def setUpClass(cls):
# head molecule
cls.peo_head = Molecule.from_file(os.path.join(test_dir, "peo_head.xyz"))
charges = [-0.1187, 0.0861, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861, 0.0861]
cls.peo_head.add_site_property("charge", charges)
s_head = 0
s_tail = 5
# chain molecule
cls.peo_bulk = Molecule.from_file(os.path.join(test_dir, "peo_bulk.xyz"))
charges = [-0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861, 0.0861]
cls.peo_bulk.add_site_property("charge", charges)
head = 0
tail = 4
# terminal molecule
cls.peo_tail = Molecule.from_file(os.path.join(test_dir, "peo_tail.xyz"))
charges = [-0.0326, 0.0861, 0.0861, -0.2792, -0.1187, 0.0861, 0.0861, 0.0861]
cls.peo_tail.add_site_property("charge", charges)
e_head = 0
e_tail = 4
cls.n_units = 25
link_distance = 1.5075
# create the polymer
cls.peo_polymer = Polymer(
cls.peo_head,
s_head,
s_tail,
cls.peo_bulk,
head,
tail,
cls.peo_tail,
e_head,
e_tail,
cls.n_units,
link_distance,
)
# linear chain
cls.peo_polymer_linear = Polymer(
cls.peo_head,
s_head,
s_tail,
cls.peo_bulk,
head,
tail,
cls.peo_tail,
e_head,
e_tail,
cls.n_units,
link_distance,
linear_chain=True,
)
def run_task(self, fw_spec):
molecules = self["constituent_molecules"]
mols_number = self["mols_number"]
input_filename = self["input_filename"]
forcefield = self["forcefield"]
topologies = self["topologies"]
user_settings = self.get("user_settings", {})
data_filename = self.get("data_filename",
user_settings.get("data_file", "lammps.data"))
final_molecule = self["final_molecule"]
# if the final molecule was generated using packmol
if fw_spec.get("packed_mol", None):
final_molecule = fw_spec["packed_mol"]
elif isinstance(final_molecule, six.string_types):
final_molecule = Molecule.from_file(final_molecule)
#molecules, mols_number, final_molecule
lammps_ff_data = LammpsData.from_ff_and_topologies(
forcefield, topologies, self["box_size"])
lammps_input_set = LammpsInputSet.from_file(
"ff-inputset",
self["input_file"],
user_settings=user_settings,
lammps_data=lammps_ff_data,
data_filename=data_filename,
is_forcefield=True)
lammps_input_set.write_input(input_filename, data_filename)
def import_Structure(type, config): if type == 'xyz': molecule = Molecule.from_file(config['filename']) lattice = Lattice([config["lattice_parameters"]["vectors"]['i'],config["lattice_parameters"]["vectors"]["j"],config["lattice_parameters"]["vectors"]["k"]]) return Structure(lattice, generate_atom_list(molecule.species), generate_coordinate_list(molecule)) else: return None
def test_get_atoms_from_molecule(self):
m = Molecule.from_file(os.path.join(test_dir, "acetylene.xyz"))
atoms = aio.AseAtomsAdaptor.get_atoms(m)
ase_composition = Composition(atoms.get_chemical_formula())
self.assertEqual(ase_composition, m.composition)
self.assertTrue(atoms.cell is None or not atoms.cell.any())
self.assertTrue(atoms.get_pbc() is None or not atoms.get_pbc().any())
def run_task(self, fw_spec):
molecules = self["constituent_molecules"]
mols_number = self["mols_number"]
input_filename = self["input_filename"]
forcefield = self["forcefield"]
topologies = self["topologies"]
user_settings = self.get("user_settings", {})
data_filename = self.get("data_filename", user_settings.get("data_file", "lammps.data"))
final_molecule = self["final_molecule"]
# if the final molecule was generated using packmol
if fw_spec.get("packed_mol", None):
final_molecule = fw_spec["packed_mol"]
elif isinstance(final_molecule, six.string_types):
