def get_mp_structure(cls, mpid):
"""
Get a structure from MP.
:param mpid: Materials Project id.
:return: Structure
"""
m = MPRester()
return m.get_structure_by_material_id(mpid)
def Phonopy (self,mpid,supcell):
from pymatgen.io.vasp.outputs import Poscar
from pymatgen.io.vasp.inputs import Kpoints, Poscar
from pymatgen.io.vasp.outputs import Potcar
from pymatgen.io.vasp.sets import MPNMRSet
from pymatgen.io.phonopy import get_displaced_structures
from pymatgen.symmetry.bandstructure import HighSymmKpath
import shutil
import os
import subprocess
from pymatgen import Structure
from pymatgen.io.vasp.sets import MPRelaxSet
from pymatgen.ext.matproj import MPRester
import shutil
from shutil import copyfile
import sys
os.chdir(self.dire)
print (os.getcwd())
# isExists=os.path.exists(mpid+"isotope")
# if not isExists:
# os.mkdir( mpid+"isotope" )
# print ("Directory created")
# else:
# print (' directory already exists')
# pat = os.path.join(self.dire, mpid+"isotope")
# diree = os.chdir(pat)
# print (os.getcwd())
# print ("Directory entered ")
mpr = MPRester()
mp_id = mpid
structure = mpr.get_structure_by_material_id(mp_id)
relax = MPRelaxSet(structure)
relax.write_input(mp_id+"isotope")
print ("Input created")
pat = os.path.join(self.dire, mpid+"isotope")
os.chdir(pat)
print (os.getcwd())
print ("Directory entered ")
eb=str("phonopy -d --dim="+supcell)
with open('command.bat', 'w') as file_object:
file_object.write(eb )
subprocess.Popen("command.bat")
for filenames in os.walk(pat):
print (filenames)
def benchmark_input_scf(request):
pseudos = abidata.pseudos("14si.pspnc", "6c.pspnc", "3li.pspnc", "9f.pspnc",
"12mg.pspnc", "8o.pspnc", "31ga.pspnc", "7n.pspnc")
rest = MPRester()
structure = rest.get_structure_by_material_id(request.param)
try:
return ebands_input(structure, pseudos, kppa=100, ecut=6).split_datasets()[0]
except Exception:
#to deal with missing pseudos
pytest.skip('Cannot create input for material {}.'.format(request.param))
def benchmark_input_scf(request):
pseudos = abidata.pseudos("14si.pspnc", "6c.pspnc", "3li.pspnc", "9f.pspnc",
"12mg.pspnc", "8o.pspnc", "31ga.pspnc", "7n.pspnc")
rest = MPRester()
structure = rest.get_structure_by_material_id(request.param)
try:
return ebands_input(structure, pseudos, kppa=100, ecut=6).split_datasets()[0]
except:
#to deal with missing pseudos
pytest.skip('Cannot create input for material {}.'.format(request.param))
def xrd(self, ):
import os
os.chdir(r"D:\Desktop\VASP practical\workdir")
from pymatgen import Lattice, Structure
from pymatgen.analysis.diffraction.xrd import XRDCalculator
from IPython.display import Image, display
from pymatgen.ext.matproj import MPRester
mpr = MPRester()
mp_id = self.mp_id
structure = mpr.get_structure_by_material_id(mp_id)
c = XRDCalculator()
print(c)
c.show_plot(structure)
print(os.getcwd())
def phase(self, judge='', appendage=""):
import os
import re
os.chdir(r"F:\VASP practical\Input")
print(os.getcwd())
from pymatgen import Structure
from pymatgen.io.vasp.sets import MPRelaxSet
from pymatgen.ext.matproj import MPRester
import shutil
mpr = MPRester()
mp_id = self.mp_id
structure = mpr.get_structure_by_material_id(mp_id)
structure.make_supercell(self.supercell)
custom_settings = {"NPAR": 4} # user custom incar settings
relax = MPRelaxSet(structure, user_incar_settings=custom_settings)
relax.write_input(mp_id + '---' + 'phase')
os.chdir("./" + mp_id + '---' + '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 = 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)
#将两个参数写入INCAR
os.chdir(r"D:\Desktop\VASP practical\workdir")
print(os.getcwd())
def phase_sol(self, EB_K_2, judge='', appendage=""):
import os
os.chdir(r"F:\VASP practical\Input")
print(os.getcwd())
from pymatgen import Structure
from pymatgen.io.vasp.sets import MPRelaxSet
from pymatgen.ext.matproj import MPRester
import shutil
mpr = MPRester()
mp_id = self.mp_id
structure = mpr.get_structure_by_material_id(mp_id)
custom_settings = {"NPAR": 4} # user custom incar settings
relax = MPRelaxSet(structure, user_incar_settings=custom_settings)
relax.write_input(mp_id + '---' + "sol" + str(EB_K_2) + 'phase')
os.chdir("./" + mp_id + '---' + "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())
#!/usr/bin/env python3
from pymatgen.ext.matproj import MPRester
from pymatgen.core import Composition
import pandas as pd
import os
import argparse
parser = argparse.ArgumentParser()
parser.add_argument("--key" ,dest="MPkey",type=str ,action="store", help="materials project key")
parser.add_argument("--id",dest='mp_id',type=str,action='store',help='materials project id')
args = parser.parse_args()
mpr = MPRester(args.MPkey)
structure = mpr.get_structure_by_material_id(args.mp_id)
structure.to (fmt='POSCAR',filename="{}-{}.vasp".format(args.mp_id,structure.composition.reduced_formula))
def Wullff(self,
formate,
surface_energy,
pic_name,
directions=(3, 4, 4),
x=0.47,
y=-16):
from pymatgen.core.surface import SlabGenerator, generate_all_slabs, Structure, Lattice
# Import the neccesary tools for making a Wulff shape
from pymatgen.analysis.wulff import WulffShape
from pymatgen.ext.matproj import MPRester
from pymatgen.io.cif import CifParser
import matplotlib.pyplot as plt
import matplotlib.image as mpimg
import pandas as pd
import os
if 'cif' in str(formate):
os.chdir(r"D:\Desktop\VASP practical\Cif library")
print(os.getcwd())
structure = CifParser(str(pic_name) + '.cif')
struct = structure.get_structures()[0]
else:
mpr = MPRester()
mp_id = formate
struct = mpr.get_structure_by_material_id(mp_id)
surface_energies = surface_energy
miller_list = surface_energies.keys()
e_surf_list = surface_energies.values()
font2 = {
'family': 'Times New Roman',
'fontsize': '40',
'weight': 'bold',
}
wulffshape = WulffShape(struct.lattice, miller_list, e_surf_list)
print(wulffshape.area_fraction_dict)
os.chdir(self.dire)
dict1 = wulffshape.area_fraction_dict
xx = []
yy = []
for key, value in dict1.items():
xx.append(key)
yy.append(value)
cc = wulffshape.effective_radius
bb = wulffshape.volume
dd = wulffshape.shape_factor
print(wulffshape.effective_radius)
res = pd.DataFrame({'Slab': xx, 'area': yy}) #构造原始数据文件
df = res.sort_values(by='area', ascending=True)
with open(str(pic_name) + '.txt', 'w') as f:
f.write('effective radius:' + str(cc) + ' ' + "volume:" +
str(bb) + ' ' + "shape factor:" + str(dd))
print(cc)
# os.chdir(r"D:\Desktop\VASP practical\workdir")
df.to_excel(str(pic_name) + ".xlsx") #生成Excel文件，并存到指定文件路径下
wulffshape.get_plot(bar_on=True,
aspect_ratio=(8, 8),
bar_pos=[0, 0.85, 1.1, 0.045],
direction=directions)
plt.title(str(pic_name), font2, x=x, y=y)
plt.savefig(str(pic_name) + ".png",
bbox_inches='tight',
transparent=True,
dpi=600,
format='png')
plt.show
os.chdir(r"D:\Desktop\VASP practical\workdir")
print('finished')
def compute_environments(chemenv_configuration):
string_sources = {
"cif": {
"string": "a Cif file",
"regexp": r".*\.cif$"
},
"mp": {
"string": "the Materials Project database",
"regexp": r"mp-[0-9]+$"
},
}
questions = {"c": "cif"}
questions["m"] = "mp"
lgf = LocalGeometryFinder()
lgf.setup_parameters()
allcg = AllCoordinationGeometries()
strategy_class = strategies_class_lookup[
chemenv_configuration.package_options["default_strategy"]["strategy"]]
# TODO: Add the possibility to change the parameters and save them in the chemenv_configuration
default_strategy = strategy_class()
default_strategy.setup_options(
chemenv_configuration.package_options["default_strategy"]
["strategy_options"])
max_dist_factor = chemenv_configuration.package_options[
"default_max_distance_factor"]
firsttime = True
while True:
if len(questions) > 1:
found = False
print(
"Enter the source from which the structure is coming or <q> to quit :"
)
for key_character, qq in questions.items():
print(" - <{}> for a structure from {}".format(
key_character, string_sources[qq]["string"]))
test = input(" ... ")
if test == "q":
break
if test not in list(questions.keys()):
for key_character, qq in questions.items():
if re.match(string_sources[qq]["regexp"],
str(test)) is not None:
found = True
source_type = qq
if not found:
print("Wrong key, try again ...")
continue
else:
source_type = questions[test]
else:
found = False
source_type = list(questions.values())[0]
if found and len(questions) > 1:
input_source = test
if source_type == "cif":
if not found:
input_source = input("Enter path to cif file : ")
cp = CifParser(input_source)
structure = cp.get_structures()[0]
elif source_type == "mp":
if not found:
input_source = input(
'Enter materials project id (e.g. "mp-1902") : ')
a = MPRester()
structure = a.get_structure_by_material_id(input_source)
lgf.setup_structure(structure)
print("Computing environments for {} ... ".format(
structure.composition.reduced_formula))
se = lgf.compute_structure_environments(
maximum_distance_factor=max_dist_factor)
print("Computing environments finished")
while True:
test = input(
"See list of environments determined for each (unequivalent) site ? "
'("y" or "n", "d" with details, "g" to see the grid) : ')
strategy = default_strategy
if test in ["y", "d", "g"]:
strategy.set_structure_environments(se)
for eqslist in se.equivalent_sites:
site = eqslist[0]
isite = se.structure.index(site)
try:
if strategy.uniquely_determines_coordination_environments:
ces = strategy.get_site_coordination_environments(
site)
else:
ces = strategy.get_site_coordination_environments_fractions(
site)
except NeighborsNotComputedChemenvError:
continue
if ces is None:
continue
if len(ces) == 0:
continue
comp = site.species
# ce = strategy.get_site_coordination_environment(site)
if strategy.uniquely_determines_coordination_environments:
ce = ces[0]
if ce is None:
continue
thecg = allcg.get_geometry_from_mp_symbol(ce[0])
mystring = "Environment for site #{} {} ({}) : {} ({})\n".format(
str(isite),
comp.get_reduced_formula_and_factor()[0],
str(comp),
thecg.name,
ce[0],
)
else:
mystring = "Environments for site #{} {} ({}) : \n".format(
str(isite),
comp.get_reduced_formula_and_factor()[0],
str(comp),
)
for ce in ces:
cg = allcg.get_geometry_from_mp_symbol(ce[0])
csm = ce[1]["other_symmetry_measures"][
"csm_wcs_ctwcc"]
mystring += " - {} ({}): {:.2f} % (csm : {:2f})\n".format(
cg.name, cg.mp_symbol, 100.0 * ce[2], csm)
if (test in ["d", "g"] and strategy.
uniquely_determines_coordination_environments):
if thecg.mp_symbol != UNCLEAR_ENVIRONMENT_SYMBOL:
mystring += " <Continuous symmetry measures> "
mingeoms = se.ce_list[isite][
thecg.
coordination_number][0].minimum_geometries()
for mingeom in mingeoms:
csm = mingeom[1]["other_symmetry_measures"][
"csm_wcs_ctwcc"]
mystring += "{} : {:.2f} ".format(
mingeom[0], csm)
print(mystring)
if test == "g":
while True:
test = input(
"Enter index of site(s) (e.g. 0 1 2, separated by spaces) for which you want to see the grid "
"of parameters : ")
try:
indices = [int(x) for x in test.split()]
print(str(indices))
for isite in indices:
if isite < 0:
raise IndexError
se.plot_environments(
isite, additional_condition=se.AC.ONLY_ACB)
break
except ValueError:
print("This is not a valid site")
except IndexError:
print("This site is out of the site range")
if no_vis:
test = input('Go to next structure ? ("y" to do so)')
if test == "y":
break
continue
test = input(
'View structure with environments ? ("y" for the unit cell or "m" for a supercell or "n") : '
)
if test in ["y", "m"]:
if test == "m":
mydeltas = []
while True:
try:
test = input("Enter multiplicity (e.g. 3 2 2) : ")
nns = test.split()
for i0 in range(int(nns[0])):
for i1 in range(int(nns[1])):
for i2 in range(int(nns[2])):
mydeltas.append(
np.array(
[1.0 * i0, 1.0 * i1, 1.0 * i2],
np.float))
break
except (ValueError, IndexError):
print("Not a valid multiplicity")
else:
mydeltas = [np.zeros(3, np.float)]
if firsttime:
vis = StructureVis(show_polyhedron=False,
show_unit_cell=True)
vis.show_help = False
firsttime = False
vis.set_structure(se.structure)
strategy.set_structure_environments(se)
for isite, site in enumerate(se.structure):
try:
ces = strategy.get_site_coordination_environments(site)
except NeighborsNotComputedChemenvError:
continue
if len(ces) == 0:
continue
ce = strategy.get_site_coordination_environment(site)
if ce is not None and ce[0] != UNCLEAR_ENVIRONMENT_SYMBOL:
for mydelta in mydeltas:
psite = PeriodicSite(
site.species,
site.frac_coords + mydelta,
site.lattice,
properties=site.properties,
)
vis.add_site(psite)
neighbors = strategy.get_site_neighbors(psite)
draw_cg(
vis,
psite,
neighbors,
cg=lgf.allcg.get_geometry_from_mp_symbol(
ce[0]),
perm=ce[1]["permutation"],
)
vis.show()
test = input('Go to next structure ? ("y" to do so) : ')
if test == "y":
break
print("")
def get_input_set(mprester: MPRester, mpnum: int) -> MPRelaxSet:
return MPRelaxSet(mprester.get_structure_by_material_id(f"mp-{mpnum}"),
potcar_functional="PW91")
if __name__ == "__main__":
# download test data
materials = {
"Si_227": "mp-149", # F cubic
"Fe_229": "mp-13", # I cubic
"S_58": "mp-558014", # P orthorhombic
"Rb2P3_69": "mp-2079", # I orthorhombic
"K2Au3_71": "mp-8700", # F orthorhombic
"LaI3_63": "mp-27979", # C orthorhombic
"KCeF4_123": "mp-1223451", # P tetragonal
"RbO2_129": "mp-12105", # I tetragonal
"BaN2_15": "mp-1001", # C monoclinic
"TiNi_11": "mp-1048", # P monoclinic
"CaC2_2": "mp-642822", # triclinic
"KNO3_160": "mp-6920", # rhombohedral
"ZnO_186": "mp-2133", # hexagonal
}
from pymatgen.ext.matproj import MPRester
_mpr = MPRester()
_module_dir = Path(__file__).resolve().parent
_structure_dir = _module_dir / "test_data" / "structures"
if not _structure_dir.exists():
_structure_dir.mkdir()
for name, mp_id in materials.items():
_s = _mpr.get_structure_by_material_id(mp_id)
dumpfn(_s, _structure_dir / f"{name}.json.gz")
def compute_environments(chemenv_configuration):
string_sources = {'cif': {'string': 'a Cif file', 'regexp': r'.*\.cif$'},
'mp': {'string': 'the Materials Project database',
'regexp': r'mp-[0-9]+$'}}
questions = {'c': 'cif'}
questions['m'] = 'mp'
lgf = LocalGeometryFinder()
lgf.setup_parameters()
allcg = AllCoordinationGeometries()
strategy_class = strategies_class_lookup[chemenv_configuration.package_options['default_strategy']['strategy']]
#TODO: Add the possibility to change the parameters and save them in the chemenv_configuration
default_strategy = strategy_class()
default_strategy.setup_options(chemenv_configuration.package_options['default_strategy']['strategy_options'])
max_dist_factor = chemenv_configuration.package_options['default_max_distance_factor']
firsttime = True
while True:
if len(questions) > 1:
found = False
print('Enter the source from which the structure is coming or <q> to quit :')
for key_character, qq in questions.items():
print(' - <{}> for a structure from {}'.format(key_character, string_sources[qq]['string']))
test = input(' ... ')
if test == 'q':
break
if test not in list(questions.keys()):
for key_character, qq in questions.items():
if re.match(string_sources[qq]['regexp'], str(test)) is not None:
found = True
source_type = qq
if not found:
print('Wrong key, try again ...')
