def test_write_my_dynamical_matrix_file_without_disp_mass(self):
myvc = VaspChecker(name="childdir")
mydm = myvc.read_my_dynamical_matrix_file("dynamics")
myvc.write_my_dynmat_without_disp_or_mass(mydm)
myread = MAST.utility.MASTFile("dynamics/DYNMAT_for_PHON")
myread2 = MAST.utility.MASTFile("childdir/DYNMAT")
self.assertEqual(myread2.data, myread.data)
def test_write_my_dynamical_matrix_file_without_disp_mass(self):
myvc = VaspChecker(name="childdir")
mydm = myvc.read_my_dynamical_matrix_file("dynamics")
myvc.write_my_dynmat_without_disp_or_mass(mydm)
myread = MAST.utility.MASTFile("dynamics/DYNMAT_for_PHON")
myread2 = MAST.utility.MASTFile("childdir/DYNMAT")
self.assertEqual(myread2.data, myread.data)
def test_vasp_kpoints_setup_from_keyword(self):
kdict = dict()
kdict["mast_kpoints"] = [3, 3, 3, "M"]
myvc = VaspChecker(name="childdir", program_keys=kdict)
mykpt = myvc._vasp_kpoints_setup()
kpt_compare = pymatgen.io.vaspio.Kpoints.from_file("files/KPOINTS_333M")
self.assertEqual(kpt_compare.kpts[0][0], mykpt.kpts[0][0])
self.assertEqual(kpt_compare.kpts[0][1], mykpt.kpts[0][1])
self.assertEqual(kpt_compare.kpts[0][2], mykpt.kpts[0][2])
self.assertEqual(kpt_compare.num_kpts, mykpt.num_kpts)
self.assertEqual(kpt_compare.style, mykpt.style)
os.remove("childdir/KPOINTS")
kdict["mast_kpoints"] = [1, 2, 5, "G"]
myvc = VaspChecker(name="childdir", program_keys=kdict)
mykpt = myvc._vasp_kpoints_setup()
kpt_compare = pymatgen.io.vaspio.Kpoints.from_file("files/KPOINTS_125G")
self.assertEqual(kpt_compare.kpts[0][0], mykpt.kpts[0][0])
self.assertEqual(kpt_compare.kpts[0][1], mykpt.kpts[0][1])
self.assertEqual(kpt_compare.kpts[0][2], mykpt.kpts[0][2])
self.assertEqual(kpt_compare.num_kpts, mykpt.num_kpts)
self.assertEqual(kpt_compare.style, mykpt.style)
os.remove("childdir/KPOINTS")
kdict["mast_kpoints"] = [2, 2, 2, "throw error"]
myvc = VaspChecker(name="childdir", program_keys=kdict)
self.assertRaises(MASTError, myvc._vasp_kpoints_setup)
def test_set_up_program_input(self):
my_structure = pymatgen.io.vaspio.Poscar.from_file("structure/POSCAR_Al").structure
kdict = dict()
kdict["IBRION"] = "2"
kdict["ISIF"] = "3"
kdict["ISMEAR"] = "1"
kdict["LCHARG"] = "FALSE"
kdict["LWAVE"] = "FALSE"
kdict["NSW"] = "191"
kdict["PREC"] = "Accurate"
kdict["SIGMA"] = "0.2"
kdict["mast_kpoints"] = [1, 1, 1, "G"]
kdict["mast_xc"] = "pw91"
myvc = VaspChecker(name="childdir", program_keys=kdict, structure=my_structure)
myvc.set_up_program_input()
myincar = pymatgen.io.vaspio.Incar.from_file("childdir/INCAR")
myposcar = pymatgen.io.vaspio.Poscar.from_file("childdir/POSCAR")
mypotcar = pymatgen.io.vaspio.Potcar.from_file("childdir/POTCAR")
mykpts = pymatgen.io.vaspio.Kpoints.from_file("childdir/KPOINTS")
compare_incar = pymatgen.io.vaspio.Incar.from_file("ready/INCAR")
compare_poscar = pymatgen.io.vaspio.Poscar.from_file("ready/POSCAR")
compare_potcar = pymatgen.io.vaspio.Potcar.from_file("ready/POTCAR")
compare_kpoints = pymatgen.io.vaspio.Kpoints.from_file("ready/KPOINTS")
self.assertEqual(myincar, compare_incar)
self.assertEqual(myposcar.structure, compare_poscar.structure)
self.assertEqual(mykpts.kpts[0][0], compare_kpoints.kpts[0][0])
self.assertEqual(mykpts.kpts[0][1], compare_kpoints.kpts[0][1])
self.assertEqual(mykpts.kpts[0][2], compare_kpoints.kpts[0][2])
self.assertEqual(mykpts.num_kpts, compare_kpoints.num_kpts)
self.assertEqual(mykpts.style, compare_kpoints.style)
self.assertEqual(mypotcar, compare_potcar)
def test_set_up_program_input(self):
my_structure = pymatgen.io.vaspio.Poscar.from_file(
"structure/POSCAR_Al").structure
kdict = dict()
kdict['IBRION'] = "2"
