code stringlengths 3 6.57k |
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ExtraFrameworkAnalyzer(atoms) |
EF_O_index_list.append(EFAnalyzer.get_extraframework_cluster() |
mode(tuple(EF_O_index_list) |
read(folder_path + '/%s.traj' % traj_name, ':') |
os.path.join(folder_path, traj_name) |
read(folder_path + '/%s.traj' % sample_zeolite, ':') |
os.path.join(folder_path, sample_zeolite) |
Path(output_dir) |
mkdir(parents=True, exist_ok=True) |
get_EF_O_index(traj[0:100]) |
enumerate(traj) |
get_capped_cluster(atoms, output_dir, 'cluster_' + str(count) |
label_pdb(output_dir, 'cluster_%s' % str(count) |
cluster_traj.append(cluster) |
print(sample_zeolite, count) |
print(sample_zeolite, count, 'failed!') |
view(cluster_traj) |
reformat_inputs(bond_param_dict, angle_param_dict) |
bond_param_dict.items() |
bond_type.append(list(types) |
param_list.extend([val for val in np.array(indices) |
angle_param_dict.items() |
angle_type.append(list(types) |
param_list.extend([val for val in np.array(indices) |
optimization (only run once) |
shorten_index_list_by_types(bond_type_index_dict, include_property_type=included_bond_type) |
shorten_index_list_by_types(angle_type_index_dict, include_property_type=included_angle_type) |
set_up_openMM_system(folder_path, cluster_tag_number, shortened_bond_list) |
enumerate(ini_bond_param_dict.items() |
list(param[count * len(indices) |
len(indices) |
len(indices) |
enumerate(ini_angle_param_dict.items() |
len(indices) |
len(indices) |
copy.deepcopy(info_dict) |
my_dict.items() |
predicted_f.append([force_list for force_list in ff_forces]) |
get_DFT_forces_single(atoms, atom_index) |
self.atoms.get_forces() |
np.linalg.norm(f_vec) |
function (MSE) |
k (Boltzmann's constant) |
np.reshape(np.array(np.reshape(predicted_f, [-1, 3]) |
np.array(np.reshape(DFT_f, [-1, 3]) |
print(np.mean(weighted_residue ** 2) |
np.mean(weighted_residue ** 2) |
print(res.success) |
make_parity_plot(ff_forces, dft_forces, atom_name) |
plt.figure() |
plt.subplots() |
plt.plot(dft_forces, ff_forces, 'o') |
plt.xlabel('DFT_force', fontsize=18) |
plt.ylabel('FF_force', fontsize=18) |
np.min([ax.get_xlim() |
ax.get_ylim() |
np.max([ax.get_xlim() |
ax.get_ylim() |
ax.plot(lims, lims, 'k-', alpha=0.75, zorder=0) |
ax.set_aspect('equal') |
ax.set_xlim(lims) |
ax.set_ylim(lims) |
plt.title('Force fitting on %s' % atom_name, fontsize=18) |
plt.show() |
func() |
time.perf_counter() |
prep_topologies(folder_path, sample_zeolite, traj_name, del_unlabeled_pdb=True) |
reformat_inputs(ini_bond_param_dict, ini_angle_param_dict) |
read(os.path.join(folder_path, traj_name) |
get_bonds(cluster, mult=2) |
get_property_types(cluster, bond_index_list) |
get_angles(cluster, mult=2) |
get_property_types(cluster, angle_index_list) |
get_type_index_pair(bond_type_dict, whole_bond_type_list, bond_index_list) |
get_type_index_pair(angle_type_dict, whole_angle_type_list, angle_index_list) |
os.path.join(folder_path, traj_name) |
os.listdir(os.path.join(folder_path, traj_name) |
np.arange(0, len(files) |
int(cluster_tag_number) |
print(cluster_tag_number) |
open(output_path + '/info_dict_%s.pickle' % numb_skip, 'wb') |
pickle.dump(info_dict, f) |
open(folder_path + '/EF_index_dict.pickle', 'rb') |
pickle.load(f) |
read(folder_path + '/%s.traj' % traj_name, '0::%s' % numb_skip) |
DFT_f.append([get_DFT_forces_single(atoms, atom_index=val) |
EF_index_dict.get(zeolite) |
print(np.array(DFT_f) |
read(folder_path + '/%s.traj' % traj_name, '-1') |
DFT_E.append(atoms.calc.results['energy']) |
open(os.path.join(folder_path, traj_name) |
pickle.load(f) |
open(folder_path + '/cluster_EF_index_dict.pickle', 'rb') |
pickle.load(f) |
copy.deepcopy(info_dict) |
np.exp(-(np.array(DFT_E) |
len(traj[0]) |
weights.extend([value, value, value, value, value, value, value, value, value]) |
get_fitting_parameters(ini_param, my_dict, DFT_f, np.array(weights) |
cluster_EF_index_dict.get(zeolite) |
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