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
#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<-----------------------------------------------------------------------------------------------------")
<<<<<<< HEAD
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
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)
class VASP:
"""Class to handle all of the VASP input and output files.
Args:
specs (dict or str): Either a dictionary containing all of the
necessary settings or a path to a folder that
contains all of the files needed.
root (str): Path to the calculation folder
incar (dict): Dictionary containing the INCAR tags to be used
potcars (dict): Dictionary containing the necessary settings to
find the correct POTCARS.
<directory> : where the potcars are located
<>
kpoints (dict): KPOINTS settings
crystal (CRYSTAL OBJ): Crystal description
"""
def __init__(self, specs,systemSpecies = None, directory = None):
from aBuild.database.crystal import Crystal
#Initialize from a dictionary
if isinstance(specs,dict):
if self._all_present(specs):
self.POTCAR = POTCAR(specs["potcars"])
self.KPOINTS = KPOINTS(specs["kpoints"])
if isinstance(specs["crystal"],Crystal):
self.crystal = specs["crystal"]
else:
self.crystal = Crystal(specs["crystal"],specs["species"])
self.handleSpecialTags(specs)
self.INCAR = INCAR(specs["incar"])
else:
msg.fatal("I don't have all the necessary information to initialize: {}".format(specs.keys()))
#Initialize from a path
elif isinstance(specs, str):
self.POTCAR = POTCAR(path.join(specs,'POTCAR'))
self.KPOINTS = KPOINTS(path.join(specs,'KPOINTS'))
self.crystal = Crystal(path.join(specs,'POSCAR'),systemSpecies,crystalSpecies = self.POTCAR.species)
self.directory = specs
else:
msg.fatal("Unable to initialize a VASP object from the data that you passed in:", specs)
if directory is not None:
self.directory = directory
def _all_present(self,specs):
required = ["incar","potcars","kpoints","crystal","species"]
for tag in required:
if tag not in specs.keys():
return False
return True
def handleSpecialTags(self,specs):
special = ["AFM","FM"]
if "FM" in specs.keys():
specs["incar"]["ispin"] = 2
specs["incar"]["magmom"] = ''
for idx,species in enumerate(sorted(specs["FM"],reverse = True)):
specs["incar"]["magmom"] += ' '.join(map(str, [ specs["FM"][species] ] * self.crystal.atom_counts[idx]))
specs["incar"]["magmom"] += ' '
elif "AFM" in specs.keys():
if self.crystal.AFMPlanes == None:
self.crystal.getAFMPlanes([1,0,0])
if self.crystal.AFMPlanes == None:
msg.info("You supposedly had an AFM crystal, but I'm not finding the planes")
return
specs["incar"]["ispin"] = 2
#Put in nonzero spin values
specs["incar"]["magmom"] = ' '.join(map(str,self.crystal.AFMPlanes)) + ' '
atomsLeft = self.crystal.nAtoms - len(self.crystal.AFMPlanes)
specs["incar"]["magmom"] += ' '.join(map(str,[0 for x in range(atomsLeft)]))
# VASP does not like to have zeros in the atom_counts list
# but I want to keep track of which atoms are in the crystal.
# This routine is just here to remove any zeros before I write to
# the POSCAR file.
def check_atom_counts_zero(self):
from numpy import array,any
print(self.crystal.atom_counts, 'atom counts')
print(any(self.crystal.atom_counts == 0))
if any(self.crystal.atom_counts == 0):
from numpy import where
idxKeep = list(where( self.crystal.atom_counts > 0)[0])
self.POTCAR.species = list(array(self.POTCAR.species)[idxKeep])
self.crystal.atom_counts = self.crystal.atom_counts[idxKeep]
def _check_tag_exists(self,file,tag):
from aBuild.utility import grep
lines = grep(file,tag)
if lines == []:
return False
else:
return True
def _check_file_exists(self,file):
files = os.listdir('./')
if file in files:
return True
else:
return False
def status(self):
from os import path
from time import time
from aBuild.utility import grep
import os
fTagStatic = '------------------------ aborting loop because EDIFF is reached ----------------------------------------\n'
fTagRelax = ' writing wavefunctions'
ctime = time()
print('checking directory {}'.format(self.directory))
with chdir(self.directory):
outcar = self._check_file_exists('OUTCAR')
incar = self._check_file_exists('INCAR')
kpoints = self._check_file_exists('KPOINTS')
potcar = self._check_file_exists('POTCAR')
poscar = self._check_file_exists('POSCAR')
output = self._check_file_exists('vasp_output')
oszicar = self._check_file_exists('OSZICAR')
inputs = incar and kpoints and potcar and poscar
''' Check to see if the input files are present
if they aren't, no need to proceed, just return
'not setup'
'''
if not inputs:
return 'not setup'
''' If the OUTCAR file is present, we know that we're
either running, finished successfully, or finished
with errors!
