def step1():
"""
get substrate bulk structures from materialsproject for
Pt, Ag, Cu, Ni, Al, Au, Pd, Ir and do 3d relaxation(ISIF=3)
get 2d structures from the provided poscars(just poscar_graphene)
and relax in x and y only(vasp_noz bin)
- POSCAR_graphene must be made available in the directory
- creates required input files and submits the jobs to the que
- 8 + 1 jobs
- returns: step1_sub.json step1_2d.json
"""
#job directory for the runs
job_dir_sub = 'step1_sub'
job_dir_2d = 'step1_2d'
# create list of all substrate poscars
poscars_sub = []
poscars_2d = []
# substrate structures
for sub in substrates:
struct_sub = get_struct_from_mp(sub)
sa_sub = SpacegroupAnalyzer(struct_sub)
struct_sub = sa_sub.get_conventional_standard_structure()
poscars_sub.append(Poscar(struct_sub))
# 2d structures
for td in mat2ds:
poscars_2d.append(Poscar.from_file(td))
# setup calibrate and run'em
turn_knobs_sub = OrderedDict(
[
('POSCAR', poscars_sub)
])
turn_knobs_2d = OrderedDict(
[
('POSCAR', poscars_2d)
])
# normal binary
qadapter_sub, job_cmd_sub = get_run_cmmnd(nnodes=nnodes, nprocs=nprocs,
walltime=walltime,
job_bin=bin_sub, mem=mem)
# binary with z constraint
qadapter_2d, job_cmd_2d = get_run_cmmnd(nnodes=nnodes, nprocs=nprocs,
walltime=walltime,
job_bin=bin_2d, mem=mem)
run_cal(turn_knobs_sub, qadapter_sub, job_cmd_sub, job_dir_sub,
'step1_sub', incar=incar_sub, kpoints=kpoints_sub)
run_cal(turn_knobs_2d, qadapter_2d, job_cmd_2d, job_dir_2d,
'step1_2d', incar=incar_2d, kpoints=kpoints_2d)
return ['step1_sub.json', 'step1_2d.json']
#-----------------------------------
#nanopartcle specifications
#-----------------------------------
#max radius in angstroms
rmax = 15
#surface families to be chopped off
hkl_family = [(1, 0, 0), (1, 1, 1)]
#surfac energies could be in any units, will be normalized
surface_energies = [28, 25]
#-----------------------------------
#intial structure
#-----------------------------------
#caution: set the structure wrt which the the miller indices are
#specified. use your own key
structure = get_struct_from_mp('PbS', MAPI_KEY="")
#primitve ---> conventional cell
sa = SpacegroupAnalyzer(structure)
structure_conventional = sa.get_conventional_standard_structure()
#-----------------------------------
# create nanoparticle
#-----------------------------------
nanoparticle = Nanoparticle(structure_conventional,
rmax=rmax,
hkl_family=hkl_family,
surface_energies=surface_energies)
nanoparticle.create()
nanoparticle.to(fmt='xyz', filename='nanoparticle.xyz')
from mpinterfaces.nanoparticle import Nanoparticle
# -----------------------------------
# nanoparticle specifications
# -----------------------------------
# max radius in angstroms
rmax = 15
# surface families to be chopped off
hkl_family = [(1, 0, 0), (1, 1, 1)]
# surfac energies could be in any units, will be normalized
surface_energies = [28, 25]
# -----------------------------------
# initial structure
# -----------------------------------
# caution: set the structure wrt which the the miller indices are
# specified. use your own key
structure = get_struct_from_mp('PbS', MAPI_KEY="")
# primitive ---> conventional cell
sa = SpacegroupAnalyzer(structure)
structure_conventional = sa.get_conventional_standard_structure()
# -----------------------------------
# create nanoparticle
# -----------------------------------
nanoparticle = Nanoparticle(structure_conventional, rmax=rmax,
hkl_family=hkl_family,
surface_energies=surface_energies)
nanoparticle.create()