continue
else:
source_type = questions[test]
else:
found = False
source_type = list(questions.values())[0]
if found and len(questions) > 1:
input_source = test
if source_type == 'cif':
if not found:
input_source = input('Enter path to cif file : ')
cp = CifParser(input_source)
structure = cp.get_structures()[0]
elif source_type == 'mp':
if not found:
input_source = input('Enter materials project id (e.g. "mp-1902") : ')
a = MPRester()
structure = a.get_structure_by_material_id(input_source)
lgf.setup_structure(structure)
print('Computing environments for {} ... '.format(structure.composition.reduced_formula))
se = lgf.compute_structure_environments(maximum_distance_factor=max_dist_factor)
print('Computing environments finished')
while True:
test = input('See list of environments determined for each (unequivalent) site ? '
'("y" or "n", "d" with details, "g" to see the grid) : ')
strategy = default_strategy
if test in ['y', 'd', 'g']:
strategy.set_structure_environments(se)
for eqslist in se.equivalent_sites:
site = eqslist[0]
isite = se.structure.index(site)
try:
if strategy.uniquely_determines_coordination_environments:
ces = strategy.get_site_coordination_environments(site)
else:
ces = strategy.get_site_coordination_environments_fractions(site)
except NeighborsNotComputedChemenvError:
continue
if ces is None:
continue
if len(ces) == 0:
continue
comp = site.species_and_occu
#ce = strategy.get_site_coordination_environment(site)
if strategy.uniquely_determines_coordination_environments:
ce = ces[0]
if ce is None:
continue
thecg = allcg.get_geometry_from_mp_symbol(ce[0])
mystring = 'Environment for site #{} {} ({}) : {} ({})\n'.format(str(isite),
comp.get_reduced_formula_and_factor()[0],
str(comp),
thecg.name,
ce[0])
else:
mystring = 'Environments for site #{} {} ({}) : \n'.format(str(isite),
comp.get_reduced_formula_and_factor()[0],
str(comp))
for ce in ces:
cg = allcg.get_geometry_from_mp_symbol(ce[0])
csm = ce[1]['other_symmetry_measures']['csm_wcs_ctwcc']
mystring += ' - {} ({}): {:.2f} % (csm : {:2f})\n'.format(cg.name, cg.mp_symbol,
100.0*ce[2],
csm)
if test in ['d', 'g'] and strategy.uniquely_determines_coordination_environments:
if thecg.mp_symbol != UNCLEAR_ENVIRONMENT_SYMBOL:
mystring += ' <Continuous symmetry measures> '
mingeoms = se.ce_list[isite][thecg.coordination_number][0].minimum_geometries()
for mingeom in mingeoms:
csm = mingeom[1]['other_symmetry_measures']['csm_wcs_ctwcc']
mystring += '{} : {:.2f} '.format(mingeom[0], csm)
print(mystring)
if test == 'g':
while True:
test = input('Enter index of site(s) (e.g. 0 1 2, separated by spaces) for which you want to see the grid of parameters : ')
try:
indices=[int(x) for x in test.split()]
print(str(indices))
for isite in indices:
if isite <0:
raise IndexError
se.plot_environments(isite, additional_condition=se.AC.ONLY_ACB)
break
except ValueError:
print('This is not a valid site')
except IndexError:
print('This site is out of the site range')
if no_vis:
test = input('Go to next structure ? ("y" to do so)')
if test == 'y':
break
continue
test = input('View structure with environments ? ("y" for the unit cell or "m" for a supercell or "n") : ')
if test in ['y', 'm']:
if test == 'm':
mydeltas = []
while True:
try:
test = input('Enter multiplicity (e.g. 3 2 2) : ')
nns = test.split()
for i0 in range(int(nns[0])):
for i1 in range(int(nns[1])):
for i2 in range(int(nns[2])):
mydeltas.append(np.array([1.0*i0, 1.0*i1, 1.0*i2], np.float))
break
except (ValueError,IndexError):
print('Not a valid multiplicity')
else:
mydeltas = [np.zeros(3, np.float)]
if firsttime:
vis = StructureVis(show_polyhedron=False, show_unit_cell=True)
vis.show_help = False
firsttime = False
vis.set_structure(se.structure)
strategy.set_structure_environments(se)
for isite, site in enumerate(se.structure):
try:
ces = strategy.get_site_coordination_environments(site)
except NeighborsNotComputedChemenvError:
continue
if len(ces) == 0:
continue
ce = strategy.get_site_coordination_environment(site)
if ce is not None and ce[0] != UNCLEAR_ENVIRONMENT_SYMBOL:
for mydelta in mydeltas:
psite = PeriodicSite(site._species, site._fcoords + mydelta, site._lattice,
properties=site._properties)
vis.add_site(psite)
neighbors = strategy.get_site_neighbors(psite)
draw_cg(vis, psite, neighbors, cg=lgf.allcg.get_geometry_from_mp_symbol(ce[0]),
perm=ce[1]['permutation'])
vis.show()
test = input('Go to next structure ? ("y" to do so) : ')
if test == 'y':
break
print('')
class MPResterTest(unittest.TestCase):
def setUp(self):
self.rester = MPRester()
warnings.simplefilter("ignore")
def tearDown(self):
warnings.resetwarnings()
def test_get_all_materials_ids_doc(self):
mids = self.rester.get_materials_ids("Al2O3")
random.shuffle(mids)
doc = self.rester.get_doc(mids.pop(0))
self.assertEqual(doc["pretty_formula"], "Al2O3")
def test_get_data(self):
props = ["energy", "energy_per_atom", "formation_energy_per_atom",
"nsites", "unit_cell_formula", "pretty_formula", "is_hubbard",
"elements", "nelements", "e_above_hull", "hubbards",
"is_compatible", "task_ids",
"density", "icsd_ids", "total_magnetization"]
# unicode literals have been reintroduced in py>3.2
expected_vals = [-191.3359011, -6.833425039285714, -2.5515769497278913,
28, {'P': 4, 'Fe': 4, 'O': 16, 'Li': 4},
"LiFePO4", True, ['Li', 'O', 'P', 'Fe'], 4, 0.0,
{'Fe': 5.3, 'Li': 0.0, 'O': 0.0, 'P': 0.0}, True,
{'mp-19017', 'mp-540081', 'mp-601412'},
3.464840709092822,
[159107, 154117, 160776, 99860, 181272, 166815,
260571, 92198, 165000, 155580, 38209, 161479, 153699,
260569, 260570, 200155, 260572, 181341, 181342,
72545, 56291, 97764, 162282, 155635],
15.9996841]
for (i, prop) in enumerate(props):
if prop not in ['hubbards', 'unit_cell_formula', 'elements',
'icsd_ids', 'task_ids']:
val = self.rester.get_data("mp-19017", prop=prop)[0][prop]
self.assertAlmostEqual(expected_vals[i], val, places=2)
elif prop in ["elements", "icsd_ids", "task_ids"]:
upstream_vals = set(
self.rester.get_data("mp-19017", prop=prop)[0][prop])
self.assertLessEqual(set(expected_vals[i]), upstream_vals)
else:
self.assertEqual(expected_vals[i],
self.rester.get_data("mp-19017",
prop=prop)[0][prop])
props = ['structure', 'initial_structure', 'final_structure', 'entry']
for prop in props:
obj = self.rester.get_data("mp-19017", prop=prop)[0][prop]
if prop.endswith("structure"):
self.assertIsInstance(obj, Structure)
elif prop == "entry":
obj = self.rester.get_data("mp-19017", prop=prop)[0][prop]
self.assertIsInstance(obj, ComputedEntry)
#Test chemsys search
data = self.rester.get_data('Fe-Li-O', prop='unit_cell_formula')
self.assertTrue(len(data) > 1)
elements = {Element("Li"), Element("Fe"), Element("O")}
for d in data:
self.assertTrue(
set(Composition(d['unit_cell_formula']).elements).issubset(
elements))
self.assertRaises(MPRestError, self.rester.get_data, "Fe2O3",
"badmethod")
def test_get_data(self):
# Test getting supported properties
self.assertNotEqual(self.rester.get_task_data("mp-30"), [])
# Test aliasing
data = self.rester.get_task_data("mp-30", "energy")
self.assertAlmostEqual(data[0]["energy"], -4.09929227, places=2)
def test_get_materials_id_from_task_id(self):
self.assertEqual(self.rester.get_materials_id_from_task_id(
"mp-540081"), "mp-19017")
def test_get_materials_id_references(self):
# nosetests pymatgen/matproj/tests/test_matproj.py:MPResterTest.test_get_materials_id_references
m = MPRester()
data = m.get_materials_id_references('mp-123')
self.assertTrue(len(data) > 1000)
def test_find_structure(self):
# nosetests pymatgen/matproj/tests/test_matproj.py:MPResterTest.test_find_structure
m = MPRester()
ciffile = os.path.join(test_dir, 'Fe3O4.cif')
data = m.find_structure(ciffile)
self.assertTrue(len(data) > 1)
s = CifParser(ciffile).get_structures()[0]
data = m.find_structure(s)
self.assertTrue(len(data) > 1)
def test_get_entries_in_chemsys(self):
syms = ["Li", "Fe", "O"]
entries = self.rester.get_entries_in_chemsys(syms)
elements = set([Element(sym) for sym in syms])
for e in entries:
self.assertIsInstance(e, ComputedEntry)
self.assertTrue(set(e.composition.elements).issubset(elements))
def test_get_structure_by_material_id(self):
s1 = self.rester.get_structure_by_material_id("mp-1")
self.assertEqual(s1.formula, "Cs1")
def test_get_entry_by_material_id(self):
e = self.rester.get_entry_by_material_id("mp-19017")
self.assertIsInstance(e, ComputedEntry)
self.assertTrue(e.composition.reduced_formula, "LiFePO4")
def test_query(self):
criteria = {'elements': {'$in': ['Li', 'Na', 'K'], '$all': ['O']}}
props = ['pretty_formula', 'energy']
data = self.rester.query(criteria=criteria, properties=props)
self.assertTrue(len(data) > 6)
data = self.rester.query(criteria="*2O", properties=props)
self.assertGreaterEqual(len(data), 52)
self.assertIn("Li2O", (d["pretty_formula"] for d in data))
def test_get_exp_thermo_data(self):
data = self.rester.get_exp_thermo_data("Fe2O3")
self.assertTrue(len(data) > 0)
for d in data:
self.assertEqual(d.formula, "Fe2O3")
def test_get_dos_by_id(self):
dos = self.rester.get_dos_by_material_id("mp-2254")
self.assertIsInstance(dos, CompleteDos)
def test_get_bandstructure_by_material_id(self):
bs = self.rester.get_bandstructure_by_material_id("mp-2254")
self.assertIsInstance(bs, BandStructureSymmLine)
bs_unif = self.rester.get_bandstructure_by_material_id(
"mp-2254", line_mode=False)
self.assertIsInstance(bs_unif, BandStructure)
self.assertNotIsInstance(bs_unif, BandStructureSymmLine)
def test_get_phonon_data_by_material_id(self):
bs = self.rester.get_phonon_bandstructure_by_material_id("mp-661")
self.assertIsInstance(bs, PhononBandStructureSymmLine)
dos = self.rester.get_phonon_dos_by_material_id("mp-661")
self.assertIsInstance(dos, CompletePhononDos)
ddb_str = self.rester.get_phonon_ddb_by_material_id("mp-661")
self.assertIsInstance(ddb_str, str)
def test_get_structures(self):
structs = self.rester.get_structures("Mn3O4")
self.assertTrue(len(structs) > 0)
def test_get_entries(self):
entries = self.rester.get_entries("TiO2")
self.assertTrue(len(entries) > 1)
for e in entries:
self.assertEqual(e.composition.reduced_formula, "TiO2")
entries = self.rester.get_entries("TiO2", inc_structure=True)
self.assertTrue(len(entries) > 1)
for e in entries:
self.assertEqual(e.structure.composition.reduced_formula, "TiO2")
# all_entries = self.rester.get_entries("Fe", compatible_only=False)
# entries = self.rester.get_entries("Fe", compatible_only=True)
# self.assertTrue(len(entries) < len(all_entries))
entries = self.rester.get_entries("Fe", compatible_only=True,
property_data=["cif"])
self.assertIn("cif", entries[0].data)
for e in self.rester.get_entries("CdO2", inc_structure=False):
self.assertIsNotNone(e.data["oxide_type"])
# test if it will retrieve the conventional unit cell of Ni
entry = self.rester.get_entry_by_material_id(
"mp-23", inc_structure=True, conventional_unit_cell=True)
Ni = entry.structure
self.assertEqual(Ni.lattice.a, Ni.lattice.b)
self.assertEqual(Ni.lattice.a, Ni.lattice.c)
self.assertEqual(Ni.lattice.alpha, 90)
self.assertEqual(Ni.lattice.beta, 90)
self.assertEqual(Ni.lattice.gamma, 90)
# Ensure energy per atom is same
primNi = self.rester.get_entry_by_material_id(
"mp-23", inc_structure=True, conventional_unit_cell=False)
self.assertEqual(primNi.energy_per_atom, entry.energy_per_atom)
Ni = self.rester.get_structure_by_material_id(
"mp-23", conventional_unit_cell=True)
self.assertEqual(Ni.lattice.a, Ni.lattice.b)
self.assertEqual(Ni.lattice.a, Ni.lattice.c)
self.assertEqual(Ni.lattice.alpha, 90)
self.assertEqual(Ni.lattice.beta, 90)
self.assertEqual(Ni.lattice.gamma, 90)
# Test case where convs are different from initial and final
th = self.rester.get_structure_by_material_id(
"mp-37", conventional_unit_cell=True)
th_entry = self.rester.get_entry_by_material_id(
"mp-37", inc_structure=True, conventional_unit_cell=True)
th_entry_initial = self.rester.get_entry_by_material_id(
"mp-37", inc_structure="initial", conventional_unit_cell=True)
self.assertEqual(th, th_entry.structure)
self.assertEqual(len(th_entry.structure), 4)
self.assertEqual(len(th_entry_initial.structure), 2)
# Test if the polymorphs of Fe are properly sorted
# by e_above_hull when sort_by_e_above_hull=True
Fe_entries = self.rester.get_entries("Fe", sort_by_e_above_hull=True)
self.assertEqual(Fe_entries[0].data["e_above_hull"], 0)
def test_get_pourbaix_entries(self):
pbx_entries = self.rester.get_pourbaix_entries(["Fe"])
for pbx_entry in pbx_entries:
self.assertTrue(isinstance(pbx_entry, PourbaixEntry))
# Ensure entries are pourbaix compatible
pbx = PourbaixDiagram(pbx_entries)
# Try binary system
pbx_entries = self.rester.get_pourbaix_entries(["Fe", "Cr"])
pbx = PourbaixDiagram(pbx_entries)
# TODO: Shyue Ping: I do not understand this test. You seem to
# be grabbing Zn-S system, but I don't see proper test for anything,
# including Na ref. This test also takes a long time.
# Test Zn-S, which has Na in reference solids
# pbx_entries = self.rester.get_pourbaix_entries(["Zn", "S"])
def test_get_exp_entry(self):
entry = self.rester.get_exp_entry("Fe2O3")
self.assertEqual(entry.energy, -825.5)
def test_submit_query_delete_snl(self):
s = Structure([[5, 0, 0], [0, 5, 0], [0, 0, 5]], ["Fe"], [[0, 0, 0]])
# d = self.rester.submit_snl(
# [s, s], remarks=["unittest"],
# authors="Test User <*****@*****.**>")
# self.assertEqual(len(d), 2)
# data = self.rester.query_snl({"about.remarks": "unittest"})
# self.assertEqual(len(data), 2)
# snlids = [d["_id"] for d in data]
# self.rester.delete_snl(snlids)
# data = self.rester.query_snl({"about.remarks": "unittest"})
# self.assertEqual(len(data), 0)
def test_get_stability(self):
entries = self.rester.get_entries_in_chemsys(["Fe", "O"])
modified_entries = []
for entry in entries:
# Create modified entries with energies that are 0.01eV higher
# than the corresponding entries.
if entry.composition.reduced_formula == "Fe2O3":
modified_entries.append(
ComputedEntry(entry.composition,
entry.uncorrected_energy + 0.01,
parameters=entry.parameters,
entry_id="mod_{}".format(entry.entry_id)))
rest_ehulls = self.rester.get_stability(modified_entries)
all_entries = entries + modified_entries
compat = MaterialsProjectCompatibility()
all_entries = compat.process_entries(all_entries)
pd = PhaseDiagram(all_entries)
for e in all_entries:
if str(e.entry_id).startswith("mod"):
for d in rest_ehulls:
if d["entry_id"] == e.entry_id:
data = d
break
self.assertAlmostEqual(pd.get_e_above_hull(e),
data["e_above_hull"])
def test_get_reaction(self):
rxn = self.rester.get_reaction(["Li", "O"], ["Li2O"])
self.assertIn("Li2O", rxn["Experimental_references"])
def test_get_substrates(self):
substrate_data = self.rester.get_substrates('mp-123', 5, [1, 0, 0])
substrates = [sub_dict['sub_id'] for sub_dict in substrate_data]
self.assertIn("mp-2534", substrates)
def test_get_surface_data(self):
data = self.rester.get_surface_data("mp-126") # Pt
self.assertIn("surfaces", data)
surfaces = data["surfaces"]
self.assertTrue(len(surfaces) > 0)
surface = surfaces.pop()
self.assertIn("miller_index", surface)
self.assertIn("surface_energy", surface)
self.assertIn("is_reconstructed", surface)
data_inc = self.rester.get_surface_data("mp-126", inc_structures=True)
self.assertIn("structure", data_inc["surfaces"][0])
def test_get_wulff_shape(self):
ws = self.rester.get_wulff_shape("mp-126")
self.assertTrue(isinstance(ws, WulffShape))
def test_get_cohesive_energy(self):
ecoh = self.rester.get_cohesive_energy("mp-13")
self.assertTrue(ecoh, 5.04543279)
def test_get_interface_reactions(self):
kinks = self.rester.get_interface_reactions("LiCoO2", "Li3PS4")
self.assertTrue(len(kinks) > 0)
kink = kinks[0]
self.assertIn("energy", kink)
self.assertIn("ratio", kink)
self.assertIn("rxn", kink)
self.assertTrue(isinstance(kink['rxn'], Reaction))
kinks_open_O = self.rester.get_interface_reactions(
"LiCoO2", "Li3PS4", open_el="O", relative_mu=-1)
self.assertTrue(len(kinks_open_O) > 0)
with warnings.catch_warnings(record=True) as w:
warnings.filterwarnings("always", message="The reactant.+")
self.rester.get_interface_reactions("LiCoO2", "MnO9")
self.assertTrue("The reactant" in str(w[-1].message))
def test_parse_criteria(self):
crit = MPRester.parse_criteria("mp-1234 Li-*")
self.assertIn("Li-O", crit["$or"][1]["chemsys"]["$in"])
self.assertIn({"task_id": "mp-1234"}, crit["$or"])
crit = MPRester.parse_criteria("Li2*")
self.assertIn("Li2O", crit["pretty_formula"]["$in"])
self.assertIn("Li2I", crit["pretty_formula"]["$in"])
self.assertIn("CsLi2", crit["pretty_formula"]["$in"])
crit = MPRester.parse_criteria("Li-*-*")
self.assertIn("Li-Re-Ru", crit["chemsys"]["$in"])
self.assertNotIn("Li-Li", crit["chemsys"]["$in"])
comps = MPRester.parse_criteria("**O3")["pretty_formula"]["$in"]
for c in comps:
self.assertEqual(len(Composition(c)), 3, "Failed in %s" % c)
chemsys = MPRester.parse_criteria("{Fe,Mn}-O")["chemsys"]["$in"]
self.assertEqual(len(chemsys), 2)
comps = MPRester.parse_criteria("{Fe,Mn,Co}O")["pretty_formula"]["$in"]
self.assertEqual(len(comps), 3, comps)
#Let's test some invalid symbols
self.assertRaises(ValueError, MPRester.parse_criteria, "li-fe")
self.assertRaises(ValueError, MPRester.parse_criteria, "LO2")
crit = MPRester.parse_criteria("POPO2")
self.assertIn("P2O3", crit["pretty_formula"]["$in"])
dir_name = input_filename.replace('.csv', '')
os.mkdir(dir_name)
print('\nDirectory "' + dir_name +
'" is created. All CIF files will be stored in this folder. \n')
# loop through all names
entries = []
for name in tqdm(names):
data_handler.try_url('https://www.materialsproject.org')
results = m.query(name, properties=['material_id',
'spacegroup.number']) # query
for result in results:
material_id = result['material_id']
sgn = result['spacegroup.number']
if sgn != 1 and sgn != 2: # exclude triclinics
structure = m.get_structure_by_material_id(
material_id, conventional_unit_cell=True)
symmetrized_structure = SpacegroupAnalyzer(
structure).get_symmetrized_structure()
entry = [name, sgn, material_id]
entries.append(entry)
CifWriter(symmetrized_structure,
symprec=0.01).write_file(dir_name + '/' + name + '_' +
str(sgn) + '_' + material_id +
'.cif')
# export csv
hdr = ['name', 'spacegroup_number', 'material_id']
export_filename = 'export_' + input_filename
data_handler.export_csv(entries, export_filename, header=hdr)
print('\nSuccess!\n')
fileNotUsed = 0
training_data = []
binNumber = np.array([])
types = {
"Triclinic": 0,
"Monoclinic": 0,
"Orthorhombic": 0,
"Tetragonal": 0,
"Trigonal": 0,
"Hexagonal": 0,
"Cubic": 0
}
for fileNumber, material_id in enumerate(inputs):
structure = m.get_structure_by_material_id(material_id)
poscar = Poscar(structure).get_string()
# Basis vector of the unit cell of lattice [(x1, y1, z1), (x2, y2, z2), (x3, y3, z3)]
lattice_vector = np.array([])
# Atom type (Element1, Element2, ...)
atom_type = np.array([])
# Atom type (# of Element1, # of Element2, ...)
atom_number = np.array([])
# Atom position [(x1, y1, z1), (x2, y2, z2), (x3, y3, z3), ...]
r = np.array([])
line = 0
print(f"Processing {fileNumber + 1} / {len(inputs)} files.")