kdict['ISIF'] = "3"
kdict['ISMEAR'] = "1"
kdict['LCHARG'] = "FALSE"
kdict['LWAVE'] = "FALSE"
kdict['NSW'] = "191"
kdict['PREC'] = "Accurate"
kdict['SIGMA'] = "0.2"
kdict['mast_kpoints'] = [1, 1, 1, "G"]
kdict['mast_xc'] = "pw91"
myvc = VaspChecker(name="childdir",
program_keys=kdict,
structure=my_structure)
myvc.set_up_program_input()
myincar = pymatgen.io.vaspio.Incar.from_file("childdir/INCAR")
myposcar = pymatgen.io.vaspio.Poscar.from_file("childdir/POSCAR")
mypotcar = pymatgen.io.vaspio.Potcar.from_file("childdir/POTCAR")
mykpts = pymatgen.io.vaspio.Kpoints.from_file("childdir/KPOINTS")
compare_incar = pymatgen.io.vaspio.Incar.from_file("ready/INCAR")
compare_poscar = pymatgen.io.vaspio.Poscar.from_file("ready/POSCAR")
compare_potcar = pymatgen.io.vaspio.Potcar.from_file("ready/POTCAR")
compare_kpoints = pymatgen.io.vaspio.Kpoints.from_file("ready/KPOINTS")
self.assertEqual(myincar, compare_incar)
self.assertEqual(myposcar.structure, compare_poscar.structure)
self.assertEqual(mykpts.kpts[0][0], compare_kpoints.kpts[0][0])
self.assertEqual(mykpts.kpts[0][1], compare_kpoints.kpts[0][1])
self.assertEqual(mykpts.kpts[0][2], compare_kpoints.kpts[0][2])
self.assertEqual(mykpts.num_kpts, compare_kpoints.num_kpts)
self.assertEqual(mykpts.style, compare_kpoints.style)
self.assertEqual(mypotcar, compare_potcar)
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)
def test_vasp_poscar_setup_no_poscar(self):
compare_pos = pymatgen.io.vaspio.Poscar.from_file(os.path.join(testdir, "structure", "POSCAR_perfect"))
myvc = VaspChecker(name="childdir", structure=compare_pos.structure)
self.assertFalse(os.path.isfile(os.path.join(testdir, "childdir", "POSCAR")))
myvc._vasp_poscar_setup()
mypos = pymatgen.io.vaspio.Poscar.from_file(os.path.join(testdir, "childdir", "POSCAR"))
self.assertEqual(mypos.structure, compare_pos.structure)
def test_read_my_displacement_file(self):
myvc = VaspChecker(name="dynamics")
mydisp = myvc.read_my_displacement_file(myvc.keywords["name"], "XDATCAR_vasp522")
self.assertEqual(mydisp["numatoms"], 4)
self.assertEqual(mydisp["configs"][6][0], " 0.00000000 0.00000000 0.00286262\n")
mydisp = myvc.read_my_displacement_file(myvc.keywords["name"], "XDATCAR_vasp5211")
self.assertEqual(mydisp["numatoms"], 4)
self.assertEqual(mydisp["configs"][2][1], " 0.50244722 0.50000000 0.00000000\n")
def test_write_final_structure_file(self):
myvc = VaspChecker(name="childdir")
finalstruc = pymatgen.io.vaspio.Poscar.from_file(
"structure/CONTCAR").structure
myvc.write_final_structure_file(finalstruc)
mystruc = pymatgen.io.vaspio.Poscar.from_file(
"childdir/CONTCAR").structure
self.assertEqual(mystruc, finalstruc)
def test_forward_initial_structure(self):
myvc = VaspChecker(name="structure")
myvc.forward_initial_structure_file(os.path.join(testdir, "childdir"))
istrp = pymatgen.io.vaspio.Poscar.from_file(
"structure/POSCAR").structure
istrc = pymatgen.io.vaspio.Poscar.from_file(
"childdir/POSCAR").structure
self.assertEqual(istrp, istrc)
def test_get_final_structure(self):
myvc = VaspChecker(name="structure")
nodir = myvc.get_final_structure_from_directory()
compare_nodir = pymatgen.io.vaspio.Poscar.from_file("structure/CONTCAR").structure
self.assertEqual(nodir, compare_nodir)
withdir = myvc.get_final_structure_from_directory("withdir")
compare_withdir = pymatgen.io.vaspio.Poscar.from_file("withdir/CONTCAR").structure
self.assertEqual(withdir, compare_withdir)
def test_get_max_enmax_from_potcar(self):
mypotcar = pymatgen.io.vaspio.Potcar.from_file(os.path.join(testdir, "files", "POTCAR_LNO_PW91"))
myvc = VaspChecker(name="childdir")
maxenmax = myvc._get_max_enmax_from_potcar(mypotcar)
self.assertEqual(maxenmax, 367.921)
mypotcar = pymatgen.io.vaspio.Potcar.from_file(os.path.join(testdir, "files", "POTCAR_LTO_PW91"))
maxenmax = myvc._get_max_enmax_from_potcar(mypotcar)
self.assertEqual(maxenmax, 400)
def test_combine_dynamical_matrix(self):
myvc = VaspChecker(name="dynamics_split")
myvc.combine_dynamical_matrix_files()
shutil.move(os.path.join(testdir, "dynamics_split/DYNMAT"), os.path.join(testdir, "childdir"))
shutil.move(os.path.join(testdir, "dynamics_split/DYNMAT_combined"), os.path.join(testdir, "childdir"))
dynmat_compare = myvc.read_my_dynamical_matrix_file(myvc.keywords["name"], "DYNMAT_compare")
dynmat_combined = myvc.read_my_dynamical_matrix_file("childdir", "DYNMAT_combined")
self.assertEqual(dynmat_compare, dynmat_combined)
def test_get_non_mast_keywords(self):
kdict = dict()
kdict["mast_nokeyword"] = "hello"
kdict["mast_charge"] = "1"
kdict["IBRION"] = "3"
kdict["skip_keyword"] = "skip"
myvc = VaspChecker(name="childdir", program_keys=kdict)
keydict = myvc._vasp_incar_get_non_mast_keywords()
self.assertEqual(keydict, {"IBRION": "3"})
def test_get_non_mast_keywords(self):
kdict = dict()
kdict['mast_nokeyword'] = "hello"
kdict['mast_charge'] = "1"
kdict['IBRION'] = "3"
kdict['skip_keyword'] = "skip"
myvc = VaspChecker(name="childdir", program_keys=kdict)
keydict = myvc._vasp_incar_get_non_mast_keywords()
self.assertEqual(keydict, {"IBRION": "3"})
def test_get_max_enmax_from_potcar(self):
mypotcar = pymatgen.io.vaspio.Potcar.from_file(
os.path.join(testdir, "files", "POTCAR_LNO_PW91"))
myvc = VaspChecker(name="childdir")
maxenmax = myvc._get_max_enmax_from_potcar(mypotcar)
self.assertEqual(maxenmax, 367.921)
mypotcar = pymatgen.io.vaspio.Potcar.from_file(
os.path.join(testdir, "files", "POTCAR_LTO_PW91"))
maxenmax = myvc._get_max_enmax_from_potcar(mypotcar)
self.assertEqual(maxenmax, 400)
def test_write_my_displacement_file(self):
myvc = VaspChecker(name="childdir")
mydisp = myvc.read_my_displacement_file("dynamics", "XDATCAR_vasp5211")
myvc.write_my_displacement_file(mydisp)
mydisp2 = myvc.read_my_displacement_file()
self.assertEqual(mydisp, mydisp2)
mydisp = myvc.read_my_displacement_file("dynamics", "XDATCAR_vasp522")
myvc.write_my_displacement_file(mydisp)
mydisp2 = myvc.read_my_displacement_file()
self.assertEqual(mydisp, mydisp2)
def test_combine_displacement_files(self):
myvc = VaspChecker(name="dynamics_split")
myvc.combine_displacement_files()
shutil.move(os.path.join(testdir, "dynamics_split/XDATCAR"), os.path.join(testdir, "childdir"))
shutil.move(os.path.join(testdir, "dynamics_split/XDATCAR_combined"), os.path.join(testdir, "childdir"))
disp_compare = myvc.read_my_displacement_file(myvc.keywords["name"], "XDATCAR_compare")
disp_combined = myvc.read_my_displacement_file("childdir", "XDATCAR_combined")
print "COMPARE"
for key, value in disp_compare.iteritems():
self.assertEqual(value, disp_combined[key])
def test_vasp_poscar_setup_mast_coordinates(self):
kdict = dict()
kdict["mast_coordinates"] = ["structure/POSCAR_coordinates"] # note that the input is a list of strings
myvc = VaspChecker(name="childdir", program_keys=kdict)
perf_pos = pymatgen.io.vaspio.Poscar.from_file(os.path.join(testdir, "structure", "POSCAR_perfect"))
perf_pos.write_file(os.path.join(testdir, "childdir", "POSCAR"))
coord_pos = pymatgen.io.vaspio.Poscar.from_file(os.path.join(testdir, "structure", "POSCAR_coordinates"))
grafted_pos = pymatgen.io.vaspio.Poscar.from_file(os.path.join(testdir, "structure", "POSCAR_grafted"))
mypos = myvc._vasp_poscar_setup()
self.assertEqual(mypos.structure, grafted_pos.structure)
def test_get_final_structure(self):
myvc = VaspChecker(name="structure")
nodir = myvc.get_final_structure_from_directory()
compare_nodir = pymatgen.io.vaspio.Poscar.from_file(
"structure/CONTCAR").structure
self.assertEqual(nodir, compare_nodir)
withdir = myvc.get_final_structure_from_directory("withdir")
compare_withdir = pymatgen.io.vaspio.Poscar.from_file(
"withdir/CONTCAR").structure
self.assertEqual(withdir, compare_withdir)
def test_read_my_dynamical_matrix_file(self):
myvc = VaspChecker(name="dynamics")
mydm = myvc.read_my_dynamical_matrix_file()
self.assertEqual(mydm["numspec"], 1)
self.assertEqual(mydm["numatoms"], 4)
self.assertEqual(mydm["numdisp"], 3)
self.assertEqual(mydm["massline"], " 55.847\n")
self.assertEqual(mydm["atoms"][1][1]["displine"], "0.0100 0.0000 0.0000")
self.assertEqual(mydm["atoms"][1][3]["displine"], "0.0000 0.0000 0.0100")
self.assertEqual(mydm["atoms"][1][1]["dynmat"][0], " -0.101036 0.000000 0.000000\n")
self.assertEqual(mydm["atoms"][1][3]["dynmat"][2], " 0.000000 0.000000 0.000000\n")
def test_read_my_displacement_file(self):
myvc = VaspChecker(name="dynamics")
mydisp = myvc.read_my_displacement_file(myvc.keywords['name'],
"XDATCAR_vasp522")
self.assertEqual(mydisp['numatoms'], 4)
self.assertEqual(mydisp['configs'][6][0],
" 0.00000000 0.00000000 0.00286262\n")
mydisp = myvc.read_my_displacement_file(myvc.keywords['name'],
"XDATCAR_vasp5211")
self.assertEqual(mydisp['numatoms'], 4)
self.assertEqual(mydisp['configs'][2][1],
" 0.50244722 0.50000000 0.00000000\n")
def test_softlink_wavefunction_file(self):
import subprocess
myvc = VaspChecker(name="files")
myvc.softlink_wavefunction_file("childdir")
myfiles = dirutil.walkfiles("childdir")
print myfiles
# self.assertTrue("childdir/CHGCAR" in myfiles)
listme = subprocess.Popen("ls -l childdir", stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
listres = listme.communicate()[0]
listme.wait()
print listres
self.assertTrue("files/WAVECAR" in listres)
def test_write_my_displacement_file(self):
myvc = VaspChecker(name="childdir")
mydisp = myvc.read_my_displacement_file("dynamics", "XDATCAR_vasp5211")
myvc.write_my_displacement_file(mydisp)
mydisp2 = myvc.read_my_displacement_file()
self.assertEqual(mydisp, mydisp2)
mydisp = myvc.read_my_displacement_file("dynamics", "XDATCAR_vasp522")
myvc.write_my_displacement_file(mydisp)
mydisp2 = myvc.read_my_displacement_file()
self.assertEqual(mydisp, mydisp2)
def test_vasp_kpoints_setup_from_keyword(self):
kdict = dict()
kdict['mast_kpoints'] = [3, 3, 3, "M"]
myvc = VaspChecker(name="childdir", program_keys=kdict)
mykpt = myvc._vasp_kpoints_setup()
kpt_compare = pymatgen.io.vaspio.Kpoints.from_file(
"files/KPOINTS_333M")
self.assertEqual(kpt_compare.kpts[0][0], mykpt.kpts[0][0])
self.assertEqual(kpt_compare.kpts[0][1], mykpt.kpts[0][1])
self.assertEqual(kpt_compare.kpts[0][2], mykpt.kpts[0][2])
self.assertEqual(kpt_compare.num_kpts, mykpt.num_kpts)
self.assertEqual(kpt_compare.style, mykpt.style)
os.remove("childdir/KPOINTS")
kdict['mast_kpoints'] = [1, 2, 5, "G"]
myvc = VaspChecker(name="childdir", program_keys=kdict)
mykpt = myvc._vasp_kpoints_setup()
kpt_compare = pymatgen.io.vaspio.Kpoints.from_file(
"files/KPOINTS_125G")
self.assertEqual(kpt_compare.kpts[0][0], mykpt.kpts[0][0])
self.assertEqual(kpt_compare.kpts[0][1], mykpt.kpts[0][1])
self.assertEqual(kpt_compare.kpts[0][2], mykpt.kpts[0][2])
self.assertEqual(kpt_compare.num_kpts, mykpt.num_kpts)
self.assertEqual(kpt_compare.style, mykpt.style)
os.remove("childdir/KPOINTS")
kdict['mast_kpoints'] = [2, 2, 2, "throw error"]