final_molecule = Molecule.from_file(final_molecule)
#molecules, mols_number, final_molecule
lammps_ff_data = LammpsData.from_ff_and_topologies(forcefield, topologies, self["box_size"])
lammps_input_set = LammpsInputSet.from_file("ff-inputset", self["input_file"],
user_settings=user_settings,
lammps_data=lammps_ff_data,
data_filename=data_filename,
is_forcefield=True)
lammps_input_set.write_input(input_filename, data_filename)
def run_task(self, fw_spec):
molecules = self["constituent_molecules"]
mols_number = self["mols_number"]
input_filename = self["input_filename"]
forcefield = self["forcefield"]
topologies = self["topologies"]
user_settings = self.get("user_settings", {})
data_filename = user_settings.get("data_file", "lammps.data")
final_molecule = self["final_molecule"]
if isinstance(final_molecule, six.string_types):
final_molecule = Molecule.from_file(final_molecule)
lammps_ff_data = LammpsForceFieldData.from_forcefield_and_topology(
molecules, mols_number, self["box_size"], final_molecule,
forcefield, topologies)
lammps_input_set = LammpsInputSet.from_file(
"forcefield",
self["input_file"],
user_settings=user_settings,
lammps_data=lammps_ff_data,
data_filename=data_filename,
is_forcefield=True)
lammps_input_set.write_input(input_filename, data_filename)
def get_surface_indices_2(xyz_file, bond_distance):
mol = Molecule.from_file(xyz_file)
bulk_coordination = 4
surface_i = []
for i in range(len(mol.sites)):
neighbors = mol.get_neighbors(mol.sites[i], bond_distance)
if len(neighbors) < bulk_coordination:
surface_i.append(i)
return surface_i
def phase_sol(self, EB_K_2, judge='', appendage=""):
import os
from pymatgen import Structure
from pymatgen.io.vasp.sets import MPRelaxSet
from pymatgen import Structure, Lattice, MPRester, Molecule
import shutil
ass = self.cif_route
print(ass)
# os.chdir(r"D:\Desktop\VASP practical\Input")
# print (os.getcwd())
# Note that you must provide your own API Key, which can
# be accessed via the Dashboard at materialsproject.org
#mpr = MPRester()#密钥
molecule = Molecule.from_file(ass)
structure = molecule.get_boxed_structure(self.a, self.b, self.c)
print(structure)
os.chdir(r"D:\Desktop\VASP practical\Input")
print(os.getcwd())
custom_settings = {"NELMIN": 5} # user custom incar settings
relax = MPRelaxSet(structure, user_incar_settings=custom_settings)
os.chdir(r"D:\Desktop\VASP practical\Input")
print(os.getcwd())
relax.write_input(ass + '---' + "sol" + str(EB_K_2) + 'phase')
os.chdir("./" + ass + '---' + "sol" + str(EB_K_2) + 'phase')
#定义一个更改当前目录的变量
dire2 = './vaspstd_sub'
#确立脚本名称
shutil.copy(r"C:\Users\41958\.spyder-py3\vaspstd_sub", dire2)
eb = str(EB_K_2) #将介电常数参数作为字符串
ls = str('TURE') #加入开启溶剂参数
with open('INCAR', 'a') as file_object:
file_object.write('LSOL = ' + ls + '\n' + 'EB_K = ' + eb)
#将两个参数写入INCAR
eb = appendage #储存WAVECAR
with open('INCAR', 'r') as f1:
lines = f1.readlines()
with open('INCAR', 'w') as f2:
for line in lines:
if judge in line:
continue
f2.write(line)
with open('INCAR', 'a') as f3:
f3.write(eb)
os.chdir(r"D:\Desktop\VASP practical\workdir")
print(os.getcwd())
def topmost():
m = Molecule.from_file('snapshot4.xyz')
for j, i in enumerate(m.sites):
if i.z > 26.5 and i.species_string is 'La':
m.remove_sites([j])
m.insert(j, Element.Ag, i.coords)
if i.z > 25 and i.species_string is 'Al':
m.remove_sites([j])
m.insert(j, Element.Mg, i.coords)
if i.z > 25 and i.species_string is 'O':
m.remove_sites([j])
m.insert(j, Element.N, i.coords)
print(m)
def setUpClass(cls):
