def test_init_pypospack(self):
atoms = ase.build.bulk('Cu','fcc', cubic=True)
sim_cell_init = crystal.SimulationCell(atoms)
sim_cell_copy = crystal.SimulationCell(sim_cell_init)
#check to see if we produce the correct object
assert isinstance(sim_cell_copy,crystal.SimulationCell)
#check to see if the lattice parameter is correct
assert sim_cell_copy.a0 == sim_cell_init.a0
#check to see that the H matrix is an nd.array
assert isinstance(sim_cell_copy.H,np.ndarray)
#check to see that the shape of the H matrix is correct
assert sim_cell_copy.H.shape == (3,3)
#check to see that the H matrix is correct
for i in range(3):
for j in range(3):
assert abs(sim_cell_copy.H[i,j]-sim_cell_init.H[i,j]) < 1e-6
#check to see that the number of atoms are correct
assert len(sim_cell_init.atomic_basis) == len(sim_cell_copy.atomic_basis)
for i,a in enumerate(sim_cell_init.atomic_basis):
#check to see that the symbols are correct
assert sim_cell_copy.atomic_basis[i].symbol == sim_cell_init.atomic_basis[i].symbol
#check to see that the positions are correct
direct_x_init = sim_cell_init.atomic_basis[i].position
direct_x_final = sim_cell_copy.atomic_basis[i].position
for j in range(3):
assert abs(direct_x_init[j]-direct_x_final[j]) < 1e-6
def test_init_ase_cell(self):
atoms = ase.build.bulk('Cu','fcc', cubic=True)
sim_cell = crystal.SimulationCell(atoms)
#check to see if we produce the correct object
assert isinstance(sim_cell,crystal.SimulationCell)
#check to see that lattice parameter is correct
assert sim_cell.a0 == 1
#check to see that the H matrix is an nd.array
assert isinstance(sim_cell.H,np.ndarray)
#check to see that the shape of the H matrix is correct
assert sim_cell.H.shape == (3,3)
#check to see that the H matrix is correct
for i in range(3):
for j in range(3):
assert abs(atoms.cell[i,j]-sim_cell.H[i,j]) < 1e-6
#check to see that the number of atoms are correct
assert len(atoms) == len(sim_cell.atomic_basis)
#check to see that the positions are correct
for i,a in enumerate(atoms):
assert sim_cell.atomic_basis[i].symbol == a.symbol
direct_x_ase = crystal.cartesian2direct(a.position,atoms.cell)
direct_x_pypospack = sim_cell.atomic_basis[i].position
for j in range(3):
assert abs(direct_x_ase[j]-direct_x_pypospack[j]) < 1e-6
def test_poscar_init_ppp():
""" test if we can build from pypospack.crystal """
symbol = 'Cu'
sg = 'fcc'
a = 3.6
obj_ppp_1 = crystal.SimulationCell(
ase.build.bulk(symbol,sg,a=a,cubic=True))
obj_ppp_2 = vasp.Poscar(obj_ppp_1)
def test_poscar_init_ase():
""" test if we can build from ase """
symbol = 'Cu'
sg = 'fcc'
a = 3.6
obj_ppp = crystal.SimulationCell(
ase.build.bulk(symbol,sg,a=a,cubic=True))
poscar = vasp.Poscar(obj_ppp)
class test_poscar_init_fcc_unit(unittest.TestCase):
def setUp(self):
self.symbol = 'Cu'
self.sg = 'fcc'
self.a = 3.6
def test_poscar_init_ase(unittest.TestCase):
""" test if we can build from ase """
obj_ppp = crystal.SimulationCell(
ase.build.bulk(symbol,sg,a=a,cubic=True))
poscar = vasp.Poscar(obj_ppp)
self.assert
def gulp_positions_to_string(self, structure='POSCAR'):
""" returns the gulp position section to create simulation cell
Args:
structure (str): the filename of the POSCAR format file. Default
is 'POSCAR'. If an object which subclasses the
pyposmat.crystal.SimulationCell class is passed, this method
will use this that class instead.
