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compatibility updates
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@rjacobs914
rjacobs914 committed Oct 10, 2017
1 parent daf5d08 commit f0b413b
Showing 1 changed file with 54 additions and 34 deletions.
88 changes: 54 additions & 34 deletions VASP_Setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@
import gzip
import shutil
import subprocess
import numpy as np
from pymatgen.matproj.rest import MPRester
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.io.vasp.inputs import Poscar
Expand Down Expand Up @@ -179,19 +180,15 @@ def __init__(self):
pass

def write_predefined_incar_file(self, simulation_type, xc_functional, number_of_nodes, cores_per_node,
disable_symmetry, poscar="POSCAR", material_type="insulator", write_chgcar=False,
write_wavecar=False):
disable_symmetry, poscar="POSCAR", material_type="insulator", write_chgcar=False, write_wavecar=False):
if os.path.exists(os.getcwd()+"/"+poscar):
element_names = PoscarAnalyzer(poscar).get_element_names()
else:
raise IOError('No POSCAR file exists in the working directory')

incar_dict = {"ENCUT": 500, "IBRION": 2, "ISMEAR": 0, "ISPIN": 2, "LORBIT": 11, "NEDOS": 2000, "PREC": "Accurate",
"NELM": 250, "TIME": 0.05, "ALGO": "All"}
if not xc_functional == 'HSE':
incar_dict.update(NPAR=number_of_nodes)
if xc_functional == 'HSE':
incar_dict.update(NPAR=number_of_nodes*cores_per_node)
"NELM": 250, "TIME": 0.05, "ALGO": "All", "NPAR": number_of_nodes}

if disable_symmetry == bool(True):
incar_dict.update(ISYM=0)

Expand Down Expand Up @@ -256,8 +253,13 @@ def write_predefined_incar_file(self, simulation_type, xc_functional, number_of_
incar_dict.update(LDAUJ=ldauj_str)
incar_dict.update(LDAUU=ldauu_str)
incar_dict.update(LDAUL=ldaul_str)
elif xc_functional == "PBEsol":
incar_dict.update(GGA="PS")
elif xc_functional == "SCAN":
incar_dict.update(METAGGA="RTPSS")
incar_dict.update(LASPH="True")
else:
raise ValueError('"xc_functional" must be set to one of "GGA", "GGA-PW91", "HSE", or "GGA+U"')
raise ValueError('"xc_functional" must be set to one of "GGA", "GGA-PW91", "HSE", "GGA+U", "PBEsol", or "SCAN"')

incar_file = open("INCAR", "w")
for key, value in incar_dict.items():
Expand Down Expand Up @@ -556,32 +558,43 @@ def make_poscar_supercell(self, scaling_matrix):

def make_poscar_rescaled(self, cell_rescale_dict, is_strained=False):
psr = PoscarAnalyzer(poscar=self.poscar)
lattice_parameters = psr.get_lattice_parameters
atom_positions = psr.get_atom_positions_direct
element_names = psr.get_element_names
atom_amounts = psr.get_atom_amounts
lattice_parameters_old = psr.get_lattice_parameters()
atom_positions = psr.get_atom_positions_direct()
element_names = psr.get_element_names()
atom_amounts = psr.get_atom_amounts()

#lattice_parameters_x = np.array(cell_rescale_dict["x"])
#lattice_parameters_y = np.array(cell_rescale_dict["y"])
#lattice_parameters_z = np.array(cell_rescale_dict["z"])
#print lattice_parameters_x
#print lattice_parameters_y
#print lattice_parameters_z
#lattice_parameters = np.concatenate((lattice_parameters_x, lattice_parameters_y))
#lattice_parameters = np.concatenate((lattice_parameters, lattice_parameters_z))
lattice_parameters = np.array((cell_rescale_dict["x"], cell_rescale_dict["y"], cell_rescale_dict["z"]))
#print lattice_parameters