# head molecule
cls.peo_head = Molecule.from_file(os.path.join(test_dir, "peo_head.xyz"))
charges = [-0.1187, 0.0861, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861, 0.0861]
cls.peo_head.add_site_property("charge", charges)
s_head = 0
s_tail = 5
# chain molecule
cls.peo_bulk = Molecule.from_file(os.path.join(test_dir, "peo_bulk.xyz"))
charges = [-0.0326, 0.0861, 0.0861, -0.2792, -0.0326, 0.0861, 0.0861]
cls.peo_bulk.add_site_property("charge", charges)
head = 0
tail = 4
# terminal molecule
cls.peo_tail = Molecule.from_file(os.path.join(test_dir, "peo_tail.xyz"))
charges = [-0.0326, 0.0861, 0.0861, -0.2792, -0.1187, 0.0861, 0.0861, 0.0861]
cls.peo_tail.add_site_property("charge", charges)
e_head = 0
e_tail = 4
cls.n_units = 25
link_distance = 1.5075
# create the polymer
cls.peo_polymer = Polymer(cls.peo_head, s_head, s_tail,
cls.peo_bulk, head, tail,
cls.peo_tail, e_head, e_tail,
cls.n_units, link_distance)
# linear chain
cls.peo_polymer_linear = Polymer(cls.peo_head, s_head, s_tail,
cls.peo_bulk, head, tail,
cls.peo_tail, e_head, e_tail,
cls.n_units, link_distance, linear_chain=True)
def setUpClass(cls):
ethanol_coords = [[0.00720, -0.56870, 0.00000],
[-1.28540, 0.24990, 0.00000],
[1.13040, 0.31470, 0.00000],
[0.03920, -1.19720, 0.89000],
[0.03920, -1.19720, -0.89000],
[-1.31750, 0.87840, 0.89000],
[-1.31750, 0.87840, -0.89000],
[-2.14220, -0.42390, -0.00000],
[1.98570, -0.13650, -0.00000]]
water_coords = [[9.626, 6.787, 12.673], [9.626, 8.420, 12.673],
[10.203, 7.604, 12.673]]
cls.ethanol_atoms = ["C", "C", "O", "H", "H", "H", "H", "H", "H"]
cls.water_atoms = ["H", "H", "O"]
ethanol = Molecule(cls.ethanol_atoms, ethanol_coords)
water = Molecule(cls.water_atoms, water_coords)
cls.mols = [ethanol, water]
cls.cocktail = Molecule.from_file(
os.path.join(test_dir, "cocktail.xyz"))
cls.packmol_config = [{"number": 1}, {"number": 15}]
def _get_gaussian_ff_top_single(self, filename=None):
"""
run antechamber using gaussian output file, then run parmchk
to generate missing force field parameters. Store and return
the force field and topology information in ff_mol.
Args:
filename: gaussian output file of the molecule
Returns:
Amberff namedtuple object that contains information on force field and
topology
"""
scratch = tempfile.gettempdir()
Amberff = namedtuple("Amberff", ["force_field", "topology"])
with ScratchDir(scratch,
copy_from_current_on_enter=True,
copy_to_current_on_exit=True) as d:
# self._convert_to_pdb(mol, 'mol.pdb')
# self.molname = filename.split('.')[0]
self._run_antechamber(filename)
self._run_parmchk()
# if antechamber can't find parameters go to gaff_example.dat
try:
mol = Molecule.from_file('mol.rtf')
print('mol.rtf file exists')
except TopCorruptionException:
correct_corrupted_top_files('mol.rtf', 'gaff_data.txt')
top = Topology.from_file('mol.rtf')
print('mol.rtf file does not exist')
try:
gff = ForceField.from_file('mol.frcmod')
except FFCorruptionException:
correct_corrupted_frcmod_files('ANTECHAMBER.FRCMOD',
'gaff_data.txt')
gff = ForceField.from_file('ANTECHAMBER.FRCMOD')
# gff.set_atom_mappings('ANTECHAMBER_AC.AC')
# gff.read_charges()
# decorate the molecule with the sire property "atomname"
#mol.add_site_property("atomname", (list(gff.atom_index.values())))
return Amberff(gff, top)
def setUpClass(cls):
ethanol_coords = [[0.00720, -0.56870, 0.00000],
[-1.28540, 0.24990, 0.00000],
[1.13040, 0.31470, 0.00000],
[0.03920, -1.19720, 0.89000],
[0.03920, -1.19720, -0.89000],
[-1.31750, 0.87840, 0.89000],
