def test_decimal(self):
struct = Structure.from_str(
"""Mg2 Al4 O8
1.0
5.003532 0.000000 2.888790
1.667844 4.717375 2.888790
0.000000 0.000000 5.777581
O Mg Al
8 2 4
direct
0.736371 0.736371 0.736371 O
0.263629 0.263629 0.709114 O
0.263629 0.709114 0.263629 O
0.709114 0.263629 0.263629 O
0.736371 0.290886 0.736371 O
0.290886 0.736371 0.736371 O
0.263629 0.263629 0.263629 O
0.736371 0.736371 0.290886 O
0.125000 0.125000 0.125000 Mg
0.875000 0.875000 0.875000 Mg
0.500000 0.500000 0.000000 Al
0.500000 0.500000 0.500000 Al
0.000000 0.500000 0.500000 Al
0.500000 0.000000 0.500000 Al""",
fmt="poscar",
)
bp = BuckinghamPotential(bush_lewis_flag="bush")
gio = GulpIO()
input = gio.buckingham_input(struct, ["relax conp"])
caller = GulpCaller()
gout = caller.run(input)
def test_run(self):
mgo_latt = [[4.212, 0, 0], [0, 4.212, 0], [0, 0, 4.212]]
mgo_specie = ["Mg"] * 4 + ["O"] * 4
mgo_frac_cord = [
[0, 0, 0],
[0.5, 0.5, 0],
[0.5, 0, 0.5],
[0, 0.5, 0.5],
[0.5, 0, 0],
[0, 0.5, 0],
[0, 0, 0.5],
[0.5, 0.5, 0.5],
]
mgo_uc = Structure(mgo_latt, mgo_specie, mgo_frac_cord, True, True)
gio = GulpIO()
gin = gio.keyword_line("optimise", "conp")
gin += gio.structure_lines(mgo_uc, symm_flg=False)
# gin += self.gc.gulp_lib('catlow.lib')
gin += "species\nMg core 2.00000\nO core 0.86902\nO shel -2.86902\n"
gin += "buck\n"
gin += "Mg core O shel 946.627 0.31813 0.00000 0.0 10.0\n"
gin += "O shel O shel 22764.000 0.14900 27.87900 0.0 12.0\n"
gin = gin
gc = GulpCaller()
"""Some inherent checks are in the run_gulp function itself.
They should be suffcient for raising errors."""
gout = gc.run(gin)
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()
from pymatgen.command_line.gulp_caller import GulpCaller, GulpIO
from pymatgen import Structure
import numpy as np
import matplotlib.pyplot as plt
def get_energy(dis):
gin = f'''conv
cart
Zn core 0 0 0
O core 0 0 {dis}
library ABOP.lib
'''
gout = gc.run(gin)
return gio.get_energy(gout)
if __name__ == '__main__':
gc = GulpCaller('/opt/gulp-5.1/Src/gulp')
gio = GulpIO()
arr = []
for i in np.linspace(1, 2.5, 20):
arr.append(get_energy(i))
print(arr[-1])
plt.plot(np.linspace(1, 2.5, 20), arr)
plt.show()
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()