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:
structure = rmd.get_structure(run_specs)
elif os.path.isfile('../POSCAR'):
structure = mg.Structure.from_file('../POSCAR')
rmd.insert_elem_types(run_specs, structure)
kpoints = rmd.read_kpoints(run_specs, structure)
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']
energy = fitting_results['energy']
structures = fitting_results['structures']
elif isinstance(run_volume_dirname, list):
volume = []
energy = []
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:
structure = rmd.get_structure(run_specs)
elif os.path.isfile('../POSCAR'):
structure = mg.Structure.from_file('../POSCAR')
rmd.insert_elem_types(run_specs, structure)
kpoints = rmd.read_kpoints(run_specs, structure)
# first SC run
incar.write_file('INCAR')
kpoints.write_file('KPOINTS')
structure.to(filename='POSCAR')
rmd.write_potcar(run_specs)
rmd.run_vasp()
# second non-SC run
incar.update(run_specs['dos']['incar'])
kpoints = rmd.read_kpoints(run_specs['dos'], structure)
structure = mg.Structure.from_file('CONTCAR')
incar.write_file('INCAR')
kpoints.write_file('KPOINTS')
relaxation parameters, and the second and after runs with high relaxation
parameters.
"""
# pre-config
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()
# 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)
stack_oszicar()
# write input files and run vasp
structure.to(filename='POSCAR')
incar.write_file('INCAR')
kpoints.write_file('KPOINTS')
rmd.write_potcar(run_specs)
rmd.run_vasp()
# rerun once according to the specs
if 'rerun' in run_specs:
stack_oszicar()
structure = mg.Structure.from_file('CONTCAR')
structure.to(filename='POSCAR')
if 'incar' in run_specs['rerun']:
KPAR_NPAR_test
change: [[4,1], [4,2], [4,4], [4,8], [4,16], [8,1], [8,2],
[8,4], [8,8], [16,1], [16,2], [16,4], [32,1], [32,2]]
"""
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 = rmd.read_kpoints(run_specs, structure)
KPAR_NPAR_change = np.array(run_specs['KPAR_NPAR_test']['change'])
energy = np.zeros(len(KPAR_NPAR_change))
time = np.zeros(len(KPAR_NPAR_change))
kpoints.write_file('KPOINTS')
structure.to(filename='POSCAR')
rmd.write_potcar(run_specs)
# main workflow
for i, KPAR_NPAR in enumerate(KPAR_NPAR_change):
incar['KPAR'] = KPAR_NPAR[0]
incar['NPAR'] = KPAR_NPAR[1]
incar.write_file('INCAR')
rmd.run_vasp()
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()
rmd.chdir(rmd.get_run_dir(run_specs))
rmd.filedump(run_specs, filename)
rmd.init_stdout()
# read settings
incar = rmd.read_incar(run_specs)
structure = rmd.get_structure(run_specs)
kpoints = rmd.read_kpoints(run_specs, structure)
# write input files and run vasp
incar.write_file('INCAR')
kpoints.write_file('KPOINTS')
structure.to(filename='POSCAR')
rmd.write_potcar(run_specs)
rmd.run_vasp()
# static
structure = mg.Structure.from_file('CONTCAR')
structure.to(filename='POSCAR')
if 'incar' in run_specs['static']:
incar.update(run_specs['static']['incar'])
incar.write_file('INCAR')
if 'kpoints' in run_specs['static']: