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 _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