myvc = VaspChecker(name="childdir", program_keys=kdict)
self.assertRaises(MASTError, myvc._vasp_kpoints_setup)
def test_vasp_poscar_setup_mast_coordinates(self):
kdict = dict()
kdict['mast_coordinates'] = [
"structure/POSCAR_coordinates"
] #note that the input is a list of strings
myvc = VaspChecker(name="childdir", program_keys=kdict)
perf_pos = pymatgen.io.vaspio.Poscar.from_file(
os.path.join(testdir, "structure", "POSCAR_perfect"))
perf_pos.write_file(os.path.join(testdir, "childdir", "POSCAR"))
coord_pos = pymatgen.io.vaspio.Poscar.from_file(
os.path.join(testdir, "structure", "POSCAR_coordinates"))
grafted_pos = pymatgen.io.vaspio.Poscar.from_file(
os.path.join(testdir, "structure", "POSCAR_grafted"))
mypos = myvc._vasp_poscar_setup()
self.assertEqual(mypos.structure, grafted_pos.structure)
def test_softlink_wavefunction_file(self):
import subprocess
myvc = VaspChecker(name="files")
myvc.softlink_wavefunction_file("childdir")
myfiles = dirutil.walkfiles("childdir")
print myfiles
#self.assertTrue("childdir/CHGCAR" in myfiles)
listme = subprocess.Popen("ls -l childdir",
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=True)
listres = listme.communicate()[0]
listme.wait()
print listres
self.assertTrue("files/WAVECAR" in listres)
def test_add_selective_dynamics(self):
mystruc = pymatgen.io.vaspio.Poscar.from_file(os.path.join(testdir, "structure", "POSCAR_Al")).structure
myvc = VaspChecker(name="childdir", structure=mystruc)
myvc._vasp_poscar_setup()
sdarr = np.zeros([4, 3], bool)
sdarr[0][0] = True
sdarr[1][1] = True
sdarr[2][2] = True
sdarr[3][0] = True
sdarr[3][1] = True
myvc.add_selective_dynamics_to_structure_file(sdarr)
after_pos = pymatgen.io.vaspio.Poscar.from_file(os.path.join(testdir, "childdir", "POSCAR"))
compare_pos = pymatgen.io.vaspio.Poscar.from_file(os.path.join(testdir, "structure", "POSCAR_Al_sd"))
self.assertEqual(after_pos.structure, compare_pos.structure)
self.assertEqual(after_pos.selective_dynamics, compare_pos.selective_dynamics)
def test_read_my_dynamical_matrix_file(self):
myvc = VaspChecker(name="dynamics")
mydm = myvc.read_my_dynamical_matrix_file()
self.assertEqual(mydm['numspec'], 1)
self.assertEqual(mydm['numatoms'], 4)
self.assertEqual(mydm['numdisp'], 3)
self.assertEqual(mydm['massline'], " 55.847\n")
self.assertEqual(mydm['atoms'][1][1]['displine'],
"0.0100 0.0000 0.0000")
self.assertEqual(mydm['atoms'][1][3]['displine'],
"0.0000 0.0000 0.0100")
self.assertEqual(mydm['atoms'][1][1]['dynmat'][0],
" -0.101036 0.000000 0.000000\n")
self.assertEqual(mydm['atoms'][1][3]['dynmat'][2],
" 0.000000 0.000000 0.000000\n")
def test_is_started(self):
myvc = VaspChecker(name="notready1")
self.assertFalse(myvc.is_started())
myvc = VaspChecker(name="ready")
self.assertFalse(myvc.is_started())
myvc = VaspChecker(name="started")
self.assertTrue(myvc.is_started())
myvc = VaspChecker(name="done")
self.assertTrue(myvc.is_started())
def test_vasp_kpoints_setup_from_metafile(self):
kdict = dict()
mymeta = MASTFile("childdir/metadata.txt")
mymeta.data.append("kpoints = 3x1x7 G 0.5 0.2 .1\n")
mymeta.to_file("childdir/metadata.txt")
mymeta2 = MASTFile("childdir/metadata.txt")
print mymeta2.data
myvc = VaspChecker(name="childdir", program_keys=kdict)
mykpt = myvc._vasp_kpoints_setup()
kpt_compare = pymatgen.io.vaspio.Kpoints.from_file("files/KPOINTS_317G")
self.assertEqual(kpt_compare.kpts[0][0], mykpt.kpts[0][0])
self.assertEqual(kpt_compare.kpts[0][1], mykpt.kpts[0][1])
self.assertEqual(kpt_compare.kpts[0][2], mykpt.kpts[0][2])
self.assertEqual(kpt_compare.num_kpts, mykpt.num_kpts)
self.assertEqual(kpt_compare.style, mykpt.style)
# self.assertEqual(kpt_compare.kpts_shift, mykpt.kpts_shift)
self.assertEqual((0.5, 0.2, 0.1), mykpt.kpts_shift)
def test_vasp_kpoints_setup_from_metafile(self):
kdict = dict()
mymeta = MASTFile("childdir/metadata.txt")
mymeta.data.append("kpoints = 3x1x7 G 0.5 0.2 .1\n")
mymeta.to_file("childdir/metadata.txt")
mymeta2 = MASTFile("childdir/metadata.txt")
print mymeta2.data
myvc = VaspChecker(name="childdir", program_keys=kdict)
mykpt = myvc._vasp_kpoints_setup()
kpt_compare = pymatgen.io.vaspio.Kpoints.from_file(
"files/KPOINTS_317G")
self.assertEqual(kpt_compare.kpts[0][0], mykpt.kpts[0][0])
self.assertEqual(kpt_compare.kpts[0][1], mykpt.kpts[0][1])
self.assertEqual(kpt_compare.kpts[0][2], mykpt.kpts[0][2])
self.assertEqual(kpt_compare.num_kpts, mykpt.num_kpts)
self.assertEqual(kpt_compare.style, mykpt.style)
#self.assertEqual(kpt_compare.kpts_shift, mykpt.kpts_shift)
self.assertEqual((0.5, 0.2, 0.1), mykpt.kpts_shift)
def test_vasp_potcar_setup(self):
kdict = dict()
kdict["mast_xc"] = "pbe"
my_poscar = pymatgen.io.vaspio.Poscar.from_file("structure/POSCAR_Al")
myvc = VaspChecker(name="childdir", program_keys=kdict)
mypotcar = myvc._vasp_potcar_setup(my_poscar)
mypotcar = pymatgen.io.vaspio.Potcar.from_file("childdir/POTCAR")
potcar_compare = pymatgen.io.vaspio.Potcar.from_file("files/POTCAR_Al_PBE")
self.assertEqual(potcar_compare[0], mypotcar[0])
kdict["mast_xc"] = "pw91"
kdict["mast_pp_setup"] = {"La": "La", "Ni": "Ni_pv", "O": "O_s"}
my_poscar = pymatgen.io.vaspio.Poscar.from_file("structure/POSCAR_LNO")
myvc = VaspChecker(name="childdir", program_keys=kdict)
mypotcar = myvc._vasp_potcar_setup(my_poscar)
mypotcar = pymatgen.io.vaspio.Potcar.from_file("childdir/POTCAR")
potcar_compare = pymatgen.io.vaspio.Potcar.from_file("files/POTCAR_LNO_PW91")
self.assertEqual(potcar_compare[0], mypotcar[0])
def test_combine_dynamical_matrix(self):
myvc = VaspChecker(name="dynamics_split")
myvc.combine_dynamical_matrix_files()
shutil.move(os.path.join(testdir, "dynamics_split/DYNMAT"),
os.path.join(testdir, "childdir"))
shutil.move(os.path.join(testdir, "dynamics_split/DYNMAT_combined"),
os.path.join(testdir, "childdir"))
dynmat_compare = myvc.read_my_dynamical_matrix_file(
myvc.keywords['name'], "DYNMAT_compare")
dynmat_combined = myvc.read_my_dynamical_matrix_file(
"childdir", "DYNMAT_combined")
self.assertEqual(dynmat_compare, dynmat_combined)
def test_combine_displacement_files(self):
myvc = VaspChecker(name="dynamics_split")
myvc.combine_displacement_files()
shutil.move(os.path.join(testdir, "dynamics_split/XDATCAR"),
os.path.join(testdir, "childdir"))
shutil.move(os.path.join(testdir, "dynamics_split/XDATCAR_combined"),
os.path.join(testdir, "childdir"))
disp_compare = myvc.read_my_displacement_file(myvc.keywords['name'],
"XDATCAR_compare")
disp_combined = myvc.read_my_displacement_file("childdir",
"XDATCAR_combined")
print "COMPARE"
for key, value in disp_compare.iteritems():
self.assertEqual(value, disp_combined[key])
def test_add_selective_dynamics(self):
mystruc = pymatgen.io.vaspio.Poscar.from_file(
os.path.join(testdir, "structure", "POSCAR_Al")).structure
myvc = VaspChecker(name="childdir", structure=mystruc)
myvc._vasp_poscar_setup()
sdarr = np.zeros([4, 3], bool)
sdarr[0][0] = True
sdarr[1][1] = True
sdarr[2][2] = True
sdarr[3][0] = True
sdarr[3][1] = True
myvc.add_selective_dynamics_to_structure_file(sdarr)
after_pos = pymatgen.io.vaspio.Poscar.from_file(
os.path.join(testdir, "childdir", "POSCAR"))
compare_pos = pymatgen.io.vaspio.Poscar.from_file(
os.path.join(testdir, "structure", "POSCAR_Al_sd"))
self.assertEqual(after_pos.structure, compare_pos.structure)