# -- Reading from poscar (vasp format)
class MPResterTest(PymatgenTest):
_multiprocess_shared_ = True
def setUp(self):
self.rester = MPRester()
warnings.simplefilter("ignore")
def tearDown(self):
warnings.simplefilter("default")
self.rester.session.close()
def test_get_all_materials_ids_doc(self):
mids = self.rester.get_materials_ids("Al2O3")
random.shuffle(mids)
doc = self.rester.get_doc(mids.pop(0))
self.assertEqual(doc["pretty_formula"], "Al2O3")
def test_get_xas_data(self):
# Test getting XAS data
data = self.rester.get_xas_data("mp-19017", "Li")
self.assertEqual("mp-19017,Li", data["mid_and_el"])
self.assertAlmostEqual(data["spectrum"]["x"][0], 55.178, places=2)
self.assertAlmostEqual(data["spectrum"]["y"][0], 0.0164634, places=2)
def test_get_data(self):
props = {
"energy",
"energy_per_atom",
"formation_energy_per_atom",
"nsites",
"unit_cell_formula",
"pretty_formula",
"is_hubbard",
"elements",
"nelements",
"e_above_hull",
"hubbards",
"is_compatible",
"task_ids",
"density",
"icsd_ids",
"total_magnetization",
}
mpid = "mp-1143"
vals = requests.get(
f"http://legacy.materialsproject.org/materials/{mpid}/json/")
expected_vals = vals.json()
for prop in props:
if prop not in [
"hubbards",
"unit_cell_formula",
"elements",
"icsd_ids",
"task_ids",
]:
val = self.rester.get_data(mpid, prop=prop)[0][prop]
if prop in ["energy", "energy_per_atom"]:
prop = "final_" + prop
self.assertAlmostEqual(expected_vals[prop], val, 2,
f"Failed with property {prop}")
elif prop in ["elements", "icsd_ids", "task_ids"]:
upstream_vals = set(
self.rester.get_data(mpid, prop=prop)[0][prop])
self.assertLessEqual(set(expected_vals[prop]), upstream_vals)
else:
self.assertEqual(
expected_vals[prop],
self.rester.get_data(mpid, prop=prop)[0][prop],
)
props = ["structure", "initial_structure", "final_structure", "entry"]
for prop in props:
obj = self.rester.get_data(mpid, prop=prop)[0][prop]
if prop.endswith("structure"):
self.assertIsInstance(obj, Structure)
elif prop == "entry":
obj = self.rester.get_data(mpid, prop=prop)[0][prop]
self.assertIsInstance(obj, ComputedEntry)
# Test chemsys search
data = self.rester.get_data("Fe-Li-O", prop="unit_cell_formula")
self.assertTrue(len(data) > 1)
elements = {Element("Li"), Element("Fe"), Element("O")}
for d in data:
self.assertTrue(
set(Composition(
d["unit_cell_formula"]).elements).issubset(elements))
self.assertRaises(MPRestError, self.rester.get_data, "Fe2O3",
"badmethod")
def test_get_materials_id_from_task_id(self):
self.assertEqual(
self.rester.get_materials_id_from_task_id("mp-540081"), "mp-19017")
def test_get_materials_id_references(self):
# nosetests pymatgen/matproj/tests/test_matproj.py:MPResterTest.test_get_materials_id_references
m = MPRester()
data = m.get_materials_id_references("mp-123")
self.assertTrue(len(data) > 1000)
def test_find_structure(self):
# nosetests pymatgen/matproj/tests/test_matproj.py:MPResterTest.test_find_structure
m = MPRester()
ciffile = self.TEST_FILES_DIR / "Fe3O4.cif"
data = m.find_structure(str(ciffile))
self.assertTrue(len(data) > 1)
s = CifParser(ciffile).get_structures()[0]
data = m.find_structure(s)
self.assertTrue(len(data) > 1)
def test_get_entries_in_chemsys(self):
syms = ["Li", "Fe", "O"]
syms2 = "Li-Fe-O"
entries = self.rester.get_entries_in_chemsys(syms)
entries2 = self.rester.get_entries_in_chemsys(syms2)
elements = {Element(sym) for sym in syms}
for e in entries:
self.assertIsInstance(e, ComputedEntry)
self.assertTrue(set(e.composition.elements).issubset(elements))
e1 = {i.entry_id for i in entries}
e2 = {i.entry_id for i in entries2}
self.assertTrue(e1 == e2)
stable_entries = self.rester.get_entries_in_chemsys(
syms, additional_criteria={"e_above_hull": {
"$lte": 0.001
}})
self.assertTrue(len(stable_entries) < len(entries))
def test_get_structure_by_material_id(self):
s1 = self.rester.get_structure_by_material_id("mp-1")
self.assertEqual(s1.formula, "Cs1")
# requesting via task-id instead of mp-id
self.assertWarns(Warning, self.rester.get_structure_by_material_id,
"mp-698856")
# requesting unknown mp-id
self.assertRaises(MPRestError,
self.rester.get_structure_by_material_id,
"mp-does-not-exist")
def test_get_entry_by_material_id(self):
e = self.rester.get_entry_by_material_id("mp-19017")
self.assertIsInstance(e, ComputedEntry)
self.assertTrue(e.composition.reduced_formula, "LiFePO4")
def test_query(self):
criteria = {"elements": {"$in": ["Li", "Na", "K"], "$all": ["O"]}}
props = ["pretty_formula", "energy"]
data = self.rester.query(criteria=criteria,
properties=props,
chunk_size=0)
self.assertTrue(len(data) > 6)
data = self.rester.query(criteria="*2O",
properties=props,
chunk_size=0)
self.assertGreaterEqual(len(data), 52)
self.assertIn("Li2O", (d["pretty_formula"] for d in data))
def test_query_chunk_size(self):
criteria = {"nelements": 2, "elements": "O"}
props = ["pretty_formula"]
data1 = self.rester.query(criteria=criteria,
properties=props,
chunk_size=0)
data2 = self.rester.query(criteria=criteria,
properties=props,
chunk_size=500)
self.assertEqual({d["pretty_formula"]
for d in data1},
{d["pretty_formula"]
for d in data2})
self.assertIn("Al2O3", {d["pretty_formula"] for d in data1})
def test_get_exp_thermo_data(self):
data = self.rester.get_exp_thermo_data("Fe2O3")
self.assertTrue(len(data) > 0)
for d in data:
self.assertEqual(d.formula, "Fe2O3")
def test_get_dos_by_id(self):
dos = self.rester.get_dos_by_material_id("mp-2254")
self.assertIsInstance(dos, CompleteDos)
def test_get_bandstructure_by_material_id(self):
bs = self.rester.get_bandstructure_by_material_id("mp-2254")
self.assertIsInstance(bs, BandStructureSymmLine)
bs_unif = self.rester.get_bandstructure_by_material_id("mp-2254",
line_mode=False)
self.assertIsInstance(bs_unif, BandStructure)
self.assertNotIsInstance(bs_unif, BandStructureSymmLine)
def test_get_phonon_data_by_material_id(self):
bs = self.rester.get_phonon_bandstructure_by_material_id("mp-661")
self.assertIsInstance(bs, PhononBandStructureSymmLine)
dos = self.rester.get_phonon_dos_by_material_id("mp-661")
self.assertIsInstance(dos, CompletePhononDos)
ddb_str = self.rester.get_phonon_ddb_by_material_id("mp-661")
self.assertIsInstance(ddb_str, str)
def test_get_structures(self):
structs = self.rester.get_structures("Mn3O4")
self.assertTrue(len(structs) > 0)
def test_get_entries(self):
entries = self.rester.get_entries("TiO2")
self.assertTrue(len(entries) > 1)
for e in entries:
self.assertEqual(e.composition.reduced_formula, "TiO2")
entries = self.rester.get_entries("TiO2", inc_structure=True)
self.assertTrue(len(entries) > 1)
for e in entries:
self.assertEqual(e.structure.composition.reduced_formula, "TiO2")
# all_entries = self.rester.get_entries("Fe", compatible_only=False)
# entries = self.rester.get_entries("Fe", compatible_only=True)
# self.assertTrue(len(entries) < len(all_entries))
entries = self.rester.get_entries("Fe",
compatible_only=True,
property_data=["cif"])
self.assertIn("cif", entries[0].data)
for e in self.rester.get_entries("CdO2", inc_structure=False):
self.assertIsNotNone(e.data["oxide_type"])
# test if it will retrieve the conventional unit cell of Ni
entry = self.rester.get_entry_by_material_id(
"mp-23", inc_structure=True, conventional_unit_cell=True)
Ni = entry.structure
self.assertEqual(Ni.lattice.a, Ni.lattice.b)
self.assertEqual(Ni.lattice.a, Ni.lattice.c)
self.assertEqual(Ni.lattice.alpha, 90)
self.assertEqual(Ni.lattice.beta, 90)
self.assertEqual(Ni.lattice.gamma, 90)
# Ensure energy per atom is same
primNi = self.rester.get_entry_by_material_id(
"mp-23", inc_structure=True, conventional_unit_cell=False)
self.assertEqual(primNi.energy_per_atom, entry.energy_per_atom)
Ni = self.rester.get_structure_by_material_id(
"mp-23", conventional_unit_cell=True)
self.assertEqual(Ni.lattice.a, Ni.lattice.b)
self.assertEqual(Ni.lattice.a, Ni.lattice.c)
self.assertEqual(Ni.lattice.alpha, 90)
self.assertEqual(Ni.lattice.beta, 90)
self.assertEqual(Ni.lattice.gamma, 90)
# Test case where convs are different from initial and final
# th = self.rester.get_structure_by_material_id(
# "mp-37", conventional_unit_cell=True)
# th_entry = self.rester.get_entry_by_material_id(
# "mp-37", inc_structure=True, conventional_unit_cell=True)
# th_entry_initial = self.rester.get_entry_by_material_id(
# "mp-37", inc_structure="initial", conventional_unit_cell=True)
# self.assertEqual(th, th_entry.structure)
# self.assertEqual(len(th_entry.structure), 4)
# self.assertEqual(len(th_entry_initial.structure), 2)
# Test if the polymorphs of Fe are properly sorted
# by e_above_hull when sort_by_e_above_hull=True
Fe_entries = self.rester.get_entries("Fe", sort_by_e_above_hull=True)
self.assertEqual(Fe_entries[0].data["e_above_hull"], 0)
def test_get_pourbaix_entries(self):
# test input chemsys as a list of elements
pbx_entries = self.rester.get_pourbaix_entries(["Fe", "Cr"])
for pbx_entry in pbx_entries:
self.assertTrue(isinstance(pbx_entry, PourbaixEntry))
# test input chemsys as a string
pbx_entries = self.rester.get_pourbaix_entries("Fe-Cr")
for pbx_entry in pbx_entries:
self.assertTrue(isinstance(pbx_entry, PourbaixEntry))
# fe_two_plus = [e for e in pbx_entries if e.entry_id == "ion-0"][0]
# self.assertAlmostEqual(fe_two_plus.energy, -1.12369, places=3)
#
# feo2 = [e for e in pbx_entries if e.entry_id == "mp-25332"][0]
# self.assertAlmostEqual(feo2.energy, 3.56356, places=3)
#
# # Test S, which has Na in reference solids
# pbx_entries = self.rester.get_pourbaix_entries(["S"])
# so4_two_minus = pbx_entries[9]
# self.assertAlmostEqual(so4_two_minus.energy, 0.301511, places=3)
# Ensure entries are Pourbaix compatible
PourbaixDiagram(pbx_entries)
def test_get_exp_entry(self):
entry = self.rester.get_exp_entry("Fe2O3")
self.assertEqual(entry.energy, -825.5)
# def test_submit_query_delete_snl(self):
# s = Structure([[5, 0, 0], [0, 5, 0], [0, 0, 5]], ["Fe"], [[0, 0, 0]])
# d = self.rester.submit_snl(
# [s, s], remarks=["unittest"],
# authors="Test User <*****@*****.**>")
# self.assertEqual(len(d), 2)
# data = self.rester.query_snl({"about.remarks": "unittest"})
# self.assertEqual(len(data), 2)
# snlids = [d["_id"] for d in data]
# self.rester.delete_snl(snlids)
# data = self.rester.query_snl({"about.remarks": "unittest"})
# self.assertEqual(len(data), 0)
def test_get_stability(self):
entries = self.rester.get_entries_in_chemsys(["Fe", "O"])
modified_entries = []
for entry in entries:
# Create modified entries with energies that are 0.01eV higher
# than the corresponding entries.
if entry.composition.reduced_formula == "Fe2O3":
modified_entries.append(
ComputedEntry(
entry.composition,
entry.uncorrected_energy + 0.01,
parameters=entry.parameters,
entry_id=f"mod_{entry.entry_id}",
))
rest_ehulls = self.rester.get_stability(modified_entries)
all_entries = entries + modified_entries
compat = MaterialsProject2020Compatibility()
all_entries = compat.process_entries(all_entries)
pd = PhaseDiagram(all_entries)
for e in all_entries:
if str(e.entry_id).startswith("mod"):
for d in rest_ehulls:
if d["entry_id"] == e.entry_id:
data = d
break
self.assertAlmostEqual(pd.get_e_above_hull(e),
data["e_above_hull"])
def test_get_reaction(self):
rxn = self.rester.get_reaction(["Li", "O"], ["Li2O"])
self.assertIn("Li2O", rxn["Experimental_references"])
def test_get_substrates(self):
substrate_data = self.rester.get_substrates("mp-123", 5, [1, 0, 0])
substrates = [sub_dict["sub_id"] for sub_dict in substrate_data]
self.assertIn("mp-2534", substrates)
def test_get_surface_data(self):
data = self.rester.get_surface_data("mp-126") # Pt
one_surf = self.rester.get_surface_data("mp-129",
miller_index=[-2, -3, 1])
self.assertAlmostEqual(one_surf["surface_energy"],
2.99156963,
places=2)
self.assertArrayAlmostEqual(one_surf["miller_index"], [3, 2, 1])
self.assertIn("surfaces", data)
surfaces = data["surfaces"]
self.assertTrue(len(surfaces) > 0)
surface = surfaces.pop()
self.assertIn("miller_index", surface)
self.assertIn("surface_energy", surface)
self.assertIn("is_reconstructed", surface)
data_inc = self.rester.get_surface_data("mp-126", inc_structures=True)
self.assertIn("structure", data_inc["surfaces"][0])
def test_get_wulff_shape(self):
ws = self.rester.get_wulff_shape("mp-126")
self.assertTrue(isinstance(ws, WulffShape))
def test_get_cohesive_energy(self):
ecoh = self.rester.get_cohesive_energy("mp-13")
self.assertTrue(ecoh, 5.04543279)
def test_get_gb_data(self):
mo_gbs = self.rester.get_gb_data(chemsys="Mo")
self.assertEqual(len(mo_gbs), 10)
mo_gbs_s5 = self.rester.get_gb_data(pretty_formula="Mo", sigma=5)
self.assertEqual(len(mo_gbs_s5), 3)
mo_s3_112 = self.rester.get_gb_data(
material_id="mp-129",
sigma=3,
gb_plane=[1, -1, -2],
include_work_of_separation=True,
)
self.assertEqual(len(mo_s3_112), 1)
gb_f = mo_s3_112[0]["final_structure"]
self.assertArrayAlmostEqual(gb_f.rotation_axis, [1, 1, 0])
self.assertAlmostEqual(gb_f.rotation_angle, 109.47122, places=4)
self.assertAlmostEqual(mo_s3_112[0]["gb_energy"], 0.47965, places=2)
self.assertAlmostEqual(mo_s3_112[0]["work_of_separation"],
6.318144,
places=2)
self.assertIn("Mo24", gb_f.formula)
hcp_s7 = self.rester.get_gb_data(material_id="mp-87",
gb_plane=[0, 0, 0, 1],
include_work_of_separation=True)
self.assertAlmostEqual(hcp_s7[0]["gb_energy"], 1.12, places=2)
self.assertAlmostEqual(hcp_s7[0]["work_of_separation"], 2.47, places=2)
def test_get_interface_reactions(self):
kinks = self.rester.get_interface_reactions("LiCoO2", "Li3PS4")
self.assertTrue(len(kinks) > 0)
kink = kinks[0]
self.assertIn("energy", kink)
self.assertIn("ratio_atomic", kink)
self.assertIn("rxn", kink)
self.assertTrue(isinstance(kink["rxn"], Reaction))
kinks_open_O = self.rester.get_interface_reactions("LiCoO2",
"Li3PS4",
open_el="O",
relative_mu=-1)
self.assertTrue(len(kinks_open_O) > 0)
with warnings.catch_warnings(record=True) as w:
warnings.filterwarnings("always", message="The reactant.+")
self.rester.get_interface_reactions("LiCoO2", "MnO9")
self.assertTrue("The reactant" in str(w[-1].message))
def test_download_info(self):
material_ids = ["mvc-2970"]
task_types = [TaskType.GGA_OPT, TaskType.GGAU_UNIFORM]
file_patterns = ["vasprun*", "OUTCAR*"]
meta, urls = self.rester.get_download_info(material_ids,
task_types=task_types,
file_patterns=file_patterns)
self.assertDictEqual(
dict(meta),
{
"mvc-2970": [{
"task_id": "mp-1738602",
"task_type": "GGA+U NSCF Uniform"
}],
},
)
self.assertEqual(
urls[0],
"https://nomad-lab.eu/prod/rae/api/raw/query?file_pattern=vasprun*&file_pattern=OUTCAR*&external_id=mp"
"-1738602",
)
def test_parse_criteria(self):
crit = MPRester.parse_criteria("mp-1234 Li-*")
self.assertIn("Li-O", crit["$or"][1]["chemsys"]["$in"])
self.assertIn({"task_id": "mp-1234"}, crit["$or"])
crit = MPRester.parse_criteria("Li2*")
self.assertIn("Li2O", crit["pretty_formula"]["$in"])
self.assertIn("Li2I", crit["pretty_formula"]["$in"])
self.assertIn("CsLi2", crit["pretty_formula"]["$in"])
crit = MPRester.parse_criteria("Li-*-*")
self.assertIn("Li-Re-Ru", crit["chemsys"]["$in"])
self.assertNotIn("Li-Li", crit["chemsys"]["$in"])
comps = MPRester.parse_criteria("**O3")["pretty_formula"]["$in"]
for c in comps:
self.assertEqual(len(Composition(c)), 3, f"Failed in {c}")
chemsys = MPRester.parse_criteria("{Fe,Mn}-O")["chemsys"]["$in"]
self.assertEqual(len(chemsys), 2)
comps = MPRester.parse_criteria("{Fe,Mn,Co}O")["pretty_formula"]["$in"]
self.assertEqual(len(comps), 3, comps)
# Let's test some invalid symbols
self.assertRaises(ValueError, MPRester.parse_criteria, "li-fe")
self.assertRaises(ValueError, MPRester.parse_criteria, "LO2")
crit = MPRester.parse_criteria("POPO2")
self.assertIn("P2O3", crit["pretty_formula"]["$in"])
def test_include_user_agent(self):
headers = self.rester.session.headers
self.assertIn("user-agent",
headers,
msg="Include user-agent header by default")
m = re.match(
r"pymatgen/(\d+)\.(\d+)\.(\d+)\.?(\d+)? \(Python/(\d+)\.(\d)+\.(\d+) ([^\/]*)/([^\)]*)\)",
headers["user-agent"],
)
self.assertIsNotNone(
m, msg=f"Unexpected user-agent value {headers['user-agent']}")
self.rester = MPRester(include_user_agent=False)
self.assertNotIn("user-agent",
self.rester.session.headers,
msg="user-agent header unwanted")
def test_database_version(self):
with MPRester(notify_db_version=True) as mpr:
db_version = mpr.get_database_version()
self.assertIsInstance(db_version, str)
yaml = YAML()
with open(MP_LOG_FILE) as f:
d = yaml.load(f)
self.assertEqual(d["MAPI_DB_VERSION"]["LAST_ACCESSED"], db_version)
self.assertIsInstance(d["MAPI_DB_VERSION"]["LOG"][db_version], int)
def test_pourbaix_heavy(self):
entries = self.rester.get_pourbaix_entries(["Li", "Mg", "Sn", "Pd"])
_ = PourbaixDiagram(entries, nproc=4, filter_solids=False)
entries = self.rester.get_pourbaix_entries(
["Ba", "Ca", "V", "Cu", "F"])
_ = PourbaixDiagram(entries, nproc=4, filter_solids=False)
entries = self.rester.get_pourbaix_entries(
["Ba", "Ca", "V", "Cu", "F", "Fe"])
_ = PourbaixDiagram(entries, nproc=4, filter_solids=False)
entries = self.rester.get_pourbaix_entries(
["Na", "Ca", "Nd", "Y", "Ho", "F"])
_ = PourbaixDiagram(entries, nproc=4, filter_solids=False)
def test_pourbaix_mpr_pipeline(self):
data = self.rester.get_pourbaix_entries(["Zn"])
pbx = PourbaixDiagram(data, filter_solids=True, conc_dict={"Zn": 1e-8})
pbx.find_stable_entry(10, 0)
data = self.rester.get_pourbaix_entries(["Ag", "Te"])
pbx = PourbaixDiagram(data,
filter_solids=True,
conc_dict={
"Ag": 1e-8,
"Te": 1e-8
})
self.assertEqual(len(pbx.stable_entries), 29)
test_entry = pbx.find_stable_entry(8, 2)
self.assertEqual(sorted(test_entry.entry_id), ["ion-10", "mp-499"])
# Test against ion sets with multiple equivalent ions (Bi-V regression)
entries = self.rester.get_pourbaix_entries(["Bi", "V"])
pbx = PourbaixDiagram(entries,
filter_solids=True,
conc_dict={
"Bi": 1e-8,
"V": 1e-8
})
self.assertTrue(
all([
"Bi" in entry.composition and "V" in entry.composition
for entry in pbx.all_entries
]))
def from_pymatgen_structure(
structure=None,
formula=None,
space_grp=None,
MP_key=None,
conventional_standard_structure=True,
):
"""
Create a Crystal object from a pymatgen Structure object.
