_ops a: %s" % symm_ops)
# ['(x,x-y,-z+1/2)', '(-x+y,y,-z+1/2)', ...]
# Insert decimal points after integers
symm_ops = [re.sub(r'(\d+)', r'\1.', x) for x in symm_ops]
logger.debug("crystal/read: icsd_cif_a: symm_ops b: %s" % symm_ops)
# ['(x,x-y,-z+1./2.)', '(-x+y,y,-z+1./2.)', ...]
# _atom_site_* lines are like:
# Mo1 Mo4+ 2 c 0.3333 0.6667 0.25 1. 0
logger.debug("crystal/read: icsd_cif_a: pos_big: %s" % pos_big)
logger.debug("crystal/read: icsd_cif_a: pos_end: %s" % pos_end)
wyckoff = [[x.split()[0], [x.split()[4], x.split()[5], x.split()[6]], x.split()[7]]
for x in lines[pos_big + 1:pos_end]]
logger.debug("crystal/read: icsd_cif_a: wyckoff a: %s" % wyckoff)
# [['Mo1', ['0.3333', '0.6667', '0.25'], '1.'], ['S1', ['0.3333', '0.6667', '0.621(4)'], '1.']]
wyckoff = [w for w in wyckoff if int(float(w[-1][:4]) + 0.5) != 0]
logger.debug("crystal/read: icsd_cif_a: wyckoff b: %s" % wyckoff)
# [['Mo1', ['0.3333', '0.6667', '0.25'], '1.'], ['S1', ['0.3333', '0.6667', '0.621(4)'], '1.']]
# Setting up a good wyckoff list
for w in wyckoff:
# Strip trailing numerals from w[0] == 'Mo1'
pom = 0
for i in range(len(w[0])):
try:
int(w[0][i])
if pom == 0:
pom = i
except:
pass
w[0] = w[0][:pom]
# Strip trailing standard uncertainty, if any, from w[1], ..., w[3]
for i in range(3):
if '(' in w[1][i]:
index = w[1][i].index('(')
else:
index = len(w[1][i])
w[1][i] = float(w[1][i][:index])
# Delete w[4]
del w[-1]
##########################################
# List of unique symbols ["Mo", "S"]
symbols = list({w[0] for w in wyckoff})
logger.debug("crystal/read: icsd_cif_a: symbols: %s" % symbols)
# List of position vectors for each symbol
positions = [[] for i in range(len(symbols))]
for w in wyckoff:
symbol = w[0]
x, y, z = w[1][0], w[1][1], w[1][2]
logger.debug("symbol: %s x: %s y: %s z: %s" % (symbol, x, y, z))
for i in range(len(symm_ops)):
# Set pom = new position based on symmetry transform
pom = list(eval(symm_ops[i]))
logger.debug("i: %s pom a: %s" % (i, pom))
# [0.3333, -0.3334, 0.25]
# Move positions to range [0,1]:
for j in range(len(pom)):
if pom[j] < 0.:
pom[j] = pom[j] + 1.
if pom[j] >= 0.999:
pom[j] = pom[j] - 1.
logger.debug("i: %s pom b: %s" % (i, pom))
# [0.3333, 0.6666, 0.25]
# If pom is not in positions[symbol], append pom
if not any(norm(array(u) - array(pom)) < 0.01 for u in positions[symbols.index(symbol)]):
ix = symbols.index(symbol)
positions[ix].append(pom)
logger.debug("new positions for %s: %s" % (symbol, repr(positions[ix])))
################ CELL ####################
a1 = a * array([1., 0., 0.])
a2 = b * array([cos(gamma * pi / 180.), sin(gamma * pi / 180.), 0.])
c1 = c * cos(beta * pi / 180.)
c2 = c / sin(gamma * pi / 180.) * (-cos(beta * pi / 180.) *
cos(gamma * pi / 180.) + cos(alpha * pi / 180.))