[-1.31750, 0.87840, -0.89000],
[-2.14220, -0.42390, -0.00000],
[1.98570, -0.13650, -0.00000]]
water_coords = [[9.626, 6.787, 12.673],
[9.626, 8.420, 12.673],
[10.203, 7.604, 12.673]]
cls.ethanol_atoms = ["C", "C", "O", "H", "H", "H", "H", "H", "H"]
cls.water_atoms = ["H", "H", "O"]
ethanol = Molecule(cls.ethanol_atoms, ethanol_coords)
water = Molecule(cls.water_atoms, water_coords)
cls.mols = [ethanol, water]
cls.cocktail = Molecule.from_file(
os.path.join(test_dir, "cocktail.xyz"))
cls.packmol_config = [{"number": 1}, {"number": 15}]
def phase(self):
import os
import re
from pymatgen import Structure
from pymatgen.io.vasp.sets import MPRelaxSet
from pymatgen import Structure, Lattice, MPRester, Molecule
import shutil
ass = self.cif_route
print(ass)
for dirpath, dirnames, filenames in os.walk(self.cif_route):
# print(dirpath)
for name in filenames:
path = os.path.join(self.cif_route, name)
molecule = Molecule.from_file(path)
molecule.apply_operation()
structure = molecule.get_boxed_structure(
self.a, self.b, self.c)
os.chdir(r"E:\VASP practical\Input")
print(os.getcwd())
structure.make_supercell(self.supercell)
custom_settings = {"NELMIN": 5} # user custom incar settings
relax = MPRelaxSet(structure,
user_incar_settings=custom_settings)
os.chdir(r"E:\VASP practical\Input")
print(os.getcwd())
relax.write_input(str(name))
os.chdir("./" + str(name))
#定义一个更改当前目录的变量
dire2 = './vaspstd_sub'
#确立脚本名称
shutil.copy(r"C:\Users\41958\.spyder-py3\vaspstd_sub", dire2)
os.chdir(r"D:\Desktop\VASP practical\workdir")
print(os.getcwd())
def read_structures_from_file(fname):
'''
read structure according to filename
Args:
fname: (str) input filename
Returns:
structure: Structure obj. or None
'''
try:
atoms=read(fname)
return ase2pmg(atoms)
except:
try:
return Molecule.from_file(fname)
except:
try:
return Structure.from_file(fname)
except:
print("Parsing error: %s"%fname)
return None
def xrd(self, ):
import os
from pymatgen import Lattice, Structure
from pymatgen.analysis.diffraction.xrd import XRDCalculator
from IPython.display import Image, display
from pymatgen import Structure, Lattice, MPRester, Molecule
ass = self.cif_route
print(ass)
# os.chdir(r"D:\Desktop\VASP practical\Input")
# print (os.getcwd())
# Note that you must provide your own API Key, which can
# be accessed via the Dashboard at materialsproject.org
#mpr = MPRester()#密钥
molecule = Molecule.from_file(ass)
structure = molecule.get_boxed_structure(self.a, self.b, self.c)
print(structure)
os.chdir(r"D:\Desktop\VASP practical\Input")
print(os.getcwd())
c = XRDCalculator()
c.show_plot(structure)
print(os.getcwd())
def setUp(self):
self.benzene = Molecule.from_file(os.path.join(test_dir, "benzene.xyz"))
self.acetylene = Molecule.from_file(os.path.join(test_dir, "acetylene.xyz"))
def loadSingleMol(path):
singleMol = Molecule.from_file(os.path.join(path, 'singlemolecule/singleMol.xyz'))
return singleMol
#%%
from pymatgen import Structure, Molecule
import os
os.chdir(
'/home/jinho93/new/oxides/perobskite/lanthanum-aluminate/periodic_step/vasp/my015/from-gulp/421/wan/same-nbands/post'
)
p = 0
ion = 0
ele = 0
m = Molecule.from_file('wannier90_centres.xyz')
s = Structure.from_file('POSCAR')
for i in m.sites:
# while i.x < 0:
# i.x += s.lattice.a
# while i.x > s.lattice.a:
# i.x -= s.lattice.a
# while i.y < 0:
# i.y += s.lattice.b
# while i.y > s.lattice.b:
# i.y -= s.lattice.b
while i.z < 0:
i.z += s.lattice.c
while i.z > s.lattice.c:
i.z -= s.lattice.c
while i.y < 0:
i.y += s.lattice.b
while i.y > s.lattice.b:
i.y -= s.lattice.b
# if i.species_string == 'La':
#%%
from pymatgen import Molecule, Structure
import os
import numpy as np
from pymatgen.core.lattice import Lattice
os.chdir('/home/jinho93/oxides/perobskite/lanthanum-aluminate/slab/nvt.para.6/island/len-19/step1')
s = Molecule.from_file('POSCAR.xyz')
sp = []
coords = []
for i in s.sites:
if i.x < 7 and i.y < 7:
sp.append(i.specie)
coords.append(i.coords)
new = Structure(Lattice(np.identity(3) * 7.648200),sp, coords, coords_are_cartesian=True)
new.to('POSCAR', 'ini_pot/reduced')
# %%
#%%
from pymatgen.command_line.gulp_caller import GulpIO
gio = GulpIO()
gio.buckingham_input(new, keywords=['conv'], uc=False)
# %%
def fix_absorbed(self,
need_miller_index,
mole,
num,
selective_dynamic,
min_slab_size_1=8.0,
min_vacuum_size_1=15,
judge='fuchdi',
appendage=""):
from pymatgen import Structure, Lattice, MPRester, Molecule
import pymatgen.core.structure
import pymatgen.core.sites
from pymatgen.analysis.adsorption import AdsorbateSiteFinder, reorient_z, plot_slab
from pymatgen.core.surface import generate_all_slabs
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from matplotlib import pyplot as plt
from pymatgen.ext.matproj import MPRester
from pymatgen.io.vasp.inputs import Poscar
from pymatgen.io.vasp.sets import MVLSlabSet
from pymatgen.io.cif import CifWriter
import os
import shutil
from openbabel import openbabel
from pymatgen.core.surface import Slab, SlabGenerator, generate_all_slabs, Structure, Lattice, ReconstructionGenerator
mp_id = self.mp_id
os.chdir(r"F:\VASP practical\Input")
print(os.getcwd())
# Note that you must provide your own API Key, which can
# be accessed via the Dashboard at materialsproject.org
mpr = MPRester()
struct = mpr.get_structure_by_material_id(mp_id)
struct = SpacegroupAnalyzer(
struct).get_conventional_standard_structure()
# fcc_ni = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3.5), ["Ni", "Ni"],
# [[0, 0, 0], [0.5, 0.5, 0.5]])
slab = SlabGenerator(struct,
miller_index=need_miller_index,
min_slab_size=min_slab_size_1,
min_vacuum_size=min_vacuum_size_1,
center_slab=True)
for n, slabs in enumerate(slab.get_slabs()):
if str(n) in str(num):
slabs_bak = slabs.copy() #可能的晶面
slabs.make_supercell(self.supercell)
print(n)
#晶胞扩充
asf_ni_111 = AdsorbateSiteFinder(
slabs, selective_dynamics=selective_dynamic)
ads_sites = asf_ni_111.find_adsorption_sites()
# print(ads_sites)
assert len(ads_sites) == 4
fig0 = plt.figure()
ax = fig0.add_subplot(111)
plot_slab(slabs, ax, adsorption_sites=False)
fig1 = plt.figure()
ax = fig1.add_subplot(111)
os.chdir(r"D:\Desktop\VASP practical\Cif library")
print(os.getcwd())
obConversion = openbabel.OBConversion()
obConversion.SetInAndOutFormats("pdb", "gjf")
mol = openbabel.OBMol()
print(mol)
c = obConversion.ReadFile(mol, "CH3OH.pdb")
obConversion.WriteFile(mol, "CH3OH.pdb" + '1.gjf')
adsorbate = Molecule.from_file("CH3OH.pdb" + '.gjf')
os.chdir(r"F:\VASP practical\Input")
print(os.getcwd())
print(adsorbate.sites)
ads_structs = asf_ni_111.add_adsorbate(
adsorbate,
(20, 20, 20),
translate=False,
)
# ads_structs = asf_ni_111.generate_adsorption_structures(adsorbate,
# repeat=[1, 1, 1])
# A = Poscar(ads_structs[0])
A = Poscar(reorient_z(ads_structs)) #将切面转换为Poscar
open('POSCAR', 'w').write(str(A))
p = Poscar.from_file('POSCAR')
# w = CifWriter(A.struct)
# w.write_file('mystructure.cif')
path = r'F:\VASP practical\Input\POSCAR' # 文件路径
if os.path.exists(path): # 如果文件存在
# 删除文件，可使用以下两种方法。
os.remove(path)
#os.unlink(path)
else:
print('no such file:%s' % my_file) # 则返回文件不存在
# w = CifWriter(A.struct)
# w.write_file('mystructure.cif')
relax = p.structure #将Poscar 转换为结构信息
custom_settings = {"NPAR": 4} # 用户的INCAR 设置
relaxs = MVLSlabSet(relax, user_incar_settings=custom_settings)
# Vasp输入文件生成器
dire = str(mp_id) + str(selective_dynamic) + str(mole) + str(
need_miller_index).replace(" ", "") + str(n)
# print (relax)
relaxs.write_input(dire)
os.chdir("./" + dire)
print(os.getcwd())
fig0.savefig('slab.png',
bbox_inches='tight',
transparent=True,
dpi=600,
format='png')
plot_slab(ads_structs, ax, adsorption_sites=False, decay=0.09)
fig1.savefig('slab_adsobate.png',
bbox_inches='tight',
transparent=True,
dpi=600,
format='png')
#定义一个更改当前目录的变量
dire2 = './vaspstd_sub'
#确立脚本名称
shutil.copy(r"C:\Users\41958\.spyder-py3\vaspstd_sub", dire2)
eb = appendage #添加其他INCAR参数
with open('INCAR', 'r') as f1:
lines = f1.readlines()
with open('INCAR', 'w') as f2:
for line in lines:
if judge in line:
continue
f2.write(line)
with open('INCAR', 'a') as f3:
f3.write(eb)
# open('POSCAR001', 'w').write(str(Poscar(reorient_z(ads_structs[0]))))
os.chdir(r"D:\Desktop\VASP practical\workdir")
print(os.getcwd())
print('finished')
# my_lattace = Lattace('mp-698074')#半水石膏
# # my_lattace.phase_out()#生成晶胞优化的输入文件
# go = my_lattace.phase_sol(66,judge='LWAVE', appendage= '\nLWAVE = Ture')
# print('yoo')
import os
import numpy as np
from pymatgen import Molecule
os.chdir('/home/jinho93/oxides/perobskite/lanthanum-aluminate/periodic_step/gulp/2.100/2.conf')
h = Molecule.from_file('head.xyz')
t = Molecule.from_file('300k/tail.xyz')
rms = np.array([np.sqrt(np.mean(y**2)) for y in (t.cart_coords - h.cart_coords)])
g = open('reg.xyz', 'w')
oxygen_list = np.array(range(540))[rms > 1.]
oxygen_list += 2
with open('lao.xyz') as f:
for i in range(200):
for j in range(542):
if j in oxygen_list:
tmp = f.readline()
tmp = tmp.replace('O', 'F')
g.write(tmp)
else:
g.write(f.readline())
g.close()
def test_get_molecule(self):
m = Molecule.from_file(os.path.join(test_dir, "acetylene.xyz"))
atoms = aio.AseAtomsAdaptor.get_atoms(m)
self.assertEqual(
aio.AseAtomsAdaptor.get_molecule(atoms).formula, "H2 C2")
from pymatgen import Molecule
import os
import numpy as np
import operator
import collections
def prettyPrint(pdict):
for key, val in pdict.items():
print(key, ":", val)
# this should be part of the workflow ref
atomList = ['Si', 'C', 'P', 'N', 'S', 'O']
origin = Molecule.from_file('./data/mol2mol/centermol.xyz')
target = Molecule.from_file('./data/mol2mol/targetmol.xyz')
transVec = target.center_of_mass - origin.center_of_mass
eleCountDict = collections.OrderedDict()
for ele in list(set(origin.species)):
if origin.species.count(ele) == 1:
eleCountDict[ele] = origin.species.count(ele)
def getMolVec(mol, singAtomDict):
molVec = np.array([])
# list of index indicating those atoms used in building the vector
indexVecList = list()
for key in singAtomDict.keys():
def setUp(self):
self.benzene = Molecule.from_file(os.path.join(test_dir, "benzene.xyz"))
self.acetylene = Molecule.from_file(os.path.join(test_dir, "acetylene.xyz"))
print(pymatgen.__file__)
# In[3]:
import sys
print(sys.version)
# ### Trabalhando com moléculas
# In[4]:
from pymatgen import Molecule
# In[5]:
water = Molecule.from_file("water.xyz")
print(water)
# In[6]:
print(water[0])
# In[7]:
print(water[1])
# In[8]:
print(water[2])
# In[9]:
"""
import pymatgen.io.vasp.outputs
