def regenerate(s1_name, s2_name, rotation, initial_coordinate, sim_par, sim_dir, export_dir, colorify=True, index=1, format='cif'):
"""
Reconstruct interpenetrated structure for given MOFs with rotation and initial coordinate.
"""
s1_mof = MOF(os.path.join(sim_dir['mof_dir'], s1_name + '.cif'))
s2_mof = MOF(os.path.join(sim_dir['mof_dir'], s2_name + '.cif'))
s2_mof_length = len(s2_mof)
first_point = initial_coordinate
x_angle, y_angle, z_angle = [math.radians(a) for a in rotation]
structure = {'atom_names': [], 'atom_coors': [], 'pbc_coors': []}
for idx in range(s2_mof_length):
if idx == 0:
atom_name = s2_mof.atom_names[idx]
rot_coor = s2_mof.atom_coors[idx]
rot_coor = xyz_rotation(rot_coor, [x_angle, y_angle, z_angle])
translation_vector = sub3(first_point, rot_coor)
else:
atom_name = s2_mof.atom_names[idx]
rot_coor = s2_mof.atom_coors[idx]
rot_coor = xyz_rotation(rot_coor, [x_angle, y_angle, z_angle])
new_coor = add3(rot_coor, translation_vector)
pbc_coor = pbc3(new_coor, s1_mof.to_frac, s1_mof.to_car)
structure['atom_coors'].append(new_coor)
structure['pbc_coors'].append(pbc_coor)
structure['atom_names'].append(atom_name)
new_structure = {'atom_names': structure['atom_names'], 'name': s2_mof.name}
if sim_par['export_pbc']:
new_structure['atom_coors'] = structure['pbc_coors']
else:
new_structure['atom_coors'] = structure['atom_coors']
# Export structure file
new_s2_mof = MOF(new_structure, file_format='dict')
joined_mof = s1_mof.join(new_s2_mof, colorify=False)
joined_mof.name += '_' + str(index)
joined_mof.export(export_dir, file_format=format)
if colorify:
new_s2_mof = MOF(new_structure, file_format='dict')
joined_mof_color = s1_mof.join(new_s2_mof, colorify=True)
joined_mof_color.name += '_' + str(index) + 'C'
joined_mof_color.export(export_dir, file_format=format)
def reshape(mof, rotation, initial_coordinate):
"""
Apply rotation and translation operations to given MOF
- rotation = [x_angle, y_angle, z_angle] in degrees
- initial_coordinate = [x, y, z] in cartesian coordinates
"""
first_point = initial_coordinate
x_angle, y_angle, z_angle = [math.radians(a) for a in rotation]
structure = {'atom_names': [], 'atom_coors': [], 'name': mof.name}
rot_coor = mof.packed_coors[0][0]
translation_vector = sub3(first_point, rot_coor)
for unit_cell in mof.packed_coors:
for atom_coor in unit_cell:
rot_coor = atom_coor
rot_coor = xyz_rotation(rot_coor, [x_angle, y_angle, z_angle])
new_coor = add3(rot_coor, translation_vector)
structure['atom_coors'].append(new_coor)
structure['atom_names'] = len(mof.packed_coors) * mof.atom_names
return structure
def check_interpenetration(sim_par, base_mof, mobile_mof, emap, atom_list):
"""
Run interpenetration algorithm with given simulation parameters and energy map.
Returns simulation summary and structural information on the discovered structures.
