Ejemplo n.º 1
0
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 != '/path/to/vdw_kernel.bindat':
            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()})
        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.add_vacuum(20 - utl.get_spacing(), 0.9)
            # 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 QUEUE == 'pbs':
            utl.write_pbs_runjob(directory, 1, 16, '800mb', '6:00:00',
                                 VASP_2D)
            submission_command = 'qsub runjob'

        elif QUEUE == 'slurm':
            utl.write_slurm_runjob(directory, 16, '800mb', '6:00:00',
                                   VASP_2D)
            submission_command = 'sbatch runjob'

        if submit:
            os.system(submission_command)
Ejemplo n.º 2
0
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 != '/path/to/vdw_kernel.bindat':
            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()})
        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.add_vacuum(20 - utl.get_spacing(), 0.9)
            # 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 QUEUE == 'pbs':
            utl.write_pbs_runjob(directory, 1, 16, '800mb', '6:00:00', VASP_2D)
            submission_command = 'qsub runjob'

        elif QUEUE == 'slurm':
            utl.write_slurm_runjob(directory, 16, '800mb', '6:00:00', VASP_2D)
            submission_command = 'sbatch runjob'

        if submit:
            os.system(submission_command)
Ejemplo n.º 3
0
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.add_vacuum(20 - utl.get_spacing(), 0.8)
    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.
    new_sites = []
    for site in structure.sites:
        new_sites.append((site.specie,
                          [site.coords[0], site.coords[1],
                           site.coords[2] + thickness + 3.5]))

    for site in new_sites:
        structure.append(site[0], site[1], coords_are_cartesian=True)

    #structure.get_sorted_structure().to('POSCAR', 'POSCAR')
    structure.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 != '/path/to/vdw_kernel.bindat':
                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,
                               'MAGMOM': utl.get_magmom_string()})
            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')

            if QUEUE == 'pbs':
                utl.write_pbs_runjob(dir, 1, 4, '800mb', '1:00:00', VASP)
                submission_command = 'qsub runjob'

            elif QUEUE == 'slurm':
                utl.write_slurm_runjob(dir, 4, '800mb', '1:00:00', VASP)
                submission_command = 'sbatch runjob'

            if submit:
                os.system(submission_command)

            os.chdir('../')

    os.chdir('../../')
Ejemplo n.º 4
0
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.add_vacuum(20 - utl.get_spacing(), 0.8)
    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.
    new_sites = []
    for site in structure.sites:
        new_sites.append((site.specie,
                          [site.coords[0], site.coords[1],
                           site.coords[2] + thickness + 3.5]))

    for site in new_sites:
        structure.append(site[0], site[1], coords_are_cartesian=True)

    #structure.get_sorted_structure().to('POSCAR', 'POSCAR')
    structure.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 != '/path/to/vdw_kernel.bindat':
                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()})
            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')

            if QUEUE == 'pbs':
                utl.write_pbs_runjob(dir, 1, 8, '1000mb', '2:00:00', VASP)
                submission_command = 'qsub runjob'

            elif QUEUE == 'slurm':
                utl.write_slurm_runjob(dir, 8, '1000mb', '2:00:00', VASP)
                submission_command = 'sbatch runjob'

            if submit:
                os.system(submission_command)

            os.chdir('../')

    os.chdir('../../')