How to use pymatgen - 10 common examples

def bcc (ele_name = 'ele', a = 3.2144871302356037) :
    latt = Lattice.cubic(a)
    return Structure(latt,
                     [ele_name, ele_name],
                     [[0, 0, 0],
                      [0.5, 0.5, 0.5],
                     ]

def create_random_reader(num_atoms):
    lattice = pmg.Lattice.from_parameters(1, 1, 1, 90, 90, 90)
    positions = np.array([(_, _, _) for _ in np.linspace(0, 1, num_atoms)])
    symbols = ['H'] * num_atoms

    return MDReader(
        energy=random.random(),
        stress=np.random.random((3, 3)),
        forces=np.random.random((num_atoms, 3)),
        structure=pmg.Structure(lattice, symbols, positions))

def test_make_confs_0(self):
        if not os.path.exists(os.path.join(self.equi_path, 'CONTCAR')):
            with self.assertRaises(RuntimeError):
                self.elastic.make_confs(self.target_path, self.equi_path)
        shutil.copy(os.path.join(self.source_path, 'CONTCAR'), os.path.join(self.equi_path, 'CONTCAR'))
        task_list = self.elastic.make_confs(self.target_path, self.equi_path)
        dfm_dirs = glob.glob(os.path.join(self.target_path, 'task.*'))

        incar0 = Incar.from_file(os.path.join('vasp_input', 'INCAR.rlx'))
        incar0['ISIF'] = 4

        self.assertEqual(os.path.realpath(os.path.join(self.equi_path, 'CONTCAR')),
                         os.path.realpath(os.path.join(self.target_path, 'POSCAR')))
        ref_st = Structure.from_file(os.path.join(self.target_path, 'POSCAR'))
        dfm_dirs.sort()
        for ii in dfm_dirs:
            st_file = os.path.join(ii, 'POSCAR')
            self.assertTrue(os.path.isfile(st_file))
            strain_json_file = os.path.join(ii, 'strain.json')
            self.assertTrue(os.path.isfile(strain_json_file))
            strain_json = loadfn(strain_json_file)

task_path = re.sub('confs', global_task_name, conf_path)
    task_path = os.path.join(task_path, vasp_str)
    os.makedirs(task_path, exist_ok=True)
    cwd = os.getcwd()
    os.chdir(task_path)
    if os.path.isfile('POSCAR') :
        os.remove('POSCAR')
    os.symlink(os.path.relpath(equi_contcar), 'POSCAR')
    os.chdir(cwd)
    task_poscar = os.path.join(task_path, 'POSCAR')
    # stress
    equi_outcar = os.path.join(equi_path, 'OUTCAR')
    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 = [-norm_def, -0.5*norm_def, 0.5*norm_def, norm_def]
    shear_strains = [-shear_def, -0.5*shear_def, 0.5*shear_def, shear_def]
    dfm_ss = DeformedStructureSet(ss, 
                                  symmetry = False, 
                                  norm_strains = norm_strains,
                                  shear_strains = shear_strains)
    n_dfm = len(dfm_ss)
    # 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()
        kspacing =float(re.findall((r"KSPACING(.+?)\n"),fc)[0].replace('=',''))
        kgamma =('T' in re.findall((r"KGAMMA(.+?)\n"),fc)[0])

equi_path = os.path.join(equi_path, vasp_str)
    equi_contcar = os.path.join(equi_path, 'CONTCAR')
    assert os.path.exists(equi_contcar),"Please compute the equilibrium state using vasp first"
    task_path = re.sub('confs', global_task_name, conf_path)
    task_path = os.path.join(task_path, vasp_str)
    os.makedirs(task_path, exist_ok=True)
    cwd = os.getcwd()
    os.chdir(task_path)
    if os.path.isfile('POSCAR') :
        os.remove('POSCAR')
    os.symlink(os.path.relpath(equi_contcar), 'POSCAR')
    os.chdir(cwd)
    task_poscar = os.path.join(task_path, 'POSCAR')
    # gen strcture
    print("task poscar: ", task_poscar)
    ss = Structure.from_file(task_poscar)
    # gen defects
    vds = InterstitialGenerator(ss, insert_ele)
    dss = []
    for jj in vds :
        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']

def test_interpolation(self):
        ep1 = pymatgen.io.vaspio.Poscar.from_file("POSCAR_ep1").structure
        ep2 = pymatgen.io.vaspio.Poscar.from_file("POSCAR_ep2").structure
        compare_im1 = pymatgen.io.vaspio.Poscar.from_file("POSCAR_im1").structure
        compare_im2 = pymatgen.io.vaspio.Poscar.from_file("POSCAR_im2").structure
        compare_im3 = pymatgen.io.vaspio.Poscar.from_file("POSCAR_im3").structure
        sxtend = StructureExtensions(struc_work1 = ep1, struc_work2 = ep2)
        slist = sxtend.do_interpolation(3)
        self.assertEqual(slist[0],ep1)
        self.assertEqual(slist[1],compare_im1)
        self.assertEqual(slist[2],compare_im2)
        self.assertEqual(slist[3],compare_im3)
        self.assertEqual(slist[4],ep2)
    def test_get_sd_array(self):

