How to use dpgen - 10 common examples

if  'user_incar' in jdata.keys():
        user_incar_path = jdata['user_incar']
        assert(os.path.exists(user_incar_path))
        user_incar_path = os.path.abspath(user_incar_path)
        fc = open(user_incar_path).read()
        kspacing =float(re.findall((r"KSPACING(.+?)\n"),fc)[0].replace('=',''))
        kgamma =('T' in re.findall((r"KGAMMA(.+?)\n"),fc)[0])
    else :
        fp_params = jdata['vasp_params']
        ecut = fp_params['ecut']
        ediff = fp_params['ediff']
        npar = fp_params['npar']
        kpar = fp_params['kpar']
        kspacing = fp_params['kspacing']
        kgamma = fp_params['kgamma']
        fc = vasp.make_vasp_phonon_incar(ecut, ediff, npar, kpar, kspacing = None, kgamma = None)
    with open(os.path.join(task_path, 'INCAR'), 'w') as fp :
        fp.write(fc)
    # gen potcar
    with open(task_poscar,'r') as fp :
        lines = fp.read().split('\n')
        ele_list = lines[5].split()
    potcar_map = jdata['potcar_map']
    potcar_list = []
    for ii in ele_list :
        assert(os.path.exists(potcar_map[ii]))
        potcar_list.append(potcar_map[ii])
    with open(os.path.join(task_path,'POTCAR'), 'w') as outfile:
        for fname in potcar_list:
            with open(fname) as infile:
                outfile.write(infile.read())
    # gen kpoints

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)

task_poscar = os.path.join(task_path, 'POSCAR')
    cwd = os.getcwd()
    os.chdir(task_path)
    if os.path.isfile('POSCAR') :
        os.remove('POSCAR')
    os.symlink(os.path.relpath(conf_poscar), 'POSCAR')
    os.chdir(cwd)    
    with open(task_poscar,'r') as fp :
        lines = fp.read().split('\n')
        ele_list = lines[5].split()
    
    print(task_path)
    # make conf.lmp  
    conf_file = os.path.join(task_path, 'conf.lmp')
    lammps.cvt_lammps_conf(task_poscar, os.path.relpath(conf_file))
    ptypes = vasp.get_poscar_types(task_poscar)
    lammps.apply_type_map(conf_file, type_map, ptypes) 
    # make lammps.in
    ntypes=len(ele_list)
    unitcell=get_structure_from_poscar(task_poscar)
    if task_type=='deepmd':
        fc = lammps.make_lammps_phonon('conf.lmp', 
                                    unitcell.masses, 
                                    lammps.inter_deepmd,
                                    model_name)
    if task_type=='meam':
        fc = lammps.make_lammps_phonon('conf.lmp', 
                                    unitcell.masses, 
                                    lammps.inter_meam,
                                    model_param)      
    f_lammps_in = os.path.join(task_path, 'lammps.in')
    with open(f_lammps_in, 'w') as fp :

task_poscar = os.path.join(task_path, 'POSCAR')
    cwd = os.getcwd()
    os.chdir(task_path)
    if os.path.isfile('POSCAR') :
        os.remove('POSCAR')
    os.symlink(os.path.relpath(conf_poscar), 'POSCAR')
    os.chdir(cwd)    
    with open(task_poscar,'r') as fp :
        lines = fp.read().split('\n')
        ele_list = lines[5].split()
    
    print(task_path)
    # make conf.lmp  
    conf_file = os.path.join(task_path, 'conf.lmp')
    lammps.cvt_lammps_conf(task_poscar, os.path.relpath(conf_file))
    ptypes = vasp.get_poscar_types(task_poscar)
    lammps.apply_type_map(conf_file, type_map, ptypes) 
    # make lammps.in
    ntypes=len(ele_list)
    unitcell=get_structure_from_poscar(task_poscar)
    if task_type=='deepmd':
        fc = lammps.make_lammps_phonon('conf.lmp', 
                                    unitcell.masses, 
                                    lammps.inter_deepmd,
                                    model_name)
    if task_type=='meam':
        fc = lammps.make_lammps_phonon('conf.lmp', 
                                    unitcell.masses, 
                                    lammps.inter_meam,
                                    model_param)      
    f_lammps_in = os.path.join(task_path, 'lammps.in')

cwd = os.getcwd()
    os.chdir(task_path)
    if os.path.isfile('POSCAR') :
        os.remove('POSCAR')
    os.symlink(os.path.relpath(conf_poscar), 'POSCAR')
    os.chdir(cwd)    
    with open(task_poscar,'r') as fp :
        lines = fp.read().split('\n')
        ele_list = lines[5].split()
    
    print(task_path)
    # make conf.lmp  
    conf_file = os.path.join(task_path, 'conf.lmp')
    lammps.cvt_lammps_conf(task_poscar, os.path.relpath(conf_file))
    ptypes = vasp.get_poscar_types(task_poscar)
    lammps.apply_type_map(conf_file, type_map, ptypes) 
    # make lammps.in
    ntypes=len(ele_list)
    unitcell=get_structure_from_poscar(task_poscar)
    if task_type=='deepmd':
        fc = lammps.make_lammps_phonon('conf.lmp', 
                                    unitcell.masses, 
                                    lammps.inter_deepmd,
                                    model_name)
    if task_type=='meam':
        fc = lammps.make_lammps_phonon('conf.lmp', 
                                    unitcell.masses, 
                                    lammps.inter_meam,
                                    model_param)      
    f_lammps_in = os.path.join(task_path, 'lammps.in')
    with open(f_lammps_in, 'w') as fp :
        fp.write(fc)