filename = '/Users/jiedeng/Documents/tmp/jd848/project_folder/pv+hf/3k/solid0/r3/cont1/recal/OUTCAR'
out=pymatgen.io.vasp.outputs.Outcar(filename)
import pymatgen.io.xyz
xyz = '/Users/jiedeng/Documents/tmp/jd848/project_folder/pv+hf/3k/solid0/r3/cont1/recal/asap/ASAP-desc.xyz'
file=pymatgen.io.xyz.XYZ(xyz)
file=pymatgen.io.xyz.XYZ()
from pymatgen import Lattice, Structure, Molecule
file = Molecule.from_file(xyz)
struct.get_neighbor_list(r=2, sites = struct[:32]) # no detailed info which site corresponds to which
struct.get_neighbor_list(r=2, sites = struct[:2]) # no detailed info which site corresponds to which
struct=Structure.from_file('/Users/jiedeng/Documents/tmp/jd848/project_folder/pv+hf/3k/solid0/r3/cont1/CONTCAR')
import pymatgen.analysis.local_env
brunnernn = pymatgen.analysis.local_env.BrunnerNN_real()
brunnernn.get_nn_info(struct,1)
task_geo = WritegaussianGeoTask()
task_geo_dbinsert = GaussianGeomOptDBInsertionTask()
task_freq_esp = WritegaussianFreqESPTask()
task_freq_esp_dbinsert = GaussianFreqESPDBInsertionTask()
task_lammps_inp = WritelammpsInputTask()
task_lammps_log_dbinsert = WritelammpsOutputTask()
task_lammps_prop_dbinsert = ParselammpsProperties()
coords = []
sp = []
solvent_molecules_path = os.path.join(rubicon.__path__[0],
'workflows/test_mols/test_lammps')
moleculelist = glob.glob(solvent_molecules_path + '/*.pdb')
for filename in moleculelist:
mol = Molecule.from_file(filename)
file_name = os.path.basename(filename)
mol_with_site_prop = Molecule(
mol.species,
mol.cart_coords,
site_properties={
"mol_name":
[os.path.splitext(file_name)[0]] * len(mol.cart_coords)
})
fw1 = Firework(
[task_geo],
name='Gaussian geometry optimization',
spec={
"molecule": mol,
"mol_name": os.path.splitext(file_name)[0],
"charge": 0,
import matplotlib.pyplot as plt
import os
mole = False
os.chdir(
'/home/jinho93/oxides/perobskite/lanthanum-aluminate/periodic_step/vasp/from-100/'
)
# os.chdir('/home/jinho93/oxides/wurtzite/zno/cp2k/1.aimd/3.16A/30/3.fix')
if mole:
from pymatgen import Molecule
s = Molecule.from_file('tail.xyz')
s2 = Molecule.from_file('113th.xyz')
else:
from pymatgen import Structure
s = Structure.from_file('POSCAR')
s2 = Structure.from_file('ini/POSCAR')
x = []
y = []
fx = []
fy = []
for site, site2 in zip(s.sites, s2.sites):
if site.species_string == 'O':
x.append(site.y)
y.append(site.z)
fx.append(site.y - site2.y)
fy.append(site.z - site2.z)
if site.c < 0.305:
print(site.z, site2.z)
# fig = plt.figure(figsize=(5.46, 8.56))
#%%
import math
from pymatgen import Structure, Molecule, Lattice
import os
os.chdir(
'/home/jinho93/oxides/perobskite/lanthanum-aluminate/slab/gulp/nonstochio/La-vac/two'
)
m = Molecule.from_file('tail.xyz')
l = Lattice.from_lengths_and_angles([11.46615, 15.2882, 50], [90, 90, 90])
s = Structure(l, m.species, m.cart_coords, coords_are_cartesian=True)
s.make_supercell([[4, 0, 0], [0, 3, 0], [0, 0, 1]])
s.make_supercell([[1, 1, 0], [1, -1, 0], [0, 0, 1]])
s.sort()
# ll = Lattice.from_lengths_and_angles([s.lattice.a / 2, s.lattice.b / 2, s.lattice.c], s.lattice.angles)
ll = Lattice.from_lengths_and_angles(s.lattice.abc, s.lattice.angles)
s = Structure(ll, s.species, s.cart_coords, coords_are_cartesian=True)
indi = []
for i, site in enumerate(s.sites):
if site.x + site.y < ll.b / math.sqrt(2):
indi.append(i)
# s.remove_sites(indi)
# s = Structure(ll, s.species, s.cart_coords, coords_are_cartesian=True)
# s.to('POSCAR', 'POSCAR')
results = {}
for i, s in enumerate(struct.sites):
neighbor_list = []