If a Materials Project API key is installed, you may pass
the Materials Project ID of a structure, which will be
fetched through the MP API. For setup information see:
https://pymatgen.org/usage.html#setting-the-pmg-mapi-key-in-the-config-file.
Alternatively, Materials Porject API key can be pass as an argument through
the function (MP_key). To get your API key, please visit Materials Project website
and login/sign up using your email id. Once logged in, go to the dashboard
to generate your own API key (https://materialsproject.org/dashboard).
Note that pymatgen typically prefers to return primitive unit cells,
which can be overridden by setting conventional_standard_structure=True.
Args:
structure: (pymatgen Structure or str), if specified as a string, it will be considered
as a Materials Project ID of a structure, otherwise it will accept only
pymatgen Structure object. if None, MP database will be queried using the
specified formula and/or space groups for the available structure
formula: (str), pretty formula to search in the MP database, (note that the forumlas in MP
database are not always formatted in the conventional order. Please
visit Materials Project website for information (https://materialsproject.org/)
if None, structure argument must not be None
space_grp: (int) space group number of the forumula provided to query MP database. If None, MP will search
for all the available space groups for the formula provided and will consider the
one with lowest unit cell volume, only specify when using formula to search MP
database
MP_key: (str) Materials Project API key
conventional_standard_structure: (bool) if True, conventional standard unit cell will be returned
instead of the primitive unit cell pymatgen returns
"""
import pymatgen as mg
from pymatgen.ext.matproj import MPRester
if structure is not None:
if isinstance(structure, str):
mpr = MPRester(MP_key)
structure = mpr.get_structure_by_material_id(structure)
assert isinstance(structure, mg.core.Structure
), "structure must be pymatgen Structure object"
structure = (mg.symmetry.analyzer.SpacegroupAnalyzer(
structure).get_conventional_standard_structure()
if conventional_standard_structure else structure)
else:
mpr = MPRester(MP_key)
if formula is None:
raise Exception(
"Atleast a formula needs to be provided to query from MP database!!"
)
query = mpr.query(
criteria={"pretty_formula": formula},
properties=["structure", "icsd_ids", "spacegroup"],
)
if space_grp:
query = [
query[i] for i in range(len(query))
if mg.symmetry.analyzer.SpacegroupAnalyzer(
query[i]["structure"]).get_space_group_number() ==
space_grp
]
selected = query[np.argmin([
query[i]["structure"].lattice.volume for i in range(len(query))
])]
structure = (mg.symmetry.analyzer.SpacegroupAnalyzer(
selected["structure"]).get_conventional_standard_structure()
if conventional_standard_structure else
selected["structure"])
positions = structure.frac_coords #: fractional atomic coordinates
cell = np.array([
structure.lattice.a,
structure.lattice.b,
structure.lattice.c,
structure.lattice.alpha,
structure.lattice.beta,
structure.lattice.gamma,
])
numbers = np.array([s.species.elements[0].Z for s in structure])
return Crystal(positions, numbers, cell)
def slab(self, miller_index_1, min_slab_size_1=8.0, min_vacuum_size_1=15):
from pymatgen.analysis.adsorption import AdsorbateSiteFinder, plot_slab, reorient_z
from pymatgen.core.surface import Slab, SlabGenerator, generate_all_slabs, Structure, Lattice, ReconstructionGenerator
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.core.structure import Structure
from pymatgen.ext.matproj import MPRester
from matplotlib import pyplot as plt
from pymatgen.io.vasp.inputs import Poscar
from pymatgen.io.vasp.sets import MVLSlabSet
import shutil
import os
mpr = MPRester() #密钥
mp_id = self.mp_id #通过mp_id来索引结构
struct = mpr.get_structure_by_material_id(mp_id)
#获取结构信息
struct = SpacegroupAnalyzer(
struct).get_conventional_standard_structure()
#空间群分析
need_miller_index = miller_index_1 #通过米勒指数，确定要切的晶面
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)
#晶面生成器参数
gh = str(miller_index_1).replace(" ", "")
for n, slabs in enumerate(slab.get_slabs()):
slabs_bak = slabs.copy() #可能的晶面
slabs.make_supercell(self.supercell)
#晶胞扩充
cc = slabs.surface_area
os.chdir(r"F:\VASP practical\Input")
print(os.getcwd())
print(n)
A = Poscar(slabs) #将切面转换为Poscar
relax = A.structure #将Poscar 转换为结构信息
custom_settings = {"NPAR": 4} # 用户的INCAR 设置
relax = MVLSlabSet(relax, user_incar_settings=custom_settings)
#Vasp输入文件生成器
fig = plt.figure() #绘图--确立画布
ax = fig.add_subplot(111) #绘图--确立位置
plot_slab(slabs, ax, adsorption_sites=False) #绘图
dire = str(mp_id) + "---" + str(gh) + '----' + str(n)
#设置一个用作存储输入文件的名称
plt.show()
# plt.savefig(dire)#将该名称用于保存图片
relax.write_input(str(gh) + '--' + str(n)) #将生成的VASP输入文件写入存储
dire_1 = str(gh) + '--' + str(n)
diree = os.chdir("./" + dire_1)
fig.savefig('slab.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)
#将脚本写入VASP输入文件所在文件夹
with open('surface_area', 'w') as f:
f.write(str(cc))
print(cc)
# os.chdir("../")
#将当前目录改为默认目录
os.chdir(r"D:\Desktop\VASP practical\workdir")
print(os.getcwd())
print('finished')
def run_task(self, fw_spec):
logging.basicConfig(
filename='chemenv_structure_environments.log',
format='%(levelname)s:%(module)s:%(funcName)s:%(message)s',
level=logging.DEBUG)
lgf = LocalGeometryFinder()
lgf.setup_parameters(
centering_type='centroid',
include_central_site_in_centroid=True,
structure_refinement=lgf.STRUCTURE_REFINEMENT_NONE)
if 'chemenv_parameters' in fw_spec:
for param, value in fw_spec['chemenv_parameters'].items():
lgf.setup_parameter(param, value)
identifier = fw_spec['identifier']
if 'structure' in fw_spec:
structure = fw_spec['structure']
else:
if identifier[
'source'] == 'MaterialsProject' and 'material_id' in identifier:
if not 'mapi_key' in fw_spec:
raise ValueError(
'The mapi_key should be provided to get the structure from the Materials Project'
)
a = MPRester(fw_spec['mapi_key'])
structure = a.get_structure_by_material_id(
identifier['material_id'])
else:
raise ValueError(
'Either structure or identifier with source = MaterialsProject and material_id '
'should be provided')
info = {}
# Compute the structure environments
lgf.setup_structure(structure)
if 'valences' in fw_spec:
valences = fw_spec['valences']
else:
try:
bva = BVAnalyzer()
valences = bva.get_valences(structure=structure)
info['valences'] = {'origin': 'BVAnalyzer'}
except:
valences = 'undefined'
info['valences'] = {'origin': 'None'}
excluded_atoms = None
if 'excluded_atoms' in fw_spec:
excluded_atoms = fw_spec['excluded_atoms']
se = lgf.compute_structure_environments(only_cations=False,
valences=valences,
excluded_atoms=excluded_atoms)
# Write to json file
if 'json_file' in fw_spec:
json_file = fw_spec['json_file']
else:
json_file = 'structure_environments.json'
f = open(json_file, 'w')
json.dump(se.as_dict(), f)
f.close()
# Save to database
if 'mongo_database' in fw_spec:
database = fw_spec['mongo_database']
entry = {
'identifier':
identifier,
'elements':
[elmt.symbol for elmt in structure.composition.elements],
'nelements':
len(structure.composition.elements),
'pretty_formula':
structure.composition.reduced_formula,
'nsites':
len(structure)
}
saving_option = fw_spec['saving_option']
if saving_option == 'gridfs':
gridfs_msonables = {
'structure': structure,
'structure_environments': se
}
elif saving_option == 'storefile':
gridfs_msonables = None
if 'se_prefix' in fw_spec:
se_prefix = fw_spec['se_prefix']
if not se_prefix.isalpha():
raise ValueError(
'Prefix for structure_environments file is "{}" '
'while it should be alphabetic'.format(se_prefix))
else:
se_prefix = ''
if se_prefix:
se_rfilename = '{}_{}.json'.format(
se_prefix, fw_spec['storefile_basename'])
else:
se_rfilename = '{}.json'.format(
fw_spec['storefile_basename'])
se_rfilepath = '{}/{}'.format(fw_spec['storefile_dirpath'],
se_rfilename)
storage_server = fw_spec['storage_server']
storage_server.put(localpath=json_file,
remotepath=se_rfilepath,
overwrite=True,
makedirs=False)
entry['structure_environments_file'] = se_rfilepath
else:
raise ValueError(
'Saving option is "{}" while it should be '
'"gridfs" or "storefile"'.format(saving_option))
criteria = {'identifier': identifier}
if database.collection.find(criteria).count() == 1:
database.update_entry(query=criteria,
entry_update=entry,
gridfs_msonables=gridfs_msonables)
else:
database.insert_entry(entry=entry,
gridfs_msonables=gridfs_msonables)
class MPResterTest(unittest.TestCase):
def setUp(self):
self.rester = MPRester()
def test_get_data(self):
props = ["energy", "energy_per_atom", "formation_energy_per_atom",
"nsites", "unit_cell_formula", "pretty_formula", "is_hubbard",
"elements", "nelements", "e_above_hull", "hubbards",
"is_compatible", "task_ids",
"density", "icsd_ids", "total_magnetization"]
# unicode literals have been reintroduced in py>3.2
expected_vals = [-191.33812137, -6.833504334642858, -2.551358929370749,
28, {k: v for k, v in {'P': 4, 'Fe': 4, 'O': 16, 'Li': 4}.items()},
"LiFePO4", True, ['Li', 'O', 'P', 'Fe'], 4, 0.0,
{k: v for k, v in {'Fe': 5.3, 'Li': 0.0, 'O': 0.0, 'P': 0.0}.items()}, True,
[u'mp-601412', u'mp-19017', u'mp-796535', u'mp-797820',
u'mp-540081', u'mp-797269'],
3.4662026991351147,
[159107, 154117, 160776, 99860, 181272, 166815,
260571, 92198, 165000, 155580, 38209, 161479, 153699,
260569, 260570, 200155, 260572, 181341, 181342,
72545, 56291, 97764, 162282, 155635],
16.0002716]
for (i, prop) in enumerate(props):
if prop not in ['hubbards', 'unit_cell_formula', 'elements',
'icsd_ids', 'task_ids']:
val = self.rester.get_data("mp-19017", prop=prop)[0][prop]
self.assertAlmostEqual(expected_vals[i], val)
elif prop in ["elements", "icsd_ids", "task_ids"]:
self.assertEqual(set(expected_vals[i]),
set(self.rester.get_data("mp-19017",
prop=prop)[0][prop]))
else:
self.assertEqual(expected_vals[i],
self.rester.get_data("mp-19017",
prop=prop)[0][prop])
props = ['structure', 'initial_structure', 'final_structure', 'entry']
for prop in props:
obj = self.rester.get_data("mp-19017", prop=prop)[0][prop]
if prop.endswith("structure"):
self.assertIsInstance(obj, Structure)
elif prop == "entry":
obj = self.rester.get_data("mp-19017", prop=prop)[0][prop]
self.assertIsInstance(obj, ComputedEntry)
#Test chemsys search
data = self.rester.get_data('Fe-Li-O', prop='unit_cell_formula')
self.assertTrue(len(data) > 1)
elements = {Element("Li"), Element("Fe"), Element("O")}
for d in data:
self.assertTrue(
set(Composition(d['unit_cell_formula']).elements).issubset(
elements))
self.assertRaises(MPRestError, self.rester.get_data, "Fe2O3",
"badmethod")
def test_get_materials_id_from_task_id(self):
self.assertEqual(self.rester.get_materials_id_from_task_id(
"mp-540081"), "mp-19017")
def test_get_materials_id_references(self):
# nosetests pymatgen/matproj/tests/test_matproj.py:MPResterTest.test_get_materials_id_references
m = MPRester()
data = m.get_materials_id_references('mp-123')
self.assertTrue(len(data) > 1000)
def test_find_structure(self):
# nosetests pymatgen/matproj/tests/test_matproj.py:MPResterTest.test_find_structure
m = MPRester()
ciffile = os.path.join(test_dir, 'Fe3O4.cif')
data = m.find_structure(ciffile)
self.assertTrue(len(data) > 1)
s = CifParser(ciffile).get_structures()[0]
data = m.find_structure(s)
self.assertTrue(len(data) > 1)
def test_get_entries_in_chemsys(self):
syms = ["Li", "Fe", "O"]
entries = self.rester.get_entries_in_chemsys(syms)
elements = set([Element(sym) for sym in syms])
for e in entries:
self.assertIsInstance(e, ComputedEntry)
self.assertTrue(set(e.composition.elements).issubset(elements))
def test_get_structure_by_material_id(self):
s1 = self.rester.get_structure_by_material_id("mp-1")
self.assertEqual(s1.formula, "Cs1")
def test_get_entry_by_material_id(self):
e = self.rester.get_entry_by_material_id("mp-19017")
self.assertIsInstance(e, ComputedEntry)
self.assertTrue(e.composition.reduced_formula, "LiFePO4")
def test_query(self):
criteria = {'elements': {'$in': ['Li', 'Na', 'K'], '$all': ['O']}}
props = ['pretty_formula', 'energy']
data = self.rester.query(criteria=criteria, properties=props)
self.assertTrue(len(data) > 6)
data = self.rester.query(criteria="*2O", properties=props)
self.assertGreaterEqual(len(data), 52)
self.assertIn("Li2O", (d["pretty_formula"] for d in data))
def test_get_exp_thermo_data(self):
data = self.rester.get_exp_thermo_data("Fe2O3")
self.assertTrue(len(data) > 0)
for d in data:
self.assertEqual(d.formula, "Fe2O3")
def test_get_dos_by_id(self):
dos = self.rester.get_dos_by_material_id("mp-2254")
self.assertIsInstance(dos, CompleteDos)
def test_get_bandstructure_by_material_id(self):
bs = self.rester.get_bandstructure_by_material_id("mp-2254")
self.assertIsInstance(bs, BandStructureSymmLine)
def test_get_structures(self):
structs = self.rester.get_structures("Mn3O4")
self.assertTrue(len(structs) > 0)
def test_get_entries(self):
entries = self.rester.get_entries("TiO2")
self.assertTrue(len(entries) > 1)
for e in entries:
self.assertEqual(e.composition.reduced_formula, "TiO2")
entries = self.rester.get_entries("TiO2", inc_structure="final")
self.assertTrue(len(entries) > 1)
for e in entries:
self.assertEqual(e.structure.composition.reduced_formula, "TiO2")
# all_entries = self.rester.get_entries("Fe", compatible_only=False)
# entries = self.rester.get_entries("Fe", compatible_only=True)
# self.assertTrue(len(entries) < len(all_entries))
entries = self.rester.get_entries("Fe", compatible_only=True,
property_data=["cif"])
self.assertIn("cif", entries[0].data)
for e in self.rester.get_entries("CdO2", inc_structure=False):
self.assertIsNotNone(e.data["oxide_type"])
def test_get_exp_entry(self):
entry = self.rester.get_exp_entry("Fe2O3")
self.assertEqual(entry.energy, -825.5)
def test_submit_query_delete_snl(self):
s = Structure([[5, 0, 0], [0, 5, 0], [0, 0, 5]], ["Fe"], [[0, 0, 0]])
# d = self.rester.submit_snl(
# [s, s], remarks=["unittest"],
# authors="Test User <*****@*****.**>")
# self.assertEqual(len(d), 2)
# data = self.rester.query_snl({"about.remarks": "unittest"})
# self.assertEqual(len(data), 2)
# snlids = [d["_id"] for d in data]
# self.rester.delete_snl(snlids)
# data = self.rester.query_snl({"about.remarks": "unittest"})
# self.assertEqual(len(data), 0)
def test_get_stability(self):
entries = self.rester.get_entries_in_chemsys(["Fe", "O"])
modified_entries = []
for entry in entries:
# Create modified entries with energies that are 0.01eV higher
# than the corresponding entries.
if entry.composition.reduced_formula == "Fe2O3":
modified_entries.append(
ComputedEntry(entry.composition,
entry.uncorrected_energy + 0.01,
parameters=entry.parameters,
entry_id="mod_{}".format(entry.entry_id)))
rest_ehulls = self.rester.get_stability(modified_entries)
all_entries = entries + modified_entries
compat = MaterialsProjectCompatibility()
all_entries = compat.process_entries(all_entries)
pd = PhaseDiagram(all_entries)
a = PDAnalyzer(pd)
for e in all_entries:
if str(e.entry_id).startswith("mod"):
for d in rest_ehulls:
if d["entry_id"] == e.entry_id:
data = d
break
self.assertAlmostEqual(a.get_e_above_hull(e),
data["e_above_hull"])
def test_get_reaction(self):
rxn = self.rester.get_reaction(["Li", "O"], ["Li2O"])
self.assertIn("Li2O", rxn["Experimental_references"])
def test_get_substrates(self):
substrate_data = self.rester.get_substrates('mp-123', 5, [1, 0, 0])
substrates = [sub_dict['sub_id'] for sub_dict in substrate_data]
self.assertIn("mp-2534", substrates)
def test_parse_criteria(self):
crit = MPRester.parse_criteria("mp-1234 Li-*")
self.assertIn("Li-O", crit["$or"][1]["chemsys"]["$in"])
self.assertIn({"task_id": "mp-1234"}, crit["$or"])
crit = MPRester.parse_criteria("Li2*")
self.assertIn("Li2O", crit["pretty_formula"]["$in"])
self.assertIn("Li2I", crit["pretty_formula"]["$in"])
self.assertIn("CsLi2", crit["pretty_formula"]["$in"])
crit = MPRester.parse_criteria("Li-*-*")
self.assertIn("Li-Re-Ru", crit["chemsys"]["$in"])
self.assertNotIn("Li-Li", crit["chemsys"]["$in"])
comps = MPRester.parse_criteria("**O3")["pretty_formula"]["$in"]
for c in comps:
self.assertEqual(len(Composition(c)), 3, "Failed in %s" % c)
chemsys = MPRester.parse_criteria("{Fe,Mn}-O")["chemsys"]["$in"]
self.assertEqual(len(chemsys), 2)
comps = MPRester.parse_criteria("{Fe,Mn,Co}O")["pretty_formula"]["$in"]
self.assertEqual(len(comps), 3, comps)
#Let's test some invalid symbols
self.assertRaises(ValueError, MPRester.parse_criteria, "li-fe")
self.assertRaises(ValueError, MPRester.parse_criteria, "LO2")
crit = MPRester.parse_criteria("POPO2")
self.assertIn("P2O3", crit["pretty_formula"]["$in"])
class MPResterTest(unittest.TestCase):
def setUp(self):
self.rester = MPRester()
def test_get_data(self):
props = ["energy", "energy_per_atom", "formation_energy_per_atom",
"nsites", "unit_cell_formula", "pretty_formula", "is_hubbard",
"elements", "nelements", "e_above_hull", "hubbards",
"is_compatible", "task_ids",
"density", "icsd_ids", "total_magnetization"]
# unicode literals have been reintroduced in py>3.2
expected_vals = [-191.33812137, -6.833504334642858, -2.551358929370749,
28, {k: v for k, v in {'P': 4, 'Fe': 4, 'O': 16, 'Li': 4}.items()},
"LiFePO4", True, ['Li', 'O', 'P', 'Fe'], 4, 0.0,
{k: v for k, v in {'Fe': 5.3, 'Li': 0.0, 'O': 0.0, 'P': 0.0}.items()}, True,
[u'mp-601412', u'mp-19017', u'mp-796535', u'mp-797820',
u'mp-540081', u'mp-797269'],
3.4662026991351147,
[159107, 154117, 160776, 99860, 181272, 166815,
260571, 92198, 165000, 155580, 38209, 161479, 153699,
260569, 260570, 200155, 260572, 181341, 181342,
72545, 56291, 97764, 162282, 155635],
16.0002716]
for (i, prop) in enumerate(props):
if prop not in ['hubbards', 'unit_cell_formula', 'elements',
'icsd_ids', 'task_ids']:
val = self.rester.get_data("mp-19017", prop=prop)[0][prop]
self.assertAlmostEqual(expected_vals[i], val)
elif prop in ["elements", "icsd_ids", "task_ids"]:
self.assertEqual(set(expected_vals[i]),
set(self.rester.get_data("mp-19017",
prop=prop)[0][prop]))
else:
self.assertEqual(expected_vals[i],
self.rester.get_data("mp-19017",
prop=prop)[0][prop])
props = ['structure', 'initial_structure', 'final_structure', 'entry']
for prop in props:
obj = self.rester.get_data("mp-19017", prop=prop)[0][prop]
if prop.endswith("structure"):
self.assertIsInstance(obj, Structure)
elif prop == "entry":
obj = self.rester.get_data("mp-19017", prop=prop)[0][prop]
self.assertIsInstance(obj, ComputedEntry)
#Test chemsys search
data = self.rester.get_data('Fe-Li-O', prop='unit_cell_formula')
self.assertTrue(len(data) > 1)
elements = {Element("Li"), Element("Fe"), Element("O")}
for d in data:
self.assertTrue(
set(Composition(d['unit_cell_formula']).elements).issubset(
elements))
self.assertRaises(MPRestError, self.rester.get_data, "Fe2O3",
"badmethod")
def test_get_materials_id_from_task_id(self):
self.assertEqual(self.rester.get_materials_id_from_task_id(
"mp-540081"), "mp-19017")
def test_get_materials_id_references(self):
# nosetests pymatgen/matproj/tests/test_matproj.py:MPResterTest.test_get_materials_id_references
m = MPRester()
data = m.get_materials_id_references('mp-123')
self.assertTrue(len(data) > 1000)
def test_find_structure(self):
# nosetests pymatgen/matproj/tests/test_matproj.py:MPResterTest.test_find_structure
m = MPRester()
ciffile = os.path.join(test_dir, 'Fe3O4.cif')
data = m.find_structure(ciffile)
self.assertTrue(len(data) > 1)
s = CifParser(ciffile).get_structures()[0]
data = m.find_structure(s)
self.assertTrue(len(data) > 1)
def test_get_entries_in_chemsys(self):
syms = ["Li", "Fe", "O"]
entries = self.rester.get_entries_in_chemsys(syms)
elements = set([Element(sym) for sym in syms])
for e in entries:
self.assertIsInstance(e, ComputedEntry)
self.assertTrue(set(e.composition.elements).issubset(elements))
def test_get_structure_by_material_id(self):
s1 = self.rester.get_structure_by_material_id("mp-1")
self.assertEqual(s1.formula, "Cs1")
def test_get_entry_by_material_id(self):
e = self.rester.get_entry_by_material_id("mp-19017")
self.assertIsInstance(e, ComputedEntry)
self.assertTrue(e.composition.reduced_formula, "LiFePO4")
def test_query(self):
criteria = {'elements': {'$in': ['Li', 'Na', 'K'], '$all': ['O']}}
props = ['pretty_formula', 'energy']
data = self.rester.query(criteria=criteria, properties=props)
self.assertTrue(len(data) > 6)
data = self.rester.query(criteria="*2O", properties=props)
self.assertGreaterEqual(len(data), 52)
self.assertIn("Li2O", (d["pretty_formula"] for d in data))
def test_get_exp_thermo_data(self):
data = self.rester.get_exp_thermo_data("Fe2O3")
self.assertTrue(len(data) > 0)
for d in data:
self.assertEqual(d.formula, "Fe2O3")
def test_get_dos_by_id(self):
dos = self.rester.get_dos_by_material_id("mp-2254")
self.assertIsInstance(dos, CompleteDos)
def test_get_bandstructure_by_material_id(self):
bs = self.rester.get_bandstructure_by_material_id("mp-2254")
self.assertIsInstance(bs, BandStructureSymmLine)
def test_get_structures(self):
structs = self.rester.get_structures("Mn3O4")
self.assertTrue(len(structs) > 0)
def test_get_entries(self):
entries = self.rester.get_entries("TiO2")
self.assertTrue(len(entries) > 1)
for e in entries:
self.assertEqual(e.composition.reduced_formula, "TiO2")
entries = self.rester.get_entries("TiO2", inc_structure="final")
self.assertTrue(len(entries) > 1)
for e in entries:
self.assertEqual(e.structure.composition.reduced_formula, "TiO2")
# all_entries = self.rester.get_entries("Fe", compatible_only=False)
# entries = self.rester.get_entries("Fe", compatible_only=True)
# self.assertTrue(len(entries) < len(all_entries))
entries = self.rester.get_entries("Fe", compatible_only=True,
property_data=["cif"])
self.assertIn("cif", entries[0].data)
for e in self.rester.get_entries("CdO2", inc_structure=False):
self.assertIsNotNone(e.data["oxide_type"])
def test_get_exp_entry(self):
entry = self.rester.get_exp_entry("Fe2O3")
self.assertEqual(entry.energy, -825.5)
def test_submit_query_delete_snl(self):
s = Structure([[5, 0, 0], [0, 5, 0], [0, 0, 5]], ["Fe"], [[0, 0, 0]])
# d = self.rester.submit_snl(
# [s, s], remarks=["unittest"],
# authors="Test User <*****@*****.**>")
# self.assertEqual(len(d), 2)
# data = self.rester.query_snl({"about.remarks": "unittest"})
# self.assertEqual(len(data), 2)
# snlids = [d["_id"] for d in data]
# self.rester.delete_snl(snlids)
# data = self.rester.query_snl({"about.remarks": "unittest"})
# self.assertEqual(len(data), 0)
def test_get_stability(self):
entries = self.rester.get_entries_in_chemsys(["Fe", "O"])
modified_entries = []
for entry in entries:
# Create modified entries with energies that are 0.01eV higher
# than the corresponding entries.
if entry.composition.reduced_formula == "Fe2O3":
modified_entries.append(
ComputedEntry(entry.composition,
entry.uncorrected_energy + 0.01,
parameters=entry.parameters,
entry_id="mod_{}".format(entry.entry_id)))
rest_ehulls = self.rester.get_stability(modified_entries)
all_entries = entries + modified_entries
compat = MaterialsProjectCompatibility()
all_entries = compat.process_entries(all_entries)
pd = PhaseDiagram(all_entries)
for e in all_entries:
if str(e.entry_id).startswith("mod"):
for d in rest_ehulls:
if d["entry_id"] == e.entry_id:
data = d
break
self.assertAlmostEqual(pd.get_e_above_hull(e),
data["e_above_hull"])
def test_get_reaction(self):
rxn = self.rester.get_reaction(["Li", "O"], ["Li2O"])
self.assertIn("Li2O", rxn["Experimental_references"])
def test_get_substrates(self):
substrate_data = self.rester.get_substrates('mp-123', 5, [1, 0, 0])
substrates = [sub_dict['sub_id'] for sub_dict in substrate_data]
self.assertIn("mp-2534", substrates)
def test_parse_criteria(self):
crit = MPRester.parse_criteria("mp-1234 Li-*")
self.assertIn("Li-O", crit["$or"][1]["chemsys"]["$in"])
self.assertIn({"task_id": "mp-1234"}, crit["$or"])
crit = MPRester.parse_criteria("Li2*")
self.assertIn("Li2O", crit["pretty_formula"]["$in"])
self.assertIn("Li2I", crit["pretty_formula"]["$in"])
self.assertIn("CsLi2", crit["pretty_formula"]["$in"])
crit = MPRester.parse_criteria("Li-*-*")
self.assertIn("Li-Re-Ru", crit["chemsys"]["$in"])
self.assertNotIn("Li-Li", crit["chemsys"]["$in"])
comps = MPRester.parse_criteria("**O3")["pretty_formula"]["$in"]
for c in comps:
self.assertEqual(len(Composition(c)), 3, "Failed in %s" % c)
chemsys = MPRester.parse_criteria("{Fe,Mn}-O")["chemsys"]["$in"]
self.assertEqual(len(chemsys), 2)
comps = MPRester.parse_criteria("{Fe,Mn,Co}O")["pretty_formula"]["$in"]
self.assertEqual(len(comps), 3, comps)
#Let's test some invalid symbols
self.assertRaises(ValueError, MPRester.parse_criteria, "li-fe")
self.assertRaises(ValueError, MPRester.parse_criteria, "LO2")
crit = MPRester.parse_criteria("POPO2")
self.assertIn("P2O3", crit["pretty_formula"]["$in"])
def compute_environments(chemenv_configuration):
string_sources = {
'cif': {
'string': 'a Cif file',
'regexp': '.*\.cif$'
},
'mp': {
'string': 'the Materials Project database',
'regexp': 'mp-[0-9]+$'
}
}
questions = {'c': 'cif'}
if chemenv_configuration.has_materials_project_access:
questions['m'] = 'mp'
lgf = LocalGeometryFinder()
lgf.setup_parameters()
allcg = AllCoordinationGeometries()
strategy_class = strategies_class_lookup[
chemenv_configuration.package_options['default_strategy']['strategy']]
#TODO: Add the possibility to change the parameters and save them in the chemenv_configuration
default_strategy = strategy_class()
default_strategy.setup_options(
chemenv_configuration.package_options['default_strategy']
['strategy_options'])
max_dist_factor = chemenv_configuration.package_options[
'default_max_distance_factor']
firsttime = True
while True:
if len(questions) > 1:
found = False
print(
'Enter the source from which the structure is coming or <q> to quit :'
)
for key_character, qq in questions.items():
print(' - <{}> for a structure from {}'.format(
key_character, string_sources[qq]['string']))
test = input(' ... ')
if test == 'q':
break
if test not in list(questions.keys()):
for key_character, qq in questions.items():
if re.match(string_sources[qq]['regexp'],
str(test)) is not None:
found = True
source_type = qq
if not found:
print('Wrong key, try again ...')
continue
else:
source_type = questions[test]
else:
found = False
source_type = list(questions.values())[0]
if found and len(questions) > 1:
input_source = test
if source_type == 'cif':
if not found:
input_source = input('Enter path to cif file : ')
cp = CifParser(input_source)
structure = cp.get_structures()[0]
elif source_type == 'mp':
if not found:
input_source = input(
'Enter materials project id (e.g. "mp-1902") : ')
a = MPRester()
structure = a.get_structure_by_material_id(input_source)
lgf.setup_structure(structure)
print('Computing environments for {} ... '.format(
structure.composition.reduced_formula))
se = lgf.compute_structure_environments(
maximum_distance_factor=max_dist_factor)
print('Computing environments finished')
while True:
test = input(
'See list of environments determined for each (unequivalent) site ? '
'("y" or "n", "d" with details, "g" to see the grid) : ')
strategy = default_strategy
if test in ['y', 'd', 'g']:
strategy.set_structure_environments(se)
for eqslist in se.equivalent_sites:
site = eqslist[0]
isite = se.structure.index(site)
try:
if strategy.uniquely_determines_coordination_environments:
ces = strategy.get_site_coordination_environments(
site)
else:
ces = strategy.get_site_coordination_environments_fractions(
site)
except NeighborsNotComputedChemenvError:
continue
if ces is None:
continue
if len(ces) == 0:
continue
comp = site.species_and_occu
#ce = strategy.get_site_coordination_environment(site)
if strategy.uniquely_determines_coordination_environments:
ce = ces[0]
if ce is None:
continue
thecg = allcg.get_geometry_from_mp_symbol(ce[0])
mystring = 'Environment for site #{} {} ({}) : {} ({})\n'.format(
str(isite),
comp.get_reduced_formula_and_factor()[0],
str(comp), thecg.name, ce[0])
else:
mystring = 'Environments for site #{} {} ({}) : \n'.format(
str(isite),
comp.get_reduced_formula_and_factor()[0],
str(comp))
for ce in ces:
cg = allcg.get_geometry_from_mp_symbol(ce[0])
csm = ce[1]['other_symmetry_measures'][
'csm_wcs_ctwcc']
mystring += ' - {} ({}): {:.2f} % (csm : {:2f})\n'.format(
cg.name, cg.mp_symbol, 100.0 * ce[2], csm)
if test in [
'd', 'g'
] and strategy.uniquely_determines_coordination_environments:
if thecg.mp_symbol != UNCLEAR_ENVIRONMENT_SYMBOL:
mystring += ' <Continuous symmetry measures> '
mingeoms = se.ce_list[isite][
thecg.
