from pymatgen import MPRester, Structure
from pymatgen.command_line.gulp_caller import GulpCaller, GulpIO
from matplotlib import pyplot
mpr = MPRester()
mono: Structure = mpr.get_structure_by_material_id('mp-352')
ortho: Structure = mpr.get_structure_by_material_id('mp-685097')
tetra: Structure = mpr.get_structure_by_material_id('mp-1018721')
gio = GulpIO()
gc = GulpCaller()
for i in [mono, ortho, tetra]:
arr = []
arr2 = []
i.apply_strain(-.05)
for j in range(15):
gin = gio.buckingham_input(i, ['conv'], library='morse.lib', alib=True)
gout = gc.run(gin)
arr.append(i.density)
arr2.append(gio.get_energy(gout))
i.apply_strain(-.01)
i.to('POSCAR', i.get_space_group_info()[0].replace('/', '_') + '.vasp')
if i.get_space_group_info()[0] == 'P4_2/nmc':
pyplot.plot(arr, [r * 2 for r in arr2],
label=i.get_space_group_info()[0])
else:
pyplot.plot(arr, arr2, label=i.get_space_group_info()[0])
pyplot.legend()
pyplot.show()
class GulpIOTest(unittest.TestCase):
_multiprocess_shared_ = True
def setUp(self):
p = Poscar.from_file(
os.path.join(PymatgenTest.TEST_FILES_DIR, "POSCAR.Al12O18"), check_for_POTCAR=False
)
self.structure = p.structure
self.gio = GulpIO()
def test_keyword_line_with_correct_keywords(self):
kw = ("defect", "property")
inp_str = self.gio.keyword_line(*kw)
for word in kw:
self.assertIn(word, inp_str)
def test_structure_lines_default_options(self):
inp_str = self.gio.structure_lines(self.structure)
self.assertIn("cell", inp_str)
self.assertIn("frac", inp_str)
self.assertIn("space", inp_str)
def test_structure_lines_no_unitcell(self):
inp_str = self.gio.structure_lines(self.structure, cell_flg=False)
self.assertNotIn("cell", inp_str)
def test_structure_lines_no_frac_coords(self):
inp_str = self.gio.structure_lines(
self.structure, cell_flg=False, frac_flg=False
)
self.assertNotIn("cell", inp_str)
self.assertIn("cart", inp_str)
@unittest.skip("Not Implemented yet")
def test_specie_potential(self):
pass
@unittest.expectedFailure
def test_library_line_explicit_path(self):
gin = self.gio.library_line(
"/Users/mbkumar/Research/Defects/GulpExe/Libraries/catlow.lib"
)
self.assertIn("lib", gin)
def test_library_line_wrong_file(self):
with self.assertRaises(GulpError):
gin = self.gio.library_line("temp_to_fail.lib")
def test_buckingham_potential(self):
mgo_latt = [[4.212, 0, 0], [0, 4.212, 0], [0, 0, 4.212]]
mgo_specie = ["Mg", "O"] * 4
mgo_frac_cord = [
[0, 0, 0],
[0.5, 0, 0],
[0.5, 0.5, 0],
[0, 0.5, 0],
[0.5, 0, 0.5],
[0, 0, 0.5],
[0, 0.5, 0.5],
[0.5, 0.5, 0.5],
]
mgo_uc = Structure(mgo_latt, mgo_specie, mgo_frac_cord, True, True)
gin = self.gio.buckingham_potential(mgo_uc)
self.assertIn("specie", gin)
self.assertIn("buck", gin)
self.assertIn("spring", gin)
self.assertIn("Mg core", gin)
self.assertIn("O core", gin)
self.assertIn("O shel", gin)
gin = self.gio.buckingham_potential(self.structure)
self.assertIn("specie", gin)
self.assertIn("buck", gin)
self.assertIn("spring", gin)
def test_buckingham_input(self):
mgo_latt = [[4.212, 0, 0], [0, 4.212, 0], [0, 0, 4.212]]
mgo_specie = ["Mg", "O"] * 4
mgo_frac_cord = [
[0, 0, 0],
[0.5, 0, 0],
[0.5, 0.5, 0],
[0, 0.5, 0],
[0.5, 0, 0.5],
[0, 0, 0.5],
[0, 0.5, 0.5],
[0.5, 0.5, 0.5],
]
mgo_uc = Structure(mgo_latt, mgo_specie, mgo_frac_cord, True, True)
gin = self.gio.buckingham_input(mgo_uc, keywords=("optimise", "conp"))
self.assertIn("optimise", gin)
self.assertIn("cell", gin)
self.assertIn("specie", gin)
self.assertIn("buck", gin)
self.assertIn("spring", gin)
self.assertIn("Mg core", gin)
self.assertIn("O core", gin)
self.assertIn("O shel", gin)
# Improve the test
def test_tersoff_potential(self):
mgo_latt = [[4.212, 0, 0], [0, 4.212, 0], [0, 0, 4.212]]
mgo_specie = ["Mg", "O"] * 4
mgo_frac_cord = [
[0, 0, 0],
[0.5, 0, 0],
[0.5, 0.5, 0],
[0, 0.5, 0],
[0.5, 0, 0.5],
[0, 0, 0.5],
[0, 0.5, 0.5],
[0.5, 0.5, 0.5],
]
mgo_uc = Structure(mgo_latt, mgo_specie, mgo_frac_cord, True, True)
gin = self.gio.tersoff_potential(mgo_uc)
self.assertIn("specie", gin)
self.assertIn("Mg core", gin)
def test_get_energy(self):
# Output string obtained from running GULP on a terminal
out_str = """ Components of energy :
--------------------------------------------------------------------------------
Interatomic potentials = 5.61135426 eV
Monopole - monopole (real) = -4.34238722 eV
Monopole - monopole (recip)= -43.45344934 eV
Monopole - monopole (total)= -47.79583656 eV
--------------------------------------------------------------------------------
Total lattice energy :
Primitive unit cell = -42.18448230 eV
Non-primitive unit cell = -168.73792920 eV
--------------------------------------------------------------------------------
Total lattice energy (in kJmol-1):
Primitive unit cell = -4070.1577 kJ/(mole unit cells)
Non-primitive unit cell = -16280.6308 kJ/(mole unit cells)
--------------------------------------------------------------------------------
Components of energy :
--------------------------------------------------------------------------------
Interatomic potentials = 6.79846039 eV
Monopole - monopole (real) = -4.45761741 eV
Monopole - monopole (recip)= -44.60653603 eV
Monopole - monopole (total)= -49.06415344 eV
--------------------------------------------------------------------------------
Total lattice energy :
Primitive unit cell = -42.26569304 eV
Non-primitive unit cell = -169.06277218 eV
--------------------------------------------------------------------------------
Total lattice energy (in kJmol-1):
Primitive unit cell = -4077.9933 kJ/(mole unit cells)
Non-primitive unit cell = -16311.9732 kJ/(mole unit cells)
--------------------------------------------------------------------------------"""
energy = self.gio.get_energy(out_str)
self.assertEqual(energy, -169.06277218)
def test_get_relaxed_structure(self):
# Output string obtained from running GULP on a terminal
with open(os.path.join(PymatgenTest.TEST_FILES_DIR, "example21.gout"), "r") as fp:
out_str = fp.read()
struct = self.gio.get_relaxed_structure(out_str)
self.assertIsInstance(struct, Structure)
self.assertEqual(8, len(struct.sites))
self.assertEqual(4.212, struct.lattice.a)
self.assertEqual(90, struct.lattice.alpha)
@unittest.skip("Test later")
def test_tersoff_inpt(self):
gin = self.gio.tersoff_input(self.structure)
from pymatgen.command_line.gulp_caller import GulpCaller, GulpIO
from matplotlib import pyplot
import numpy as np
gio = GulpIO()
gc = GulpCaller()
arr = []
for i in np.linspace(0.5, 1, 100):
body = f'''conv
#cell
#1 1 10 90 90 90
cart
O core 0 0 -{i}
O core 0 0 {i}
Hf core 0 0 0
species
Hf core 2.4
O core -1.2
general 0 12
Hf core O core 0 0 1.0 1.
'''
gout = gc.run(body)
e = gio.get_energy(gout)
arr.append(e)
pyplot.plot(arr)
pyplot.show()
for j, i in enumerate(ortho.sites):
if str(i.specie) == 'Hf':
ortho.replace(j, species=Specie('Zr'))
break
for j, i in enumerate(ortho.sites):
if str(i.specie) == 'Hf':
ortho.replace(j, species=Specie('Zr'))
break
gio = GulpIO()
gc = GulpCaller()
for i in [mono, ortho, tetra]:
arr = []
arr2 = []
i.apply_strain(.05)
for j in range(10):
gin = gio.buckingham_input(i, ['conv'], library='morse.lib', alib=True)
gout = gc.run(gin)
print(gout)
arr.append(i.density)
arr2.append(gio.get_energy(gout) / i.volume)
i.apply_strain(-.01)
i.to('POSCAR', i.get_space_group_info()[0].replace('/', '_') + '.vasp')
if i.get_space_group_info()[0] == 'P4_2/nmc':
pyplot.plot(arr, [r * 2 for r in arr2],
label=i.get_space_group_info()[0])
else:
pyplot.plot(arr, arr2, label=i.get_space_group_info()[0])
pyplot.legend()
pyplot.show()
from pymatgen.command_line.gulp_caller import GulpIO
except:
print 'You should install pymatgen first.'
exit(0)
import sys
from monty.io import zopen
if __name__ == '__main__':
Gulp = GulpIO()
#change the Structure
#Cry_Str = Structure.from_file("POSCAR")
#gulpinput = Gulp.structure_lines(structure = Cry_Str)
#with open('gulpinput','w') as f:
#f.write(gulpinput)
#exit(0)
#output the energy
with zopen('log', "rt") as f:
contents = f.read()
energy = Gulp.get_energy(contents)
print energy
#output the relaxed structure
with zopen('log', "rt") as f:
contents = f.read()
Opt_Str = Gulp.get_relaxed_structure(contents)
Vasp_Str = Poscar(Opt_Str)
Vasp_Str.write_file('out.vasp')