Returns
str:
"""
sim_cell = None
if isinstance(structure, crystal.SimulationCell):
sim_cell = crystal.SimulationCell(poscar)
else:
sim_cell = vasp.Poscar()
try:
sim_cell.read(structure)
except FileNotFoundError as e:
msg = 'PYPOSPACK_ERROR: cannot find the POSCAR file:{}'.format(
structure)
raise
H = sim_cell.H * sim_cell.a0
str_out = "vectors\n"
str_out += "{:.10f} {:.10f} {:.10f}\n".format(H[0, 0], H[0, 1], H[0,
2])
str_out += "{:.10f} {:.10f} {:.10f}\n".format(H[1, 0], H[1, 1], H[1,
2])
str_out += "{:.10f} {:.10f} {:.10f}\n".format(H[2, 0], H[2, 1], H[2,
2])
str_out += "fractional\n"
for s in sim_cell.symbols:
for a in sim_cell.atomic_basis:
if a.symbol == s:
try:
str_out += "{} core {} {} {}\n".format(\
s,a.position[0],a.position[1],a.position[2])
except:
print(s)
print(a.symbol)
print(a.position)
raise
return str_out
def test_add_atom(self):
sim_cell = crystal.SimulationCell()
sim_cell.add_atom('Cu',[0,0,0])
def test_init_default(self):
sim_cell = crystal.SimulationCell()
assert isinstance(sim_cell,crystal.SimulationCell)
def test_init_ase(self):
atoms = ase.build.bulk('Cu','fcc', cubic=True)
sim_cell = crystal.SimulationCell(atoms)
assert isinstance(sim_cell,crystal.SimulationCell)
for i in range(3):
for j in range(3):
assert abs(sim_cell_copy.H[i,j]-sim_cell_init.H[i,j]) < 1e-6
#check to see that the number of atoms are correct
assert len(sim_cell_init.atomic_basis) == len(sim_cell_copy.atomic_basis)
for i,a in enumerate(sim_cell_init.atomic_basis):
#check to see that the symbols are correct
assert sim_cell_copy.atomic_basis[i].symbol == sim_cell_init.atomic_basis[i].symbol
#check to see that the positions are correct
direct_x_init = sim_cell_init.atomic_basis[i].position
direct_x_final = sim_cell_copy.atomic_basis[i].position
for j in range(3):
assert abs(direct_x_init[j]-direct_x_final[j]) < 1e-6
def test_add_atom(self):
sim_cell = crystal.SimulationCell()
sim_cell.add_atom('Cu',[0,0,0])
if __name__ == "__main__":
sim_cell = crystal.SimulationCell()
print(sim_cell.a0)
print(sim_cell.H)
print(type(sim_cell.atomic_basis))
for a in sim_cell.atomic_basis:
print(a.symbol,a.position)
print('add_atom')
sim_cell.add_atom('Cu',[0,0,0])
"""
This script tests the functionality of the pypospack.io.phonts module by
recreating the example in the PhonTS example/argon
"""
import copy
import numpy as np
import pypospack.io.phonts as phonts
import pypospack.crystal as crystal
# define simulation cell directly
ar_fcc = crystal.SimulationCell()
ar_fcc.a0 = 3.9620
ar_fcc.add_atom('Ar', [0.0, 0.0, 0.0])
ar_fcc.add_atom('Ar', [0.5, 0.5, 0.0])
ar_fcc.add_atom('Ar', [0.5, 0.0, 0.5])
ar_fcc.add_atom('Ar', [0.0, 0.5, 0.5])
# define simulation cell through poscar file
# poscar_filename = 'POSCAR'
# acc_fcc = vasp.Poscar()
# acc_fcc.read('POSCAR')
# this is a leonnard jones potential
# TODO: LJ is not currently implemented in pypospack.potentials
# TODO: pypospack.potentials.LeonnardJones.to_phonts_string() not implemented
phonts_potential_type = ['exp-6', 1]
phonts_potential_params = ['Ar', 'Ar', 0.010531316, 13., 3.85, 5.625, 9.625]
slurm_phonts_dict = {}
slurm_phonts_dict['filename'] = 'slurm_submit.sh'