def test_ne(self): " Test __ne__() function." # Two equal INCAR. filename1 = path + "/INCAR" filename2 = path + "/INCAR2" incar1 = InCar(filename1) incar2 = InCar(filename1) self.assertFalse(incar1 != incar2) # Different INCAR. incar1 = InCar(filename1) incar2 = InCar(filename2) self.assertTrue(incar1 != incar2)
def create_incar(xsdname, args): """""" if os.path.exists('INCAR'): return 'INCAR already exists, not changed.\n' incar = InCar() if args.task: task = args.task incar.quickgen(args.task) else: task = 'SC' content = 'INCAR -->\n' content += ' Task is %s\n' %task if PY2: pname_value_pairs = args.__dict__.iteritems() else: pname_value_pairs = args.__dict__.items() for pname, value in pname_value_pairs : if (value is not None): if pname in incar.pnames: incar.set(pname, value) else: if (pname in INCAR_PARAMETERS.keys()): incar.add(pname, value) content += " {} -> {}\n".format(pname, value) #incar.set('SYSTEM', xsdname) incar.tofile(verbos=False) content += '\n' return content
def test_rdata(self): " Test data line in INCAR can be read correctly. " filename = path + "/INCAR" incar = InCar(filename) # Test integer parameter. ref_line = "ISTART = 0 # 0 = new job, 1 = restart" pnames, datas = incar.rdata(ref_line) self.assertListEqual(pnames, ["ISTART"]) self.assertListEqual(datas, ["0"]) # Test string parameter. ref_line = "PREC = Normal # [Low/Medium/High/Accurate/Normal]" pnames, datas = incar.rdata(ref_line) self.assertListEqual(pnames, ["PREC"]) self.assertListEqual(datas, ["Normal"]) # Test comment line. ref_line = "! Electronic Structure" result = incar.rdata(ref_line) self.assertIsNone(result) # Test multi-parameter line. ref_line = "LHFCALC = .TRUE. ; HFSCREEN = 0.2 # HSE" pnames, datas = incar.rdata(ref_line) self.assertListEqual(pnames, ["LHFCALC", "HFSCREEN"]) self.assertListEqual(datas, [".TRUE.", "0.2"])
def test_parameter_add(self): " Test new parameter can be added correctly. " filename = path + "/INCAR" incar = InCar(filename) self.assertFalse(hasattr(incar, "TEST_zjshao")) incar.add("TEST_zjshao", "True") self.assertTrue(incar.TEST_zjshao, "True")
def test_parameter_set(self): " Test existed parameter can be set correctly. " filename = path + "/INCAR" incar = InCar(filename) self.assertTrue(incar.ISIF, "2") incar.set("ISIF", 3) self.assertTrue(incar.ISIF, "3")
def test_compare(self): " Make sure we can compare two InCar objects correctly. " # Two equal INCAR. filename1 = path + "/INCAR" filename2 = path + "/INCAR2" incar1 = InCar(filename1) incar2 = InCar(filename1) a_dict, b_dict = incar1.compare(incar2) self.assertDictEqual(a_dict, {}) self.assertDictEqual(b_dict, {}) # Different INCAR. incar1 = InCar(filename1) incar2 = InCar(filename2) a_dict, b_dict = incar1.compare(incar2) self.assertDictEqual(a_dict, {'ISMEAR': '1', 'LREAL': 'A'}) self.assertDictEqual(b_dict, {'ISMEAR': '2', 'LREAL': ''})
def test_parameter_del(self): " Make sure we can remove parameters correctly. " filename = path + "/INCAR" incar = InCar(filename) # Check before deletion. self.assertTrue(hasattr(incar, "ISIF")) self.assertTrue("ISIF" in incar.pnames) pname, value = incar.pop("ISIF") # Check after deletion. self.assertEqual(pname, "ISIF") self.assertEqual(value, "2") self.assertFalse(hasattr(incar, "ISIF")) self.assertFalse("ISIF" in incar.pnames)
def test_load(self): " Test all data in INCAR can be loaded. " filename = path + "/INCAR" incar = InCar(filename) ref_pnames = [ 'SYSTEM', 'ISTART', 'ISPIN', 'PREC', 'ENCUT', 'NELM', 'NELMIN', 'ISMEAR', 'SIGMA', 'LREAL', 'EDIFFG', 'ALGO', 'ISIF', 'NSW', 'IBRION', 'POTIM', 'ISYM', 'NWRITE', 'LCHARG', 'LWAVE', 'NCORE' ] ref_datas = [ 'per', '0', '2', 'Normal', '450', '400', '3', '1', '0.1', 'A', '-0.05', 'Fast', '2', '900', '1', '0.2', '0', '1', '.False.', '.False.', '4' ] for pname, data in zip(ref_pnames, ref_datas): self.assertEqual(getattr(incar, pname), data)
# Copy INCAR vasp.script subprocess.getstatusoutput( 'cp $HOME/example/INCAR $HOME/example/vasp.script ./') # Set argument parser. parser = argparse.ArgumentParser() # Add optional argument. parser.add_argument("-k", "--kpoints", help="set k-points") parser.add_argument("--nnode", help="node number used for the job") parser.add_argument("--ncpu", help="cpu number on each node") parser.add_argument("-q", "--queue", help="pbs queue type") # Add all possible arguments in INCAR file. if os.path.exists("INCAR"): incar = InCar() parameters = incar.pnames for parameter in parameters: help_info = "Set '{}' in INCAR".format(parameter) parser.add_argument("--{}".format(parameter), help=help_info) args = parser.parse_args() # Create POSCAR status, output = subprocess.getstatusoutput('ls *.xsd | head -1') xsd = XsdFile(filename=output) poscar_content = xsd.get_poscar_content(bases_const=1.0) with open('POSCAR', 'w') as f: f.write(poscar_content) # Create POTCAR
import logging from vaspy.incar import InCar SHELL_COMMAND = "find ./ -name 'INCAR'" if "__main__" == __name__: # Check command validity. status, output = commands.getstatusoutput(SHELL_COMMAND) if status: raise SystemExit("Invalid shell commands - '{}'".format(SHELL_COMMAND)) # Get InCar objects. incar_paths = (incar_path.strip() for incar_path in output.split('\n')) incars = [InCar(incar_path) for incar_path in incar_paths] # Get all possible arguments. set_list = [set(incar.pnames()) for incar in incars] possible_args = set.intersection(*set_list) # Set arguments for this script. parser = argparse.ArgumentParser() for arg in possible_args: arg_str = "--{}".format(arg) parser.add_argument(arg_str, help="set {} INCAR parameter".format(arg)) args_space = parser.parse_args() # Change parameters for all incars. for pname, value in args_space.__dict__.iteritems(): if value is None:
def setUp(self): # Create an InCar object. self.incar = InCar("./testdata/INCAR")