used. If that is set to a list of directory names, the volumes and structures will be concatenated and sorted according to the volume value. If you set a 'slice' tag in the under the tag 'phonopy', like phonopy: volumes_and_structures: slice: [null, -4] The slice is applied to the volume and structure list. """ run_specs, filename = rmd.get_run_specs_and_filename() cwd = os.getcwd() rmd.chdir(rmd.get_run_dir(run_specs)) rmd.filedump(run_specs, filename) phonopy_specs = run_specs['phonopy'] phonopy_specs['dim'] = ' '.join(map(str, phonopy_specs['dim'])) incar = rmd.read_incar(run_specs) if os.path.isfile('../properties.json'): properties = rmd.fileload('../properties.json') if 'ISPIN' not in incar: if rmd.detect_is_mag(properties['mag']): incar.update({'ISPIN': 2}) else: incar.update({'ISPIN': 1}) # higher priority for run_specs if 'poscar' in run_specs:
ISMEAR: -5 LORBIT: 10 NEDOS: 4000 ISYM: -1 LWAVE: True ISTART: 0 It will cause the INCAR and/or KPOINTS to change before starting the static run. """ # pre-config run_specs, filename = rmd.get_run_specs_and_filename() start_dir = os.getcwd() rmd.chdir(rmd.get_run_dir(run_specs)) rmd.filedump(run_specs, filename) rmd.init_stdout() # read settings # POSCAR if 'poscar' in run_specs: structure = rmd.get_structure(run_specs) elif os.path.isfile('../POSCAR'): structure = mg.Structure.from_file('../POSCAR') rmd.insert_elem_types(run_specs, structure) # INCAR incar = rmd.read_incar(run_specs) if os.path.isfile('../properties.json'):
Run convergence test with changing kpoints subdivision values, and plot figures. You should set a 'kpoints_test' tag in the specs file, like kpoints_test: density_change: [1000, 2000, 4000] force_gamma: True Obviously, 'kpoints' tag should be omitted. """ run_specs, filename = rmd.get_run_specs_and_filename() rmd.chdir(rmd.get_run_dir(run_specs)) rmd.filedump(run_specs, filename) rmd.init_stdout() rmd.infer_from_json(run_specs) structure = rmd.get_structure(run_specs) incar = rmd.read_incar(run_specs) kpoints_specs = run_specs['kpoints_test'] if 'force_gamma' in kpoints_specs: force_gamma = kpoints_specs['force_gamma'] else: force_gamma = False if 'density_change' in kpoints_specs: density_change = np.array(kpoints_specs['density_change'])
arguments of pymatgen.analysis.elasticity.strain.DeformedStructureSet(), like elastic: num_norm: 2 num_shear: 2 After the set of VASP runs, you need to use the process script process_elastic_stress_strain to solve for the elastic constants. """ # pre-config run_specs, filename = rmd.get_run_specs_and_filename() cwd = os.getcwd() rmd.chdir(rmd.get_run_dir(run_specs)) rmd.filedump(run_specs, filename) # read settings incar = rmd.read_incar(run_specs) structure = rmd.get_structure(run_specs) kpoints = rmd.read_kpoints(run_specs, structure) # elastic if 'elastic' in run_specs and ('num_norm' in run_specs['elastic'] or 'num_shear' in run_specs['elastic']): dss = elasticity.strain.DeformedStructureSet(structure, num_norm=run_specs['elastic']['num_norm'], num_shear=run_specs['elastic']['num_shear']) else: dss = elasticity.strain.DeformedStructureSet(structure) strain_list = [i.green_lagrange_strain for i in dss.deformations] rmd.filedump([i.tolist() for i in strain_list], 'strain_list.json') for idx, defo in enumerate(dss.deformations):
would use to actually run the routine script run_phonopy_qha-para.py before this. You should set a 'phonopy' tag in the specs file in the format documented in the script run_phonopy_qha-para.py. Optionally, you can set a tag 'qha_only' to be True to skip the per volume phonopy evaluation, and just run phonopy_qha, phonopy: qha_only: True """ run_specs, filename = rmd.get_run_specs_and_filename() rmd.chdir(rmd.get_run_dir(run_specs)) phonopy_specs = run_specs['phonopy'] phonopy_specs['dim'] = ' '.join(map(str, phonopy_specs['dim'])) phonopy_specs['mp'] = ' '.join(map(str, phonopy_specs['mp'])) phonopy_specs['tmax'] = str(phonopy_specs['tmax']) phonopy_specs['tstep'] = str(phonopy_specs['tstep']) run_volume_dirname = phonopy_specs['volumes_and_structures']['from']\ if 'volumes_and_structures' in phonopy_specs and \ 'from' in phonopy_specs['volumes_and_structures'] and \ phonopy_specs['volumes_and_structures']['from'] else 'run_volume' if isinstance(run_volume_dirname, str): fitting_results = rmd.fileload(os.path.join('..', run_volume_dirname, 'fitting_results.json'))[-1] volume = fitting_results['volume']
