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 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) :
conf_path = os.path.abspath(conf_dir)
conf_poscar = os.path.join(conf_path, 'POSCAR')
task_path = re.sub('confs', global_task_name, conf_path)
task_path = os.path.join(task_path, task_name)
equi_stress = Stress(np.loadtxt(os.path.join(task_path, 'equi.stress.out')))
lst_dfm_path = glob.glob(os.path.join(task_path, 'dfm-*'))
lst_strain = []
lst_stress = []
for ii in lst_dfm_path :
strain = np.loadtxt(os.path.join(ii, 'strain.out'))
stress = lammps.get_stress(os.path.join(ii, 'log.lammps'))
# convert from pressure to stress
stress = -stress
lst_strain.append(Strain(strain))
lst_stress.append(Stress(stress))
et = ElasticTensor.from_independent_strains(lst_strain, lst_stress, eq_stress = equi_stress, vasp = False)
# et = ElasticTensor.from_independent_strains(lst_strain, lst_stress, eq_stress = None)
# bar to GPa
# et = -et / 1e4
print_et(et)
result = os.path.join(task_path,'result')
result_et(et,conf_dir,result)
if 'upload_username' in jdata.keys() and task_name=='deepmd':
upload_username=jdata['upload_username']
util.insert_data('elastic','deepmd',upload_username,result)
def cmpt_vasp(jdata, conf_dir) :
conf_path = os.path.abspath(conf_dir)
conf_poscar = os.path.join(conf_path, 'POSCAR')
task_path = re.sub('confs', global_task_name, conf_path)
if 'relax_incar' in jdata.keys():
vasp_str='vasp-relax_incar'
else:
fp_params = jdata['vasp_params']
kspacing = fp_params['kspacing']
vasp_str='vasp-k%.2f' % kspacing
task_path = os.path.join(task_path, vasp_str)
equi_stress = Stress(np.loadtxt(os.path.join(task_path, 'equi.stress.out')))
lst_dfm_path = glob.glob(os.path.join(task_path, 'dfm-*'))
lst_strain = []
lst_stress = []
for ii in lst_dfm_path :
strain = np.loadtxt(os.path.join(ii, 'strain.out'))
stress = vasp.get_stress(os.path.join(ii, 'OUTCAR'))
# convert from pressure in kB to stress
stress *= -1000
lst_strain.append(Strain(strain))
lst_stress.append(Stress(stress))
et = ElasticTensor.from_independent_strains(lst_strain, lst_stress, eq_stress = equi_stress, vasp = False)
# et = ElasticTensor.from_independent_strains(lst_strain, lst_stress, eq_stress = None)
# bar to GPa
# et = -et / 1e4
print_et(et)
result = os.path.join(task_path,'result')
result_et(et,conf_dir,result)
if 'upload_username' in jdata.keys():
upload_username=jdata['upload_username']
util.insert_data('elastic','vasp',upload_username,result)
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 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)