phonopy_specs['volumes_and_structures']['slice'] else [None] * 2
volume, energy, structures = np.array(sorted(zip(volume, energy, structures)))[idx_slice[0]:idx_slice[1]].T
for V, st in zip(volume, structures):
rmd.chdir(str(np.round(V, 2)))
if run_specs['phonopy']['mode'] == 'force_set':
structure = mg.Structure.from_dict(st)
structure.to(filename='POSCAR')
call('phonopy -d --dim="' + phonopy_specs['dim'] + '" > /dev/null', shell=True)
os.remove('SPOSCAR')
disp_structures = sorted(glob.glob('POSCAR-*'))
disp_dirs = ['disp-' + i.split('POSCAR-')[1] for i in disp_structures]
for disp_d, disp_p in zip(disp_dirs, disp_structures):
rmd.chdir(disp_d)
rmd.init_stdout()
shutil.move('../' + disp_p, 'POSCAR')
incar.write_file('INCAR')
kpoints.write_file('KPOINTS')
rmd.write_potcar(run_specs)
job = str(V) + '-' + disp_d
shutil.copy(cwd + '/INPUT/deploy.job', job)
call('sed -i "/python/c time ' + rmd.VASP_EXEC + ' 2>&1 | tee -a stdout" ' + job, shell=True)
call('M ' + job, shell=True)
os.remove(job)
os.chdir('..')
elif run_specs['phonopy']['mode'] == 'force_constant':
rmd.init_stdout()
incar.write_file('INCAR')
kpoints.write_file('KPOINTS')
structure = mg.Structure.from_dict(st)
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'])
else:
density_change = np.array(range(kpoints_specs['begin'], kpoints_specs['end'], kpoints_specs['step']))