Run the full independent strain sets with changing delta values, fit the energy values from each strain set to a polynomial, extract the parameters and plot figures, and then linearly solve for the elastic constants. The strain sets used to solve the elastic constants are detailed in run_module_elastic.py. You should set a 'elastic' tag in the specs file, like elastic: cryst_sys: cubic """ run_specs, filename = rmd.get_run_specs_and_filename() rmd.chdir(rmd.get_run_dir(run_specs)) rmd.filedump(run_specs, filename) cryst_sys = run_specs['elastic']['cryst_sys'] rmd.infer_from_json(run_specs) structure = rmd.get_structure(run_specs) incar = rmd.read_incar(run_specs) kpoints = rmd.read_kpoints(run_specs, structure) is_mag = incar['ISPIN'] == 2 if 'ISPIN' in incar else False fitting_results_summary = {} rmd.chdir('nostrain') rmd.init_stdout()
Run the phonopy force set calculation for a constant volume. You should set a 'phonopy' tag in the specs file like phonopy: mode: force_set (or force_constant) dim: [2, 2, 2] mp: [31, 31, 31] tmax: 1400 tstep: 5 """ run_specs, filename = rmd.get_run_specs_and_filename() cwd = os.getcwd() rmd.chdir(rmd.get_run_dir(run_specs)) rmd.filedump(run_specs, filename) phonopy_dim = ' '.join(map(str, run_specs['phonopy']['dim'])) phonopy_mp = ' '.join(map(str, run_specs['phonopy']['mp'])) phonopy_tmax = str(run_specs['phonopy']['tmax']) phonopy_tstep = str(run_specs['phonopy']['tstep']) incar = rmd.read_incar(run_specs) if os.path.isfile('../properties.json'): properties = rmd.fileload('../properties.json') if 'ISPIN' not in incar: if rmd.detect_is_mag(properties['mag']): incar.update({'ISPIN': 2}) else: incar.update({'ISPIN': 1})
Run the phonopy force set calculation for a constant volume. You should set a 'phonopy' tag in the specs file like phonopy: mode: force_set (or force_constant) dim: [2, 2, 2] mp: [31, 31, 31] tmax: 1400 tstep: 5 """ run_specs, filename = rmd.get_run_specs_and_filename() cwd = os.getcwd() rmd.chdir(rmd.get_run_dir(run_specs)) rmd.filedump(run_specs, filename) phonopy_dim = ' '.join(map(str, run_specs['phonopy']['dim'])) phonopy_mp = ' '.join(map(str, run_specs['phonopy']['mp'])) phonopy_tmax = str(run_specs['phonopy']['tmax']) phonopy_tstep = str(run_specs['phonopy']['tstep']) rmd.infer_from_json(run_specs) structure = rmd.get_structure(run_specs) incar = rmd.read_incar(run_specs) kpoints = rmd.read_kpoints(run_specs, structure) if run_specs['phonopy']['mode'] == 'force_set': structure.to(filename='POSCAR') call('phonopy -d --dim="' + phonopy_dim + '" > /dev/null', shell=True)
Run the full independent strain sets with changing delta values, fit the energy values from each strain set to a polynomial, extract the parameters and plot figures, and then linearly solve for the elastic constants. The strain sets used to solve the elastic constants are detailed in run_module_elastic.py. You should set a 'elastic' tag in the specs file, like elastic: cryst_sys: cubic """ run_specs, filename = rmd.get_run_specs_and_filename() rmd.chdir(rmd.get_run_dir(run_specs)) rmd.filedump(run_specs, filename) cryst_sys = run_specs['elastic']['cryst_sys'] rmd.infer_from_json(run_specs) structure = rmd.get_structure(run_specs) incar = rmd.read_incar(run_specs) kpoints = rmd.read_kpoints(run_specs, structure) is_mag = incar['ISPIN'] == 2 if 'ISPIN' in incar else False fitting_results_summary = {} rmd.chdir('nostrain') rmd.init_stdout()
arguments of pymatgen.analysis.elasticity.strain.DeformedStructureSet(), like elastic: num_norm: 2 num_shear: 2 After the set of VASP runs, you need to use the process script process_elastic_stress_strain to solve for the elastic constants. """ # pre-config run_specs, filename = rmd.get_run_specs_and_filename() cwd = os.getcwd() rmd.chdir(rmd.get_run_dir(run_specs)) rmd.filedump(run_specs, filename) # read settings rmd.infer_from_json(run_specs) structure = rmd.get_structure(run_specs) incar = rmd.read_incar(run_specs) kpoints = rmd.read_kpoints(run_specs, structure) # elastic if 'elastic' in run_specs and ('num_norm' in run_specs['elastic'] or 'num_shear' in run_specs['elastic']): dss = elasticity.strain.DeformedStructureSet( structure, num_norm=run_specs['elastic']['num_norm'], num_shear=run_specs['elastic']['num_shear'])