def cmpt_vasp(jdata, conf_dir, supercell) :
if 'relax_incar' in jdata.keys():
vasp_str='vasp-relax_incar'
else:
kspacing = jdata['vasp_params']['kspacing']
vasp_str='vasp-k%.2f' % kspacing
equi_path = re.sub('confs', global_equi_name, conf_dir)
equi_path = os.path.join(equi_path, vasp_str)
equi_path = os.path.abspath(equi_path)
equi_outcar = os.path.join(equi_path, 'OUTCAR')
task_path = re.sub('confs', global_task_name, conf_dir)
task_path = os.path.join(task_path, vasp_str)
task_path = os.path.abspath(task_path)
print("# ", task_path)
equi_natoms, equi_epa, equi_vpa = vasp.get_nev(equi_outcar)
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, vasp_str)
structure_dir = os.path.basename(ii)
outcar = os.path.join(ii, 'OUTCAR')
natoms, epa, vpa = vasp.get_nev(outcar)
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 _cmpt_vasp(jdata, conf_dir, supercell, insert_ele) :
fp_params = jdata['vasp_params']
kspacing = fp_params['kspacing']
equi_path = re.sub('confs', global_equi_name, conf_dir)
equi_path = os.path.join(equi_path, 'vasp-k%.2f' % kspacing)
equi_path = os.path.abspath(equi_path)
equi_outcar = os.path.join(equi_path, 'OUTCAR')
task_path = re.sub('confs', global_task_name, conf_dir)
task_path = os.path.join(task_path, 'vasp-k%.2f' % kspacing)
task_path = os.path.abspath(task_path)
equi_natoms, equi_epa, equi_vpa = vasp.get_nev(equi_outcar)
copy_str = "%sx%sx%s" % (supercell[0], supercell[1], supercell[2])
struct_path_widecard = os.path.join(task_path, 'struct-%s-%s-*' % (insert_ele, copy_str))
print(struct_path_widecard)
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 ("Insert_ele-Struct: Inter_E(eV)\n")
for ii in struct_path_list :
structure_dir = os.path.basename(ii)
outcar = os.path.join(ii, 'OUTCAR')
natoms, epa, vpa = vasp.get_nev(outcar)
evac = epa * natoms - equi_epa * natoms
sys.stdout.write ("%s: %7.3f \n" % (structure_dir, evac))
def cmpt_vasp(jdata, conf_dir, static=False):
if 'relax_incar' in jdata.keys():
vasp_str = 'vasp-relax_incar'
else:
kspacing = jdata['vasp_params']['kspacing']
vasp_str = 'vasp-k%.2f' % (kspacing)
equi_path = re.sub('confs', global_equi_name, conf_dir)
equi_path = os.path.join(equi_path, vasp_str)
equi_path = os.path.abspath(equi_path)
equi_outcar = os.path.join(equi_path, 'OUTCAR')
task_path = re.sub('confs', global_task_name, conf_dir)
if static:
if 'scf_incar' in jdata.keys():
vasp_static_str = 'vasp-static-scf_incar'
else:
kspacing = jdata['vasp_params']['kspacing']
vasp_static_str = 'vasp-static-k%.2f' % (kspacing)
task_path = os.path.join(task_path, vasp_static_str)
else:
task_path = os.path.join(task_path, vasp_str)
task_path = os.path.abspath(task_path)
equi_natoms, equi_epa, equi_vpa = vasp.get_nev(equi_outcar)
struct_path_widecard = os.path.join(task_path, 'struct-*-m*m')
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" % (conf_dir))
sys.stdout.write("Miller_Indices: \tSurf_E(J/m^2) EpA(eV) equi_EpA(eV)\n")
result = os.path.join(task_path, 'result')
with open(result, 'w') as fp:
fp.write('conf_dir:%s\n' % (conf_dir))
fp.write("Miller_Indices: \tSurf_E(J/m^2) EpA(eV) equi_EpA(eV)\n")
for ii in struct_path_list:
structure_dir = os.path.basename(ii)
outcar = os.path.join(ii, 'OUTCAR')
natoms, epa, vpa = vasp.get_nev(outcar)
