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import numpy as np
import shlex
import re
class configuration:
"""Docstring"""
def __init__(self, properties=None, latoms=None, energy=None, lpos=None, lforces=None, pbc=None, lattice=None, config_type=None, dihedral_angle=None):
"""
properties: string that contain the properties written in the extendend xyz file (ex: 'species:S:1:pos:R:3:forces:R:3')
latoms: (string) list of atoms species as string in xyz of length n
energy: energy of the configuration
lpos: list of position (n, 3) for n atoms
lforces: list of forces (n, 3) for n atoms
lattice: list of the component of the lattice vectors of size 9
pbc: periodic boudary conditions as : F F F for False False False
config_type: 'isolated_atom' or a specific note
dihedral_angle: _JSON[a,b,c] or scalar
"""
self.properties = properties
self.latoms = latoms
self.pbc = pbc
self.config_type = config_type
# Scalar type
if type(latoms) != type(None):
self.natoms = len(latoms)
else:
self.natoms = None
if type(energy) != type(None):
self.energy = float(energy)
else:
self.energy = None
if type(dihedral_angle) != type(None):
self.dihedral_angle = float(dihedral_angle)
else:
self.dihedral_angle = None
# List type (directly transform to np.array)
if type(lpos) != type(None):
self.lpos = np.asarray([np.asarray([float(y) for y in x]) for x in lpos])
else:
self.lpos = None
if type(lforces) != type(None):
self.lforces = np.asarray([np.asarray([float(y) for y in x]) for x in lforces])
else:
self.lforces = None
if type(lattice) != type(None):
self.lattice = np.asarray([float(x) for x in lattice])
else:
self.lattice = None
def read_header(self, tupple_header):
for i in range(len(tupple_header)):
if "Lattice" in b[i]:
self.lattice = re.findall(r"[-+]?(?:\d*\.*\d+)", b[i])
elif "Properties" in b[i]:
self.properties = b[i].replace('Properties=', '')
elif "dihedral_angle" in b[i]:
self.dihedral_angle = float(re.findall(r"[-+]?(?:\d*\.*\d+)", b[i])[0])
elif "energy" in b[i]:
self.energy = float(b[i].replace('energy=', ''))
elif "pbc" in b[i]:
self.pbc = " ".join(re.split("[^FT]*", b[i]))
elif "config_type" in b[i]:
self.config_type = b[i].replace('config_type=', '')
def read_conf(self, extracted_tupple):
"""
"""
self.natoms = int(extracted_tupple[0])
self.read_header(extracted_tupple[1])
if "species:S:" in self.properties:
self.latoms = []
if "pos:R:3" in self.properties:
self.lpos = []
if "forces:R:3" in self.properties:
self.lforces = []
for i in range(self.natoms):
string = extracted_tupple[2][i].split()
if "species:S:" in self.properties:
self.latoms.append(string[0])
if "pos:R:3" in self.properties:
self.lpos.append([float(x) for x in string[1:4]])
if "forces:R:3" in self.properties:
self.lforces.append([float(x) for x in string[4:7]])
self.lpos = np.asarray(self.lpos)
self.lforces = np.asarray(self.lforces)
def write_conf(self, filename, mode='w'):
"""
mode: can be write 'w' or append 'a'
"""
if mode == "w":
with open(filename, mode=mode) as foo:
foo.write(str(self.natoms))
foo.write("\n")
# Write Header
if type(self.lattice) != type(None):
lattice = [str(x) for x in self.lattice]
foo.write(str( " Lattice=\""+ ' '.join(lattice) + "\""))
foo.write(str(" Properties=" + ''.join(self.properties)))
if self.dihedral_angle:
foo.write(str(" dihedral_angle=%s" % self.dihedral_angle))
foo.write(str(" config_type=%s" % self.config_type))
