def relax(dim=2, submit=True, force_overwrite=False): """ Writes input files and (optionally) submits a self-consistent relaxation. Should be run before pretty much anything else, in order to get the right energy and structure of the material. Args: dim (int): 2 for relaxing a 2D material, 3 for a 3D material. submit (bool): Whether or not to submit the job. force_overwrite (bool): Whether or not to overwrite files if an already converged vasprun.xml exists in the directory. """ if force_overwrite or not utl.is_converged(os.getcwd()): directory = os.getcwd().split('/')[-1] # vdw_kernel.bindat file required for VDW calculations. if VDW_KERNEL: os.system('cp {} .'.format(VDW_KERNEL)) # KPOINTS Kpoints.automatic_density(Structure.from_file('POSCAR'), 1000).write_file('KPOINTS') # INCAR INCAR_DICT.update( {'MAGMOM': utl.get_magmom_string(Structure.from_file('POSCAR'))} ) Incar.from_dict(INCAR_DICT).write_file('INCAR') # POTCAR utl.write_potcar() # Special tasks only performed for 2D materials. if dim == 2: # Ensure 20A interlayer vacuum utl.ensure_vacuum(Structure.from_file('POSCAR'), 20) # Remove all z k-points. kpts_lines = open('KPOINTS').readlines() with open('KPOINTS', 'w') as kpts: for line in kpts_lines[:3]: kpts.write(line) kpts.write(kpts_lines[3].split()[0] + ' ' + kpts_lines[3].split()[1] + ' 1') # Submission script if dim == 2: binary = VASP_TWOD_BIN elif dim == 3: binary = VASP_STD_BIN if QUEUE_SYSTEM == 'pbs': utl.write_pbs_runjob(directory, 1, 16, '800mb', '6:00:00', binary) submission_command = 'qsub runjob' elif QUEUE_SYSTEM == 'slurm': utl.write_slurm_runjob(directory, 16, '800mb', '6:00:00', binary) submission_command = 'sbatch runjob' if submit: os.system(submission_command)
def relax(dim=2, submit=True, force_overwrite=False): """ Writes input files and (optionally) submits a self-consistent relaxation. Should be run before pretty much anything else, in order to get the right energy and structure of the material. Args: dim (int): 2 for relaxing a 2D material, 3 for a 3D material. submit (bool): Whether or not to submit the job. force_overwrite (bool): Whether or not to overwrite files if an already converged vasprun.xml exists in the directory. """ if force_overwrite or not utl.is_converged(os.getcwd()): directory = os.getcwd().split('/')[-1] # vdw_kernel.bindat file required for VDW calculations. if VDW_KERNEL: os.system('cp {} .'.format(VDW_KERNEL)) # KPOINTS Kpoints.automatic_density(Structure.from_file('POSCAR'), 1000).write_file('KPOINTS') # INCAR INCAR_DICT.update( {'MAGMOM': utl.get_magmom_string(Structure.from_file('POSCAR'))}) Incar.from_dict(INCAR_DICT).write_file('INCAR') # POTCAR utl.write_potcar() # Special tasks only performed for 2D materials. if dim == 2: # Ensure 20A interlayer vacuum utl.ensure_vacuum(Structure.from_file('POSCAR'), 20) # Remove all z k-points. kpts_lines = open('KPOINTS').readlines() with open('KPOINTS', 'w') as kpts: for line in kpts_lines[:3]: kpts.write(line) kpts.write(kpts_lines[3].split()[0] + ' ' + kpts_lines[3].split()[1] + ' 1') # Submission script if dim == 2: binary = VASP_TWOD_BIN elif dim == 3: binary = VASP_STD_BIN if QUEUE_SYSTEM == 'pbs': utl.write_pbs_runjob(directory, 1, 16, '800mb', '6:00:00', binary) submission_command = 'qsub runjob' elif QUEUE_SYSTEM == 'slurm': utl.write_slurm_runjob(directory, 16, '800mb', '6:00:00', binary) submission_command = 'sbatch runjob' if submit: os.system(submission_command)
def run_gamma_calculations(submit=True, step_size=0.5): """ Setup a 2D grid of static energy calculations to plot the Gamma surface between two layers of the 2D material. These calculations are run and stored in subdirectories under 'friction/lateral'. Args: submit (bool): Whether or not to submit the jobs. step_size (float): the distance between grid points in Angstroms. """ if not os.path.isdir('friction'): os.mkdir('friction') os.chdir('friction') if not os.path.isdir('lateral'): os.mkdir('lateral') os.chdir('lateral') os.system('cp ../../CONTCAR POSCAR') # Pad the bottom layer with 20 Angstroms of vacuum. utl.ensure_vacuum(Structure.from_file('POSCAR'), 20) structure = Structure.from_file('POSCAR') n_sites_per_layer = structure.num_sites n_divs_x = int(math.ceil(structure.lattice.a / step_size)) n_divs_y = int(math.ceil(structure.lattice.b / step_size)) # Get the thickness of the material. max_height = max([site.coords[2] for site in structure.sites]) min_height = min([site.coords[2] for site in structure.sites]) thickness = max_height - min_height # Make a new layer. species, coords = [], [] for site in structure.sites: # Original site species.append(site.specie) coords.append(site.coords) # New layer site species.append(site.specie) coords.append( [site.coords[0], site.coords[1], site.coords[2] + thickness + 3.5]) Structure(structure.lattice, species, coords, coords_are_cartesian=True).to('POSCAR', 'POSCAR') for x in range(n_divs_x): for y in range(n_divs_y): dir = '{}x{}'.format(x, y) if not os.path.isdir(dir): os.mkdir(dir) # Copy input files os.chdir(dir) os.system('cp ../../../INCAR .') os.system('cp ../../../KPOINTS .') os.system('cp ../POSCAR .') if VDW_KERNEL: os.system('cp {} .'.format(VDW_KERNEL)) # Shift the top layer structure = Structure.from_file("POSCAR") all_z_coords = [s.coords[2] for s in structure.sites] top_layer = [ s for s in structure.sites if s.coords[2] > np.mean(all_z_coords) ] structure.remove_sites( [i for i, s in enumerate(structure.sites) if s in top_layer]) for site in top_layer: structure.append(site.specie, [ site.coords[0] + float(x) / float(n_divs_x), site.coords[1] + float(y) / float(n_divs_y), site.coords[2] ], coords_are_cartesian=True) structure = structure.get_sorted_structure() structure.to("POSCAR", "POSCAR") utl.write_potcar() incar_dict = Incar.from_file('INCAR').as_dict() incar_dict.update({ 'NSW': 0, 'LAECHG': False, 'LCHARG': False, 'LWAVE': False, 'LVTOT': False, 'MAGMOM': utl.get_magmom_string(structure) }) incar_dict.pop('NPAR', None) Incar.from_dict(incar_dict).write_file('INCAR') if QUEUE_SYSTEM == 'pbs': utl.write_pbs_runjob(dir, 1, 8, '1000mb', '2:00:00', VASP_STD_BIN) submission_command = 'qsub runjob' elif QUEUE_SYSTEM == 'slurm': utl.write_slurm_runjob(dir, 8, '1000mb', '2:00:00', VASP_STD_BIN) submission_command = 'sbatch runjob' if submit: os.system(submission_command) os.chdir('../') os.chdir('../../')
def run_gamma_calculations(submit=True, step_size=0.5): """ Setup a 2D grid of static energy calculations to plot the Gamma surface between two layers of the 2D material. These calculations are run and stored in subdirectories under 'friction/lateral'. Args: submit (bool): Whether or not to submit the jobs. step_size (float): the distance between grid points in Angstroms. """ if not os.path.isdir('friction'): os.mkdir('friction') os.chdir('friction') if not os.path.isdir('lateral'): os.mkdir('lateral') os.chdir('lateral') try: os.system('cp ../../CONTCAR POSCAR') except: try: os.system('cp ../../POSCAR .') except: raise IOError('No POSCAR or CONTCAR found in ' + os.path.dirname(os.path.dirname(os.getcwd()))) # Pad the bottom layer with 20 Angstroms of vacuum. utl.ensure_vacuum(Structure.from_file('POSCAR'), 20) structure = Structure.from_file('POSCAR') n_sites_per_layer = structure.num_sites n_divs_x = int(math.ceil(structure.lattice.a / step_size)) n_divs_y = int(math.ceil(structure.lattice.b / step_size)) # Get the thickness of the material. max_height = max([site.coords[2] for site in structure.sites]) min_height = min([site.coords[2] for site in structure.sites]) thickness = max_height - min_height # Make a new layer. species, coords = [], [] for site in structure.sites: # Original site species.append(site.specie) coords.append(site.coords) # New layer site species.append(site.specie) coords.append( [site.coords[0], site.coords[1], site.coords[2] + thickness + 3.5]) Structure(structure.lattice, species, coords).to('POSCAR', 'POSCAR') for x in range(n_divs_x): for y in range(n_divs_y): dir = '{}x{}'.format(x, y) if not os.path.isdir(dir): os.mkdir(dir) # Copy input files os.chdir(dir) if not os.path.exists('../../INCAR'): raise IOError('No INCAR found in ' + os.path.dirname(os.path.dirname(os.getcwd()))) if not os.path.exists('../../KPOINTS'): raise IOError('No KPOINTS found in ' + os.path.dirname(os.path.dirname(os.getcwd()))) os.system('cp ../../../INCAR .') os.system('cp ../../../KPOINTS .') os.system('cp ../POSCAR .') if VDW_KERNEL: os.system('cp {} .'