for key in cell_rescale_dict.keys():
if key == "x":
new_cell_length = float(cell_rescale_dict[key])
old_cell_length = math.sqrt((lattice_parameters[0][0])**2+(lattice_parameters[0][1])**2+(lattice_parameters[0][2])**2)
lattice_parameters[0][0] = lattice_parameters[0][0]*(new_cell_length/old_cell_length)
new_cell_length = math.sqrt((lattice_parameters[0][0])**2+(lattice_parameters[0][1])**2+(lattice_parameters[0][2])**2)
old_cell_length = math.sqrt((lattice_parameters_old[0][0])**2+(lattice_parameters_old[0][1])**2+(lattice_parameters_old[0][2])**2)
#lattice_parameters[0][0] = lattice_parameters[0][0]*(new_cell_length/old_cell_length)
if is_strained == bool(False):
for index in range(len(atom_positions[-1])):
atom_positions[0][index] *= atom_positions[0][index]*(old_cell_length/new_cell_length)

if key == "y":
new_cell_length = float(cell_rescale_dict[key])
old_cell_length = math.sqrt((lattice_parameters[1][0])**2+(lattice_parameters[1][1])**2+(lattice_parameters[1][2])**2)
lattice_parameters[1][1] = lattice_parameters[1][1]*(new_cell_length/old_cell_length)
new_cell_length = math.sqrt((lattice_parameters[1][0])**2+(lattice_parameters[1][1])**2+(lattice_parameters[1][2])**2)
old_cell_length = math.sqrt((lattice_parameters_old[1][0])**2+(lattice_parameters_old[1][1])**2+(lattice_parameters_old[1][2])**2)
#lattice_parameters[1][1] = lattice_parameters[1][1]*(new_cell_length/old_cell_length)
if is_strained == bool(False):
for index in range(len(atom_positions[-1])):
atom_positions[1][index] = atom_positions[1][index]*(old_cell_length/new_cell_length)

if key == "z":
new_cell_length = float(cell_rescale_dict[key])
old_cell_length = math.sqrt((lattice_parameters[2][0])**2+(lattice_parameters[2][1])**2+(lattice_parameters[2][2])**2)
lattice_parameters[2][2] = lattice_parameters[2][2]*(new_cell_length/old_cell_length)
new_cell_length = math.sqrt((lattice_parameters[2][0])**2+(lattice_parameters[2][1])**2+(lattice_parameters[2][2])**2)
old_cell_length = math.sqrt((lattice_parameters_old[2][0])**2+(lattice_parameters_old[2][1])**2+(lattice_parameters_old[2][2])**2)
#lattice_parameters[2][2] = lattice_parameters[2][2]*(new_cell_length/old_cell_length)
if is_strained == bool(False):
for index in range(len(atom_positions[-1])):
atom_positions[2][index] = atom_positions[2][index]*(old_cell_length/new_cell_length)
Expand All @@ -604,10 +617,16 @@ def make_poscar_rescaled(self, cell_rescale_dict, is_strained=False):
poscar_scaled.write(str(lattice_parameters[2][0])+" "+str(lattice_parameters[2][1])+" "+str(lattice_parameters[2][2])+"\n")
line_count += 1
if line_count == 5:
poscar_scaled.write(str(element_names[0])+" "+str(element_names[1])+" "+str(element_names[2])+"\n")
#poscar_scaled.write(str(element_names[0])+" "+str(element_names[1])+" "+str(element_names[2])+"\n")
for element_name in element_names:
poscar_scaled.write(str(element_name)+" ")
poscar_scaled.write("\n")
line_count += 1
if line_count == 6:
poscar_scaled.write(str(atom_amounts[0])+" "+str(atom_amounts[1])+" "+str(atom_amounts[2])+"\n")
for atom_amount in atom_amounts:
poscar_scaled.write(str(atom_amount)+" ")
#poscar_scaled.write(str(atom_amounts[0])+" "+str(atom_amounts[1])+" "+str(atom_amounts[2])+"\n")
poscar_scaled.write("\n")
line_count += 1
if line_count == 7:
poscar_scaled.write("Selective Dynamics"+"\n")
Expand Down Expand Up @@ -647,7 +666,7 @@ def make_poscar_with_dopants(self, doping_type, doping_scheme, oxidation_states=
return poscar

def make_poscar_with_vacancy(self, vacancy_species, max_supercell_size):
element_names = PoscarAnalyzer(poscar=self.poscar).get_element_names
element_names = PoscarAnalyzer(poscar=self.poscar).get_element_names()
count = 1
structure = Structure.from_file(self.poscar)
poscar_list = []
Expand Down Expand Up @@ -683,8 +702,8 @@ def make_poscar_slab(self, surface_hkl, minimum_thickness, minimum_vacuum=20, sh
poscar.write_file(poscar_placeholder)