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")
    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)
            lmp_log = os.path.join(ii, 'log.lammps')

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)

stress = vasp.get_stress(equi_outcar)
    np.savetxt(os.path.join(task_path, 'equi.stress.out'), stress)
    # gen strcture
    ss = Structure.from_file(task_poscar)
    # gen defomations
    norm_strains=np.arange(strain_start,strain_end,strain_step)
    print('gen with norm '+str(norm_strains))
    deformations=[]
    for ii in norm_strains:
        strain = Strain.from_index_amount(strain_direct, ii)
        deformations.append(strain.get_deformation_matrix())
    deformed_structures = [defo.apply_to_structure(ss)
                                    for defo in deformations]
    n_dfm = len(deformed_structures)
    # gen incar
    fc = vasp.make_vasp_relax_incar(ecut, ediff, True, False, False, npar=npar, kpar=kpar, kspacing = None, kgamma = None)
    with open(os.path.join(task_path, 'INCAR'), 'w') as fp :
        fp.write(fc)
    # gen potcar
    with open(task_poscar,'r') as fp :
        lines = fp.read().split('\n')
        ele_list = lines[5].split()
    potcar_map = jdata['potcar_map']
    potcar_list = []
    for ii in ele_list :
        assert(os.path.exists(potcar_map[ii]))
        potcar_list.append(potcar_map[ii])
    with open(os.path.join(task_path,'POTCAR'), 'w') as outfile:
        for fname in potcar_list:
            with open(fname) as infile:
                outfile.write(infile.read())
    # gen kpoints

if  'relax_incar' in jdata.keys():
        relax_incar_path = jdata['relax_incar']
        assert(os.path.exists(relax_incar_path))
        relax_incar_path = os.path.abspath(relax_incar_path)
        fc = open(relax_incar_path).read()
        kspacing =float(re.findall((r"KSPACING(.+?)\n"),fc)[0].replace('=',''))
        kgamma =('T' in re.findall((r"KGAMMA(.+?)\n"),fc)[0])
    else :
        fp_params = jdata['vasp_params']
        ecut = fp_params['ecut']
        ediff = fp_params['ediff']
        npar = fp_params['npar']
        kpar = fp_params['kpar']
        kspacing = fp_params['kspacing']
        kgamma = fp_params['kgamma']
        fc = vasp.make_vasp_relax_incar(ecut, ediff, True, False, False, npar=npar,kpar=kpar, kspacing = kspacing, kgamma = kgamma)
        
    with open(os.path.join(task_path, 'INCAR'), 'w') as fp :
        fp.write(fc)
    # gen potcar
    with open(task_poscar,'r') as fp :
        lines = fp.read().split('\n')
        ele_list = lines[5].split()
    potcar_map = jdata['potcar_map']
    potcar_list = []
    for ii in ele_list :
        assert os.path.exists(os.path.abspath(potcar_map[ii])),"No POTCAR in the potcar_map of %s"%(ii)
        potcar_list.append(os.path.abspath(potcar_map[ii]))
    with open(os.path.join(task_path,'POTCAR'), 'w') as outfile:
        for fname in potcar_list:
            with open(fname) as infile:
                outfile.write(infile.read())

dss.append(jj.generate_defect_structure(supercell))
    # gen incar
    if  'relax_incar' in jdata.keys():
        relax_incar_path = jdata['relax_incar']
        assert(os.path.exists(relax_incar_path))
        relax_incar_path = os.path.abspath(relax_incar_path)
        fc = open(relax_incar_path).read()
    else :
        fp_params = jdata['vasp_params']
        ecut = fp_params['ecut']
        ediff = fp_params['ediff']
        npar = fp_params['npar']
        kpar = fp_params['kpar']
        kspacing = fp_params['kspacing']
        kgamma = fp_params['kgamma']
        fc = vasp.make_vasp_relax_incar(ecut, ediff, True, True, True, npar=npar,kpar=kpar, kspacing = kspacing, kgamma = kgamma)
    with open(os.path.join(task_path, 'INCAR'), 'w') as fp :
        fp.write(fc)
    # gen potcar
    with open(task_poscar,'r') as fp :
        lines = fp.read().split('\n')
        ele_list = lines[5].split()
    potcar_map = jdata['potcar_map']
    potcar_list = []
    for ii in ele_list :
        assert os.path.exists(os.path.abspath(potcar_map[ii])),"No POTCAR in the potcar_map of %s"%(ii)
        potcar_list.append(os.path.abspath(potcar_map[ii]))
    with open(os.path.join(task_path,'POTCAR'), 'w') as outfile:
        for fname in potcar_list:
            with open(fname) as infile:
                outfile.write(infile.read())
    # gen tasks