a3 = array([c1, c2, sqrt(c**2 - (c1**2 + c2**2))])
cell = array([a1, a2, a3])
logger.debug("crystal/read: icsd_cif_a: a1: %s" % a1)
logger.debug("crystal/read: icsd_cif_a: a2: %s" % a2)
logger.debug("crystal/read: icsd_cif_a: a3: %s" % a3)
##########################################
from pylada.crystal import Structure, primitive
logger.debug("crystal/read: icsd_cif_a: cell: %s" % cell)
structure = Structure(
transpose(cell),
scale=1,
name=basename(filename))
for i in range(len(symbols)):
logger.debug("crystal/read: icsd_cif_a: i: %s symbol: %s len(position): %i" % (
i, symbols[i], len(positions[i])
))
# crystal/read: i: 0 symbol: Mo len position: 2
for j in range(len(positions[i])):
atpos = dot(transpose(cell), positions[i][j])
logger.debug("j: %s pos: %s" % (j, positions[i][j]))
logger.debug("atpos: " % atpos)
# j: 0 pos: [0.3333, 0.6666000000000001, 0.25]
# atpos: [ 6.32378655e-16 1.81847148e+00 3.07500000e+00]
structure.add_atom(atpos[0], atpos[1], atpos[2], symbols[i])
logger.info("crystal/read: icsd_cif_a: structure: %s" % structure)
prim = primitive(structure)
logger.info("crystal/read: icsd_cif_a: primitive structure: %s" % prim)
return prim
def main():
import re
from sys import path as python_path
from os.path import exists
from argparse import ArgumentParser
from pylada import jobfolder
from pylada.process.mpi import create_global_comm
import pylada
# below would go additional imports.
parser = ArgumentParser(prog="runone", description=re.sub("\\s+", " ", __doc__[1:]))
parser.add_argument('--logging', dest="logging", default="critical", type=str,
help="Debug level.")
parser.add_argument('--testValidProgram', dest="testValidProgram",
default=None, type=str,
help="testValidProgram")
parser.add_argument("--jobid", dest="names", nargs='+', type=str,
help="Job name", metavar="N")
parser.add_argument("--ppath", dest="ppath", default=None,
help="Directory to add to python path",
metavar="Directory")
parser.add_argument('--nbprocs', dest="nbprocs", default=pylada.default_comm['n'], type=int,
help="Number of processors with which to launch job.")
parser.add_argument('--ppn', dest="ppn", default=pylada.default_comm['ppn'], type=int,
help="Number of processors with which to launch job.")
parser.add_argument('--timeout', dest="timeout", default=300, type=int,
help="Time to wait for job-dictionary to becom available "
"before timing out (in seconds). A negative or null "
"value implies forever. Defaults to 5mn.")
parser.add_argument('pickle', metavar='FILE', type=str, help='Path to a job-folder.')
try:
options = parser.parse_args()
except SystemExit:
return
from pylada import logger
logger.setLevel(level=options.logging.upper())
from pylada.misc import setTestValidProgram
tstPgm = options.testValidProgram
if tstPgm.lower() == 'none':
tstPgm = None
setTestValidProgram(tstPgm)
from pylada.misc import testValidProgram
# additional path to look into.
if options.ppath is not None:
python_path.append(options.ppath)
if not exists(options.pickle):
print("Could not find file {0}.".format(options.pickle))
return
# Set up mpi processes.
pylada.default_comm['ppn'] = options.ppn
pylada.default_comm['n'] = options.nbprocs
if testValidProgram == None:
create_global_comm(options.nbprocs) # Sets pylada.default_comm
else:
pylada.default_comm = None # use testValidProgram
timeout = None if options.timeout <= 0 else options.timeout
jobfolder = jobfolder.load(options.pickle, timeout=timeout)
print((' ipy/lau/scattered_script: jobfolder: %s' % jobfolder))
print((' ipy/lau/scattered_script: options: %s' % options))
for name in options.names:
logger.info('ipy/lau/scattered_script: testValidProgram: %s' % testValidProgram)
logger.info('ipy/lau/scattered_script: name: %s' % name)
logger.info('ipy/lau/scattered_script: jobfolder[name]: %s' % jobfolder[name])
logger.info('ipy/lau/scattered_script: type(jobfolder[name]): %s' %
type(jobfolder[name]))
logger.info(
'ipy/lau/scattered_script: jobfolder[name].compute: %s' % jobfolder[name].compute)
logger.info(
'ipy/lau/scattered_script: type(jobfolder[name].compute): %s' \
% type(jobfolder[name].compute))
logger.info('ipy/lau/scattered_script: before compute for name: %s' % name)
comm = pylada.default_comm
if testValidProgram != None:
comm = None
jobfolder[name].compute(comm=comm, outdir=name)
logger.info('ipy/lau/scattered_script: after compute for name: %s' % name)
def icsd_cif_a(filename, make_primitive=True):
""" Reads lattice from the ICSD \*cif files.
