def __init__(self,input):
#import structure from PYMATGEN
self.key = input.APIKEY # Import API key from input
self.MaterialID = input.MATERIALID # Set class variable MaterialID from input
self.cutoff = input.ECUT
self.Ecut = input.ECUT #Class variable; in Ryberg, transfer from input file
self.kpts = input.KMESH ### KPTS from input file for a generator, class variable
#self.pseudodir = "ABINIT/ABINITPP/ATOMICDATA/" # Set the directory for pseudopotentials
self.EMAIL = input.Email #Class variable; set email for SLURM from input file
self.NCORE = input.ncore #Class Variable; number of cores, taken from input file
self.SOC = input.SOC
self.nbnd = input.NUMBANDS
self.lspinorb = '.FALSE.'
if input.SOC:
self.noncolin = '.TRUE.'
self.lspinorb = '.TRUE.'
selectconventional = input.conventional_cell
selectrelax = input.Relax
with matproj.MPRester(self.key) as m:
struct = m.get_structure_by_material_id(self.MaterialID,final=selectrelax,conventional_unit_cell=selectconventional) # GET STRUCT FROM MATERIALS PROJECT
self.struct = m.get_structure_by_material_id(self.MaterialID,final=selectrelax,conventional_unit_cell=selectconventional) # GET STRUCT FROM MATERIALS PROJECT
C = Composition(str(struct.formula))
self.seedname = str(input.seedname) # set class variable SEEDNAME from input file
self.SEEDDIR = "OUTPUT/" + 'S-' + self.seedname + '/' #set the seed directory
# MAKE DIRECTORIES
if not os.path.exists(self.SEEDDIR):
os.makedirs(self.SEEDDIR)
if not os.path.exists(self.SEEDDIR + "WT"):
os.makedirs(self.SEEDDIR + "WT")
##### Set variables
self.UNIQUE_ATOMS = np.unique(struct.species)
self.cord = struct.frac_coords
self.ntypat = np.unique(struct.atomic_numbers).size
self.natom = np.array(struct.atomic_numbers).size
self.numlist = np.array(struct.atomic_numbers)[::1]
self.atomnum = np.unique(struct.atomic_numbers)[::1]
self.typat = ""
for x in struct.atomic_numbers:
for at in self.atomnum:
if at == x:
self.typat += ''.join(map(str,np.where(self.atomnum == at)
[0] + 1)) + " "
# SOC CASE
num_bands = input.NUMBANDS
# for x in struct.species:
# PP = gb.glob(self.pseudodir + str(x) + ".*")
# readpp = minidom.parse(''.join(map(str,PP)))
# items = readpp.getElementsByTagName('atom')
# num_bands += float(items[0].attributes['valence'].value)
num_wann = num_bands - (num_bands%2) # FORCE EVEN
self.wan = num_wann
if self.SOC:
self.WTwan = self.wan/2
else:
self.WTwan = self.wan
import pandas as pd
from pymatgen.ext import matproj
from pymatgen.core import periodic_table
import util
if __name__ == '__main__':
# path
output_filepath = './query_result.csv'
elementgroup_dict = util.element_of_interest()
# open restful interface
with matproj.MPRester(api_key='9bASScRXuQNDSebS') as m:
# build criteria
criteria = {
'elements': {
'$in': elementgroup_dict['transition_metal'],
'$in': elementgroup_dict['chalcogen'],
'$nin': elementgroup_dict['others'],
},
'nelements': {
'$in': [2, 3]
},
}
properties = ['material_id', 'pretty_formula', 'spacegroup', 'nsites']
result = m.query(criteria=criteria, properties=properties)
record = [{
'material_id': row['material_id'],
def __init__(self, input):
#self.CIFDIR = "cifdir/"
self.key = input.APIKEY # Import API key from input
self.MaterialID = input.MATERIALID # Set class variable MaterialID from input
self.seedname = str(
input.seedname) # set class variable SEEDNAME from input file
self.Ecut = input.ECUT #Class variable; in Ryberg, transfer from input file
self.kpts = input.KMESH ### KPTS from input file for a generator, class variable
self.SEEDDIR = "OUTPUT/" + 'Abi-' + self.seedname + '/' #set the seed directory
self.pseudodir = "Pseudopotentials/ABINIT/ATOMICDATA/" # Set the directory for pseudopotentials
self.EMAIL = input.Email #Class variable; set email for SLURM from input file
self.NCORE = input.ncore #Class Variable; number of cores, taken from input file
self.SOC = input.SOC
selectconventional = input.conventional_cell
selectrelax = input.Relax
# MAKE DIRECTORIES
if not os.path.exists(self.SEEDDIR):
os.makedirs(self.SEEDDIR)
if not os.path.exists(self.SEEDDIR + "PP"):
os.makedirs(self.SEEDDIR + "PP")
if not os.path.exists(self.SEEDDIR + "WT"):
os.makedirs(self.SEEDDIR + "WT")
#import structure from PYMATGEN
with matproj.MPRester(self.key) as m:
struct = m.get_structure_by_material_id(
self.MaterialID,
final=selectrelax,
conventional_unit_cell=selectconventional
) # GET STRUCT FROM MATERIALS PROJECT
self.struct = m.get_structure_by_material_id(
self.MaterialID,
final=selectrelax,
conventional_unit_cell=selectconventional
) # GET STRUCT FROM MATERIALS PROJECT
C = Composition(str(struct.formula))