neighbor_data = struct.get_neighbors(s, r_cut, include_index=True)
for n in neighbor_data:
neighbor_list.append(n[2])
results[i] = neighbor_list
return results
folder = "/Users/dchannah/work/NU/melt_cdse/traj/split/si_converted/"
# f = sys.argv[1]
# print particle[0]
temps = ["400"]
frames = ["1", "2", "3", "4", "5", "6", "7", "8"]
for t in temps:
bin_dict = {}
for u_bs in [10, 15, 20, 25, 35]:
bin_dict[u_bs] = []
for f in frames:
fil = folder + t + "_" + f + ".xyz"
particle = Molecule.from_file(fil)
for r_bin in ([0, 10], [10, 15], [15, 20], [20, 25], [25, 35]):
lower_bound = r_bin[0]
upper_bound = r_bin[1]
atom_indices = get_i_in_shell(particle, lower_bound, upper_bound)
shell = get_ordering_for_sites(particle, atom_indices)
bin_dict[upper_bound].append(np.average(shell))
for u_bs in [10, 15, 20, 25, 35]:
print u_bs, str(np.average(bin_dict[u_bs]))
def test_featurize():
"""Test the featurization wrapper function."""
structure = Structure.from_file(
os.path.join(THIS_DIR, "..", "..", "examples", "structures",
"BaO2_mp-1105_computed.cif"))
x, indices, names = featurize(structure) # pylint: disable=invalid-name
assert len(x) == len(indices) == len(names) == 2
assert indices[0] == 0
assert indices[1] == 1
structure = Structure.from_file(
os.path.join(THIS_DIR, "..", "..", "examples", "structures",
"Mg_MOF_74.cif"))
x, indices, names = featurize(structure) # pylint: disable=invalid-name
assert len(x) == len(indices) == len(names) == 6
assert indices[0] == 0
assert indices[1] == 1
structure = Structure.from_file(
os.path.join(THIS_DIR, "..", "structure_data_files", "RSM0027.cif"))
x, indices, names = featurize(structure) # pylint: disable=invalid-name
assert len(x) == len(indices) == len(names) == 2
spga = SpacegroupAnalyzer(structure)
spga = SpacegroupAnalyzer(structure)
x, indices, names = featurize( # pylint: disable=invalid-name
spga.get_primitive_standard_structure())
assert len(x) == len(indices) == len(names) == 2
x, indices, names = featurize( # pylint: disable=invalid-name
spga.get_conventional_standard_structure())
assert len(x) == len(indices) == len(names) == 4
structure = Structure.from_file(
os.path.join(THIS_DIR, "..", "structure_data_files", "RSM0099.cif"))
x, indices, names = featurize(structure) # pylint: disable=invalid-name
assert len(x) == len(indices) == len(names) == 3
spga = SpacegroupAnalyzer(structure)
x, indices, names = featurize( # pylint: disable=invalid-name
spga.get_primitive_standard_structure()) # pylint: disable=invalid-name
assert len(x) == len(indices) == len(names) == 3
x, indices, names = featurize( # pylint: disable=invalid-name
spga.get_conventional_standard_structure())
assert len(x) == len(indices) == len(names) == 9
# Test Daniele's xyz file
m = Molecule.from_file( # pylint: disable=invalid-name
os.path.join(THIS_DIR, "..", "structure_data_files",
"TSS03_structuredata.xyz"))
lattice = np.array([
[6.4214088758454, 0.0, -2.0278718029537],
[-1.7281031033172, 9.4571070308166, -5.4721686991526],
[0.0, 0.0, 11.18087355],
])
s = Structure(lattice, [s.specie for s in m], m.cart_coords) # pylint: disable=invalid-name
x, indices, names = featurize(s) # pylint: disable=invalid-name
assert len(x) == len(indices) == len(names) == 2
assert indices[0] == 0
assert indices[1] == 1
def test_get_molecule(self):
m = Molecule.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "acetylene.xyz"))
atoms = aio.AseAtomsAdaptor.get_atoms(m)
self.assertEqual(aio.AseAtomsAdaptor.get_molecule(atoms).formula, "H2 C2")