coordination_number][0].minimum_geometries()
for mingeom in mingeoms:
csm = mingeom[1]['other_symmetry_measures'][
'csm_wcs_ctwcc']
mystring += '{} : {:.2f} '.format(
mingeom[0], csm)
print(mystring)
if test == 'g':
test = input(
'Enter index of site(s) for which you want to see the grid of parameters : '
)
indices = list(map(int, test.split()))
print(indices)
for isite in indices:
se.plot_environments(isite,
additional_condition=se.AC.ONLY_ACB)
if no_vis:
test = input('Go to next structure ? ("y" to do so)')
if test == 'y':
break
continue
test = input(
'View structure with environments ? ("y" for the unit cell or "m" for a supercell or "n") : '
)
if test in ['y', 'm']:
if test == 'm':
mydeltas = []
test = input('Enter multiplicity (e.g. 3 2 2) : ')
nns = test.split()
for i0 in range(int(nns[0])):
for i1 in range(int(nns[1])):
for i2 in range(int(nns[2])):
mydeltas.append(
np.array([1.0 * i0, 1.0 * i1, 1.0 * i2],
np.float))
else:
mydeltas = [np.zeros(3, np.float)]
if firsttime:
vis = StructureVis(show_polyhedron=False,
show_unit_cell=True)
vis.show_help = False
firsttime = False
vis.set_structure(se.structure)
strategy.set_structure_environments(se)
for isite, site in enumerate(se.structure):
try:
ces = strategy.get_site_coordination_environments(site)
except NeighborsNotComputedChemenvError:
continue
if len(ces) == 0:
continue
ce = strategy.get_site_coordination_environment(site)
if ce is not None and ce[0] != UNCLEAR_ENVIRONMENT_SYMBOL:
for mydelta in mydeltas:
psite = PeriodicSite(site._species,
site._fcoords + mydelta,
site._lattice,
properties=site._properties)
vis.add_site(psite)
neighbors = strategy.get_site_neighbors(psite)
draw_cg(vis,
psite,
neighbors,
cg=lgf.allcg.get_geometry_from_mp_symbol(
ce[0]),
perm=ce[1]['permutation'])
vis.show()
test = input('Go to next structure ? ("y" to do so) : ')
if test == 'y':
break
print('')
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')
class MPResterTest(PymatgenTest):
_multiprocess_shared_ = True
def setUp(self):
self.rester = MPRester()
warnings.simplefilter("ignore")
def tearDown(self):
warnings.simplefilter("default")
self.rester.session.close()
def test_get_all_materials_ids_doc(self):
mids = self.rester.get_materials_ids("Al2O3")
random.shuffle(mids)
doc = self.rester.get_doc(mids.pop(0))
self.assertEqual(doc["pretty_formula"], "Al2O3")
def test_get_xas_data(self):
# Test getting XAS data
data = self.rester.get_xas_data("mp-19017", "Li")
self.assertEqual("mp-19017,Li", data["mid_and_el"])
self.assertAlmostEqual(data["spectrum"]["x"][0], 55.178, places=2)
self.assertAlmostEqual(data["spectrum"]["y"][0], 0.0164634, places=2)
def test_get_data(self):
props = [
"energy",
"energy_per_atom",
"formation_energy_per_atom",
"nsites",
"unit_cell_formula",
"pretty_formula",
"is_hubbard",
"elements",
"nelements",
"e_above_hull",
"hubbards",
"is_compatible",
"task_ids",
"density",
"icsd_ids",
"total_magnetization",
]
expected_vals = [
-191.7661349,
-6.848790532142857,
-2.5571951564625857,
28,
{
"P": 4,
"Fe": 4,
"O": 16,
"Li": 4
},
"LiFePO4",
True,
["Li", "O", "P", "Fe"],
4,
0.0,
{
"Fe": 5.3,
"Li": 0.0,
"O": 0.0,
"P": 0.0
},
True,
{"mp-19017", "mp-540081", "mp-601412"},
3.4708958823634912,
[
159107,
154117,
160776,
99860,
181272,
166815,
260571,
92198,
165000,
155580,
38209,
161479,
153699,
260569,
260570,
200155,
260572,
181341,
181342,
72545,
56291,
97764,
162282,
155635,
],
0,
]
for (i, prop) in enumerate(props):
if prop not in [
"hubbards",
"unit_cell_formula",
"elements",
"icsd_ids",
"task_ids",
]:
val = self.rester.get_data("mp-19017", prop=prop)[0][prop]
self.assertAlmostEqual(expected_vals[i], val, 2,
"Failed with property %s" % prop)
elif prop in ["elements", "icsd_ids", "task_ids"]:
upstream_vals = set(
self.rester.get_data("mp-19017", prop=prop)[0][prop])
self.assertLessEqual(set(expected_vals[i]), upstream_vals)
else:
self.assertEqual(
expected_vals[i],
self.rester.get_data("mp-19017", prop=prop)[0][prop],
)
props = ["structure", "initial_structure", "final_structure", "entry"]
for prop in props:
obj = self.rester.get_data("mp-19017", prop=prop)[0][prop]
if prop.endswith("structure"):
self.assertIsInstance(obj, Structure)
elif prop == "entry":
obj = self.rester.get_data("mp-19017", prop=prop)[0][prop]
self.assertIsInstance(obj, ComputedEntry)
# Test chemsys search
data = self.rester.get_data("Fe-Li-O", prop="unit_cell_formula")
self.assertTrue(len(data) > 1)
elements = {Element("Li"), Element("Fe"), Element("O")}
for d in data:
self.assertTrue(
set(Composition(
d["unit_cell_formula"]).elements).issubset(elements))
self.assertRaises(MPRestError, self.rester.get_data, "Fe2O3",
"badmethod")
# Test getting supported properties
self.assertNotEqual(self.rester.get_task_data("mp-30"), [])
# Test aliasing
data = self.rester.get_task_data("mp-30", "energy")
self.assertAlmostEqual(data[0]["energy"], -4.09929227, places=2)
def test_get_materials_id_from_task_id(self):
self.assertEqual(
self.rester.get_materials_id_from_task_id("mp-540081"), "mp-19017")
def test_get_materials_id_references(self):
# nosetests pymatgen/matproj/tests/test_matproj.py:MPResterTest.test_get_materials_id_references
m = MPRester()
data = m.get_materials_id_references("mp-123")
self.assertTrue(len(data) > 1000)
def test_find_structure(self):
# nosetests pymatgen/matproj/tests/test_matproj.py:MPResterTest.test_find_structure
m = MPRester()
ciffile = self.TEST_FILES_DIR / "Fe3O4.cif"
data = m.find_structure(str(ciffile))
self.assertTrue(len(data) > 1)
s = CifParser(ciffile).get_structures()[0]
data = m.find_structure(s)
self.assertTrue(len(data) > 1)
def test_get_entries_in_chemsys(self):
syms = ["Li", "Fe", "O"]
syms2 = "Li-Fe-O"
entries = self.rester.get_entries_in_chemsys(syms)
entries2 = self.rester.get_entries_in_chemsys(syms2)
elements = set([Element(sym) for sym in syms])
for e in entries:
self.assertIsInstance(e, ComputedEntry)
self.assertTrue(set(e.composition.elements).issubset(elements))
e1 = set([i.entry_id for i in entries])
e2 = set([i.entry_id for i in entries2])
self.assertTrue(e1 == e2)
def test_get_structure_by_material_id(self):
s1 = self.rester.get_structure_by_material_id("mp-1")
self.assertEqual(s1.formula, "Cs1")
# requesting via task-id instead of mp-id
self.assertWarns(Warning, self.rester.get_structure_by_material_id,
"mp-698856")
# requesting unknown mp-id
self.assertRaises(MPRestError,
self.rester.get_structure_by_material_id,
"mp-does-not-exist")
def test_get_entry_by_material_id(self):
e = self.rester.get_entry_by_material_id("mp-19017")
self.assertIsInstance(e, ComputedEntry)
self.assertTrue(e.composition.reduced_formula, "LiFePO4")
def test_query(self):
criteria = {"elements": {"$in": ["Li", "Na", "K"], "$all": ["O"]}}
props = ["pretty_formula", "energy"]
data = self.rester.query(criteria=criteria,
properties=props,
chunk_size=0)
self.assertTrue(len(data) > 6)
data = self.rester.query(criteria="*2O",
properties=props,
chunk_size=0)
self.assertGreaterEqual(len(data), 52)
self.assertIn("Li2O", (d["pretty_formula"] for d in data))
def test_query_chunk_size(self):
criteria = {"nelements": 2, "elements": "O"}
props = ["pretty_formula"]
data1 = self.rester.query(criteria=criteria,
properties=props,
chunk_size=0)
data2 = self.rester.query(criteria=criteria,
properties=props,
chunk_size=500)
self.assertEqual({d["pretty_formula"]
for d in data1},
{d["pretty_formula"]
for d in data2})
self.assertIn("Al2O3", {d["pretty_formula"] for d in data1})
def test_get_exp_thermo_data(self):
data = self.rester.get_exp_thermo_data("Fe2O3")
self.assertTrue(len(data) > 0)
for d in data:
self.assertEqual(d.formula, "Fe2O3")
def test_get_dos_by_id(self):
dos = self.rester.get_dos_by_material_id("mp-2254")
self.assertIsInstance(dos, CompleteDos)
def test_get_bandstructure_by_material_id(self):
bs = self.rester.get_bandstructure_by_material_id("mp-2254")
self.assertIsInstance(bs, BandStructureSymmLine)
bs_unif = self.rester.get_bandstructure_by_material_id("mp-2254",
line_mode=False)
self.assertIsInstance(bs_unif, BandStructure)
self.assertNotIsInstance(bs_unif, BandStructureSymmLine)
def test_get_phonon_data_by_material_id(self):
bs = self.rester.get_phonon_bandstructure_by_material_id("mp-661")
self.assertIsInstance(bs, PhononBandStructureSymmLine)
dos = self.rester.get_phonon_dos_by_material_id("mp-661")
self.assertIsInstance(dos, CompletePhononDos)
ddb_str = self.rester.get_phonon_ddb_by_material_id("mp-661")
self.assertIsInstance(ddb_str, str)
def test_get_structures(self):
structs = self.rester.get_structures("Mn3O4")
self.assertTrue(len(structs) > 0)
def test_get_entries(self):
entries = self.rester.get_entries("TiO2")
self.assertTrue(len(entries) > 1)
for e in entries:
self.assertEqual(e.composition.reduced_formula, "TiO2")
entries = self.rester.get_entries("TiO2", inc_structure=True)
self.assertTrue(len(entries) > 1)
for e in entries:
self.assertEqual(e.structure.composition.reduced_formula, "TiO2")
# all_entries = self.rester.get_entries("Fe", compatible_only=False)
# entries = self.rester.get_entries("Fe", compatible_only=True)
# self.assertTrue(len(entries) < len(all_entries))
entries = self.rester.get_entries("Fe",
compatible_only=True,
property_data=["cif"])
self.assertIn("cif", entries[0].data)
for e in self.rester.get_entries("CdO2", inc_structure=False):
self.assertIsNotNone(e.data["oxide_type"])
# test if it will retrieve the conventional unit cell of Ni
entry = self.rester.get_entry_by_material_id(
"mp-23", inc_structure=True, conventional_unit_cell=True)
Ni = entry.structure
self.assertEqual(Ni.lattice.a, Ni.lattice.b)
self.assertEqual(Ni.lattice.a, Ni.lattice.c)
self.assertEqual(Ni.lattice.alpha, 90)
self.assertEqual(Ni.lattice.beta, 90)
self.assertEqual(Ni.lattice.gamma, 90)
# Ensure energy per atom is same
primNi = self.rester.get_entry_by_material_id(
"mp-23", inc_structure=True, conventional_unit_cell=False)
self.assertEqual(primNi.energy_per_atom, entry.energy_per_atom)
Ni = self.rester.get_structure_by_material_id(
"mp-23", conventional_unit_cell=True)
self.assertEqual(Ni.lattice.a, Ni.lattice.b)
self.assertEqual(Ni.lattice.a, Ni.lattice.c)
self.assertEqual(Ni.lattice.alpha, 90)
self.assertEqual(Ni.lattice.beta, 90)
self.assertEqual(Ni.lattice.gamma, 90)
# Test case where convs are different from initial and final
# th = self.rester.get_structure_by_material_id(
# "mp-37", conventional_unit_cell=True)
# th_entry = self.rester.get_entry_by_material_id(
# "mp-37", inc_structure=True, conventional_unit_cell=True)
# th_entry_initial = self.rester.get_entry_by_material_id(
# "mp-37", inc_structure="initial", conventional_unit_cell=True)
# self.assertEqual(th, th_entry.structure)
# self.assertEqual(len(th_entry.structure), 4)
# self.assertEqual(len(th_entry_initial.structure), 2)
# Test if the polymorphs of Fe are properly sorted
# by e_above_hull when sort_by_e_above_hull=True
Fe_entries = self.rester.get_entries("Fe", sort_by_e_above_hull=True)
self.assertEqual(Fe_entries[0].data["e_above_hull"], 0)
def test_get_pourbaix_entries(self):
# test input chemsys as a list of elements
pbx_entries = self.rester.get_pourbaix_entries(["Fe", "Cr"])
for pbx_entry in pbx_entries:
self.assertTrue(isinstance(pbx_entry, PourbaixEntry))
# test input chemsys as a string
pbx_entries = self.rester.get_pourbaix_entries("Fe-Cr")
for pbx_entry in pbx_entries:
self.assertTrue(isinstance(pbx_entry, PourbaixEntry))
fe_two_plus = [e for e in pbx_entries if e.entry_id == "ion-0"][0]
self.assertAlmostEqual(fe_two_plus.energy,
-1.6228450214319294,
places=2)
feo2 = [e for e in pbx_entries if e.entry_id == "mp-25332"][0]
self.assertAlmostEqual(feo2.energy, 2.5523680849999995, places=2)
# Test S, which has Na in reference solids
pbx_entries = self.rester.get_pourbaix_entries(["S"])
so4_two_minus = pbx_entries[9]
self.assertAlmostEqual(so4_two_minus.energy,
0.0644980568750011,
places=2)
# Ensure entries are pourbaix compatible
PourbaixDiagram(pbx_entries)
def test_get_exp_entry(self):
entry = self.rester.get_exp_entry("Fe2O3")
self.assertEqual(entry.energy, -825.5)
# def test_submit_query_delete_snl(self):
# s = Structure([[5, 0, 0], [0, 5, 0], [0, 0, 5]], ["Fe"], [[0, 0, 0]])
# d = self.rester.submit_snl(
# [s, s], remarks=["unittest"],
# authors="Test User <*****@*****.**>")
# self.assertEqual(len(d), 2)
# data = self.rester.query_snl({"about.remarks": "unittest"})
# self.assertEqual(len(data), 2)
# snlids = [d["_id"] for d in data]
# self.rester.delete_snl(snlids)
# data = self.rester.query_snl({"about.remarks": "unittest"})
# self.assertEqual(len(data), 0)
def test_get_stability(self):
entries = self.rester.get_entries_in_chemsys(["Fe", "O"])
modified_entries = []
for entry in entries:
# Create modified entries with energies that are 0.01eV higher
# than the corresponding entries.
if entry.composition.reduced_formula == "Fe2O3":
modified_entries.append(
ComputedEntry(
entry.composition,
entry.uncorrected_energy + 0.01,
parameters=entry.parameters,
entry_id="mod_{}".format(entry.entry_id),
))
rest_ehulls = self.rester.get_stability(modified_entries)
all_entries = entries + modified_entries
compat = MaterialsProjectCompatibility()
all_entries = compat.process_entries(all_entries)
pd = PhaseDiagram(all_entries)
for e in all_entries:
if str(e.entry_id).startswith("mod"):
for d in rest_ehulls:
if d["entry_id"] == e.entry_id:
data = d
break
self.assertAlmostEqual(pd.get_e_above_hull(e),
data["e_above_hull"])
def test_get_reaction(self):
rxn = self.rester.get_reaction(["Li", "O"], ["Li2O"])
self.assertIn("Li2O", rxn["Experimental_references"])
def test_get_substrates(self):
substrate_data = self.rester.get_substrates("mp-123", 5, [1, 0, 0])
substrates = [sub_dict["sub_id"] for sub_dict in substrate_data]
self.assertIn("mp-2534", substrates)
def test_get_surface_data(self):
data = self.rester.get_surface_data("mp-126") # Pt
one_surf = self.rester.get_surface_data("mp-129",
miller_index=[-2, -3, 1])
self.assertAlmostEqual(one_surf["surface_energy"],
2.99156963,
places=2)
self.assertArrayAlmostEqual(one_surf["miller_index"], [3, 2, 1])
self.assertIn("surfaces", data)
surfaces = data["surfaces"]
self.assertTrue(len(surfaces) > 0)
surface = surfaces.pop()
self.assertIn("miller_index", surface)
self.assertIn("surface_energy", surface)
self.assertIn("is_reconstructed", surface)
data_inc = self.rester.get_surface_data("mp-126", inc_structures=True)
self.assertIn("structure", data_inc["surfaces"][0])
def test_get_wulff_shape(self):
ws = self.rester.get_wulff_shape("mp-126")
self.assertTrue(isinstance(ws, WulffShape))
def test_get_cohesive_energy(self):
ecoh = self.rester.get_cohesive_energy("mp-13")
self.assertTrue(ecoh, 5.04543279)
def test_get_gb_data(self):
mo_gbs = self.rester.get_gb_data(chemsys="Mo")
self.assertEqual(len(mo_gbs), 10)
mo_gbs_s5 = self.rester.get_gb_data(pretty_formula="Mo", sigma=5)
self.assertEqual(len(mo_gbs_s5), 3)
mo_s3_112 = self.rester.get_gb_data(
material_id="mp-129",
sigma=3,
gb_plane=[1, -1, -2],
include_work_of_separation=True,
)
self.assertEqual(len(mo_s3_112), 1)
gb_f = mo_s3_112[0]["final_structure"]
self.assertArrayAlmostEqual(gb_f.rotation_axis, [1, 1, 0])
self.assertAlmostEqual(gb_f.rotation_angle, 109.47122, places=4)
self.assertAlmostEqual(mo_s3_112[0]["gb_energy"], 0.47965, places=2)
self.assertAlmostEqual(mo_s3_112[0]["work_of_separation"],
6.318144,
places=2)
self.assertIn("Mo24", gb_f.formula)
hcp_s7 = self.rester.get_gb_data(material_id="mp-87",
gb_plane=[0, 0, 0, 1],
include_work_of_separation=True)
self.assertAlmostEqual(hcp_s7[0]["gb_energy"], 1.12, places=2)
self.assertAlmostEqual(hcp_s7[0]["work_of_separation"], 2.47, places=2)
def test_get_interface_reactions(self):
kinks = self.rester.get_interface_reactions("LiCoO2", "Li3PS4")
self.assertTrue(len(kinks) > 0)
kink = kinks[0]
self.assertIn("energy", kink)
self.assertIn("ratio_atomic", kink)
self.assertIn("rxn", kink)
self.assertTrue(isinstance(kink["rxn"], Reaction))
kinks_open_O = self.rester.get_interface_reactions("LiCoO2",
"Li3PS4",
open_el="O",
relative_mu=-1)
self.assertTrue(len(kinks_open_O) > 0)
with warnings.catch_warnings(record=True) as w:
warnings.filterwarnings("always", message="The reactant.+")
self.rester.get_interface_reactions("LiCoO2", "MnO9")
self.assertTrue("The reactant" in str(w[-1].message))
def test_download_info(self):
material_ids = ["mp-32800", "mp-23494"]
task_types = [TaskType.GGA_OPT, TaskType.GGA_UNIFORM]
file_patterns = ["vasprun*", "OUTCAR*"]
meta, urls = self.rester.get_download_info(material_ids,
task_types=task_types,
file_patterns=file_patterns)
self.assertDictEqual(
dict(meta),
{
"mp-23494": [{
"task_id": "mp-1752825",
"task_type": "GGA NSCF Uniform"
}],
"mp-32800": [{
"task_id": "mp-739635",
"task_type": "GGA NSCF Uniform"
}],
},
)
prefix = "http://labdev-nomad.esc.rzg.mpg.de/fairdi/nomad/mp/api/raw/query?"