########## MAKE A CIF FILE ###
# cif = CifWriter(struct) # Start generator
# cif.write_file(self.CIFDIR + self.seedname + ".cif") #write cif file to directory
# ciffile = self.CIFDIR + self.seedname + ".cif" # define ciffile
# cif = open(ciffile) # open cif file
# parser = CifParser(ciffile) #Start Parser
self.lattice = struct.lattice
self.a = self.lattice.a
self.b = self.lattice.b
self.c = self.lattice.c
self.alpha = self.lattice.alpha
self.beta = self.lattice.beta
self.gamma = self.lattice.gamma
self.UNIQUE_ATOMS = np.unique(struct.species)
self.cord = struct.frac_coords
self.ntypat = np.unique(struct.atomic_numbers).size
self.natom = np.array(struct.atomic_numbers).size
self.atomnum = np.unique(struct.atomic_numbers)[::1]
# It has to be done this way, otherwise format would be off
self.typat = ""
for x in struct.atomic_numbers:
for at in self.atomnum:
if at == x:
self.typat += ''.join(
map(str,
np.where(self.atomnum == at)[0] + 1)) + " "
# SOC CASE
num_bands = 0
for x in struct.species:
PP = gb.glob(self.pseudodir + str(x) + ".*")
readpp = minidom.parse(''.join(map(str, PP)))
items = readpp.getElementsByTagName('atom')
num_bands += float(items[0].attributes['valence'].value)
num_wann = num_bands - (num_bands % 2) # FORCE EVEN
self.wan = num_wann
self.WTwan = num_wann
if self.SOC:
self.WTwan = self.wan / 2
def __init__(self):
self.CIFDIR = "cifdir/"
self.key = input.APIKEY # Import API key from input
self.MaterialID = input.MATERIALID # Set class variable MaterialID from input
self.seedname = str(
input.SEEDNAME) # set class variable SEEDNAME from input file
self.Ecut = input.ECUT #Class variable; in Ryberg, transfer from input file
self.kpts = input.KMESH ### KPTS from input file for a generator, class variable
self.SEEDDIR = "OUTPUT/" + 'STA-' + self.seedname + '/' #set the seed directory
#self.pseudodir = "ABINIT/ABINITPP/ATOMICDATA/" # Set the directory for pseudopotentials
self.EMAIL = input.EMAIL #Class variable; set email for SLURM from input file
self.NCORE = input.ncore #Class Variable; number of cores, taken from input file
self.SOC = input.SOC
self.nbnd = input.NUMBANDS
# MAKE DIRECTORIES
if not os.path.exists(self.SEEDDIR):
os.makedirs(self.SEEDDIR)
if not os.path.exists(self.SEEDDIR + "WT"):
os.makedirs(self.SEEDDIR + "WT")
#import structure from PYMATGEN
with matproj.MPRester(self.key) as m:
struct = m.get_structure_by_material_id(
self.MaterialID, final=True, conventional_unit_cell=False
) # GET STRUCT FROM MATERIALS PROJECT
self.struct = m.get_structure_by_material_id(
self.MaterialID, final=True, conventional_unit_cell=False
) # GET STRUCT FROM MATERIALS PROJECT
C = Composition(str(struct.formula))
########## MAKE A CIF FILE ###
cif = CifWriter(struct) # Start generator
cif.write_file(self.CIFDIR + self.seedname +
".cif") #write cif file to directory
ciffile = self.CIFDIR + self.seedname + ".cif" # define ciffile
cif = open(ciffile) # open cif file
parser = CifParser(ciffile) #Start Parser
####### PARSE VARIABLES FROM CIF ##########
chk_a = "_cell_length_a"
chk_b = "_cell_length_b"
chk_c = "_cell_length_c"
chk_alpha = "_cell_angle_alpha"
chk_beta = "_cell_angle_beta"
chk_gamma = "_cell_angle_gamma"
chk_name = "_chemical_formula_structural"
for x in cif:
if chk_a in x:
self.a = x.replace(chk_a, '').replace('\n', '')
if chk_b in x:
self.b = x.replace(chk_b, '').replace('\n', '')
if chk_c in x:
self.c = x.replace(chk_c, '').replace('\n', '')
if chk_alpha in x:
self.alpha = x.replace(chk_alpha, '').replace('\n', '')
if chk_beta in x:
self.beta = x.replace(chk_beta, '').replace('\n', '')
if chk_gamma in x:
self.gamma = x.replace(chk_gamma, '').replace('\n', '')
#if chk_name in x:
# seedname = x.replace(chk_name, '')
# seedname = seedname.replace('\n', '').translate(
# {ord(i): None for i in ' '})
self.UNIQUE_ATOMS = np.unique(struct.species)
self.cord = struct.frac_coords
self.ntypat = np.unique(struct.atomic_numbers).size
self.natom = np.array(struct.atomic_numbers).size
self.numlist = np.array(struct.atomic_numbers)[::1]
self.atomnum = np.unique(struct.atomic_numbers)[::1]
self.typat = ""
for x in struct.atomic_numbers:
for at in self.atomnum:
if at == x:
self.typat += ''.join(
map(str,
np.where(self.atomnum == at)[0] + 1)) + " "
# SOC CASE
num_bands = input.NUMBANDS
# for x in struct.species:
# PP = gb.glob(self.pseudodir + str(x) + ".*")
# readpp = minidom.parse(''.join(map(str,PP)))
# items = readpp.getElementsByTagName('atom')
# num_bands += float(items[0].attributes['valence'].value)
num_wann = num_bands - (num_bands % 2) # FORCE EVEN
self.wan = num_wann
if self.SOC:
self.WTwan = self.wan / 2