"""
# Initialize simulation parameters
structure_energy_limit = sim_par['structure_energy_limit']
atom_energy_limit = sim_par['atom_energy_limit']
# atom_energy_limit = sim_par['energy_density_limit'] * mobile_mof.ucv
energy_density_limit = sim_par['energy_density_limit']
rotation_freedom = sim_par['rotation_freedom']
summary_percent = sim_par['summary_percent']
try_all_rotations = sim_par['try_all_rotations']
# Get energy map dimensions for trilinear interpolation
emap_max = [emap[-1][0], emap[-1][1], emap[-1][2]]
emap_min = [emap[0][0], emap[0][1], emap[0][2]]
side_length = [emap_max[0] - emap_min[0] + 1, emap_max[1] - emap_min[1] + 1, emap_max[2] - emap_min[2] + 1]
x_length, y_length = int(side_length[1] * side_length[2]), int(side_length[2])
if try_all_rotations:
all_rot_degrees = possible_rotations(sim_par['rotation_freedom'])
rotation_limit = len(all_rot_degrees)
sim_par['rotation_limit'] = rotation_limit
else:
rotation_limit = sim_par['rotation_limit']
initial_coors = initial_coordinates(base_mof, emap, atom_list, atom_energy_limit)
trial_limit = len(initial_coors) * rotation_limit
div = round(trial_limit / (100 / summary_percent))
rot_freedom = 360 / rotation_freedom
# omitted_coordinates = len(emap) - len(initial_coors)
summary = {'percent': [], 'structure_count': [], 'trial_count': []}
new_structures = []
abort_ip = False
mobile_mof_length = len(mobile_mof)
structure_count = 0
structure_total_energy = 0
ucv = mobile_mof.ucv
energy_density = 0
initial_coor_index = 0
rotation_index = 0
# Interpenetration trial loop for different positions and orientations
for t in range(trial_limit):
abort_ip = False
# Interpenetration trial loop for a specific position and different orientations
for idx in range(mobile_mof_length):
if not abort_ip:
# If the interpenetration is just starting select rotation angles
if idx == 0:
# Determine random angles for rotation in 3D space
# Determine first point for interpenetrating structure
if t % rotation_limit == 0:
# Start with original orientation for first trial
x_angle, y_angle, z_angle = [0, 0, 0]
first_point = initial_coors[initial_coor_index]
initial_coor_index += 1
rotation_index = 0
elif try_all_rotations:
x_angle, y_angle, z_angle = all_rot_degrees[rotation_index]
else:
x_angle = 2 * math.pi * math.floor(random() * rot_freedom) / rot_freedom
y_angle = 2 * math.pi * math.floor(random() * rot_freedom) / rot_freedom
z_angle = 2 * math.pi * math.floor(random() * rot_freedom) / rot_freedom
rotation_index += 1
# Rotate first atom of the mobile MOF
atom_name = mobile_mof.atom_names[idx]
rot_coor = mobile_mof.atom_coors[idx]
rot_coor = xyz_rotation(rot_coor, [x_angle, y_angle, z_angle])
translation_vector = sub3(first_point, rot_coor)
# Initialize new structure dictionary
structure = {'atom_names': [], 'atom_coors': [], 'pbc_coors': []}
structure['first_point'] = first_point
structure['translation_vector'] = translation_vector
structure['atom_coors'].append(first_point)
structure['pbc_coors'].append(first_point)
structure['atom_names'].append(atom_name)
structure['rotation'] = [x_angle, y_angle, z_angle]
# If interpenetration is still going on
elif idx < mobile_mof_length - 1:
atom_name = mobile_mof.atom_names[idx]
rot_coor = mobile_mof.atom_coors[idx]
rot_coor = xyz_rotation(rot_coor, [x_angle, y_angle, z_angle])
new_coor = add3(rot_coor, translation_vector)
pbc_coor = pbc3(new_coor, base_mof.to_frac, base_mof.to_car)
emap_atom_index = energy_map_atom_index(atom_name, atom_list)
point_energy = tripolate(pbc_coor, emap_atom_index, emap, x_length, y_length)
structure_total_energy += point_energy
energy_density += point_energy / ucv
if energy_density > energy_density_limit:
structure_total_energy = 0
energy_density = 0
abort_ip = True
break # Fix this part (break interpenetration trial loop)
else:
structure['atom_coors'].append(new_coor)
structure['pbc_coors'].append(pbc_coor)
structure['atom_names'].append(atom_name)
# If interpenetration trial ended with no collision - record structure info
else:
structure['energy'] = structure_total_energy
structure['energy_density'] = energy_density
new_structures.append(structure)
structure_count += 1
structure_total_energy = 0
energy_density = 0
# Record simulation progress according to division (div) and summary
if t % div == 0:
percent_complete = round(t / trial_limit * 100)
summary['percent'].append(percent_complete)
summary['structure_count'].append(structure_count)
summary['trial_count'].append(t)
return summary, new_structures