'''
elif outcar: # OUTCAR present
sgrcon = grep('vasp_output','SGRCON')
tooclose = grep('vasp_output','HOPE')
finalenergyline = grep('OUTCAR','free energy')
generalerror = grep('vasp_output','ERROR')
# Check to make sure I've converged electonically.
if grep('OSZICAR','DAV:') != []:
electronicIteration = int(grep('OSZICAR','DAV:')[-1].split()[1])
else:
electronicIteration = 0
if grep('INCAR','nsw') != []:
nsw = int(grep('INCAR','nsw')[0].split('=')[1])
if nsw == 0:
nsw = 1
else:
nsw = 1
if grep('OSZICAR','F=') != []:
ionicIteration = int(grep('OSZICAR','F=')[-1].split()[0])
else:
ionicIteration = 1
if grep('INCAR','nelm') != []:
maxelectronic = grep('INCAR','nelm')[0].split('=')[1]
else:
maxelectronic = 60
if ionicIteration == nsw and int(electronicIteration) == int(maxelectronic):
return 'unconverged'
''' Let's first check to see if this is a static
calculation or a relaxation because the tag
to check for is different.'''
if incar:
relax = grep('INCAR','IBRION')
if '-1' not in relax or relax is []:
static = True
else:
static = False
else:
return 'not setup'
''' Check finish tag for static calc'''
if static and self._check_tag_exists('OUTCAR', fTagStatic): #finish tag found
if finalenergyline != []: #Let's double check
return 'done'
else: # Apparently not, why?
return 'idk'
''' Check finish tag for relax calc'''
elif self._check_tag_exists('OUTCAR',fTagRelax): #Looks like it's done
if finalenergyline != []: # Let's double check
return 'done'
else: # Apparently not, why?
return 'idk'
else:
''' Check how long since the last file write. If it was recent
then we're probably running.'''
time = path.getmtime('OUTCAR')
if (ctime - time) < 3600: # If the OUTCAR was modified in the last hour
# the calculation is probably still running.
return 'running'
elif sgrcon:
return 'sgrcon'
elif generalerror:
return 'error'
elif tooclose:
return 'warning'
else:
return 'too long'
else:
return 'not started'
if output:
warning = grep('output','RRRRR') != [] or grep('output','AAAAAA') != []
if warning:
return 'warning'
return folderstat
@staticmethod
def from_file(runpath):
incar = INCAR.from_file(runpath)
kpoint = KPOINTS.from_file(runpath)
potcars = POTCARS.from_file(runpath)
result = VASP(runpath = runpath,incar=incar,kpoints=kpoints,potcars=potcars)
return result
def buildFolder(self,runGetKPoints = True):
from aBuild.calculators.vasp import POSCAR
self.KPOINTS.rGP = runGetKPoints
self.INCAR.writeINCAR()
print("INCAR built")
self.crystal.write('POSCAR_orig')
print("POSCAR_orig built")
self.check_atom_counts_zero()
self.crystal.write('POSCAR')
print("POSCAR built")
self.KPOINTS.writeKPOINTS()
print("KPOINTS built")
self.POTCAR.writePOTCAR()
#print("POTCAR built")
def read_forces(self,allIonic = True):
with open('POSCAR','r') as file:
poslines = file.readlines()
if any(c.isalpha() for c in poslines[5].strip()): #It's a CONTCAR
nAtoms = sum([int(i) for i in poslines[6].split()])
else:
nAtoms = sum([int(i) for i in poslines[5].split()])
with open('OUTCAR', 'r') as file:
lines = file.readlines()
n = 0
if allIonic:
forces = []
n = 0
found = False
for line in lines:
if line.rfind('TOTAL-FORCE') > -1:
found = True
singleItForces = []
for i in range(nAtoms):
singleItForces.append(np.array([float(f) for f in
lines[n + i + 2].split()[3:6]]))
msg.info('Found forces for {} atoms.'.format(nAtoms))
if not '--' in lines[n+nAtoms + 2]:
msg.fatal('It appears that there are forces for more atoms than I was expecting!')
