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Merge pull request #154 from pyscal/add_qe
Add qe
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,5 @@ | ||
| [bumpversion] | ||
| current_version = 0.9.8 | ||
| current_version = 0.9.9 | ||
| commit = True | ||
| tag = False | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,117 @@ | ||
| import mendeleev | ||
| import numpy as np | ||
| from ase.io.espresso import read_fortran_namelist | ||
| import os | ||
| import warnings | ||
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| def _convert_tab_to_dict(tab): | ||
| keywords = ["ATOMIC_SPECIES", | ||
| "ATOMIC_POSITIONS", | ||
| "K_POINTS", | ||
| "CELL_PARAMETERS", | ||
| "OCCUPATIONS", | ||
| "CONSTRAINTS", | ||
| "ATOMIC_VELOCITIES", | ||
| "ATOMIC_FORCES", | ||
| "ADDITIONAL_K_POINTS", | ||
| "SOLVENTS", | ||
| "HUBBARD"] | ||
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| tabdict = {} | ||
| for line in tab: | ||
| firstword = line.split()[0] | ||
| secondword = " ".join(line.split()[1:]) | ||
|
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| if firstword in keywords: | ||
| tabdict[firstword] = {} | ||
| tabdict[firstword]['value'] = [] | ||
| tabdict[firstword]['extra'] = secondword | ||
| tabarr = tabdict[firstword]['value'] | ||
| else: | ||
| tabarr.append(line.strip()) | ||
| return tabdict | ||
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| def write_espresso(s, inputfile, copy_from=None, pseudo_files=None): | ||
| data = None | ||
| tab = None | ||
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| if copy_from is not None: | ||
| if os.path.exists(copy_from): | ||
| try: | ||
| with open(copy_from, 'r') as fin: | ||
| data, tab = read_fortran_namelist(fin) | ||
| except: | ||
| warnings.warn(f'Error reading {copy_from}, a clean file will be written') | ||
| copy=True | ||
|
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| if tab is not None: | ||
| tab = _convert_tab_to_dict(tab) | ||
| else: | ||
| tab = {} | ||
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| if data is None: | ||
| data = {} | ||
| data['system'] = {} | ||
| data['control'] = {} | ||
|
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| tab['CELL_PARAMETERS'] = {} | ||
| tab['CELL_PARAMETERS']['extra'] = 'angstrom' | ||
| tab['CELL_PARAMETERS']['value'] = [] | ||
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| for vec in s.box: | ||
| tab['CELL_PARAMETERS']['value'].append(' '.join([str(x) for x in vec])) | ||
|
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| cds = s.direct_coordinates | ||
| species = s.atoms.species | ||
|
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| unique_species = np.unique(species) | ||
| if pseudo_files is not None: | ||
| if not len(pseudo_files) == len(unique_species): | ||
| raise ValueError('Number of pseudo files must match number of unique species') | ||
| pseudo_dirs = [os.path.dirname(os.path.abspath(pseudo_file)) for pseudo_file in pseudo_files] | ||
| if not len(np.unique(pseudo_dirs)) == 1: | ||
| raise ValueError('All pseudo files must be in the same directory') | ||
| data['control']['pseudo_dir'] = pseudo_dirs[0] | ||
| else: | ||
| pseudo_files = ['None' for x in range(len(unique_species))] | ||
|
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| tab['ATOMIC_SPECIES'] = {} | ||
| tab['ATOMIC_SPECIES']['extra'] = '' | ||
| tab['ATOMIC_SPECIES']['value'] = [] | ||
|
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| for count, us in enumerate(unique_species): | ||
| chem = mendeleev.element(us) | ||
| tab['ATOMIC_SPECIES']['value'].append(f'{us} {chem.atomic_weight} {os.path.basename(pseudo_files[count])}') | ||
|
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| tab['ATOMIC_POSITIONS'] = {} | ||
| tab['ATOMIC_POSITIONS']['extra'] = 'crystal' | ||
| tab['ATOMIC_POSITIONS']['value'] = [] | ||
|
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| for cd, sp in zip(cds, species): | ||
| tab['ATOMIC_POSITIONS']['value'].append(f'{sp} {cd[0]} {cd[1]} {cd[2]}') | ||
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| data['system']['ibrav'] = 0 | ||
| data['system']['nat'] = len(species) | ||
| data['system']['ntyp'] = len(unique_species) | ||
|
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| with open(inputfile, 'w') as fout: | ||
| if s.sample is not None: | ||
| fout.write(f'! {s.sample.toPython()}\n\n') | ||
|
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| for key, val in data.items(): | ||
| fout.write(f'&{key.upper()}\n') | ||
| for k, v in val.items(): | ||
| if isinstance(v, str): | ||
| fout.write(f' {k} = \'{v}\',\n') | ||
| else: | ||
| fout.write(f' {k} = {v},\n') | ||
| fout.write('/\n') | ||
| fout.write('\n') | ||
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| for key, val in tab.items(): | ||
| fout.write(f'{key} {val["extra"]}\n') | ||
| fout.write('\n') | ||
| for v in val['value']: | ||
| fout.write(v) | ||
| fout.write('\n') | ||
| fout.write('\n') |
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