.format(VDW_KERNEL)) utl.write_potcar() incar_dict = Incar.from_file('INCAR').as_dict() incar_dict.update({ 'NSW': 0, 'LAECHG': False, 'LCHARG': False, 'LWAVE': False, 'LVTOT': False, 'MAGMOM': utl.get_magmom_string(Structure.from_file('POSCAR')) }) incar_dict.pop('NPAR', None) Incar.from_dict(incar_dict).write_file('INCAR') # Shift the top layer poscar_lines = open('POSCAR').readlines() with open('POSCAR', 'w') as poscar: for line in poscar_lines[:8 + n_sites_per_layer]: poscar.write(line) for line in poscar_lines[8 + n_sites_per_layer:]: split_line = line.split() new_coords = [ float(split_line[0]) + float(x) / float(n_divs_x), float(split_line[1]) + float(y) / float(n_divs_y), float(split_line[2]) ] poscar.write(' '.join([str(i) for i in new_coords]) + '\n') sub_exe = True if VASP_STD_BIN == 'None': print 'Executable is missing in ' + os.getcwd() + '/runjob' print 'Configure mpint_config.yaml file with your executable!' sub_exe = False if QUEUE_SYSTEM == 'pbs': utl.write_pbs_runjob(dir, 1, 8, '1000mb', '2:00:00', VASP_STD_BIN) submission_command = 'qsub runjob' elif QUEUE_SYSTEM == 'slurm': utl.write_slurm_runjob(dir, 8, '1000mb', '2:00:00', VASP_STD_BIN) submission_command = 'sbatch runjob' if submit and sub_exe: os.system(submission_command) os.chdir('../') os.chdir('../../')
def run_gamma_calculations(submit=True, step_size=0.5): """ Setup a 2D grid of static energy calculations to plot the Gamma surface between two layers of the 2D material. These calculations are run and stored in subdirectories under 'friction/lateral'. Args: submit (bool): Whether or not to submit the jobs. step_size (float): the distance between grid points in Angstroms. """ if not os.path.isdir('friction'): os.mkdir('friction') os.chdir('friction') if not os.path.isdir('lateral'): os.mkdir('lateral') os.chdir('lateral') os.system('cp ../../CONTCAR POSCAR') # Pad the bottom layer with 20 Angstroms of vacuum. utl.ensure_vacuum(Structure.from_file('POSCAR'), 20) structure = Structure.from_file('POSCAR') n_sites_per_layer = structure.num_sites n_divs_x = int(math.ceil(structure.lattice.a / step_size)) n_divs_y = int(math.ceil(structure.lattice.b / step_size)) # Get the thickness of the material. max_height = max([site.coords[2] for site in structure.sites]) min_height = min([site.coords[2] for site in structure.sites]) thickness = max_height - min_height # Make a new layer. species, coords = [], [] for site in structure.sites: # Original site species.append(site.specie) coords.append(site.coords) # New layer site species.append(site.specie) coords.append([site.coords[0], site.coords[1], site.coords[2] + thickness + 3.5]) Structure(structure.lattice, species, coords, coords_are_cartesian=True).to('POSCAR', 'POSCAR') for x in range(n_divs_x): for y in range(n_divs_y): dir = '{}x{}'.format(x, y) if not os.path.isdir(dir): os.mkdir(dir) # Copy input files os.chdir(dir) os.system('cp ../../../INCAR .') os.system('cp ../../../KPOINTS .') os.system('cp ../POSCAR .') if VDW_KERNEL: os.system('cp {} .'.format(VDW_KERNEL)) # Shift the top layer structure = Structure.from_file("POSCAR") all_z_coords = [s.coords[2] for s in structure.sites] top_layer = [s for s in structure.sites if s.coords[2] > np.mean(all_z_coords)] structure.remove_sites([i for i, s in enumerate(structure.sites) if s in top_layer]) for site in top_layer: structure.append( site.specie, [site.coords[0]+float(x)/float(n_divs_x), site.coords[1]+float(y)/float(n_divs_y), site.coords[2]], coords_are_cartesian=True ) structure = structure.get_sorted_structure() structure.to("POSCAR", "POSCAR") utl.write_potcar() incar_dict = Incar.from_file('INCAR').as_dict() incar_dict.update({'NSW': 0, 'LAECHG': False, 'LCHARG': False, 'LWAVE': False, 'LVTOT': False, 'MAGMOM': utl.get_magmom_string(structure)}) incar_dict.pop('NPAR', None) Incar.from_dict(incar_dict).write_file('INCAR') if QUEUE_SYSTEM == 'pbs': utl.write_pbs_runjob(dir, 1, 8, '1000mb', '2:00:00', VASP_STD_BIN) submission_command = 'qsub runjob' elif QUEUE_SYSTEM == 'slurm': utl.write_slurm_runjob(dir, 8, '1000mb', '2:00:00', VASP_STD_BIN) submission_command = 'sbatch runjob' if submit: os.system(submission_command) os.chdir('../') os.chdir('../../')