def _cmpt_deepmd_lammps(jdata, conf_dir, supercell, insert_ele, task_name) :
equi_path = re.sub('confs', global_equi_name, conf_dir)
equi_path = os.path.join(equi_path, task_name.split('-')[0])
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)
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-%s-*' % (insert_ele,copy_str))
struct_path_list = glob.glob(struct_path_widecard)
print(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")
for ii in struct_path_list :
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 cmpt_deepmd_lammps(jdata, conf_dir, task_name, static = False) :
equi_path = re.sub('confs', global_equi_name, conf_dir)
equi_path = os.path.join(equi_path, task_name.split('-')[0])
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)
equi_natoms, equi_epa, equi_vpa = lammps.get_nev(equi_log)
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)
lmp_log = os.path.join(ii, 'log.lammps')
natoms, epa, vpa = lammps.get_nev(lmp_log)
AA = lammps.get_base_area(lmp_log)
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() and task_name=='deepm':
upload_username=jdata['upload_username']
util.insert_data('surf','deepmd',upload_username,result)
def cmpt_deepmd_lammps(jdata, conf_dir, task_name, static=False):
equi_path = re.sub('confs', global_equi_name, conf_dir)
equi_path = os.path.join(equi_path, task_name.split('-')[0])
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)
equi_natoms, equi_epa, equi_vpa = lammps.get_nev(equi_log)
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")
for ii in struct_path_list:
structure_dir = os.path.basename(ii)
lmp_log = os.path.join(ii, 'log.lammps')
natoms, epa, vpa = lammps.get_nev(lmp_log)
AA = lammps.get_base_area(lmp_log)
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 cmpt_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 _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_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']
if 'relax_incar' in jdata.keys():
vasp_str = 'vasp-relax_incar'
else:
vasp_str = 'vasp-k%.2f' % 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_str)
lmps_path = os.path.join(task_path,
task_name + vasp_str.replace('vasp', ''))
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(os.path.basename(ls), 'EpA_std_err=', error)
def post_repro(vasp_path, all_tasks, ptr_data):
ptr_data += "Reproduce: VASP_path DFT_E(eV/atom) LMP_E(eV/atom) Difference(eV/atom)\n"
vasp_task = glob.glob(os.path.join(vasp_path, 'task.[0-9]*[0-9]'))
assert len(vasp_task) > 0, "Please do VASP calcualtions first"
vasp_task.sort()
vasp_ener_tot = []
lmp_ener_tot = []
res_data = {}
for ii in vasp_task:
# compute vasp
outcar = os.path.join(ii, 'OUTCAR')
vasp_ener = np.array(vasp.get_energies(outcar))
vasp_ener_file = os.path.join(ii, 'ener.vasp.out')
# compute reprod
lmp_ener = []
if len(all_tasks) < (len(vasp_ener_tot) + len(vasp_ener)):
raise RuntimeError("lammps tasks reproduced not equal to vasp")
natoms = 1
for jj in range(
len(vasp_ener_tot), (len(vasp_ener_tot) + len(vasp_ener))
): #all_tasks[len(vasp_ener_tot):(len(vasp_ener_tot) + len(vasp_ener))]:
log_lmp = os.path.join(all_tasks[jj], 'log.lammps')
if not os.path.exists(log_lmp):
raise RuntimeError("lammps reproduce not finished")
natoms, epa, vpa = lammps.get_nev(log_lmp)
lmp_ener.append(epa)
lmp_ener_tot.append(epa)
vasp_epa = list(vasp_ener)[jj - len(vasp_ener_tot)] / natoms
ptr_data += '%s %7.3f %7.3f %7.3f\n' % (vasp_task[ii], vasp_epa,
epa, epa - vasp_epa)
lmp_ener = np.array(lmp_ener)
lmp_ener = np.reshape(lmp_ener, [-1, 1])
vasp_ener_tot += list(vasp_ener)
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))
res_data[ii] = {'nframes': len(vasp_ener), 'error': error}
np.savetxt(vasp_ener_file, vasp_ener[error_start:])
if not len(vasp_ener_tot) == len(lmp_ener_tot):
raise RuntimeError("lammps tasks reproduced not equal to vasp")
# for ii in range(len(lmp_ener_tot)):
# ptr_data += '%7.3f %7.3f %7.3f\n' % (vasp_ener_tot[ii], lmp_ener_tot[ii],
# lmp_ener_tot[ii] - vasp_ener_tot[ii])
return res_data, ptr_data
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_lmp_eos(jdata, 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(key=lambda k: float(k.split('-')[-1]))
result = os.path.join(conf_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:
log_lammps = os.path.join(ii, 'log.lammps')
natoms, epa, vpa = lammps.get_nev(log_lammps)
print(vpa, epa)
fp.write('%7.3f %8.4f \n' % (vpa, epa))
fp.close()
if 'upload_username' in jdata.keys() and task_name == 'deepmd':
upload_username = jdata['upload_username']
util.insert_data('eos', 'deepmd', upload_username, result)
def comput_lmp_nev(conf_dir, task_name, 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)
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)
if write_shift and len(ele_types) > 1:
ener_shift = comput_e_shift(poscar, task_name)
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.%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, None
else:
return None, None, None, None