nanoparticle.to(fmt='xyz', filename='nanoparticle.xyz')
def get_structures():
for species in structures:
struct_species = get_struct_from_mp(species)
poscar_list.append(Poscar(struct_species))
return None
# coding: utf-8
# Copyright (c) Henniggroup.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals, print_function
import os
import sys
from collections import OrderedDict
from mpinterfaces import get_struct_from_mp
from mpinterfaces.lammps import CalibrateLammps
from mpinterfaces.utils import get_run_cmmnd
# list of structures from materialsproject
structures = get_struct_from_mp('ZnO', all_structs=True)
# scale the structures
scell_size = 12
for s in structures:
a, b, c = s.lattice.abc
s.make_supercell([int(scell_size / a),
int(scell_size / b),
int(scell_size / c)])
# lammps input paramaters
parameters = {'atom_style': 'charge',
'charges': {'Zn': 2, 'O': -2},
'minimize': '1.0e-13 1.0e-20 1000 10000',
'fix': ['fix_nve all nve',
'1 all box/relax aniso 0.0 vmax 0.001',
'1a all qeq/comb 1 0.0001 file fq.out']}
# list of pair styles
matplotlib.use('Agg')
from pymatgen.core.composition import Composition
from pymatgen.phasediagram.entries import PDEntry
from pymatgen.phasediagram.pdmaker import PhaseDiagram
from pymatgen.phasediagram.plotter import PDPlotter
from mpinterfaces import get_struct_from_mp
from mpinterfaces.lammps import CalibrateLammps
from mpinterfaces.utils import *
# all the info/warnings/outputs redirected to the log file:
# lammps_Al_O.log
logger = get_logger('lammps_Al_O')
# list of structures from materialsproject
structures = get_struct_from_mp('Al-O', all_structs=True)
# scale the structures
scell_size = 12
for s in structures:
a, b, c = s.lattice.abc
s.make_supercell(
[ceil(scell_size / a),
ceil(scell_size / b),
ceil(scell_size / c)])
# lammps input paramaters
parameters = {
'atom_style':
'charge',
'charges': {
'Al': 0,
'O': 0
import sys
from math import sqrt
from collections import OrderedDict
import numpy as np
from pymatgen.io.vasp.inputs import Incar, Poscar
from pymatgen.io.vasp.inputs import Potcar, Kpoints
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from mpinterfaces import get_struct_from_mp, Interface
from mpinterfaces.calibrate import Calibrate, CalibrateSlab
from mpinterfaces.utils import get_run_cmmnd
MAPI_KEY = os.environ.get("MAPI_KEY", "")
#get structure from materialsproject, use your own key
strt = get_struct_from_mp('PbS', MAPI_KEY=MAPI_KEY)
#convert from fcc primitive to conventional cell
#the conventional unit cell is used to create the slab
#this is important becasue the hkl specification for the required slab
#is wrt the provided unit cell
sa = SpacegroupAnalyzer(strt)
structure_conventional = sa.get_conventional_standard_structure()
strt = structure_conventional.copy()
#create slab
iface = Interface(strt, hkl=[1,1,1],
min_thick=10, min_vac=10,
supercell=[1,1,1])
# sort structure into groups of elements atoms for Potcar mapping
iface.sort()
# vasp input
incar_dict = {
from __future__ import division, unicode_literals, print_function
import os
import sys
from collections import OrderedDict
from mpinterfaces import get_struct_from_mp
from mpinterfaces.lammps import CalibrateLammps
from mpinterfaces.utils import get_run_cmmnd
# list of structures from materialsproject
structures = get_struct_from_mp("ZnO", all_structs=True)
# scale the structures
scell_size = 12
for s in structures:
a, b, c = s.lattice.abc
s.make_supercell([int(scell_size / a), int(scell_size / b), int(scell_size / c)])