It will not work in the case of other \*cif.
It is likely to produce wrong output if the site occupations are fractional.
If the occupation is > 0.5 it will treat it as 1 and
in the case occupation < 0.5 it will treat it as 0 and
it will accept all occupation = 0.5 as 1 and create a mess!
"""
from pylada import logger
import re
from copy import deepcopy
from os.path import basename
from numpy.linalg import norm
from numpy import array, transpose
from numpy import pi, sin, cos, sqrt, dot
lines = open(filename, 'r').readlines()
logger.info("crystal/read: icsd_cif_a: %s" % filename)
sym_big = 0
sym_end = 0
pos_big = 0
pos_end = 0
for l in lines:
x = l.split()
if len(x) > 0:
# CELL
if x[0] == '_cell_length_a':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
a = float(x[-1][:index])
if x[0] == '_cell_length_b':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
b = float(x[-1][:index])
if x[0] == '_cell_length_c':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
c = float(x[-1][:index])
if x[0] == '_cell_angle_alpha':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
alpha = float(x[-1][:index])
if x[0] == '_cell_angle_beta':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
beta = float(x[-1][:index])
if x[0] == '_cell_angle_gamma':
if '(' in x[-1]:
index = x[-1].index('(')
else:
index = len(x[-1])
gamma = float(x[-1][:index])
# SYMMETRY OPERATIONS
if len(x) > 0 and x[0] == '_symmetry_equiv_pos_as_xyz':
sym_big = lines.index(l)
if len(x) > 0 and x[0] == '_atom_type_symbol':
sym_end = lines.index(l)
# WYCKOFF POSITIONS
if len(x) > 0 and x[0] == '_atom_site_attached_hydrogens':
pos_big = lines.index(l)
if len(x) > 0 and x[0] == '_atom_site_B_iso_or_equiv':
pos_big = lines.index(l)
if len(x) > 0 and x[0] == '_atom_site_U_iso_or_equiv':
pos_big = lines.index(l)
if len(x) > 0 and x[0] == '_atom_site_0_iso_or_equiv':
pos_big = lines.index(l)
# if pos_end == 0 and l in ['\n', '\r\n'] and lines.index(l) > pos_big:
if pos_end == 0 and pos_big > 0 \
and (l in ['\n', '\r\n'] or l.startswith('#')) \
and lines.index(l) > pos_big:
pos_end = lines.index(l)
# _symmetry_equiv_pos_* lines are like:
# 1 'x, x-y, -z+1/2'
logger.debug("crystal/read: icsd_cif_a: sym_big: %s" % sym_big)
logger.debug("crystal/read: icsd_cif_a: sym_end: %s" % sym_end)
symm_ops = ['(' + x.split()[1][1:] + x.split()[2] + x.split()[3][:-1] + ')'
for x in lines[sym_big + 1:sym_end - 1]]
logger.debug("crystal/read: icsd_cif_a: symm_ops a: %s" % symm_ops)
# ['(x,x-y,-z+1/2)', '(-x+y,y,-z+1/2)', ...]
# Insert decimal points after integers
symm_ops = [re.sub(r'(\d+)', r'\1.', x) for x in symm_ops]
logger.debug("crystal/read: icsd_cif_a: symm_ops b: %s" % symm_ops)
# ['(x,x-y,-z+1./2.)', '(-x+y,y,-z+1./2.)', ...]
# _atom_site_* lines are like:
# Mo1 Mo4+ 2 c 0.3333 0.6667 0.25 1. 0
logger.debug("crystal/read: icsd_cif_a: pos_big: %s" % pos_big)
logger.debug("crystal/read: icsd_cif_a: pos_end: %s" % pos_end)
wyckoff = [[x.split()[0], [x.split()[4], x.split()[5], x.split()[6]], x.split()[7]]
for x in lines[pos_big + 1:pos_end]]
logger.debug("crystal/read: icsd_cif_a: wyckoff a: %s" % wyckoff)
# [['Mo1', ['0.3333', '0.6667', '0.25'], '1.'], ['S1', ['0.3333', '0.6667', '0.621(4)'], '1.']]
wyckoff = [w for w in wyckoff if int(float(w[-1][:4]) + 0.5) != 0]
logger.debug("crystal/read: icsd_cif_a: wyckoff b: %s" % wyckoff)
# [['Mo1', ['0.3333', '0.6667', '0.25'], '1.'], ['S1', ['0.3333', '0.6667', '0.621(4)'], '1.']]
# Setting up a good wyckoff list
for w in wyckoff:
# Strip trailing numerals from w[0] == 'Mo1'
pom = 0
for i in range(len(w[0])):
try:
int(w[0][i])
if pom == 0:
pom = i
except:
pass
w[0] = w[0][:pom]
# Strip trailing standard uncertainty, if any, from w[1], ..., w[3]
for i in range(3):
if '(' in w[1][i]:
index = w[1][i].index('(')
else:
index = len(w[1][i])
w[1][i] = float(w[1][i][:index])
# Delete w[4]
del w[-1]
##########################################
# List of unique symbols ["Mo", "S"]
symbols = list({w[0] for w in wyckoff})
logger.debug("crystal/read: icsd_cif_a: symbols: %s" % symbols)
# List of position vectors for each symbol
positions = [[] for i in range(len(symbols))]
for w in wyckoff:
symbol = w[0]
x, y, z = w[1][0], w[1][1], w[1][2]
logger.debug("symbol: %s x: %s y: %s z: %s" % (symbol, x, y, z))
for i in range(len(symm_ops)):
# Set pom = new position based on symmetry transform
pom = list(eval(symm_ops[i]))
logger.debug("i: %s pom a: %s" % (i, pom))
# [0.3333, -0.3334, 0.25]
# Move positions to range [0,1]:
for j in range(len(pom)):
if pom[j] < 0.:
pom[j] = pom[j] + 1.
if pom[j] >= 0.999:
pom[j] = pom[j] - 1.
logger.debug("i: %s pom b: %s" % (i, pom))
# [0.3333, 0.6666, 0.25]
# If pom is not in positions[symbol], append pom
if not any(norm(array(u) - array(pom)) < 0.01 for u in positions[symbols.index(symbol)]):
ix = symbols.index(symbol)
positions[ix].append(pom)
logger.debug("new positions for %s: %s" % (symbol, repr(positions[ix])))
################ CELL ####################
a1 = a * array([1., 0., 0.])
a2 = b * array([cos(gamma * pi / 180.), sin(gamma * pi / 180.), 0.])
c1 = c * cos(beta * pi / 180.)
c2 = c / sin(gamma * pi / 180.) * (-cos(beta * pi / 180.) *
cos(gamma * pi / 180.) + cos(alpha * pi / 180.))
a3 = array([c1, c2, sqrt(c**2 - (c1**2 + c2**2))])
cell = array([a1, a2, a3])
logger.debug("crystal/read: icsd_cif_a: a1: %s" % a1)
logger.debug("crystal/read: icsd_cif_a: a2: %s" % a2)
logger.debug("crystal/read: icsd_cif_a: a3: %s" % a3)
##########################################
from pylada.crystal import Structure, primitive
logger.debug("crystal/read: icsd_cif_a: cell: %s" % cell)
structure = Structure(
transpose(cell),
scale=1,
name=basename(filename))
for i in range(len(symbols)):
logger.debug("crystal/read: icsd_cif_a: i: %s symbol: %s len(position): %i" % (
i, symbols[i], len(positions[i])
))
# crystal/read: i: 0 symbol: Mo len position: 2
for j in range(len(positions[i])):
atpos = dot(transpose(cell), positions[i][j])
logger.debug("j: %s pos: %s" % (j, positions[i][j]))
logger.debug("atpos: " % atpos)
# j: 0 pos: [0.3333, 0.6666000000000001, 0.25]
# atpos: [ 6.32378655e-16 1.81847148e+00 3.07500000e+00]
structure.add_atom(atpos[0], atpos[1], atpos[2], symbols[i])
logger.info("crystal/read: icsd_cif_a: structure: %s" % structure)
if make_primitive:
prim = primitive(structure)
else:
prim = deepcopy(structure)
logger.info("crystal/read: icsd_cif_a: primitive structure: %s" % prim)
return prim
