-
Notifications
You must be signed in to change notification settings - Fork 16
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #11 from atztogo/develop
Collection of updates
- Loading branch information
Showing
45 changed files
with
244 additions
and
19,862 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,20 +1,6 @@ | ||
|
|
||
| AiiDA Phonopy plugin | ||
| ==================== | ||
|
|
||
| This a phonopy plugin for AiiDA. This plugin includes workflows to calculate | ||
| phonon band structure, DOS, thermal properties and mode Gruneisen parameters. | ||
| It provides interfaces for VASP, Quantum ESPRESSO and LAMMPS to calculate the | ||
| atomic forces and relax the crystal structure. | ||
|
|
||
|
|
||
| Examples | ||
| -------- | ||
| Some test calculations are found in the folder **/examples** | ||
|
|
||
| - plugins: examples of basic functionality of phonopy remote plugin. These tests require | ||
| the previous calculation of forces or force constants that should be already stored in the database | ||
| - workchains: examples of the full phonon calculation / gruneisen parameters from scratch. These workflows | ||
| require the installation of plugins for VASP, LAMMPS or QuantumESPRESSO. | ||
| - tools: example scripts for visualize the results of phonon/gruneisen workchains. These scripts require | ||
| matplotlib. | ||
| This a phonopy plugin for AiiDA. This plugin includes workflows to | ||
| calculate phonons with supercell and finite displacement approaches. | ||
| Currently it provides interfaces only to VASP. |
File renamed without changes.
File renamed without changes.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
2 changes: 1 addition & 1 deletion
2
...a_phonopy/calculations/phonopy/phonopy.py → aiida_phonopy/calcs/phonopy.py
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Empty file.
File renamed without changes.
File renamed without changes.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,16 @@ | ||
| import sys | ||
|
|
||
| class IterHarmonicApproximation(WorkChain): | ||
| _next_workchain_string = 'phonopy.phonon' | ||
| _next_workchain = WorkflowFactory(_next_workchain_string) | ||
|
|
||
| @classmethod | ||
| def define(cls, spec): | ||
| super(IterHarmonicApproximation, cls).define(spec) | ||
| spec.expose_inputs(cls._next_workchain) | ||
| spec.outline( | ||
| cls.initialize, | ||
| ) | ||
|
|
||
| def initialize(self): | ||
| self.report("initialize") |
File renamed without changes.
File renamed without changes.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,141 @@ | ||
| import sys | ||
| import phonopy | ||
| from aiida.manage.configuration import load_profile | ||
| load_profile() | ||
| from aiida.orm import Float, Bool, Str, load_node | ||
|
|
||
|
|
||
| def launch_aiida(): | ||
| import spglib | ||
| from phonopy.interface.vasp import (read_vasp_from_strings, | ||
| get_vasp_structure_lines) | ||
| from phonopy.structure.atoms import PhonopyAtoms | ||
| from aiida.plugins import DataFactory, WorkflowFactory | ||
| from aiida.engine import run, submit | ||
| from aiida_phonopy.common.utils import phonopy_atoms_to_structure | ||
|
|
||
| Dict = DataFactory('dict') | ||
| unitcell_str = """ Na Cl | ||
| 1.00000000000000 | ||
| 5.6903014761756712 0.0000000000000000 0.0000000000000000 | ||
| 0.0000000000000000 5.6903014761756712 0.0000000000000000 | ||
| 0.0000000000000000 0.0000000000000000 5.6903014761756712 | ||
| 4 4 | ||
| Direct | ||
| 0.0000000000000000 0.0000000000000000 0.0000000000000000 | ||
| 0.0000000000000000 0.5000000000000000 0.5000000000000000 | ||
| 0.5000000000000000 0.0000000000000000 0.5000000000000000 | ||
| 0.5000000000000000 0.5000000000000000 0.0000000000000000 | ||
| 0.5000000000000000 0.5000000000000000 0.5000000000000000 | ||
| 0.5000000000000000 0.0000000000000000 0.0000000000000000 | ||
| 0.0000000000000000 0.5000000000000000 0.0000000000000000 | ||
| 0.0000000000000000 0.0000000000000000 0.5000000000000000""" | ||