# lammps input paramaters
parameters = {
"atom_style": "charge",
"charges": {"Zn": 2, "O": -2},
"minimize": "1.0e-13 1.0e-20 1000 10000",
"fix": ["fix_nve all nve", "1 all box/relax aniso 0.0 vmax 0.001", "1a all qeq/comb 1 0.0001 file fq.out"],
}
# list of pair styles
pair_styles = ["comb3 polar_off"]
# list of pair coefficient files
pair_coeff_files = [os.path.join(os.getcwd(), "ffield.comb3")]
# parameters tuned: structures, pair styles and pair coefficients
turn_knobs = OrderedDict([("STRUCTURES", structures), ("PAIR_STYLES", pair_styles), ("PAIR_COEFFS", pair_coeff_files)])
# job directory and run settings
def get_grain_boundary_interface(structure=None, hkl_pair= {'hkl': [[1,0,0],[1,1,0]],\
'thickness':[10,10]}, twist = 0, tilt = 0, separation=0):
"""
Args:
structure: pymatgen structure to create grain boundary in
hkl_pair: dict of {'hkl':thickness}
twist: twist in degrees
tilt: tilt in degrees
"""
structure = get_struct_from_mp(structure, MAPI_KEY="")
sa = SpacegroupAnalyzer(structure)
structure_conventional = sa.get_conventional_standard_structure()
structure = structure_conventional.copy()
structure.sort()
#creation of lower part of grain boundary
lower= Interface(structure,\
hkl = hkl_pair['hkl'][0],
min_thick = hkl_pair['thickness'][0],
min_vac = separation+hkl_pair['thickness'][1],
primitive = False, from_ase = True, center_slab=False)
lower.to(fmt="poscar", filename="POSCAR_lower.vasp")
#creation of upper part of grain boundary
upper= Interface(structure,\
hkl = hkl_pair['hkl'][1],
min_thick = hkl_pair['thickness'][1],
min_vac = 0,
primitive = False, from_ase = True)
#find top atoms reference of lower part of gb
substrate_top_z = np.max(np.array([site.coords for site in lower])[:, 2])
# define twist and tilt vectors
twist_shift_normal = lower.lattice.matrix[2,:]/\
np.linalg.norm(lower.lattice.matrix[2,:])
tilt_normal = upper.lattice.matrix[1,:]/\
np.linalg.norm(upper.lattice.matrix[2,:])
#define twist operation SymmOp object
twist_op = SymmOp.from_axis_angle_and_translation(axis= twist_shift_normal,\
angle=twist, angle_in_radians=False,translation_vec=(0, 0, 0))
#define tilt operation SymmOp object
tilt_op = SymmOp.from_axis_angle_and_translation(axis= tilt_normal,\
angle=tilt, angle_in_radians=False,translation_vec=(0, 0, 0))
upper.apply_operation(twist_op)
upper.to(fmt="poscar", filename="POSCAR_upper.vasp")
upper.apply_operation(tilt_op)
#define shift separation along twist vector normal to upper plane
shift = -1 * twist_shift_normal / np.linalg.norm(
twist_shift_normal) * separation
#define origin to shift w.r.t top of the lower grain
origin = np.array([0, 0, substrate_top_z])
#shift sites in upper
for site in upper:
new_coords = site.coords - origin + shift
lower.append(site.specie, new_coords, coords_are_cartesian=True)
return lower
# new_sites = [site for k, site in enumerate(mol) if k not in remove_sites]
# return Molecule.from_sites(new_sites)
if __name__ == '__main__':
# nanopartcle settings
# max radius in angstroms
rmax = 15
# surface families to be chopped off
surface_families = [(1, 0, 0), (1, 1, 1)]
# could be in any units, will be normalized
surface_energies = [28, 25]
# caution: set the structure wrt which the the miller indices are specified
# use your own API key
structure = get_struct_from_mp('PbS')
# primitve ---> conventional cell
sa = SpacegroupAnalyzer(structure)
structure_conventional = sa.get_conventional_standard_structure()
nanoparticle = Nanoparticle(structure_conventional,
rmax=rmax,
