def cmpt_deepmd_lammps(jdata, conf_dir, supercell, task_name):
equi_path = re.sub('confs', global_equi_name, conf_dir)
equi_path = os.path.join(equi_path, task_name)
equi_path = os.path.abspath(equi_path)
equi_log = os.path.join(equi_path, 'log.lammps')
task_path = re.sub('confs', global_task_name, conf_dir)
task_path = os.path.join(task_path, task_name)
task_path = os.path.abspath(task_path)
print("# ", task_path)
equi_natoms, equi_epa, equi_vpa = lammps.get_nev(equi_log)
copy_str = "%sx%sx%s" % (supercell[0], supercell[1], supercell[2])
struct_path_widecard = os.path.join(task_path, 'struct-%s-*' % (copy_str))
struct_path_list = glob.glob(struct_path_widecard)
struct_path_list.sort()
if len(struct_path_list) == 0:
print("# cannot find results for conf %s supercell %s" %
(conf_dir, supercell))
sys.stdout.write("Structure: \tVac_E(eV) E(eV) equi_E(eV)\n")
for ii in struct_path_list:
struct_poscar = os.path.join(ii, 'POSCAR')
energy_shift = comput_e_shift(struct_poscar, task_name)
structure_dir = os.path.basename(ii)
lmp_log = os.path.join(ii, 'log.lammps')
natoms, epa, vpa = lammps.get_nev(lmp_log)
evac = epa * natoms - equi_epa * natoms
sys.stdout.write(
"%s: %7.3f %7.3f %7.3f \n" %
(structure_dir, evac, epa * natoms, equi_epa * natoms))
def comput_lmp_nev(conf_dir, task_name, write_stable=False):
conf_path = re.sub('confs', global_equi_name, conf_dir)
conf_path = os.path.abspath(conf_path)
poscar = os.path.join(conf_path, 'POSCAR')
if write_stable:
ele_types = vasp.get_poscar_types(poscar)
if len(ele_types) > 1:
raise RuntimeError(
'stable energy and volume only for one element, current you have %s from POSCAR'
% str(ele_types))
ener_shift = comput_e_shift(poscar, task_name)
lmp_path = os.path.join(conf_path, task_name)
log_lammps = os.path.join(lmp_path, 'log.lammps')
if os.path.isfile(log_lammps):
natoms, epa, vpa = lammps.get_nev(log_lammps)
epa = (epa * natoms - ener_shift) / natoms
if write_stable:
stable_dir = 'stables'
os.makedirs(stable_dir, exist_ok=True)
name_prefix = os.path.join(stable_dir,
'%s.%s' % (ele_types[0], task_name))
open(name_prefix + '.e', 'w').write('%.16f\n' % (epa))
open(name_prefix + '.v', 'w').write('%.16f\n' % (vpa))
return natoms, epa, vpa
else:
return None, None, None
def comput_lmp_eos(conf_dir, task_name):
conf_path = re.sub('confs', global_task_name, conf_dir)
conf_path = os.path.abspath(conf_path)
conf_path = os.path.join(conf_path, task_name)
vol_paths = glob.glob(os.path.join(conf_path, 'vol-*'))
vol_paths.sort()
print('Vpa(A^3)\tEpA(eV)')
for ii in vol_paths:
log_lammps = os.path.join(ii, 'log.lammps')
natoms, epa, vpa = lammps.get_nev(log_lammps)
print(vpa, epa)
def _cmpt_deepmd_reprod_traj(jdata, conf_dir, supercell, insert_ele,
task_name):
fp_params = jdata['vasp_params']
kspacing = fp_params['kspacing']
conf_path = os.path.abspath(conf_dir)
task_path = re.sub('confs', global_task_name, conf_path)
vasp_path = os.path.join(task_path, 'vasp-k%.2f' % kspacing)
lmps_path = os.path.join(task_path, task_name + '-k%.2f' % kspacing)
copy_str = "%sx%sx%s" % (supercell[0], supercell[1], supercell[2])
struct_widecard = os.path.join(vasp_path,
'struct-%s-%s-*' % (insert_ele, copy_str))
vasp_struct = glob.glob(struct_widecard)
vasp_struct.sort()
cwd = os.getcwd()
for vs in vasp_struct:
# compute vasp
outcar = os.path.join(vs, 'OUTCAR')
vasp_ener = np.array(vasp.get_energies(outcar))
vasp_ener_file = os.path.join(vs, 'ener.vasp.out')
# compute reprod
struct_basename = os.path.basename(vs)
ls = os.path.join(lmps_path, struct_basename)
frame_widecard = os.path.join(ls, 'frame.*')
frames = glob.glob(frame_widecard)
frames.sort()
lmp_ener = []
for ii in frames:
log_lmp = os.path.join(ii, 'log.lammps')
natoms, epa, vpa = lammps.get_nev(log_lmp)
lmp_ener.append(epa)
lmp_ener = np.array(lmp_ener)
lmp_ener = np.reshape(lmp_ener, [-1, 1])
lmp_ener_file = os.path.join(ls, 'ener.lmp.out')
vasp_ener = np.reshape(vasp_ener, [-1, 1]) / natoms
error_start = 1
lmp_ener -= lmp_ener[-1] - vasp_ener[-1]
diff = lmp_ener - vasp_ener
diff = diff[error_start:]
error = np.linalg.norm(diff) / np.sqrt(np.size(lmp_ener))
np.savetxt(vasp_ener_file, vasp_ener[error_start:])
np.savetxt(lmp_ener_file, lmp_ener[error_start:])
print(ls, error)