|
|
||
| lat, pos, num = spglib.refine_cell( | ||
| read_vasp_from_strings(unitcell_str).to_tuple()) | ||
| cell = PhonopyAtoms(cell=lat, scaled_positions=pos, numbers=num) | ||
| cell = read_vasp_from_strings( | ||
| '\n'.join(get_vasp_structure_lines(cell))) | ||
| structure = phonopy_atoms_to_structure(cell) | ||
|
|
||
| base_incar_dict = { | ||
| 'PREC': 'Accurate', | ||
| 'IBRION': -1, | ||
| 'EDIFF': 1e-8, | ||
| 'NELMIN': 5, | ||
| 'NELM': 100, | ||
| 'ENCUT': 520, | ||
| 'IALGO': 38, | ||
| 'ISMEAR': 0, | ||
| 'SIGMA': 0.01, | ||
| # 'GGA': 'PS', | ||
| 'LREAL': False, | ||
| 'lcharg': False, | ||
| 'lwave': False, | ||
| } | ||
|
|
||
| base_config = {'code_string': 'vasp544mpi@stern', | ||
| 'kpoints_density': 0.5, # k-point density, | ||
| 'potential_family': 'PBE.54', | ||
| 'potential_mapping': {'Na': 'Na_pv', 'Cl': 'Cl'}, | ||
| 'options': {'resources': {'parallel_env': 'mpi*', | ||
| 'tot_num_mpiprocs': 16}, | ||
| 'max_wallclock_seconds': 3600 * 10}} | ||
| base_parser_settings = {'add_energies': True, | ||
| 'add_forces': True, | ||
| 'add_stress': True} | ||
| forces_config = base_config.copy() | ||
| forces_config.update({'parser_settings': base_parser_settings, | ||
| 'parameters': base_incar_dict}) | ||
| nac_config = base_config.copy() | ||
| nac_parser_settings = {'add_born_charges': True, | ||
| 'add_dielectrics': True} | ||
| nac_parser_settings.update(base_parser_settings) | ||
| nac_incar_dict = {'lepsilon': True} | ||
| nac_incar_dict.update(base_incar_dict) | ||
| nac_config.update({'parser_settings': nac_parser_settings, | ||
| 'parameters': nac_incar_dict}) | ||
|
|
||
| PhononPhonopy = WorkflowFactory('phonopy.phonon') | ||
| builder = PhononPhonopy.get_builder() | ||
| builder.structure = structure | ||
| builder.calculator_settings = Dict(dict={'forces': forces_config, | ||
| 'nac': nac_config}) | ||
| builder.run_phonopy = Bool(True) | ||
| builder.remote_phonopy = Bool(True) | ||
| builder.code_string = Str('phonopy@stern') | ||
| builder.phonon_settings = Dict( | ||
| dict={'mesh': 50.0, | ||
| 'supercell_matrix': [1, 1, 1], | ||
| 'distance': 0.01, | ||
| 'is_nac': True}) | ||
| builder.symmetry_tolerance = Float(1e-5) | ||
| builder.options = Dict(dict=base_config['options']) | ||
| builder.metadata.label = "NaCl 2x2x2 phonon test on stern" | ||
| builder.metadata.description = "NaCl 2x2x2 phonon test on stern" | ||
|
|
||
| # Chose how to run the calculation | ||
| run_by_deamon = True | ||
| if not run_by_deamon: | ||
| result = run(builder) | ||
| print(result) | ||
| else: | ||
| future = submit(builder) | ||
| print(future) | ||
| print('Running workchain with pk={}'.format(future.pk)) | ||
|
|
||
|
|
||
| def dump_phonopy(pk): | ||
| n = load_node(pk) | ||
| unitcell = n.inputs.structure.get_ase() | ||
| smat = n.outputs.phonon_setting_info['supercell_matrix'] | ||
| ph = phonopy.load(unitcell=unitcell, | ||
| supercell_matrix=smat, | ||
| primitive_matrix='auto') | ||
| force_sets = n.outputs.force_sets.get_array('force_sets') | ||
| dataset = n.outputs.phonon_setting_info['displacement_dataset'] | ||
| ph.dataset = dataset | ||
| ph.forces = force_sets | ||
| if 'nac_params' in n.outputs: | ||
| borns = n.outputs.nac_params.get_array('born_charges') | ||
| epsilon = n.outputs.nac_params.get_array('epsilon') | ||
| nac_params = {'born': borns, | ||
| 'factor': 14.399652, | ||
| 'dielectric': epsilon} | ||
| ph.nac_params = nac_params | ||
|
|
||
| settings = {'force_sets': True, | ||
| 'displacements': True, | ||
| 'force_constants': False, | ||
| 'born_effective_charge': True, | ||
| 'dielectric_constant': True} | ||
| # phonopy-params.yaml is written out. | ||
| ph.save(settings=settings) | ||
| print("phonopy_params.yaml was made for PK=%d" % pk) | ||
|
|
||
|
|
||
| if __name__ == '__main__': | ||
| if len(sys.argv) < 2: | ||
| launch_aiida() | ||
| else: | ||
| dump_phonopy(int(sys.argv[1])) |
Oops, something went wrong.