hkl_family=surface_families,
surface_energies=surface_energies)
nanoparticle.create()
nanoparticle.to(fmt='xyz', filename='nanoparticle.xyz')
"""
Wulff construction using the ASE package
works only for cubic systems and doesn't support multiatom basis
from ase.cluster import wulff_construction
import sys
from math import sqrt
from collections import OrderedDict
import numpy as np
from pymatgen.io.vasp.inputs import Incar, Poscar
from pymatgen.io.vasp.inputs import Potcar, Kpoints
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from mpinterfaces import get_struct_from_mp, Interface
from mpinterfaces.calibrate import Calibrate, CalibrateSlab
from mpinterfaces.utils import get_run_cmmnd
MAPI_KEY = os.environ.get("MAPI_KEY", "")
#get structure from materialsproject, use your own key
strt = get_struct_from_mp('PbS', MAPI_KEY=MAPI_KEY)
#convert from fcc primitive to conventional cell
#the conventional unit cell is used to create the slab
#this is important becasue the hkl specification for the required slab
#is wrt the provided unit cell
sa = SpacegroupAnalyzer(strt)
structure_conventional = sa.get_conventional_standard_structure()
strt = structure_conventional.copy()
#create slab
iface = Interface(strt,
hkl=[1, 1, 1],
min_thick=10,
min_vac=10,
supercell=[1, 1, 1])
# sort structure into groups of elements atoms for Potcar mapping
iface.sort()
def makePoscars(M_elements,
X_elements,
monolayer_path,
bulk_path,
getCompeting=True):
"""
function that writes out poscars of
chem-substituted M-X monolayers
Args:
M_elements : (list) M
X_elements : (list) X
ratio : (float?)
monolayers : (str) path to poscar files of monolayers
bulks : (str) path to poscar files of bulk
Returns:
List of Poscar file objects for twod monolayers and their competitors
"""
# checing the existence of the monolayer
# and bulk directories
# these direcotries can simply contain the motifs at
# the top most level
monosDir = os.listdir(monolayer_path)
bulksDir = os.listdir(bulk_path)
# if bulks in os.listdir('inputs'):
# bulksDir = os.listdir('inputs/bulks')
# else:
# bulks = []
twod = []
competitors = []
monos = {}
bulks = {}
results = {}
# making direcotries of types of chem sub directories
results['onRatio'] = []
results['hull'] = []
# read in monolayer and bulk motifs
for mon in monosDir:
monos[mon] = Structure.from_file(monolayer_path + '/' + mon)
results[mon] = []
for bulk in bulksDir:
bulks[bulk] = Structure.from_file(bulk_path + '/' + bulk)
results[bulk + '_bulk'] = []
# perform the chem sub based on the input X and M lists
for base_name, mono in monos.items():
# os.mkdir(monolayer)
# os.chdir(monolayer)
for M in M_elements:
for X in X_elements:
coreElements = [M, X]
# naming the files .. can be set as poscar.comment
sub_spec = np.unique(mono.species)
if len(sub_spec) != len(coreElements):
print(base_name + ' DOES NOT HAVE ' + len(coreElements) +
' ELEMENTS. ENDING LOOP')
break
else:
substitutionDict = {}
counter = 0
for element in sub_spec:
substitutionDict[element] = coreElements[counter]
counter += 1
substitutedStruct = mono
substitutedStruct.replace_species(substitutionDict)
results[base_name].append(substitutedStruct)
if getCompeting:
competing = get_competing_phases_new(
mono
) # argument taken is the POSCAR in the current directory.
# Modify get_competing_phases code to allow input structure
# object?
if len(competing) == 1:
# ONRATIO
newStruct = get_struct_from_mp(
competing[0][1]) # assume the
# lowest hull distance
results['onRatio'].append(newStruct)