if static:
e0 = np.array(vasp.get_energies(outcar)) / natoms
epa = e0[0]
boxes = vasp.get_boxes(outcar)
AA = np.linalg.norm(np.cross(boxes[0][0], boxes[0][1]))
Cf = 1.60217657e-16 / (1e-20 * 2) * 0.001
evac = (epa * natoms - equi_epa * natoms) / AA * Cf
sys.stdout.write("%s:\t %7.3f %8.3f %8.3f\n" %
(structure_dir, evac, epa, equi_epa))
fp.write("%s:\t %7.3f %8.3f %8.3f\n" %
(structure_dir, evac, epa, equi_epa))
fp.close()
if 'upload_username' in jdata.keys():
upload_username = jdata['upload_username']
util.insert_data('surf', 'vasp', upload_username, result)
def _compute_lower(self, output_file, all_tasks, all_res):
output_file = os.path.abspath(output_file)
res_data = {}
ptr_data = os.path.dirname(output_file) + '\n'
if not self.reprod:
ptr_data += "Miller_Indices: \tSurf_E(J/m^2) EpA(eV) equi_EpA(eV)\n"
for ii in all_tasks:
with open(os.path.join(ii, 'inter.json')) as fp:
idata = json.load(fp)
inter_type = idata['type']
equi_path = os.path.abspath(
os.path.join(os.path.dirname(output_file),
'../relaxation'))
structure_dir = os.path.basename(ii)
if inter_type == 'vasp':
equi_outcar = os.path.join(equi_path, 'OUTCAR')
equi_natoms, equi_epa, equi_vpa = vasp.get_nev(equi_outcar)
outcar = os.path.join(ii, 'OUTCAR')
natoms, epa, vpa = vasp.get_nev(outcar)
if self.static:
e0 = np.array(vasp.get_energies(outcar)) / natoms
epa = e0[0]
boxes = vasp.get_boxes(outcar)
AA = np.linalg.norm(np.cross(boxes[0][0], boxes[0][1]))
elif inter_type in ['deepmd', 'meam', 'eam_fs', 'eam_alloy']:
equi_log = os.path.join(equi_path, 'log.lammps')
equi_natoms, equi_epa, equi_vpa = lammps.get_nev(equi_log)
lmp_log = os.path.join(ii, 'log.lammps')
natoms, epa, vpa = lammps.get_nev(lmp_log)
AA = lammps.get_base_area(lmp_log)
else:
raise RuntimeError('interaction type not supported')
Cf = 1.60217657e-16 / (1e-20 * 2) * 0.001
evac = (epa * natoms - equi_epa * natoms) / AA * Cf
ptr_data += "%s: \t%7.3f %8.3f %8.3f\n" % (
structure_dir, evac, epa, equi_epa)
res_data[structure_dir] = [evac, epa, equi_epa]
else:
if 'vasp_path' not in self.parameter:
raise RuntimeError(
"please provide the vasp_path for reproduction")
vasp_path = os.path.abspath(self.parameter['vasp_path'])
res_data, ptr_data = reproduce.post_repro(vasp_path, all_tasks,
ptr_data)
with open(output_file, 'w') as fp:
json.dump(res_data, fp, indent=4)
return res_data, ptr_data
def comput_vasp_eos(jdata, conf_dir):
conf_path = re.sub('confs', global_task_name, conf_dir)
conf_path = os.path.abspath(conf_path)
if 'relax_incar' in jdata.keys():
vasp_str = 'vasp-relax_incar'
else:
kspacing = jdata['vasp_params']['kspacing']
vasp_str = 'vasp-k%.2f' % kspacing
task_path = os.path.join(conf_path, vasp_str)
vol_paths = glob.glob(os.path.join(task_path, 'vol-*'))
vol_paths.sort(key=lambda k: float(k.split('-')[-1]))
result = os.path.join(task_path, 'result')
print('Vpa(A^3)\tEpA(eV)')
with open(result, 'w') as fp:
fp.write('conf_dir:%s\n VpA(A^3) EpA(eV)\n' % (conf_dir))
for ii in vol_paths:
outcar = os.path.join(ii, 'OUTCAR')
natoms, epa, vpa = vasp.get_nev(outcar)
print(vpa, epa)
fp.write('%7.3f %8.4f \n' % (vpa, epa))
fp.close()
if 'upload_username' in jdata.keys():
upload_username = jdata['upload_username']
util.insert_data('eos', 'vasp', upload_username, result)