self.assertEqual(after_pos.selective_dynamics,
compare_pos.selective_dynamics)
def test_vasp_potcar_setup(self):
kdict = dict()
kdict['mast_xc'] = "pbe"
my_poscar = pymatgen.io.vaspio.Poscar.from_file("structure/POSCAR_Al")
myvc = VaspChecker(name="childdir", program_keys=kdict)
mypotcar = myvc._vasp_potcar_setup(my_poscar)
mypotcar = pymatgen.io.vaspio.Potcar.from_file("childdir/POTCAR")
potcar_compare = pymatgen.io.vaspio.Potcar.from_file(
"files/POTCAR_Al_PBE")
self.assertEqual(potcar_compare[0], mypotcar[0])
kdict['mast_xc'] = "pw91"
kdict['mast_pp_setup'] = {'La': 'La', 'Ni': 'Ni_pv', 'O': 'O_s'}
my_poscar = pymatgen.io.vaspio.Poscar.from_file("structure/POSCAR_LNO")
myvc = VaspChecker(name="childdir", program_keys=kdict)
mypotcar = myvc._vasp_potcar_setup(my_poscar)
mypotcar = pymatgen.io.vaspio.Potcar.from_file("childdir/POTCAR")
potcar_compare = pymatgen.io.vaspio.Potcar.from_file(
"files/POTCAR_LNO_PW91")
self.assertEqual(potcar_compare[0], mypotcar[0])
def test_get_energy_from_energy_file(self):
myvc = VaspChecker(name="done")
myenergy = myvc.get_energy_from_energy_file()
self.assertAlmostEqual(myenergy, float(-0.83312666e01), places=7)
def test_forward_wavefunction_file(self):
myvc = VaspChecker(name="files")
myvc.forward_wavefunction_file("childdir")
self.assertTrue(os.path.isfile("childdir/WAVECAR"))
def test_get_total_electrons(self):
mypos = pymatgen.io.vaspio.Poscar.from_file("structure/POSCAR_LTO")
mypot = pymatgen.io.vaspio.Potcar.from_file("files/POTCAR_LTO_PW91")
myvc = VaspChecker()
numelec = myvc.get_total_electrons(mypos, mypot)
self.assertEqual(numelec, 328)
def test_get_valence_list(self):
mypot = pymatgen.io.vaspio.Potcar.from_file("files/POTCAR_LTO_PW91")
myvc = VaspChecker()
vlist = myvc.get_valence_list(mypot)
self.assertEqual(vlist, [11, 12, 6])
def test_get_structure_from_file(self):
myvc = VaspChecker(name="structure")
getstr = myvc.get_structure_from_file("structure/POSCAR_perfect")
mystr = pymatgen.io.vaspio.Poscar.from_file("structure/POSCAR_perfect").structure
self.assertEqual(mystr, getstr)
def test_forward_wavefunction_file(self):
myvc = VaspChecker(name="files")
myvc.forward_wavefunction_file("childdir")
self.assertTrue(os.path.isfile("childdir/WAVECAR"))
def test_has_ending_structure_file(self):
myvc = VaspChecker(name="ready")
self.assertFalse(myvc.has_ending_structure_file())
myvc = VaspChecker(name="done")
self.assertTrue(myvc.has_ending_structure_file())
def test_has_ending_structure_file(self):
myvc = VaspChecker(name="ready")
self.assertFalse(myvc.has_ending_structure_file())
myvc = VaspChecker(name="done")
self.assertTrue(myvc.has_ending_structure_file())
def test_get_total_electrons(self):
mypos = pymatgen.io.vaspio.Poscar.from_file("structure/POSCAR_LTO")
mypot = pymatgen.io.vaspio.Potcar.from_file("files/POTCAR_LTO_PW91")
myvc = VaspChecker()
numelec = myvc.get_total_electrons(mypos, mypot)
self.assertEqual(numelec, 328)
def test_write_my_dynamical_matrix_file(self):
myvc = VaspChecker(name="childdir")
mydm = myvc.read_my_dynamical_matrix_file("dynamics")
myvc.write_my_dynamical_matrix_file(mydm)
mydm2 = myvc.read_my_dynamical_matrix_file()
self.assertEqual(mydm, mydm2)
def test_get_valence_list(self):
mypot = pymatgen.io.vaspio.Potcar.from_file("files/POTCAR_LTO_PW91")
myvc = VaspChecker()
vlist = myvc.get_valence_list(mypot)
self.assertEqual(vlist, [11, 12, 6])
def test_get_energy_from_energy_file(self):
myvc = VaspChecker(name="done")
myenergy = myvc.get_energy_from_energy_file()
self.assertAlmostEqual(myenergy, float(-.83312666E+01), places=7)
def test_is_started(self):
