def scale(self, factor: float) -> LammpsData:
"""
Scales the charge in of the in self.data and returns a new one. TODO: check if non-destructive
Args:
factor: The charge scaling factor
Returns:
A recreated LammpsData obj
"""
items = {}
items["box"] = self.data.box
items["masses"] = self.data.masses
atoms = self.data.atoms.copy(deep=True)
atoms["q"] = atoms["q"] * factor
assert np.around(atoms.q.sum(), decimals=self.precision) == np.around(
self.data.atoms.q.sum() * factor, decimals=self.precision)
digit_count = 0
for q in atoms["q"]:
rounded = self.count_significant_figures(q)
if rounded > digit_count:
digit_count = rounded
print("No. of significant figures to output for charges: ",
digit_count)
items["atoms"] = atoms
items["atom_style"] = self.data.atom_style
items["velocities"] = self.data.velocities
items["force_field"] = self.data.force_field
items["topology"] = self.data.topology
return LammpsData(**items)
def write_data_file(self, organism, job_dir_path, composition_space):
"""
Writes the file (called in.data) containing the structure that LAMMPS
reads.
Args:
organism: the Organism whose structure to write
job_dir_path: the path the job directory (as a string) where the
file will be written
composition_space: the CompositionSpace of the search
"""
# get xhi, yhi and zhi from the lattice vectors
lattice_coords = organism.cell.lattice.matrix
xhi = lattice_coords[0][0]
yhi = lattice_coords[1][1]
zhi = lattice_coords[2][2]
box_size = [[0.0, xhi], [0.0, yhi], [0.0, zhi]]
# get xy, xz and yz from the lattice vectors
xy = lattice_coords[1][0]
xz = lattice_coords[2][0]
yz = lattice_coords[2][1]
# get a list of the elements from the lammps input script to
# preserve their order of appearance
num_atoms = len(composition_space.get_all_elements())
with open(self.input_script, 'r') as f:
lines = f.readlines()
for line in lines:
if 'pair_coeff' in line:
element_symbols = line.split()[-1*num_atoms:]
all_elements = []
for symbol in element_symbols:
all_elements.append(Element(symbol))
# get the dictionary of atomic masses - set the atom types to the order
# of their appearance in the lammps input script
atomic_masses_dict = {}
for i in range(len(all_elements)):
atomic_masses_dict[all_elements[i].symbol] = [
i + 1, float(all_elements[i].atomic_mass)]
# get the atoms data
atoms_data = LammpsData.get_atoms_data(
organism.cell, atomic_masses_dict, set_charge=True)
# make a LammpsData object
lammps_data = LammpsData(box_size, atomic_masses_dict.values(),
atoms_data)
# write the data to a file
# This method doesn't write the tilts, so we have to add those. It also
# writes the molecule id of each atom, so we have to remove those
lammps_data.write_data_file(job_dir_path + '/in.data')
# read the in.data file as a list of strings
with open(job_dir_path + '/in.data', 'r') as f:
lines = f.readlines()
# find the location to insert the tilts
insertion_index = 0
for line in lines:
if 'zhi' in line:
insertion_index = lines.index(line) + 1
# build the string containing the tilts and add it
tilts_string = str(xy) + ' ' + str(xz) + ' ' + str(yz) + ' xy xz yz\n'
lines.insert(insertion_index, tilts_string)
# get the index of the line where the atoms info starts
atoms_index = 0
for line in lines:
if 'Atoms' in line:
atoms_index = lines.index(line) + 2
# remove the the molecule id's
for i in range(len(organism.cell.sites)):
split_line = lines[atoms_index + i].split()
del split_line[1]
modified_line = ''
for item in split_line:
modified_line = modified_line + item + ' '
modified_line = modified_line + '\n'
lines[atoms_index + i] = modified_line
lines[-1] = lines[-1] + '\n'
# overwrite the in.data file with the new contents, including the tilts
with open(job_dir_path + '/in.data', 'w') as f:
for line in lines:
f.write('%s' % line)