def comput_vasp_nev(jdata, conf_dir, write_stable=False):
kspacing = jdata['vasp_params']['kspacing']
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, 'vasp-k%.2f' % kspacing)
vasp_path = os.path.join(conf_path, 'vasp-k%.2f' % kspacing)
outcar = os.path.join(vasp_path, 'OUTCAR')
# tag_fin = os.path.join(vasp_path, 'tag_finished')
if not os.path.isfile(outcar):
warnings.warn("cannot find OUTCAR in " + vasp_path + " skip")
elif not vasp.check_finished(outcar):
warnings.warn("incomplete job " + vasp_path + " use the last frame")
if os.path.isfile(outcar):
natoms, epa, vpa = vasp.get_nev(outcar)
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.vasp-k%.2f' % (ele_types[0], kspacing))
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 _cmpt_vasp(jdata, conf_dir, supercell, insert_ele):
if 'relax_incar' in jdata.keys():
vasp_str = 'vasp-relax_incar'
else:
kspacing = jdata['vasp_params']['kspacing']
vasp_str = 'vasp-k%.2f' % kspacing
equi_path = re.sub('confs', global_equi_name, conf_dir)
equi_path = os.path.join(equi_path, vasp_str)
equi_path = os.path.abspath(equi_path)
equi_outcar = os.path.join(equi_path, 'OUTCAR')
task_path = re.sub('confs', global_task_name, conf_dir)
task_path = os.path.join(task_path, vasp_str)
task_path = os.path.abspath(task_path)
equi_natoms, equi_epa, equi_vpa = vasp.get_nev(equi_outcar)
copy_str = "%sx%sx%s" % (supercell[0], supercell[1], supercell[2])
struct_path_widecard = os.path.join(
task_path, 'struct-%s-%s-*' % (insert_ele, copy_str))
print(struct_path_widecard)
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("Insert_ele-Struct: Inter_E(eV) E(eV) equi_E(eV)\n")
result = os.path.join(task_path, 'result')
with open(result, 'w') as fp:
fp.write('conf_dir:%s\n' % (conf_dir))
fp.write("Insert_ele-Struct: Inter_E(eV) E(eV) equi_E(eV)\n")
for ii in struct_path_list:
structure_dir = os.path.basename(ii)
outcar = os.path.join(ii, 'OUTCAR')
natoms, epa, vpa = vasp.get_nev(outcar)
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))
fp.write("%s: %7.3f %7.3f %7.3f \n" %
(structure_dir, evac, epa * natoms, equi_epa * natoms))
fp.close()
def comput_vasp_eos(jdata, conf_dir):
kspacing = jdata['vasp_params']['kspacing']
conf_path = re.sub('confs', global_task_name, conf_dir)
conf_path = os.path.abspath(conf_path)
conf_path = os.path.join(conf_path, 'vasp-k%.2f' % kspacing)
vol_paths = glob.glob(os.path.join(conf_path, 'vol-*'))
vol_paths.sort()
print('Vpa(A^3)\tEpA(eV)')
for ii in vol_paths:
outcar = os.path.join(ii, 'OUTCAR')
natoms, epa, vpa = vasp.get_nev(outcar)
print(vpa, epa)
def cmpt_vasp(jdata, conf_dir, static=False):
fp_params = jdata['vasp_params']
kspacing = fp_params['kspacing']
equi_path = re.sub('confs', global_equi_name, conf_dir)
equi_path = os.path.join(equi_path, 'vasp-k%.2f' % kspacing)
equi_path = os.path.abspath(equi_path)
equi_outcar = os.path.join(equi_path, 'OUTCAR')
task_path = re.sub('confs', global_task_name, conf_dir)
if static:
task_path = os.path.join(task_path, 'vasp-static-k%.2f' % kspacing)
else:
task_path = os.path.join(task_path, 'vasp-k%.2f' % kspacing)
task_path = os.path.abspath(task_path)
equi_natoms, equi_epa, equi_vpa = vasp.get_nev(equi_outcar)
struct_path_widecard = os.path.join(task_path, 'struct-*-m*m')
