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'])