if allIonic:
forces.append(singleItForces)
n+=1
if not found:
msg.info("Couldn't find forces for this calc")
return None
if not allIonic:
forces = singleItForces
if allIonic and len(forces) == 1:
return forces[0]
return forces
def read_fermi(self):
"""Method that reads Fermi energy from OUTCAR file"""
E_f = None
for line in open('OUTCAR', 'r'):
if line.rfind('E-fermi') > -1:
E_f = float(line.split()[2])
return E_f
def read_nbands(self):
for line in open('OUTCAR', 'r'):
line = self.strip_warnings(line)
if line.rfind('NBANDS') > -1:
nBands = int(line.split()[-1])
return nBands
def read_energy(self, allElectronic=False):
energyZ = None
energyF = None
if allElectronic:
energyF = []
energyZ = []
for line in open('OUTCAR', 'r'):
# Free energy
if line.lower().startswith(' free energy toten') or line.lower().startswith(' free energy toten'):
if allElectronic:
energyF.append(float(line.split()[-2]))
else:
energyF = float(line.split()[-2])
# Extrapolated zero point energy
if line.startswith(' energy without entropy'):
if allElectronic:
energyZ.append(float(line.split()[-1]))
else:
energyZ = float(line.split()[-1])
return energyF,energyZ
def read_stress(self):
stress = None
for line in open('OUTCAR'):
if line.find(' in kB ') != -1:
stress = -np.array([float(a) for a in line.split()[2:]])
stress = stress[[0, 1, 2, 4, 5, 3]] * 1e-1 * .00624151# * ase.units.GPa.. Gets me to Giga Pascals
return stress
def read_results(self, allElectronic = False, allIonic=False):
if self.directory is not None and self.status() in ['done','unconverged']:
with chdir(self.directory):
self.crystal.results = {}
self.crystal.results["warning"] = False
self.crystal.results["energyF"],self.crystal.results["energyZ"] = self.read_energy(allElectronic=allElectronic)
self.crystal.results["forces"] = self.read_forces(allIonic=allIonic)
self.crystal.results["stress"] = self.read_stress()
#self.POTCAR = POTCAR.from_POTCAR()
self.crystal.results["species"] = self.POTCAR.species
self.crystal.results["energypatom"] = self.crystal.results["energyF"]/self.crystal.nAtoms
if abs(self.crystal.results["energyF"]) > 1000:
self.crystal.results["warning"] = True
if 'pure' not in self.directory:
self.crystal.results["fEnth"] = self.formationEnergy
else:
self.crystal.results["fEnth"] = 0
else:
print(self.status(), 'not reading results')
self.crystal.results = None
msg.info("Unable to extract necessary information from directory! ({})".format(self.directory))
def add_to_results(self,key,item):
if self.crystal.results is None:
self.crystal.results = {}
self.crystal.results[key] = item
@property
def formationEnergy(self):
pures = []
for i in range(self.crystal.nTypes):
pureDir = path.join(path.split(self.directory)[0], 'pure' + self.crystal.species[i])
pureVASP = VASP(pureDir,systemSpecies = self.crystal.species)
pureVASP.read_results()
pures.append(pureVASP)
try:
formationEnergy = self.crystal.results["energyF"]/self.crystal.nAtoms - sum( [ pures[i].crystal.results["energyF"]/pures[i].crystal.nAtoms * self.crystal.concentrations[i] for i in range(self.crystal.nTypes)])
except:
formationEnergy = 10000
return formationEnergy