def build_ToRelax(self, enumDicts, 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')
print(enumDicts)
nEnums = len(enumDicts)
knary = len(species)
for ilat in range(nEnums):
lat = enumDicts[ilat]["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=enumDicts[ilat]["concs"]):
continue
print(thisCrystal.title)
mindist = thisCrystal.minDist
print(
mindist,
"actual min dist<-----------------------------------------------------------------------------------------------------"
)
if mindist > 2 and thisCrystal.nAtoms < 60:
if not AFM:
print('Adding to file')
#print("Atom counts after scramble {}".format(thisCrystal.atom_counts))
with open(path.join(self.root, 'to-relax.cfg'),
'a+') as f:
f.writelines('\n'.join(
thisCrystal.lines('mtprelax')))
elif thisCrystal.getAFMPlanes([1, 0, 0]):
print("Original Crystal is AFM compatible")
with open(
path.join(self.root, 'to-relax.cfg_' +
str(start)), 'a+') as f:
f.writelines('\n'.join(
thisCrystal.lines('mtprelax')))
# break
else:
print("Checking super-periodics")
superCrystal = thisCrystal.superPeriodics(2)
if superCrystal != []:
print('Found a super-Periodic that works')
print(superCrystal.basis, 'basis')
print(superCrystal.atom_counts,
'atom counts')
with open(
path.join(
self.root,
'to-relax.cfg_' + str(start)),
'a+') as f:
f.writelines('\n'.join(
superCrystal.lines('mtprelax')))
# break
else:
enumLattice = Enumerate(enumDicts[ilat])
print(end, 'end')
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("Lattice", lat, "structure:", struct)
enumLattice.generatePOSCAR(struct)
thisCrystal = Crystal(
path.join(enumLattice.root,
"poscar.{}.{}".format(lat, struct)), species)
if not AFM:
print('Writing to file!!!!!', end)
with open(
path.join(self.root, 'to_relax.cfg' + filetag),
'a+') as f:
f.writelines('\n'.join(
thisCrystal.lines('mtprelax')))
elif thisCrystal.getAFMPlanes([1, 0, 0]):
print("Original Crystal is AFM compatible")
with open(
path.join(self.root, 'to_relax.cfg' + filetag),
'a+') as f:
f.writelines('\n'.join(
thisCrystal.lines('mtprelax')))
else:
print("Checking super-periodics")
superCrystal = thisCrystal.superPeriodics(2)
if superCrystal != []:
print('Found a super-Periodic that works')
with open(
path.join(self.root,
'to_relax.cfg' + filetag),
'a+') as f:
f.writelines('\n'.join(
superCrystal.lines('mtprelax')))
# print(thisCrystal.appMinDist,' approp Min Dist')
# print(thisCrystal.minDist, 'actual min dist')
# with open(path.join(self.root,'to-relax.cfg'),'a+') as f:
# f.writelines('\n'.join(thisCrystal.lines('mtprelax') ))
delpath = path.join(enumLattice.root,
"poscar.{}.{}".format(lat, struct))
remove(delpath)
end = None
if mindist > 2 and thisCrystal.nAtoms < 60:
if not AFM:
print('Adding to file')
#print("Atom counts after scramble {}".format(thisCrystal.atom_counts))
with open(path.join(self.root,'to-relax.cfg'),'a+') as f:
f.writelines('\n'.join(thisCrystal.lines('mtprelax') ) )
elif thisCrystal.getAFMPlanes([1,0,0]):
print("Original Crystal is AFM compatible")
with open(path.join(self.root,'to-relax.cfg_' + str(start)),'a+') as f:
f.writelines('\n'.join(thisCrystal.lines('mtprelax') ))
# break
else:
print("Checking super-periodics")
superCrystal = thisCrystal.superPeriodics(2)
if superCrystal != []:
print('Found a super-Periodic that works')
print(superCrystal.basis,'basis')
print(superCrystal.atom_counts, 'atom counts')
with open(path.join(self.root,'to-relax.cfg_' + str(start)),'a+') as f:
f.writelines('\n'.join(superCrystal.lines('mtprelax') ))
# break
=======
print(thisCrystal.appMinDist, 'appropriate min distance')
################################### my changes ################################################################
# thisCrystal.validateCrystal()
if self.special_settings["AFM"]: #if there's a AFM dictionary passed in with special_settings
print("Checking if this structure can be AFM")
AFMsuccess = thisCrystal.checkAFM(self.special_settings["AFM"]["plane"],self.special_settings["AFM"]["spin_type"])#,self.special_settings["eps"] )
if not AFMsuccess:
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)
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))