# previous test
# ids = 'mp-23494,mp-688563,mp-32800,mp-746913'
ids = "mp-1752825,mp-739635"
self.assertEqual(
urls[0],
f"{prefix}file_pattern=vasprun*&file_pattern=OUTCAR*&external_id={ids}",
)
def test_parse_criteria(self):
crit = MPRester.parse_criteria("mp-1234 Li-*")
self.assertIn("Li-O", crit["$or"][1]["chemsys"]["$in"])
self.assertIn({"task_id": "mp-1234"}, crit["$or"])
crit = MPRester.parse_criteria("Li2*")
self.assertIn("Li2O", crit["pretty_formula"]["$in"])
self.assertIn("Li2I", crit["pretty_formula"]["$in"])
self.assertIn("CsLi2", crit["pretty_formula"]["$in"])
crit = MPRester.parse_criteria("Li-*-*")
self.assertIn("Li-Re-Ru", crit["chemsys"]["$in"])
self.assertNotIn("Li-Li", crit["chemsys"]["$in"])
comps = MPRester.parse_criteria("**O3")["pretty_formula"]["$in"]
for c in comps:
self.assertEqual(len(Composition(c)), 3, "Failed in %s" % c)
chemsys = MPRester.parse_criteria("{Fe,Mn}-O")["chemsys"]["$in"]
self.assertEqual(len(chemsys), 2)
comps = MPRester.parse_criteria("{Fe,Mn,Co}O")["pretty_formula"]["$in"]
self.assertEqual(len(comps), 3, comps)
# Let's test some invalid symbols
self.assertRaises(ValueError, MPRester.parse_criteria, "li-fe")
self.assertRaises(ValueError, MPRester.parse_criteria, "LO2")
crit = MPRester.parse_criteria("POPO2")
self.assertIn("P2O3", crit["pretty_formula"]["$in"])
def test_include_user_agent(self):
headers = self.rester.session.headers
self.assertIn("user-agent",
headers,
msg="Include user-agent header by default")
m = re.match(
r"pymatgen/(\d+)\.(\d+)\.(\d+)\.?(\d+)? \(Python/(\d+)\.(\d)+\.(\d+) ([^\/]*)/([^\)]*)\)",
headers["user-agent"],
)
self.assertIsNotNone(m,
msg="Unexpected user-agent value {}".format(
headers["user-agent"]))
self.rester = MPRester(include_user_agent=False)
self.assertNotIn("user-agent",
self.rester.session.headers,
msg="user-agent header unwanted")
def test_database_version(self):
with MPRester(notify_db_version=True) as mpr:
db_version = mpr.get_database_version()
self.assertIsInstance(db_version, str)
with open(SETTINGS_FILE, "rt") as f:
d = yaml.safe_load(f)
self.assertEqual(d["MAPI_DB_VERSION"]["LAST_ACCESSED"], db_version)
self.assertIsInstance(d["MAPI_DB_VERSION"]["LOG"][db_version], int)
def sol(self,
EB_K_2,
miller_index_2,
min_slab_size_2=8.0,
min_vacuum_size_2=15):
from pymatgen.analysis.adsorption import AdsorbateSiteFinder, plot_slab, reorient_z
from pymatgen.core.surface import Slab, SlabGenerator, generate_all_slabs, Structure, Lattice, ReconstructionGenerator
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.core.structure import Structure
from pymatgen.ext.matproj import MPRester
from matplotlib import pyplot as plt
from pymatgen.io.vasp.inputs import Poscar
from pymatgen.io.vasp.sets import MVLSlabSet
import shutil
import os
mpr = MPRester() #密钥
mp_id = self.mp_id #通过mp_id来索引结构
struct = mpr.get_structure_by_material_id(mp_id)
#获取结构信息
struct = SpacegroupAnalyzer(
struct).get_conventional_standard_structure()
#空间群分析
need_miller_index = miller_index_2 #通过米勒指数，确定要切的晶面
slab = SlabGenerator(struct, miller_index=need_miller_index, min_slab_size=min_slab_size_2,\
min_vacuum_size=min_vacuum_size_2, center_slab=True)
#晶面生成器参数
for n, slabs in enumerate(slab.get_slabs()):
slabs_bak = slabs.copy() #可能的晶面
slabs.make_supercell(self.supercell)
#晶胞扩充
A = Poscar(slabs) #将切面转换为Poscar
relax = A.structure #将Poscar 转换为结构信息
custom_settings = {"NPAR": 4} # 用户的INCAR 设置
relax = MVLSlabSet(relax, user_incar_settings=custom_settings)
#Vasp输入文件生成器
fig = plt.figure() #绘图--确立画布
ax = fig.add_subplot(111) #绘图--确立位置
plot_slab(slabs, ax, adsorption_sites=False) #绘图
dire = str(mp_id) + "---" + "sol" + str(EB_K_2) + str(
need_miller_index) + '----' + str(n)
#设置一个用作存储输入文件的名称
plt.savefig(dire) #将该名称用于保存图片
relax.write_input(dire) #将生成的VASP输入文件写入存储
os.chdir("./" + dire)
#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)
#将脚本写入VASP输入文件所在文件夹
eb = str(EB_K_2)
ls = str('TURE')
with open('INCAR', 'a') as file_object:
file_object.write('LSOL = ' + ls + '\n' + 'EB_K = ' + eb)
# os.chdir("../")
#将当前目录改为默认目录
os.chdir(r"D:\Desktop\VASP practical\workdir")
print(os.getcwd())
print('finished')
from pymatgen.ext.matproj import MPRester
from pymatgen.io.vasp.sets import MPRelaxSet, VaspInputSet
import pandas as pd
data = pd.read_csv('new_materials.csv')
mpr = MPRester()
user_incar_settings = {}
hubbard_off = False
i = 0
for mp_id in data['task_id']:
struct = mpr.get_structure_by_material_id(str(mp_id))
relaxed = MPRelaxSet(struct)
relaxed.write_input("/tmp/structs/%s_%s" % (mp_id, data['labels'].iloc[i]),
make_dir_if_not_present=True,
potcar_spec=True)
i += 1
class MPResterTest(unittest.TestCase):
def setUp(self):
self.rester = MPRester()
warnings.simplefilter("ignore")
def tearDown(self):
warnings.resetwarnings()
def test_get_all_materials_ids_doc(self):
mids = self.rester.get_materials_ids("Al2O3")
random.shuffle(mids)
doc = self.rester.get_doc(mids.pop(0))
self.assertEqual(doc["pretty_formula"], "Al2O3")
def test_get_data(self):
props = ["energy", "energy_per_atom", "formation_energy_per_atom",
"nsites", "unit_cell_formula", "pretty_formula", "is_hubbard",
"elements", "nelements", "e_above_hull", "hubbards",
"is_compatible", "task_ids",
"density", "icsd_ids", "total_magnetization"]
# unicode literals have been reintroduced in py>3.2
expected_vals = [-191.33812137, -6.833504334642858, -2.551358929370749,
28, {k: v for k, v in {'P': 4, 'Fe': 4, 'O': 16, 'Li': 4}.items()},
"LiFePO4", True, ['Li', 'O', 'P', 'Fe'], 4, 0.0,
{k: v for k, v in {'Fe': 5.3, 'Li': 0.0, 'O': 0.0, 'P': 0.0}.items()}, True,
[u'mp-601412', u'mp-19017', u'mp-796535', u'mp-797820',
u'mp-540081', u'mp-797269'],
3.4662026991351147,
[159107, 154117, 160776, 99860, 181272, 166815,
260571, 92198, 165000, 155580, 38209, 161479, 153699,
260569, 260570, 200155, 260572, 181341, 181342,
72545, 56291, 97764, 162282, 155635],
16.0002716]
for (i, prop) in enumerate(props):
if prop not in ['hubbards', 'unit_cell_formula', 'elements',
'icsd_ids', 'task_ids']:
val = self.rester.get_data("mp-19017", prop=prop)[0][prop]
self.assertAlmostEqual(expected_vals[i], val)
elif prop in ["elements", "icsd_ids", "task_ids"]:
self.assertEqual(set(expected_vals[i]),
set(self.rester.get_data("mp-19017",
prop=prop)[0][prop]))
else:
self.assertEqual(expected_vals[i],
self.rester.get_data("mp-19017",
prop=prop)[0][prop])
props = ['structure', 'initial_structure', 'final_structure', 'entry']
for prop in props:
obj = self.rester.get_data("mp-19017", prop=prop)[0][prop]
if prop.endswith("structure"):
self.assertIsInstance(obj, Structure)
elif prop == "entry":
obj = self.rester.get_data("mp-19017", prop=prop)[0][prop]
self.assertIsInstance(obj, ComputedEntry)
#Test chemsys search
data = self.rester.get_data('Fe-Li-O', prop='unit_cell_formula')
self.assertTrue(len(data) > 1)
elements = {Element("Li"), Element("Fe"), Element("O")}
for d in data:
self.assertTrue(
set(Composition(d['unit_cell_formula']).elements).issubset(
elements))
self.assertRaises(MPRestError, self.rester.get_data, "Fe2O3",
"badmethod")
def test_get_materials_id_from_task_id(self):
self.assertEqual(self.rester.get_materials_id_from_task_id(
"mp-540081"), "mp-19017")
def test_get_materials_id_references(self):
# nosetests pymatgen/matproj/tests/test_matproj.py:MPResterTest.test_get_materials_id_references
m = MPRester()
data = m.get_materials_id_references('mp-123')
self.assertTrue(len(data) > 1000)
def test_find_structure(self):
# nosetests pymatgen/matproj/tests/test_matproj.py:MPResterTest.test_find_structure
m = MPRester()
ciffile = os.path.join(test_dir, 'Fe3O4.cif')
data = m.find_structure(ciffile)
self.assertTrue(len(data) > 1)
s = CifParser(ciffile).get_structures()[0]
data = m.find_structure(s)
self.assertTrue(len(data) > 1)
def test_get_entries_in_chemsys(self):
syms = ["Li", "Fe", "O"]
entries = self.rester.get_entries_in_chemsys(syms)
elements = set([Element(sym) for sym in syms])
for e in entries:
self.assertIsInstance(e, ComputedEntry)
self.assertTrue(set(e.composition.elements).issubset(elements))
def test_get_structure_by_material_id(self):
s1 = self.rester.get_structure_by_material_id("mp-1")
self.assertEqual(s1.formula, "Cs1")
def test_get_entry_by_material_id(self):
e = self.rester.get_entry_by_material_id("mp-19017")
self.assertIsInstance(e, ComputedEntry)
self.assertTrue(e.composition.reduced_formula, "LiFePO4")
def test_query(self):
criteria = {'elements': {'$in': ['Li', 'Na', 'K'], '$all': ['O']}}
props = ['pretty_formula', 'energy']
data = self.rester.query(criteria=criteria, properties=props)
self.assertTrue(len(data) > 6)
data = self.rester.query(criteria="*2O", properties=props)
self.assertGreaterEqual(len(data), 52)
self.assertIn("Li2O", (d["pretty_formula"] for d in data))
def test_get_exp_thermo_data(self):
data = self.rester.get_exp_thermo_data("Fe2O3")
self.assertTrue(len(data) > 0)
for d in data:
self.assertEqual(d.formula, "Fe2O3")
def test_get_dos_by_id(self):
dos = self.rester.get_dos_by_material_id("mp-2254")
self.assertIsInstance(dos, CompleteDos)
def test_get_bandstructure_by_material_id(self):
bs = self.rester.get_bandstructure_by_material_id("mp-2254")
self.assertIsInstance(bs, BandStructureSymmLine)
bs_unif = self.rester.get_bandstructure_by_material_id(
"mp-2254", line_mode=False)
self.assertIsInstance(bs_unif, BandStructure)
self.assertNotIsInstance(bs_unif, BandStructureSymmLine)
def test_get_phonon_data_by_material_id(self):
bs = self.rester.get_phonon_bandstructure_by_material_id("mp-661")
self.assertIsInstance(bs, PhononBandStructureSymmLine)
dos = self.rester.get_phonon_dos_by_material_id("mp-661")
self.assertIsInstance(dos, CompletePhononDos)
ddb_str = self.rester.get_phonon_ddb_by_material_id("mp-661")
self.assertIsInstance(ddb_str, str)
def test_get_structures(self):
structs = self.rester.get_structures("Mn3O4")
self.assertTrue(len(structs) > 0)
def test_get_entries(self):
entries = self.rester.get_entries("TiO2")
self.assertTrue(len(entries) > 1)
for e in entries:
self.assertEqual(e.composition.reduced_formula, "TiO2")
entries = self.rester.get_entries("TiO2", inc_structure=True)
self.assertTrue(len(entries) > 1)
for e in entries:
self.assertEqual(e.structure.composition.reduced_formula, "TiO2")
# all_entries = self.rester.get_entries("Fe", compatible_only=False)
# entries = self.rester.get_entries("Fe", compatible_only=True)
# self.assertTrue(len(entries) < len(all_entries))
entries = self.rester.get_entries("Fe", compatible_only=True,
property_data=["cif"])
self.assertIn("cif", entries[0].data)
for e in self.rester.get_entries("CdO2", inc_structure=False):
self.assertIsNotNone(e.data["oxide_type"])
# test if it will retrieve the conventional unit cell of Ni
entry = self.rester.get_entry_by_material_id(
"mp-23", inc_structure=True, conventional_unit_cell=True)
Ni = entry.structure
self.assertEqual(Ni.lattice.a, Ni.lattice.b)
self.assertEqual(Ni.lattice.a, Ni.lattice.c)
self.assertEqual(Ni.lattice.alpha, 90)
self.assertEqual(Ni.lattice.beta, 90)
self.assertEqual(Ni.lattice.gamma, 90)
# Ensure energy per atom is same
primNi = self.rester.get_entry_by_material_id(
"mp-23", inc_structure=True, conventional_unit_cell=False)
self.assertEqual(primNi.energy_per_atom, entry.energy_per_atom)
Ni = self.rester.get_structure_by_material_id(
"mp-23", conventional_unit_cell=True)
self.assertEqual(Ni.lattice.a, Ni.lattice.b)
self.assertEqual(Ni.lattice.a, Ni.lattice.c)
self.assertEqual(Ni.lattice.alpha, 90)
self.assertEqual(Ni.lattice.beta, 90)
self.assertEqual(Ni.lattice.gamma, 90)
# Test case where convs are different from initial and final
th = self.rester.get_structure_by_material_id(
"mp-37", conventional_unit_cell=True)
th_entry = self.rester.get_entry_by_material_id(
"mp-37", inc_structure=True, conventional_unit_cell=True)
th_entry_initial = self.rester.get_entry_by_material_id(
"mp-37", inc_structure="initial", conventional_unit_cell=True)
self.assertEqual(th, th_entry.structure)
self.assertEqual(len(th_entry.structure), 4)
self.assertEqual(len(th_entry_initial.structure), 2)
def test_get_pourbaix_entries(self):
pbx_entries = self.rester.get_pourbaix_entries(["Fe"])
for pbx_entry in pbx_entries:
self.assertTrue(isinstance(pbx_entry, PourbaixEntry))
# Ensure entries are pourbaix compatible
pbx = PourbaixDiagram(pbx_entries)
# Try binary system
pbx_entries = self.rester.get_pourbaix_entries(["Fe", "Cr"])
pbx = PourbaixDiagram(pbx_entries)
# Test Zn-S, which has Na in reference solids
pbx_entries = self.rester.get_pourbaix_entries(["Zn", "S"])
def test_get_exp_entry(self):
entry = self.rester.get_exp_entry("Fe2O3")
self.assertEqual(entry.energy, -825.5)
def test_submit_query_delete_snl(self):
s = Structure([[5, 0, 0], [0, 5, 0], [0, 0, 5]], ["Fe"], [[0, 0, 0]])
# d = self.rester.submit_snl(
# [s, s], remarks=["unittest"],
# authors="Test User <*****@*****.**>")
# self.assertEqual(len(d), 2)
# data = self.rester.query_snl({"about.remarks": "unittest"})
# self.assertEqual(len(data), 2)
# snlids = [d["_id"] for d in data]
# self.rester.delete_snl(snlids)
# data = self.rester.query_snl({"about.remarks": "unittest"})
# self.assertEqual(len(data), 0)
def test_get_stability(self):
entries = self.rester.get_entries_in_chemsys(["Fe", "O"])
modified_entries = []
for entry in entries:
# Create modified entries with energies that are 0.01eV higher
# than the corresponding entries.
if entry.composition.reduced_formula == "Fe2O3":
modified_entries.append(
ComputedEntry(entry.composition,
entry.uncorrected_energy + 0.01,
parameters=entry.parameters,
entry_id="mod_{}".format(entry.entry_id)))
rest_ehulls = self.rester.get_stability(modified_entries)
all_entries = entries + modified_entries
compat = MaterialsProjectCompatibility()
all_entries = compat.process_entries(all_entries)
pd = PhaseDiagram(all_entries)
for e in all_entries:
if str(e.entry_id).startswith("mod"):
for d in rest_ehulls:
if d["entry_id"] == e.entry_id:
data = d
break
self.assertAlmostEqual(pd.get_e_above_hull(e),
data["e_above_hull"])
def test_get_reaction(self):
rxn = self.rester.get_reaction(["Li", "O"], ["Li2O"])
self.assertIn("Li2O", rxn["Experimental_references"])
def test_get_substrates(self):
substrate_data = self.rester.get_substrates('mp-123', 5, [1, 0, 0])
substrates = [sub_dict['sub_id'] for sub_dict in substrate_data]
self.assertIn("mp-2534", substrates)
def test_get_surface_data(self):
data = self.rester.get_surface_data("mp-126") # Pt
self.assertIn("surfaces", data)
surfaces = data["surfaces"]
self.assertTrue(len(surfaces) > 0)
surface = surfaces.pop()
self.assertIn("miller_index", surface)
self.assertIn("surface_energy", surface)
self.assertIn("is_reconstructed", surface)
data_inc = self.rester.get_surface_data("mp-126", inc_structures=True)
self.assertIn("structure", data_inc["surfaces"][0])
def test_get_wulff_shape(self):
ws = self.rester.get_wulff_shape("mp-126")
self.assertTrue(isinstance(ws, WulffShape))
def test_get_interface_reactions(self):
kinks = self.rester.get_interface_reactions("LiCoO2", "Li3PS4")
self.assertTrue(len(kinks) > 0)
kink = kinks[0]
self.assertIn("energy", kink)
self.assertIn("ratio", kink)
self.assertIn("rxn", kink)
self.assertTrue(isinstance(kink['rxn'], Reaction))
kinks_open_O = self.rester.get_interface_reactions(
"LiCoO2", "Li3PS4", open_el="O", relative_mu=-1)
self.assertTrue(len(kinks_open_O) > 0)
with warnings.catch_warnings(record=True) as w:
warnings.filterwarnings("always", message="The reactant.+")
self.rester.get_interface_reactions("LiCoO2", "MnO3")
self.assertTrue("The reactant" in str(w[-1].message))
def test_parse_criteria(self):
crit = MPRester.parse_criteria("mp-1234 Li-*")
self.assertIn("Li-O", crit["$or"][1]["chemsys"]["$in"])
self.assertIn({"task_id": "mp-1234"}, crit["$or"])
crit = MPRester.parse_criteria("Li2*")
self.assertIn("Li2O", crit["pretty_formula"]["$in"])
self.assertIn("Li2I", crit["pretty_formula"]["$in"])
self.assertIn("CsLi2", crit["pretty_formula"]["$in"])
crit = MPRester.parse_criteria("Li-*-*")
self.assertIn("Li-Re-Ru", crit["chemsys"]["$in"])
self.assertNotIn("Li-Li", crit["chemsys"]["$in"])
comps = MPRester.parse_criteria("**O3")["pretty_formula"]["$in"]
for c in comps:
self.assertEqual(len(Composition(c)), 3, "Failed in %s" % c)
chemsys = MPRester.parse_criteria("{Fe,Mn}-O")["chemsys"]["$in"]
self.assertEqual(len(chemsys), 2)
comps = MPRester.parse_criteria("{Fe,Mn,Co}O")["pretty_formula"]["$in"]
self.assertEqual(len(comps), 3, comps)
#Let's test some invalid symbols
self.assertRaises(ValueError, MPRester.parse_criteria, "li-fe")
self.assertRaises(ValueError, MPRester.parse_criteria, "LO2")
crit = MPRester.parse_criteria("POPO2")
self.assertIn("P2O3", crit["pretty_formula"]["$in"])
class MPResterTest(PymatgenTest):
_multiprocess_shared_ = True
def setUp(self):
self.rester = MPRester()
warnings.simplefilter("ignore")
def tearDown(self):
warnings.simplefilter("default")
self.rester.session.close()
def test_get_all_materials_ids_doc(self):
mids = self.rester.get_materials_ids("Al2O3")
random.shuffle(mids)
doc = self.rester.get_doc(mids.pop(0))
self.assertEqual(doc["pretty_formula"], "Al2O3")
def test_get_xas_data(self):
# Test getting XAS data
data = self.rester.get_xas_data("mp-19017", "Li")
self.assertEqual("mp-19017,Li", data['mid_and_el'])
self.assertAlmostEqual(data['spectrum']['x'][0], 55.178, places=2)
self.assertAlmostEqual(data['spectrum']['y'][0], 0.0164634, places=2)
def test_get_data(self):
props = ["energy", "energy_per_atom", "formation_energy_per_atom",
"nsites", "unit_cell_formula", "pretty_formula", "is_hubbard",
"elements", "nelements", "e_above_hull", "hubbards",
"is_compatible", "task_ids",
"density", "icsd_ids", "total_magnetization"]
# unicode literals have been reintroduced in py>3.2
expected_vals = [-191.3359011, -6.833425039285714, -2.5515769497278913,
28, {'P': 4, 'Fe': 4, 'O': 16, 'Li': 4},
"LiFePO4", True, ['Li', 'O', 'P', 'Fe'], 4, 0.0,
{'Fe': 5.3, 'Li': 0.0, 'O': 0.0, 'P': 0.0}, True,
{'mp-19017', 'mp-540081', 'mp-601412'},
3.464840709092822,
[159107, 154117, 160776, 99860, 181272, 166815,
260571, 92198, 165000, 155580, 38209, 161479, 153699,
260569, 260570, 200155, 260572, 181341, 181342,
72545, 56291, 97764, 162282, 155635],
15.9996841]
for (i, prop) in enumerate(props):
if prop not in ['hubbards', 'unit_cell_formula', 'elements',
'icsd_ids', 'task_ids']:
val = self.rester.get_data("mp-19017", prop=prop)[0][prop]
self.assertAlmostEqual(expected_vals[i], val, places=2)
elif prop in ["elements", "icsd_ids", "task_ids"]:
upstream_vals = set(
self.rester.get_data("mp-19017", prop=prop)[0][prop])
self.assertLessEqual(set(expected_vals[i]), upstream_vals)
else:
self.assertEqual(expected_vals[i],
self.rester.get_data("mp-19017",
prop=prop)[0][prop])
props = ['structure', 'initial_structure', 'final_structure', 'entry']
for prop in props:
obj = self.rester.get_data("mp-19017", prop=prop)[0][prop]
if prop.endswith("structure"):
self.assertIsInstance(obj, Structure)
elif prop == "entry":
obj = self.rester.get_data("mp-19017", prop=prop)[0][prop]
self.assertIsInstance(obj, ComputedEntry)
# Test chemsys search
data = self.rester.get_data('Fe-Li-O', prop='unit_cell_formula')
self.assertTrue(len(data) > 1)
elements = {Element("Li"), Element("Fe"), Element("O")}
for d in data:
self.assertTrue(
set(Composition(d['unit_cell_formula']).elements).issubset(
elements))
self.assertRaises(MPRestError, self.rester.get_data, "Fe2O3",
"badmethod")
def test_get_data(self):
# Test getting supported properties
self.assertNotEqual(self.rester.get_task_data("mp-30"), [])
# Test aliasing
data = self.rester.get_task_data("mp-30", "energy")
self.assertAlmostEqual(data[0]["energy"], -4.09929227, places=2)
def test_get_materials_id_from_task_id(self):
self.assertEqual(self.rester.get_materials_id_from_task_id(
"mp-540081"), "mp-19017")
def test_get_materials_id_references(self):
# nosetests pymatgen/matproj/tests/test_matproj.py:MPResterTest.test_get_materials_id_references
m = MPRester()
data = m.get_materials_id_references('mp-123')
self.assertTrue(len(data) > 1000)
def test_find_structure(self):
# nosetests pymatgen/matproj/tests/test_matproj.py:MPResterTest.test_find_structure
m = MPRester()
ciffile = self.TEST_FILES_DIR / 'Fe3O4.cif'
data = m.find_structure(str(ciffile))
self.assertTrue(len(data) > 1)
s = CifParser(ciffile).get_structures()[0]
data = m.find_structure(s)
self.assertTrue(len(data) > 1)
def test_get_entries_in_chemsys(self):
syms = ["Li", "Fe", "O"]
entries = self.rester.get_entries_in_chemsys(syms)
elements = set([Element(sym) for sym in syms])
for e in entries:
self.assertIsInstance(e, ComputedEntry)
self.assertTrue(set(e.composition.elements).issubset(elements))
def test_get_structure_by_material_id(self):
s1 = self.rester.get_structure_by_material_id("mp-1")
self.assertEqual(s1.formula, "Cs1")
def test_get_entry_by_material_id(self):
e = self.rester.get_entry_by_material_id("mp-19017")
self.assertIsInstance(e, ComputedEntry)
self.assertTrue(e.composition.reduced_formula, "LiFePO4")
def test_query(self):
criteria = {'elements': {'$in': ['Li', 'Na', 'K'], '$all': ['O']}}
props = ['pretty_formula', 'energy']
data = self.rester.query(
criteria=criteria, properties=props, chunk_size=0)
self.assertTrue(len(data) > 6)
data = self.rester.query(
criteria="*2O", properties=props, chunk_size=0)
self.assertGreaterEqual(len(data), 52)
self.assertIn("Li2O", (d["pretty_formula"] for d in data))
def test_query_chunk_size(self):
criteria = {"nelements": 2, "elements": "O"}
props = ['pretty_formula']
data1 = self.rester.query(
criteria=criteria, properties=props, chunk_size=0)
data2 = self.rester.query(
criteria=criteria, properties=props, chunk_size=500)
self.assertEqual({d['pretty_formula'] for d in data1},
{d['pretty_formula'] for d in data2})
self.assertIn("Al2O3", {d['pretty_formula'] for d in data1})
def test_get_exp_thermo_data(self):
data = self.rester.get_exp_thermo_data("Fe2O3")
self.assertTrue(len(data) > 0)
for d in data:
self.assertEqual(d.formula, "Fe2O3")
def test_get_dos_by_id(self):
dos = self.rester.get_dos_by_material_id("mp-2254")
self.assertIsInstance(dos, CompleteDos)
def test_get_bandstructure_by_material_id(self):
bs = self.rester.get_bandstructure_by_material_id("mp-2254")
self.assertIsInstance(bs, BandStructureSymmLine)
bs_unif = self.rester.get_bandstructure_by_material_id(
"mp-2254", line_mode=False)
self.assertIsInstance(bs_unif, BandStructure)
self.assertNotIsInstance(bs_unif, BandStructureSymmLine)
def test_get_phonon_data_by_material_id(self):
bs = self.rester.get_phonon_bandstructure_by_material_id("mp-661")
self.assertIsInstance(bs, PhononBandStructureSymmLine)
dos = self.rester.get_phonon_dos_by_material_id("mp-661")
self.assertIsInstance(dos, CompletePhononDos)
ddb_str = self.rester.get_phonon_ddb_by_material_id("mp-661")
self.assertIsInstance(ddb_str, str)
def test_get_structures(self):
structs = self.rester.get_structures("Mn3O4")
self.assertTrue(len(structs) > 0)
def test_get_entries(self):
entries = self.rester.get_entries("TiO2")
self.assertTrue(len(entries) > 1)
for e in entries:
self.assertEqual(e.composition.reduced_formula, "TiO2")
entries = self.rester.get_entries("TiO2", inc_structure=True)
self.assertTrue(len(entries) > 1)
for e in entries:
self.assertEqual(e.structure.composition.reduced_formula, "TiO2")
# all_entries = self.rester.get_entries("Fe", compatible_only=False)
# entries = self.rester.get_entries("Fe", compatible_only=True)
# self.assertTrue(len(entries) < len(all_entries))
entries = self.rester.get_entries("Fe", compatible_only=True,
property_data=["cif"])
self.assertIn("cif", entries[0].data)
for e in self.rester.get_entries("CdO2", inc_structure=False):
self.assertIsNotNone(e.data["oxide_type"])
# test if it will retrieve the conventional unit cell of Ni
entry = self.rester.get_entry_by_material_id(
"mp-23", inc_structure=True, conventional_unit_cell=True)
Ni = entry.structure
self.assertEqual(Ni.lattice.a, Ni.lattice.b)
self.assertEqual(Ni.lattice.a, Ni.lattice.c)
self.assertEqual(Ni.lattice.alpha, 90)
self.assertEqual(Ni.lattice.beta, 90)
self.assertEqual(Ni.lattice.gamma, 90)
# Ensure energy per atom is same
primNi = self.rester.get_entry_by_material_id(
"mp-23", inc_structure=True, conventional_unit_cell=False)
self.assertEqual(primNi.energy_per_atom, entry.energy_per_atom)
Ni = self.rester.get_structure_by_material_id(
"mp-23", conventional_unit_cell=True)
self.assertEqual(Ni.lattice.a, Ni.lattice.b)
self.assertEqual(Ni.lattice.a, Ni.lattice.c)
self.assertEqual(Ni.lattice.alpha, 90)
self.assertEqual(Ni.lattice.beta, 90)
self.assertEqual(Ni.lattice.gamma, 90)
# Test case where convs are different from initial and final
th = self.rester.get_structure_by_material_id(
"mp-37", conventional_unit_cell=True)
th_entry = self.rester.get_entry_by_material_id(
"mp-37", inc_structure=True, conventional_unit_cell=True)
th_entry_initial = self.rester.get_entry_by_material_id(
"mp-37", inc_structure="initial", conventional_unit_cell=True)
self.assertEqual(th, th_entry.structure)
self.assertEqual(len(th_entry.structure), 4)
self.assertEqual(len(th_entry_initial.structure), 2)
# Test if the polymorphs of Fe are properly sorted
# by e_above_hull when sort_by_e_above_hull=True
Fe_entries = self.rester.get_entries("Fe", sort_by_e_above_hull=True)
self.assertEqual(Fe_entries[0].data["e_above_hull"], 0)
def test_get_pourbaix_entries(self):
pbx_entries = self.rester.get_pourbaix_entries(["Fe", "Cr"])
for pbx_entry in pbx_entries:
self.assertTrue(isinstance(pbx_entry, PourbaixEntry))
# Ensure entries are pourbaix compatible
pbx = PourbaixDiagram(pbx_entries)
# Try binary system
#pbx_entries = self.rester.get_pourbaix_entries(["Fe", "Cr"])
#pbx = PourbaixDiagram(pbx_entries)
# TODO: Shyue Ping: I do not understand this test. You seem to
# be grabbing Zn-S system, but I don't see proper test for anything,
# including Na ref. This test also takes a long time.
# Test Zn-S, which has Na in reference solids
# pbx_entries = self.rester.get_pourbaix_entries(["Zn", "S"])
def test_get_exp_entry(self):
entry = self.rester.get_exp_entry("Fe2O3")
self.assertEqual(entry.energy, -825.5)
def test_submit_query_delete_snl(self):
s = Structure([[5, 0, 0], [0, 5, 0], [0, 0, 5]], ["Fe"], [[0, 0, 0]])
# d = self.rester.submit_snl(
# [s, s], remarks=["unittest"],
# authors="Test User <*****@*****.**>")
# self.assertEqual(len(d), 2)
# data = self.rester.query_snl({"about.remarks": "unittest"})
# self.assertEqual(len(data), 2)
# snlids = [d["_id"] for d in data]
# self.rester.delete_snl(snlids)
# data = self.rester.query_snl({"about.remarks": "unittest"})
# self.assertEqual(len(data), 0)
def test_get_stability(self):
entries = self.rester.get_entries_in_chemsys(["Fe", "O"])
modified_entries = []
for entry in entries:
# Create modified entries with energies that are 0.01eV higher
# than the corresponding entries.
if entry.composition.reduced_formula == "Fe2O3":
modified_entries.append(
ComputedEntry(entry.composition,
entry.uncorrected_energy + 0.01,
parameters=entry.parameters,
entry_id="mod_{}".format(entry.entry_id)))
rest_ehulls = self.rester.get_stability(modified_entries)
all_entries = entries + modified_entries
compat = MaterialsProjectCompatibility()
all_entries = compat.process_entries(all_entries)
pd = PhaseDiagram(all_entries)
for e in all_entries:
if str(e.entry_id).startswith("mod"):
for d in rest_ehulls:
if d["entry_id"] == e.entry_id:
data = d
break
self.assertAlmostEqual(pd.get_e_above_hull(e),
data["e_above_hull"])
def test_get_reaction(self):
rxn = self.rester.get_reaction(["Li", "O"], ["Li2O"])
self.assertIn("Li2O", rxn["Experimental_references"])
def test_get_substrates(self):
substrate_data = self.rester.get_substrates('mp-123', 5, [1, 0, 0])
substrates = [sub_dict['sub_id'] for sub_dict in substrate_data]
self.assertIn("mp-2534", substrates)
def test_get_surface_data(self):
data = self.rester.get_surface_data("mp-126") # Pt
one_surf = self.rester.get_surface_data('mp-129', miller_index=[-2, -3, 1])
self.assertAlmostEqual(one_surf['surface_energy'], 2.99156963, places=2)
self.assertArrayAlmostEqual(one_surf['miller_index'], [3, 2, 1])
self.assertIn("surfaces", data)
surfaces = data["surfaces"]
self.assertTrue(len(surfaces) > 0)
surface = surfaces.pop()
self.assertIn("miller_index", surface)
self.assertIn("surface_energy", surface)
self.assertIn("is_reconstructed", surface)
data_inc = self.rester.get_surface_data("mp-126", inc_structures=True)
self.assertIn("structure", data_inc["surfaces"][0])
def test_get_wulff_shape(self):
ws = self.rester.get_wulff_shape("mp-126")
self.assertTrue(isinstance(ws, WulffShape))
def test_get_cohesive_energy(self):
ecoh = self.rester.get_cohesive_energy("mp-13")
self.assertTrue(ecoh, 5.04543279)
def test_get_gb_data(self):
mo_gbs = self.rester.get_gb_data(chemsys='Mo')
self.assertEqual(len(mo_gbs), 10)
mo_gbs_s5 = self.rester.get_gb_data(pretty_formula='Mo', sigma=5)
self.assertEqual(len(mo_gbs_s5), 3)
mo_s3_112 = self.rester.get_gb_data(material_id='mp-129', sigma=3,
gb_plane=[1, -1, -2],
include_work_of_separation=True)
self.assertEqual(len(mo_s3_112), 1)
gb_f = mo_s3_112[0]['final_structure']
self.assertArrayAlmostEqual(gb_f.rotation_axis, [1, 1, 0])
self.assertAlmostEqual(gb_f.rotation_angle, 109.47122, places=4)
self.assertAlmostEqual(mo_s3_112[0]['gb_energy'], 0.47965, places=2)
self.assertAlmostEqual(mo_s3_112[0]['work_of_separation'], 6.318144, places=2)
self.assertIn("Mo24", gb_f.formula)
hcp_s7 = self.rester.get_gb_data(material_id='mp-87', gb_plane=[0, 0, 0, 1],
include_work_of_separation=True)
self.assertAlmostEqual(hcp_s7[0]['gb_energy'], 1.12, places=2)
self.assertAlmostEqual(hcp_s7[0]['work_of_separation'], 2.46, places=2)
def test_get_interface_reactions(self):
kinks = self.rester.get_interface_reactions("LiCoO2", "Li3PS4")
self.assertTrue(len(kinks) > 0)
kink = kinks[0]
self.assertIn("energy", kink)
self.assertIn("ratio_atomic", kink)
self.assertIn("rxn", kink)
self.assertTrue(isinstance(kink['rxn'], Reaction))
kinks_open_O = self.rester.get_interface_reactions(
"LiCoO2", "Li3PS4", open_el="O", relative_mu=-1)
self.assertTrue(len(kinks_open_O) > 0)
with warnings.catch_warnings(record=True) as w:
warnings.filterwarnings("always", message="The reactant.+")
self.rester.get_interface_reactions("LiCoO2", "MnO9")
self.assertTrue("The reactant" in str(w[-1].message))
def test_parse_criteria(self):
crit = MPRester.parse_criteria("mp-1234 Li-*")
self.assertIn("Li-O", crit["$or"][1]["chemsys"]["$in"])
self.assertIn({"task_id": "mp-1234"}, crit["$or"])
crit = MPRester.parse_criteria("Li2*")
self.assertIn("Li2O", crit["pretty_formula"]["$in"])
self.assertIn("Li2I", crit["pretty_formula"]["$in"])
self.assertIn("CsLi2", crit["pretty_formula"]["$in"])
crit = MPRester.parse_criteria("Li-*-*")
self.assertIn("Li-Re-Ru", crit["chemsys"]["$in"])
self.assertNotIn("Li-Li", crit["chemsys"]["$in"])
comps = MPRester.parse_criteria("**O3")["pretty_formula"]["$in"]
for c in comps:
self.assertEqual(len(Composition(c)), 3, "Failed in %s" % c)
chemsys = MPRester.parse_criteria("{Fe,Mn}-O")["chemsys"]["$in"]
self.assertEqual(len(chemsys), 2)
comps = MPRester.parse_criteria("{Fe,Mn,Co}O")["pretty_formula"]["$in"]
self.assertEqual(len(comps), 3, comps)
#Let's test some invalid symbols
self.assertRaises(ValueError, MPRester.parse_criteria, "li-fe")
self.assertRaises(ValueError, MPRester.parse_criteria, "LO2")
crit = MPRester.parse_criteria("POPO2")
self.assertIn("P2O3", crit["pretty_formula"]["$in"])
def test_include_user_agent(self):
headers = self.rester.session.headers
self.assertIn("user-agent", headers, msg="Include user-agent header by default")
m = re.match(
r"pymatgen/(\d+)\.(\d+)\.(\d+) \(Python/(\d+)\.(\d)+\.(\d+) ([^\/]*)/([^\)]*)\)",
headers['user-agent'])
self.assertIsNotNone(m, msg="Unexpected user-agent value {}".format(headers['user-agent']))
self.assertEqual(m.groups()[:3], tuple(pmg_version.split(".")))
self.assertEqual(
m.groups()[3:6],
tuple(str(n) for n in (sys.version_info.major, sys.version_info.minor, sys.version_info.micro))
)
self.rester = MPRester(include_user_agent=False)
self.assertNotIn("user-agent", self.rester.session.headers, msg="user-agent header unwanted")
class mp_query(object):
def __init__(self, api_key):
self.mpr = MPRester(api_key)
def find_access_strings(self, search):
data = self.mpr.get_data(search)
material_ids = [datum['material_id'] for datum in data]
return material_ids
def mp_structure(self, material_id, standardize=True):
struct = self.mpr.get_structure_by_material_id(material_id)
if standardize:
struct = SpacegroupAnalyzer(struct).get_conventional_standard_structure()
return struct
def make_structures(self, search):
material_ids = self.find_access_strings(search)
structures = []
for ID in material_ids:
struct = self.mp_structure(ID)
structures.append(struct)
return structures
def search_summary(self, search, print_energies=True, barplot=False, write_files=False, format='cif'):
data = self.mpr.get_data(search)
energies = []
for datum in data:
f = datum['pretty_formula']
sn = str(datum['spacegroup']['number'])
ss = datum['spacegroup']['symbol']
i = datum['material_id']
te = float(datum['energy'])
ae = float(datum['energy_per_atom'])
struct = self.mp_structure(i, standardize=False)
ase_atoms = AseAtomsAdaptor.get_atoms(struct)
composition = ase_atoms.get_chemical_formula()
if write_files:
write(f + '_' + sn + '.' + format, ase_atoms, format=format)
energies.append((f, sn, ss, te, ae, composition))
energies.sort(key = lambda x: x[4])
if print_energies:
print('formula spacegroup_number spacegroup_symbol total_energy energy_per_atom composition')
for l in energies:
print('{:7} {:<17} {:<17} {:<12.5f} {:<15f} {:<11}'.format(*l))
if barplot:
energies = np.asarray(energies)
epa = np.array(map(float, energies[:,4]))
epa -= min(epa)
xticks = [i + '_' + j for i,j in energies[:,0:2]]
ind = np.arange(len(energies))
fig = plt.figure()
plt.ylabel('Relative energy per atom / eV')
plt.xlabel('Material')
plt.xticks(ind, xticks, rotation=90)
fig.set_size_inches(6.5,3)
plt.savefig(search + '.tiff', dpi=300, bbox_inches='tight')
