jax-md/jax_md/io.py at main · dominicrufa/jax-md

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# Licensed under the Apache License, Version 2.0 (the "License");

# you may not use this file except in compliance with the License.

# You may obtain a copy of the License at

# https://www.apache.org/licenses/LICENSE-2.0

# Unless required by applicable law or agreed to in writing, software

# distributed under the License is distributed on an "AS IS" BASIS,

# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

# See the License for the specific language governing permissions and

# limitations under the License.

import jax.numpy as np

def _xyz_vec2str(x):

"""Convert a vector to string.

"""

return "\t".join([str(i) for i in x])

def write_xyz(filename, *args):

"""Write arrays to xyz file format.

Args:

filename: Output filename.

args: Arguments can be 1D or 2D arrays where length (along axis=0) is equal to number of atoms.

Examples:

write_xyz('minimize.xyz', R)

write_xyz('minimize.xyz', species, R)

write_xyz('minimize.xyz', species, R, velocities, forces)

"""

vars = [arg[:, np.newaxis] if len(arg.shape)==1 else arg for arg in args]

vars = np.hstack(vars)

with open(filename, "w+") as f:

N = len(vars)

str_ = f"{N}" + "\n\n"

f.write(str_)

for j in range(N):

str_ = f"{j+1}\t" + _xyz_vec2str(vars[j, :]) + "\n"

f.write(str_)