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 build_ToRelax(self, enums, species, AFM=False, start=1, end=None):
from aBuild.enumeration import Enumerate
from aBuild.utility import unpackProtos, getAllPerms, getProtoPaths
from aBuild.database.crystal import Crystal
from os import remove, path
print('Building to_relax.cfg')
nEnums = len(enums)
knary = len(species)
for ilat in range(nEnums):
lat = enums[ilat].lattice.lattice_name
if lat == 'protos':
structures = getProtoPaths(knary)
for struct in structures:
print("Proto structure:", struct)
scrambleOrder = getAllPerms(knary,
justCyclic='uniqueUnaries'
in struct)
for scramble in scrambleOrder:
thisCrystal = Crystal(struct, species)
#print("Atom counts before scramble {}".format(thisCrystal.atom_counts))
thisCrystal.scrambleAtoms(scramble)
if not thisCrystal.concsOK(
concRestrictions=enums[ilat]["concs"]):
continue
mindist = thisCrystal.minDist
if mindist > 2:
with open(path.join(self.root, 'to_relax.cfg'),
'a+') as f:
f.writelines('\n'.join(
thisCrystal.lines('mtprelax')))
else:
enumLattice = enums[ilat]
if end == None:
end = enumLattice.nConfigs + 1
filetag = ''
else:
filetag = '_' + str(start)
#for struct in range(enumLattice.nConfigs+1):
for struct in range(start, end):
print("Generating {} crystal structure # {}.".format(
lat, struct))
enumLattice.generatePOSCAR(struct)
# When initializing a crystal object from a poscar generated by makestr.x, I know that the crystal species is
# the same as the system species because it generates zeros in the atom counts list.
print('initializing object')
thisCrystal = Crystal.from_poscar(
path.join(enumLattice.root,
"poscar.{}.{}".format(lat, struct)), species)
thisCrystal.set_latpar(modify=enumLattice.latticeExpand)
with open(path.join(self.root, 'to_relax.cfg' + filetag),
'a+') as f:
f.writelines('\n'.join(thisCrystal.lines('mtprelax')))
delpath = path.join(enumLattice.root,
"poscar.{}.{}".format(lat, struct))
remove(delpath)