myvc = VaspChecker(name="notready1")
self.assertFalse(myvc.is_started())
myvc = VaspChecker(name="ready")
self.assertFalse(myvc.is_started())
myvc = VaspChecker(name="started")
self.assertTrue(myvc.is_started())
myvc = VaspChecker(name="done")
self.assertTrue(myvc.is_started())
def test_write_final_structure_file(self):
myvc = VaspChecker(name="childdir")
finalstruc = pymatgen.io.vaspio.Poscar.from_file("structure/CONTCAR").structure
myvc.write_final_structure_file(finalstruc)
mystruc = pymatgen.io.vaspio.Poscar.from_file("childdir/CONTCAR").structure
self.assertEqual(mystruc, finalstruc)
def test_write_my_dynamical_matrix_file(self):
myvc = VaspChecker(name="childdir")
mydm = myvc.read_my_dynamical_matrix_file("dynamics")
myvc.write_my_dynamical_matrix_file(mydm)
mydm2 = myvc.read_my_dynamical_matrix_file()
self.assertEqual(mydm, mydm2)
def test_has_starting_structure_file(self):
myvc = VaspChecker(name="notready3")
self.assertFalse(myvc.has_starting_structure_file())
myvc = VaspChecker(name="ready")
self.assertTrue(myvc.has_starting_structure_file())
myvc = VaspChecker(name="notready1")
self.assertTrue(myvc.has_starting_structure_file())
myvc = VaspChecker(name="notready2")
self.assertTrue(myvc.has_starting_structure_file())
myvc = VaspChecker(name="notready4")
self.assertTrue(myvc.has_starting_structure_file())
myvc = VaspChecker(name="notready5")
self.assertTrue(myvc.has_starting_structure_file())
def test_forward_initial_structure(self):
myvc = VaspChecker(name="structure")
myvc.forward_initial_structure_file(os.path.join(testdir, "childdir"))
istrp = pymatgen.io.vaspio.Poscar.from_file("structure/POSCAR").structure
istrc = pymatgen.io.vaspio.Poscar.from_file("childdir/POSCAR").structure
self.assertEqual(istrp, istrc)
def test_scale_mesh(self):
myvc = VaspChecker()
mystr = pymatgen.io.vaspio.Poscar.from_file("ready/POSCAR").structure
myk = myvc.scale_mesh(mystr, 2000)
self.assertEqual(myvc.keywords["program_keys"]["mast_kpoints"], [8, 8, 8, "M"])
def test_scale_mesh(self):
myvc = VaspChecker()
mystr = pymatgen.io.vaspio.Poscar.from_file("ready/POSCAR").structure
myk = myvc.scale_mesh(mystr, 2000)
self.assertEqual(myvc.keywords['program_keys']['mast_kpoints'],
[8, 8, 8, 'M'])
def test_get_structure_from_file(self):
myvc = VaspChecker(name="structure")
getstr = myvc.get_structure_from_file("structure/POSCAR_perfect")
mystr = pymatgen.io.vaspio.Poscar.from_file(
"structure/POSCAR_perfect").structure
self.assertEqual(mystr, getstr)
def test_has_starting_structure_file(self):
myvc = VaspChecker(name="notready3")
self.assertFalse(myvc.has_starting_structure_file())
myvc = VaspChecker(name="ready")
self.assertTrue(myvc.has_starting_structure_file())
myvc = VaspChecker(name="notready1")
self.assertTrue(myvc.has_starting_structure_file())
myvc = VaspChecker(name="notready2")
self.assertTrue(myvc.has_starting_structure_file())
myvc = VaspChecker(name="notready4")
self.assertTrue(myvc.has_starting_structure_file())
myvc = VaspChecker(name="notready5")
self.assertTrue(myvc.has_starting_structure_file())
def test_forward_dynamical_matrix(self):
myvc = VaspChecker(name="dynamics")
myvc.forward_dynamical_matrix_file(os.path.join(testdir, "childdir"))
dp = myvc.read_my_dynamical_matrix_file("dynamics")
dc = myvc.read_my_dynamical_matrix_file("childdir")
self.assertEqual(dp, dc)
def test_forward_dynamical_matrix(self):
myvc = VaspChecker(name="dynamics")
myvc.forward_dynamical_matrix_file(os.path.join(testdir, "childdir"))
dp = myvc.read_my_dynamical_matrix_file("dynamics")
dc = myvc.read_my_dynamical_matrix_file("childdir")
self.assertEqual(dp, dc)