def adsorbedSurface(self):
"""
Adds adsorbates to bare surface
"""
from pymatgen.analysis.adsorption import AdsorbateSiteFinder, get_rot
slab = copy.deepcopy(self.bareSurface())
asf = AdsorbateSiteFinder(slab)
b_sites = asf.find_adsorption_sites(distance=1.1,
symm_reduce=0)['bridge']
o_sites = asf.find_adsorption_sites(distance=1.1,
symm_reduce=0)['ontop']
h_sites = asf.find_adsorption_sites(distance=1.1,
symm_reduce=0)['hollow']
for ads, sites in self.adsorbates.items():
a = molDict[ads]
for (kind, num) in map(alphaNumSplit, sites):
asf = AdsorbateSiteFinder(slab)
if kind == 'B': slab = asf.add_adsorbate(a, b_sites[int(num)])
elif kind == 'O':
slab = asf.add_adsorbate(a, o_sites[int(num)])
elif kind == 'H':
slab = asf.add_adsorbate(a, h_sites[int(num)])
else:
raise ValueError, "Bad site character in " + str(sites)
return slab
def adsorbedSurface(surfpckl, facet, adsorbates):
"""
Adds adsorbates to bare surface
"""
magmomInit = 3
magElems = ['Fe', 'Mn', 'Cr', 'Co', 'Ni']
initASE = pickle.loads(surfpckl)
constrnts = initASE.constraints
tags = initASE.get_tags().tolist()
slab = makePMGSlabFromASE(initASE, facet)
asf = AdsorbateSiteFinder(slab)
b_sites = asf.find_adsorption_sites(distance=1.1, symm_reduce=0)['bridge']
o_sites = asf.find_adsorption_sites(distance=1.1, symm_reduce=0)['ontop']
h_sites = asf.find_adsorption_sites(distance=1.1, symm_reduce=0)['hollow']
for ads, sites in adsorbates.items():
a = gas.molDict[ads]
for (kind, num) in [printParse.alphaNumSplit(x) for x in sites]:
asf = AdsorbateSiteFinder(slab)
if kind == 'B': slab = asf.add_adsorbate(a, b_sites[int(num) - 1])
elif kind == 'O':
slab = asf.add_adsorbate(a, o_sites[int(num) - 1])
elif kind == 'H':
slab = asf.add_adsorbate(a, h_sites[int(num) - 1])
else:
raise ValueError, "Bad site character in " + str(sites)
aseSlab = AseAtomsAdaptor.get_atoms(slab)
magmoms = [
magmomInit if (magmomInit and e in magElems) else 0
for e in aseSlab.get_chemical_symbols()
]
newtags = np.zeros(len(aseSlab))
for i, t in enumerate(tags):
newtags[i] = t
aseSlab.set_tags(newtags)
aseSlab.set_constraint(constrnts)
aseSlab.set_pbc([1, 1, 1])
aseSlab.set_initial_magnetic_moments(magmoms)
aseSlab.wrap()
return aseSlab
def adsorbedSurface(baresurface,adsorbates): """ Adds adsorbates to bare surface """ slab = baresurface.copy() asf = AdsorbateSiteFinder(slab) b_sites = asf.find_adsorption_sites(distance=1.1,symm_reduce=0)['bridge'] o_sites = asf.find_adsorption_sites(distance=1.1,symm_reduce=0)['ontop'] h_sites = asf.find_adsorption_sites(distance=1.1,symm_reduce=0)['hollow'] for ads,sites in adsorbates.items(): a = molDict[ads] for (kind,num) in [alphaNumSplit(x) for x in sites]: asf = AdsorbateSiteFinder(slab) if kind == 'B': slab=asf.add_adsorbate(a,b_sites[int(num)-1]) elif kind == 'O': slab=asf.add_adsorbate(a,o_sites[int(num)-1]) elif kind == 'H': slab=asf.add_adsorbate(a,h_sites[int(num)-1]) else: raise ValueError, "Bad site character in "+str(sites) return slab
def save_site_combos(slab, adsorbate, path, coverage, height=0.9,
dist_reduce=2.1, symm_reduce=False, ref_species=None,no_bridge=False):
coord_combos = create_coord_combos(slab, coverage, ref_species=ref_species, height=height, dist_reduce=dist_reduce)
if symm_reduce:
coord_combos = combo_symm_reduce(slab,coord_combos)
if no_bridge:
coord_combos = [name for name in coord_combos if 'bridge' not in list(name.keys())[0]]
print(len(coord_combos))
for combo in coord_combos:
fin_slab = slab.copy()
sites = list(combo.values())[0]
dirname = list(combo.keys())[0]
#sf = AdsorbateSiteFinder(fin_slab)
for site in sites:
sf = AdsorbateSiteFinder(fin_slab)
fin_slab = sf.add_adsorbate(adsorbate,site,reorient=False)
fin_slab = fin_slab.get_sorted_structure()
#appends the specified adsorbate to the slab in the selected sites if the distance between the sites is more than a specified number of angstroms
if not os.path.exists('%s\\%s' %(path, dirname)):
os.makedirs('%s\\%s' %(path, dirname))
fin_slab.to('poscar','%s\\%s\\POSCAR'%(path, dirname))
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')
# ### Verificar a possibilidade de adsorção do CO2
# In[45]:
CO2_x = Molecule(["O", "C", "O"], [[-1.16, 0, 0], [0, 0, 0], [1.16, 0, 0]])
CO2_y = Molecule(["O", "C", "O"], [[0, -1.16, 0], [0, 0, 0], [0, 1.16, 0]])
CO2_z = Molecule(["O", "C", "O"], [[0, 0, -1.16], [0, 0, 0], [0, 0, 1.16]])
# In[46]:
ads_sites = asf.find_adsorption_sites()
ads_coords = ads_sites['ontop'][0]
# In[47]:
x_struct = asf.add_adsorbate(CO2_x, ads_coords, repeat=[2, 2, 1])
y_struct = asf.add_adsorbate(CO2_y, ads_coords, repeat=[2, 2, 1])
z_struct = asf.add_adsorbate(CO2_z, ads_coords, repeat=[2, 2, 1])
# In[48]:
for struc, ax, title in zip([x_struct, y_struct, z_struct],
plt.subplots(1, 3, figsize=[15, 45])[1],
["x", "y", "z"]):
plot_slab(struc, ax, adsorption_sites=False)
ax.set_title(r"CO$_2$ in the %s direction" % title)
ax.set_xlim(-1, 10)
ax.set_ylim(-3, 8)
ax.set_xticks([])
ax.set_yticks([])
plt.show()