# chem sub
## how about more than 2 ? this would just be the case in ternaries, etc.
elif len(competing) == 2:
# HULL
newStruct1 = get_struct_from_mp(competing[0][1])
newStruct2 = get_struct_from_mp(competing[1][1])
results['hull'].append(newStruct1)
results['hull'].append(newStruct2)
# write_potcar(pathToPOTCAR)
# relax(submit=False)
# same for bulks
for base_name, bulk in bulks.items():
for M in M_elements:
for X in X_elements:
coreElements = [M, X]
sub_spec = np.unique(bulk.species)
if len(sub_spec) != len(coreElements):
print(base_name + ' DOES NOT HAVE ' + len(coreElements) +
' ELEMENTS. ENDING LOOP')
break
else:
substitutionDict = {}
counter = 0
for element in sub_spec:
substitutionDict[element] = coreElements[counter]
counter += 1
substitutedStruct = bulk
substitutedStruct.replace_species(substitutionDict)
results[base_name + '_bulk'].append(substitutedStruct)
return results
def get_grain_boundary_interface(structure=None, hkl_pair= {'hkl': [[1,0,0],[1,1,0]],\
'thickness':[10,10]}, twist = 0, tilt = 0, separation=0):
"""
Args:
structure: pymatgen structure to create grain boundary in
hkl_pair: dict of {'hkl':thickness}
twist: twist in degrees
tilt: tilt in degrees
"""
structure = get_struct_from_mp(structure, MAPI_KEY="")
sa = SpacegroupAnalyzer(structure)
structure_conventional = sa.get_conventional_standard_structure()
structure = structure_conventional.copy()
structure.sort()
#creation of lower part of grain boundary
lower= Interface(structure,\
hkl = hkl_pair['hkl'][0],
min_thick = hkl_pair['thickness'][0],
min_vac = separation+hkl_pair['thickness'][1],
primitive = False, from_ase = True, center_slab=False)
lower.to(fmt="poscar", filename="POSCAR_lower.vasp")
#creation of upper part of grain boundary
upper= Interface(structure,\
hkl = hkl_pair['hkl'][1],
min_thick = hkl_pair['thickness'][1],
min_vac = 0,
primitive = False, from_ase = True)
#find top atoms reference of lower part of gb
substrate_top_z = np.max(np.array([site.coords for site in lower])[:,2])
# define twist and tilt vectors
twist_shift_normal = lower.lattice.matrix[2,:]/\
np.linalg.norm(lower.lattice.matrix[2,:])
tilt_normal = upper.lattice.matrix[1,:]/\
np.linalg.norm(upper.lattice.matrix[2,:])
#define twist operation SymmOp object
twist_op = SymmOp.from_axis_angle_and_translation(axis= twist_shift_normal,\
angle=twist, angle_in_radians=False,translation_vec=(0, 0, 0))
#define tilt operation SymmOp object
tilt_op = SymmOp.from_axis_angle_and_translation(axis= tilt_normal,\
angle=tilt, angle_in_radians=False,translation_vec=(0, 0, 0))
upper.apply_operation(twist_op)
upper.to(fmt="poscar", filename="POSCAR_upper.vasp")
upper.apply_operation(tilt_op)
#define shift separation along twist vector normal to upper plane
shift = -1*twist_shift_normal/np.linalg.norm(twist_shift_normal) * separation
#define origin to shift w.r.t top of the lower grain
origin = np.array([0,0, substrate_top_z])
#shift sites in upper
for site in upper:
new_coords = site.coords - origin + shift
lower.append(site.specie, new_coords, coords_are_cartesian=True)
return lower
# new_sites = [site for k, site in enumerate(mol) if k not in remove_sites]
# return Molecule.from_sites(new_sites)
if __name__ == '__main__':
# nanopartcle settings
# max radius in angstroms
rmax = 15
# surface families to be chopped off
surface_families = [(1, 0, 0), (1, 1, 1)]
# could be in any units, will be normalized
surface_energies = [28, 25]
# caution: set the structure wrt which the the miller indices are specified
# use your own API key
structure = get_struct_from_mp('PbS')
# primitve ---> conventional cell
sa = SpacegroupAnalyzer(structure)
structure_conventional = sa.get_conventional_standard_structure()
nanoparticle = Nanoparticle(structure_conventional, rmax=rmax,
hkl_family=surface_families,
surface_energies=surface_energies)
nanoparticle.create()
nanoparticle.to(fmt='xyz', filename='nanoparticle.xyz')
"""
Wulff construction using the ASE package
works only for cubic systems and doesn't support multiatom basis
from ase.cluster import wulff_construction
def get_structures():
for species in structures:
struct_species = get_struct_from_mp(species)
poscar_list.append(Poscar(struct_species))
return None