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("Miller_Indices: \tSurf_E(J/m^2) EpA(eV) equi_EpA(eV)\n")
for ii in struct_path_list:
structure_dir = os.path.basename(ii)
outcar = os.path.join(ii, 'OUTCAR')
natoms, epa, vpa = vasp.get_nev(outcar)
if static:
e0 = np.array(vasp.get_energies(outcar)) / natoms
epa = e0[0]
boxes = vasp.get_boxes(outcar)
AA = np.linalg.norm(np.cross(boxes[0][0], boxes[0][1]))
Cf = 1.60217657e-16 / (1e-20 * 2) * 0.001
evac = (epa * natoms - equi_epa * natoms) / AA * Cf
sys.stdout.write("%s:\t %7.3f %8.3f %8.3f\n" %
(structure_dir, evac, epa, equi_epa))
def _compute_lower(self, output_file, all_tasks, all_res):
output_file = os.path.abspath(output_file)
res_data = {}
ptr_data = os.path.dirname(output_file) + '\n'
if not self.reprod:
ptr_data += "Insert_ele-Struct: Inter_E(eV) E(eV) equi_E(eV)\n"
for ii in all_tasks:
with open(os.path.join(ii, 'inter.json')) as fp:
idata = json.load(fp)
inter_type = idata['type']
equi_path = os.path.abspath(
os.path.join(os.path.dirname(output_file),
'../relaxation'))
structure_dir = os.path.basename(ii)
if inter_type == 'vasp':
equi_outcar = os.path.join(equi_path, 'OUTCAR')
equi_natoms, equi_epa, equi_vpa = vasp.get_nev(equi_outcar)
elif inter_type in ['deepmd', 'meam', 'eam_fs', 'eam_alloy']:
equi_log = os.path.join(equi_path, 'log.lammps')
equi_natoms, equi_epa, equi_vpa = lammps.get_nev(equi_log)
else:
raise RuntimeError('interaction type not supported')
natoms = len(all_res[ii]['force']) / 3
epa = all_res[ii]['energy'] / natoms
evac = epa * natoms - equi_epa * natoms
ptr_data += "%s: %7.3f %7.3f %7.3f \n" % (
structure_dir, evac, epa * natoms, equi_epa * natoms)
res_data[structure_dir] = [
evac, epa * natoms, equi_epa * natoms
]
else:
if 'vasp_path' not in self.parameter:
raise RuntimeError(
"please provide the vasp_path for reproduction")
vasp_path = os.path.abspath(self.parameter['vasp_path'])
res_data, ptr_data = reproduce.post_repro(vasp_path, all_tasks,
ptr_data)
with open(output_file, 'w') as fp:
json.dump(res_data, fp, indent=4)
return res_data, ptr_data
def comput_vasp_nev(jdata, conf_dir, write_shift=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')
ele_types = vasp.get_poscar_types(poscar)
if 'relax_incar' in jdata.keys():
vasp_str = 'vasp-relax_incar'
else:
kspacing = jdata['vasp_params']['kspacing']
vasp_str = 'vasp-k%.2f' % kspacing
vasp_path = os.path.join(conf_path, vasp_str)
outcar = os.path.join(vasp_path, 'OUTCAR')
# tag_fin = os.path.join(vasp_path, 'tag_finished')
if not os.path.isfile(outcar):
warnings.warn("cannot find OUTCAR in " + vasp_path + " skip")
elif not vasp.check_finished(outcar):
warnings.warn("incomplete job " + vasp_path + " use the last frame")
if os.path.isfile(outcar):
natoms, epa, vpa = vasp.get_nev(outcar)
if write_shift and len(ele_types) > 1:
ener_shift = comput_e_shift(poscar, vasp_str)
shift = (epa * natoms - ener_shift) / natoms
return natoms, epa, vpa, shift
if len(ele_types) == 1:
stable_dir = 'stables'
os.makedirs(stable_dir, exist_ok=True)
name_prefix = os.path.join(stable_dir,
'%s.' % (ele_types[0]) + vasp_str)
open(name_prefix + '.e', 'w').write('%.16f\n' % (epa))
open(name_prefix + '.v', 'w').write('%.16f\n' % (vpa))
return natoms, epa, vpa, None
else:
return None, None, None, None
