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.command_line.gulp_caller import GulpIO from MDAnalysis import Universe gio = GulpIO() gio
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()
with zopen(filen, "rt") as f:
contents = f.read()
energy = Gulp.get_energy(contents)
if lave:
contents = open(filen, 'r').readlines()
for line in contents:
if 'Total number atoms/shells' in line:
num = int(re.findall('\d+', line)[0])
break
else:
num = 1
return energy / num
if __name__ == '__main__':
Gulp = GulpIO()
num = int(sys.argv[1])
if num == 1:
#write input file of gulp
Cry_Str = Structure.from_file("POSCAR")
with open('gulpinput', 'w') as f:
f.write(Gulp.keyword_line('opti conj conp nosymmetry qok'))
f.write(Gulp.keyword_line('switch_min bfgs gnorm 0.5\n'))
gulpinput = Gulp.structure_lines(structure=Cry_Str, symm_flg=False)
f.write(gulpinput)
f.write(Gulp.keyword_line('maxcyc 500'))
f.write(Gulp.keyword_line('library self_build.lib'))
f.write(Gulp.keyword_line('dump every gulpopt'))
def setUp(self):
p = Poscar.from_file(os.path.join(test_dir, 'POSCAR.Al12O18'),
check_for_POTCAR=False)
self.structure = p.structure
self.gio = GulpIO()