kdict['mast_neb_settings']['lines']=neblines
        ingdir = "writedir/neb_labelinit-labelfin"
        topmetad = MASTFile("files/top_metadata_neb")
        topmetad.to_file("writedir/metadata.txt")
        metad = MASTFile("files/metadata_neb")
        metad.to_file("%s/metadata.txt" % ingdir)
        unsorted_init = MASTFile("unsorted/parent_structure_labelinit")
        #unsorted_init = MASTFile("unsorted/parent_structure_labelinit_scrambled")
        unsorted_init.to_file("%s/parent_structure_labelinit" % ingdir)
        unsorted_fin = MASTFile("unsorted/parent_structure_labelfin")
        unsorted_fin.to_file("%s/parent_structure_labelfin" % ingdir)
        my_structure=pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
        mywi = ChopIngredient(name=ingdir,program_keys=kdict,structure=my_structure)
        [sinit, sfin] = mywi.get_parent_structures()
        init_compare = pymatgen.io.vaspio.Poscar.from_file("files/parent_structure_labelinit").structure
        fin_compare = pymatgen.io.vaspio.Poscar.from_file("files/parent_structure_labelfin").structure
        #print sinit
        #print init_compare
        #print sfin
        #print fin_compare
        self.assertEqual(sinit.sites, init_compare.sites)
        self.assertEqual(sinit.lattice, init_compare.lattice)
        self.assertEqual(sfin.sites, fin_compare.sites)
        self.assertEqual(sfin.lattice, fin_compare.lattice)
        #self.testclass.get_parent_structures()

def test_complete_subfolders(self):
        #raise SkipTest
        ingdir="%s/writedir/single_label1" % testdir
        recipedir="%s/writedir" % testdir
        topmetad = MASTFile("files/top_metadata_single")
        topmetad.data.append("origin_dir = %s/files\n" % testdir) #give origin directory
        topmetad.to_file("writedir/metadata.txt")
        metad = MASTFile("files/metadata_single")
        metad.to_file("%s/metadata.txt" % ingdir)
        kdict=dict()
        kdict['mast_program'] = 'vasp'
        kdict['mast_kpoints'] = [2,2,2,"M"]
        kdict['mast_xc'] = 'pw91'
        my_structure = pymatgen.io.vaspio.Poscar.from_file("files/perfect_structure").structure
        mywr = ChopIngredient(name=ingdir, program_keys = kdict, structure=my_structure)
        myoutcar = MASTFile("files/OUTCAR_completed")
        myoszicar = MASTFile("files/OSZICAR_completed")
        for subdir in ['00','01','02','03','04']:
            subname = "%s/%s" % (ingdir, subdir)
            os.mkdir(subname)
            mywr.keywords['name'] = subname
            mywr.checker.keywords['name'] = subname
            mywr.write_singlerun()
            mywr.write_submit_script()
            myoutcar.to_file("%s/OUTCAR" % subname)
            myoszicar.to_file("%s/OSZICAR" % subname)
        myci = ChopIngredient(name=ingdir,program_keys=kdict, structure=my_structure)
        self.assertTrue(myci.complete_subfolders())
        os.remove("%s/04/OUTCAR" % ingdir)
        self.assertFalse(myci.complete_subfolders())

def test_vasp_poscar_setup_has_poscar(self):
        compare_pos = pymatgen.io.vaspio.Poscar.from_file(os.path.join(testdir, "structure","POSCAR_perfect"))
        compare_pos.write_file(os.path.join(testdir,"childdir","POSCAR"))
        myvc = VaspChecker(name="childdir")
        mypos = myvc._vasp_poscar_setup()
        self.assertEqual(mypos.structure, compare_pos.structure)

import pymatgen
import numpy as np
from MAST.ingredients.pmgextend.vasp_extensions import *
from MAST.ingredients.frozenphonons import *
mypos = pymatgen.io.vaspio.Poscar.from_file("//home/tam/bin/git/MAST4pymatgen/test/nebtest/ep1/CONTCAR")
mypos.write_file("//home/tam/bin/git/MAST4pymatgen/test/nebtest/POSCAR_no_frozen")
mypos2 = make_one_unfrozen_atom_poscar(mypos, 3)
mypos.write_file("//home/tam/bin/git/MAST4pymatgen/test/nebtest/POSCAR_no_frozen_maybe")
mypos2.write_file("//home/tam/bin/git/MAST4pymatgen/test/nebtest/POSCAR_frozen_3")

myph = FrozenPhonons(parent_path="//home/tam/bin/git/MAST4pymatgen/test/nebtest/ep1",dir_name="//home/tam/bin/git/MAST4pymatgen/test/phtest/frozen",program="vasp")
myph.generate_files()