def test_atoms_load__loads_lmpdat_from_file_or_path():
with Path("tests/uio66/uio66-linker.lmpdat") as path:
atoms = Atoms.load(path, atom_format="atomic")
assert len(atoms) == 16
with Path("tests/uio66/uio66-linker.lmpdat").open() as fd:
atoms = Atoms.load(fd, filetype="lmpdat", atom_format="atomic")
assert len(atoms) == 16
def test_atoms_load__loads_cif_from_file_or_path():
with Path("tests/uio66/uio66-linker.cif") as path:
atoms = Atoms.load(path)
assert len(atoms) == 16
with Path("tests/uio66/uio66-linker.cif").open() as fd:
atoms = Atoms.load(fd, filetype="cif")
assert len(atoms) == 16
import csv
import sys
import time
import numpy as np
from mofun import Atoms, replace_pattern_in_structure, find_pattern_in_structure
all_repldims = [(1, 1, 1), (2, 2, 2)]
# all_repldims = [(1,1,1), (2,2,2), (4,4,4)]
# all_repldims = [(1,1,1), (2,2,2), (4,4,4), (8,8,8)]
uio66 = Atoms.load("uio66.cif")
uio67 = Atoms.load("uio67.cif")
uio66_linker = Atoms.load("uio66-linker.cml")
uio67_linker = Atoms.load("uio67-linker.cml")
output_csv = csv.writer(sys.stdout)
output_csv.writerow([
"mof", "repl", "num-atoms", "matches-found", "matches-expected",
"process-time-seconds", "perf-counter-seconds"
])
for repldims in all_repldims:
structure = uio66.replicate(repldims=repldims)
time_s = time.process_time()
perf_s = time.perf_counter()
patterns = find_pattern_in_structure(structure, uio66_linker)
output_csv.writerow(
("uio66", "%dx%dx%dx" % repldims, len(structure),
def mofun_cli(inputpath,
outputpath,
find_path=None,
replace_path=None,
replace_fraction=1.0,
axis1a_idx=0,
axis1b_idx=-1,
axis2_idx=None,
dumppath=None,
chargefile=None,
replicate=None,
mic=None,
framework_element=None,
pp=False):
atoms = Atoms.load(inputpath)
# upate positions from lammps dump file
if dumppath is not None:
# update positions in original atoms file with new positions
dumpatoms = ase.io.read(dumppath, format="lammps-dump-text")
assert len(dumpatoms.positions) == len(atoms.positions)
atoms.positions = dumpatoms.positions
# update charges
if chargefile is not None:
charges = np.array(
[float(line.strip()) for line in chargefile if line.strip() != ''])
assert len(charges) == len(atoms.positions)
atoms.charges = charges
if replicate is not None:
atoms = atoms.replicate(replicate)
# replicate to meet minimum image convention, if necessary
if mic is not None:
repls = np.array(np.ceil(2 * mic / np.diag(atoms.cell)), dtype=int)
atoms = atoms.replicate(repls)
if pp:
assign_pair_params_to_structure(atoms)
if replace_path is not None and find_path is None:
print("Cannot perform a replace operation without a find operation")
elif find_path is not None:
search_pattern = Atoms.load(find_path)
if replace_path is not None:
replace_pattern = Atoms.load(replace_path)
atoms = replace_pattern_in_structure(
atoms,
search_pattern,
replace_pattern,
axis1a_idx=axis1a_idx,
axis1b_idx=axis1b_idx,
axis2_idx=axis2_idx,
replace_fraction=replace_fraction)
else:
results = find_pattern_in_structure(atoms, search_pattern)
print("Found %d instances of the search_pattern in the structure" %
len(results))
print(results)
# set framework elements to specified element-only works on ASE exports
if framework_element is not None:
atoms.symbols[atoms.atom_groups == 0] = framework_element
if outputpath.suffix in ['.lmpdat', '.mol']:
atoms.save(outputpath)
else:
print("INFO: Trying output using ASE")
aseatoms = atoms.to_ase()
if framework_element is not None:
aseatoms.symbols[atoms.atom_groups == 0] = framework_element
aseatoms.set_pbc(True)
aseatoms.write(outputpath)
