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