psr = PoscarAnalyzer(poscar=poscar_placeholder)
atom_coordinates = psr.get_atom_positions_direct
total_atoms = psr.get_total_atoms
atom_coordinates = psr.get_atom_positions_direct()
total_atoms = psr.get_total_atoms()
atom_coord_min = min(atom_coordinates[2])
for index in range(len(atom_coordinates[2])):
atom_coordinates[2][index] -= atom_coord_min
Expand Down Expand Up @@ -719,7 +738,7 @@ def trim_poscar_slab(self, surface_trimming_dict, atom_position_tolerance = 0.01
# Keep removing layers until the desired number of layers has been reached
while surface_layer_count < surface_trimming_dict[key]:
poscar_slab = open(self.poscar, "r")
element_names = PoscarAnalyzer(poscar=self.poscar).get_element_names
element_names = PoscarAnalyzer(poscar=self.poscar).get_element_names()
list_z_coords = []; list_z_coords_unique = []; trimmed_slab_coords = [];
# Specify where coordinates start in POSCAR, whether SD has been specified or not
line_where_coords_start = 8
Expand Down Expand Up @@ -763,10 +782,10 @@ def trim_poscar_slab(self, surface_trimming_dict, atom_position_tolerance = 0.01
for entry in element_names:
atom_count = 0
for line in trimmed_slab_coords:
if entry in line:
atom_count += 1
#if entry in line:
atom_count += 1
atom_count_list.append(atom_count)
print atom_count_list
#print atom_count_list

poscar_slab = open(self.poscar, "r")
line_count = 0
Expand All @@ -789,7 +808,7 @@ def trim_poscar_slab(self, surface_trimming_dict, atom_position_tolerance = 0.01

poscar_slab_trimmed.close()
poscar_slab.close()
shutil.move(os.getcwd() + "/" + poscar_placeholder, os.getcwd() + "/" + self.poscar)
shutil.move(os.getcwd() + "/" + "POSCAR_placeholder", os.getcwd() + "/" + "POSCAR")
surface_layer_count += 1
structure = Structure.from_file(self.poscar)
poscar = Poscar(structure=structure)
Expand All @@ -798,13 +817,13 @@ def trim_poscar_slab(self, surface_trimming_dict, atom_position_tolerance = 0.01
def add_selective_dynamics(self, number_of_layers, top_and_bottom = True, layer_thickness=2.0):
#Typically a z_tolerance equal to 0.5*layer_spacing - delta will make a single layer marked "T T T".
pa = PoscarAnalyzer(poscar=self.poscar)
lattice_parameters = pa.get_lattice_parameters
lattice_parameters = pa.get_lattice_parameters()
# Normalize layer thickness by c lattice parameter
layer_thickness = layer_thickness/math.sqrt(lattice_parameters[2][0]**2+lattice_parameters[2][1]**2+lattice_parameters[2][2]**2)
#delta = 0.25*layer_thickness
#z_tolerance = (0.5*layer_thickness) + (layer_thickness*(number_of_layers-1)) - delta
z_tolerance = (0.5*layer_thickness) + (layer_thickness*(number_of_layers-1))
atom_positions = pa.get_atom_positions_direct
atom_positions = pa.get_atom_positions_direct()

# Create selective dynamics selection based on z-axis atom position
z_coords = []
Expand Down Expand Up @@ -859,7 +878,8 @@ def add_selective_dynamics(self, number_of_layers, top_and_bottom = True, layer_

poscar_nosd.close()
poscar_sd.close()
shutil.move(os.getcwd() + "/" + str(poscar_sd), os.getcwd() + "/" + self.poscar)
#shutil.move(os.getcwd() + "/" + str(poscar_sd), os.getcwd() + "/" + self.poscar)
shutil.move(os.getcwd() + "/" + "POSCAR_placeholder", os.getcwd() + "/" + "POSCAR")
structure = Structure.from_file(self.poscar)
poscar = Poscar(structure=structure)
return poscar
Expand Down

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