foo.write(str(" energy=%s" % self.energy))
if self.pbc:
foo.write(str(" pbc=\"" + " ".join(self.pbc) + "\""))
# Write xyz
for i in range(len(self.latoms)):
foo.write("\n")
foo.write(str(self.latoms[i] + '{:15.8f}'.format(self.lpos[i][0]) + '{:15.8f}'.format(self.lpos[i][1]) + '{:15.8f}'.format(self.lpos[i][2])))
if type(self.lforces) != type(None):
foo.write(str('{:15.8f}'.format(self.lforces[i][0]) + '{:15.8f}'.format(self.lforces[i][1]) + '{:15.8f}'.format(self.lforces[i][2])))
elif mode == "a":
with open(filename, mode=mode) as foo:
foo.write(str(self.natoms))
foo.write("\n")
# Write Header
if type(self.lattice) != type(None):
lattice = [str(x) for x in self.lattice]
foo.write(str( " Lattice=\""+ ' '.join(lattice) + "\""))
foo.write(str(" Properties=" + ''.join(self.properties)))
if self.dihedral_angle:
foo.write(str(" dihedral_angle=%s" % self.dihedral_angle))
foo.write(str(" config_type=%s" % self.config_type))
foo.write(str(" energy=%s" % self.energy))
if self.pbc:
foo.write(str(" pbc=\"" + " ".join(self.pbc) + "\""))
# Write xyz
for i in range(len(self.latoms)):
foo.write("\n")
foo.write(str(self.latoms[i] + '{:15.8f}'.format(self.lpos[i][0]) + '{:15.8f}'.format(self.lpos[i][1]) + '{:15.8f}'.format(self.lpos[i][2])))
if type(self.lforces) != type(None):
foo.write(str('{:15.8f}'.format(self.lforces[i][0]) + '{:15.8f}'.format(self.lforces[i][1]) + '{:15.8f}'.format(self.lforces[i][2])))
foo.write("\n")
def extract_data(conf_data):
"""
Input the 'string_data' variable of the 'read_extended_file' function. It outputs the content of the extended file such as tupple containing 3 element, time the number of configuration.
tupple[x][0]: the number of atom in the configuration
tupple[x][1]: the header of the configuration
tupple[x][2]: the xyz file of the configuration (element, position, forces)
"""
index_properties = [i for i, value in enumerate(conf_data) if ("Properties" in value)]
ltupple = []
for i in index_properties:
number = int(conf_data[i-1])
# print(i+1, i + number+1)
xyz = conf_data[i+1:i + number+1]
properties = shlex.split(conf_data[i])
ltupple.append((number, properties, xyz))
return ltupple
def read_extended_file(filepath):
"""
Input an extended file to get directly the 'configuration' object defined by the class above. It reads all the configurations of the file.
"""
# Load data in string
with open(filepath) as foo:
string_data = foo.readlines()
string_data = [x.replace('\n', '') for x in string_data]
# extract all conf in tupples
extracted_data = extract_data(string_data)
# put tupples into configuration object
lconfs = []
for i in range(len(extracted_data)):
conf = configuration()
conf.read_conf(extracted_data[i])
lconfs.append(conf)
return lconfs
dsys = dpdata.LabeledSystem('/Users/atetenoire/server/ruthenium_CO_O/deepmd_sorted_event_filtered_mixed/075ML/size_200000/', fmt='deepmd/npy')
for i in tqdm.tqdm(range(len(dsys.__dict__['data']['energies']))):
a = configuration(properties='species:S:1:pos:R:3:forces:R:3', latoms=latom_names, energy=dsys.__dict__['data']['energies'][i], lpos=dsys.__dict__['data']['coords'][i], lforces=dsys.__dict__['data']['forces'][i], pbc=['T', 'T', 'T'], lattice=dsys.__dict__['data']['cells'][i].flatten(), config_type='AIMDEF_075ML', dihedral_angle=None)
a.write_conf('mace_training_test/075ML/size_200000.xyz', mode='a')
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