def init_enum(self,enumdicts,systemSpecies,runGetKpoints = True):
from aBuild.enumeration import Enumerate
from aBuild.calculators.vasp import VASP
from aBuild.database.crystal import Crystal
from aBuild.jobs import Job
from random import randrange
from aBuild.utility import chdir
from numpy import array
from os import remove, path
# from crystal import Crystal
from os import path
import os
# if not path.isdir(self.root):
# os.mkdir(self.root)
print("Building database from enumerations")
self.crystals = []
# configIndex = startPoint = self._starting_point
#########################my changes#########################3
iterations = 0
########################################################
for eDict in enumdicts:
enumController = Enumerate(eDict)
if enumController.nEnumStructs == 0:
msg.warn('There are no enumerated structures for lattice type {}. Not building any VASP folders for them.'.format(self.enumDicts[index]["name"]))
enumController.buildInputFile()
enumController.enumerate()
def enumerate(self,dataset):
from aBuild.enumeration import Enumerate
self.dataset = dataset
for index in range(self.nEnums):
enumController = Enumerate(self.enumDicts[index])
enumController.buildInputFile(False)
enumController.enumerate(False)
def init_enum(enumdicts, systemSpecies):
from aBuild.enumeration import Enumerate
from aBuild.calculators.vasp import VASP
from aBuild.database.crystal import Crystal
from aBuild.jobs import Job
from random import randrange
from aBuild.utility import chdir
from numpy import array
from os import remove, path
# from crystal import Crystal
from os import path
import os
print("Building database from enumerations")
crystals = []
# configIndex = startPoint = self._starting_point
for eDict in enumdicts:
enumController = Enumerate(eDict)
if enumController.nEnumStructs == 0:
msg.warn(
'There are no enumerated structures for lattice type {}. Not building any VASP folders for them.'
.format(eDict["lattice"]))
enumController.buildInputFile()
enumController.enumerate()
# Loop to generate random structures for a given lattice type
for i in range(eDict["nconfigs"]):
print('Adding {} structure # {} to database'.format(
eDict["lattice"], rStruct))
with open('structNums', 'a+') as f:
f.write(eDict["name"] + ' ' + str(i) + '\n')
enumController.generatePOSCAR(i)
poscarpath = path.join(
enumController.root,
"poscar.{}.{}".format(eDict["name"], rStruct))
thisCrystal = Crystal.from_poscar(
poscarpath, systemSpecies
) #title = ' '.join([self.enumDicts[index]["lattice"]," str #: {}"]).format(rStruct)
crystals.append(thisCrystal)
delpath = path.join(
enumController.root,
"poscar.{}.{}".format(eDict["name"], rStruct))
remove(delpath)
return dataset(crystals)
def init_enum(self, enumdicts, systemSpecies, runGetKpoints=True):
from aBuild.enumeration import Enumerate
from aBuild.calculators.vasp import VASP
from aBuild.database.crystal import Crystal
from aBuild.jobs import Job
from random import randrange
from aBuild.utility import chdir
# from crystal import Crystal
from os import path
import os
# if not path.isdir(self.root):
# os.mkdir(self.root)
print("Building database from enumerations")
self.crystals = []
# configIndex = startPoint = self._starting_point
for eDict in enumdicts:
enumController = Enumerate(eDict)
if enumController.nEnumStructs == 0:
msg.warn(
'There are no enumerated structures for lattice type {}. Not building any VASP folders for them.'
.format(self.enumDicts[index]["lattice"]))
enumController.buildInputFile()
enumController.enumerate()
# Loop to generate random structures for a given lattice type
for i in range(eDict["nconfigs"]):
rStruct = randrange(1, enumController.nEnumStructs)
print('Adding {} structure # {} to database'.format(
eDict["lattice"], rStruct))
with open('structNums', 'a+') as f:
f.write(eDict["lattice"] + ' ' + str(rStruct) + '\n')
#print("Building VASP folder for {} structure #: {}".format(eDict["lattice"],rStruct))
enumController.generatePOSCAR(rStruct)
poscarpath = path.join(
enumController.root,
"poscar.{}.{}".format(eDict["lattice"], rStruct))
thisCrystal = Crystal(
poscarpath, systemSpecies=systemSpecies
) #title = ' '.join([self.enumDicts[index]["lattice"]," str #: {}"]).format(rStruct)
self.crystals.append(thisCrystal)
def init_enum(self, enumdicts, systemSpecies, runGetKpoints=True):
from aBuild.enumeration import Enumerate
from aBuild.calculators.vasp import VASP
from aBuild.database.crystal import Crystal
from aBuild.jobs import Job
from random import randrange
from aBuild.utility import chdir
from numpy import array
from os import remove, path
# from crystal import Crystal
from os import path
import os
# if not path.isdir(self.root):
# os.mkdir(self.root)
print("Building database from enumerations")
self.crystals = []
# configIndex = startPoint = self._starting_point
for eDict in enumdicts:
enumController = Enumerate(eDict)
if enumController.nEnumStructs == 0:
msg.warn(
'There are no enumerated structures for lattice type {}. Not building any VASP folders for them.'
.format(self.enumDicts[index]["lattice"]))
enumController.buildInputFile()
enumController.enumerate()
# Loop to generate random structures for a given lattice type
for i in range(eDict["nconfigs"]):
rStruct = 16254 #randrange(1,enumController.nEnumStructs)
print('Adding {} structure # {} to database'.format(
eDict["lattice"], rStruct))
with open('structNums', 'a+') as f:
f.write(eDict["name"] + ' ' + str(rStruct) + '\n')
#print("Building VASP folder for {} structure #: {}".format(eDict["lattice"],rStruct))
enumController.generatePOSCAR(rStruct)
poscarpath = path.join(
enumController.root,
"poscar.{}.{}".format(eDict["name"], rStruct))
thisCrystal = Crystal(
poscarpath, systemSpecies=systemSpecies
) #title = ' '.join([self.enumDicts[index]["lattice"]," str #: {}"]).format(rStruct)
if self.restrictions is None:
self.crystals.append(thisCrystal)
elif thisCrystal.getAFMPlanes([1, 0, 0]):
print('parent is AFM compatible')
self.crystals.append(thisCrystal)
import sys
sys.exit()
else:
superCrystal = thisCrystal.superPeriodics(2)
if superCrystal != []:
print('super periodic structures is AFM compatible')
print(superCrystal.minDist, 'minDist')
print(superCrystal.basis, ' basis')
print(array(superCrystal.Bv_direct), 'direct')
print(array(superCrystal.Bv_cartesian), 'cartesian')
self.crystals.append(superCrystal)
import sys
sys.exit()
else:
print("Can't find an AFM compatible structure")
import sys
sys.exit()
# self.crystals.append(thisCrystal)
delpath = path.join(
enumController.root,
"poscar.{}.{}".format(eDict["name"], rStruct))
remove(delpath)