Example #1
0
import os
import sys

from ase import Atoms, Atom, QuasiNewton, PickleTrajectory

from gpaw import *
from gpaw.cluster import Cluster
from gpaw.utilities.viewmol import ViewmolTrajectory, write_viewmol

s = Cluster([Atom('H'), Atom('H', (0, 0, 3))])
s.minimal_box(2)
c = GPAW(h=0.3, nbands=2)
s.set_calculator(c)

vfname = 'traj.vmol'
pfname = 'traj.pickle'
vmt = ViewmolTrajectory(s, vfname)
traj = PickleTrajectory(pfname, 'w', s)
#c.attach(vmt.add, 100000)
#sys.exit()

# Find the theoretical bond length:
dyn = QuasiNewton(s)
dyn.attach(traj.write)
dyn.attach(vmt.add)
dyn.run(fmax=0.05)

traj = PickleTrajectory(pfname, 'r')
vfname2 = 'pickle.vmol'
write_viewmol(traj, vfname2)
Example #2
0
def run_slab(adsorbate, geometry, xc, code):

    parameters = initialize_parameters(code, 0.1, h)
    parameters['xc'] = xc

    tag = 'Ru001'

    if adsorbate != 'None':
        name = adsorbate + tag
    else:
        name = tag

    if geometry == 'fix':
        slab = read_trajectory(code + '_' + name + '.traj')
    else:
        adsorbate_heights = {'N': 1.108, 'O': 1.257}

        slab = hcp0001('Ru',
                       size=(2, 2, 4),
                       a=2.72,
                       c=1.58 * 2.72,
                       vacuum=5.0 + add_vacuum,
                       orthogonal=True)
        slab.center(axis=2)

        if adsorbate != 'None':
            add_adsorbate(slab, adsorbate, adsorbate_heights[adsorbate], 'hcp')

    slab.set_constraint(FixAtoms(mask=slab.get_tags() >= 3))

    if code != 'elk':
        parameters['nbands'] = 80
        parameters['kpts'] = [4, 4, 1]
    #
    if code == 'gpaw':
        from gpaw import GPAW as Calculator
        from gpaw.mpi import rank
        parameters['txt'] = code + '_' + name + '.txt'
        from gpaw.mixer import Mixer, MixerSum
        parameters['mixer'] = Mixer(beta=0.2, nmaxold=5, weight=100.0)
    if code == 'dacapo':
        from ase.calculators.dacapo import Dacapo as Calculator
        rank = 0
        parameters['txtout'] = code + '_' + name + '.txt'
    if code == 'abinit':
        from ase.calculators.abinit import Abinit as Calculator
        rank = 0
        parameters['label'] = code + '_' + name
    if code == 'elk':
        from ase.calculators.elk import ELK as Calculator
        rank = 0
        parameters['autokpt'] = True
        elk_dir = 'elk_' + str(parameters['rgkmax'])
        conv_param = 1.0
        parameters['dir'] = elk_dir + '_' + name
    #
    calc = Calculator(**parameters)
    #
    slab.set_calculator(calc)
    try:
        if geometry == 'fix':
            slab.get_potential_energy()
            traj = PickleTrajectory(code + '_' + name + '.traj', mode='w')
            traj.write(slab)
        else:
            opt = QuasiNewton(slab,
                              logfile=code + '_' + name + '.qn',
                              trajectory=code + '_' + name + '.traj')
            opt.run(fmax=fmax)
    except:
        raise
Example #3
0
import os
import sys

from ase import Atoms, Atom, QuasiNewton, PickleTrajectory

from gpaw import *
from gpaw.cluster import Cluster
from gpaw.utilities.viewmol import ViewmolTrajectory, write_viewmol

s = Cluster([Atom('H'), Atom('H',(0,0,3))])
s.minimal_box(2)
c = GPAW(h=0.3, nbands=2)
s.set_calculator(c)

vfname='traj.vmol'
pfname='traj.pickle'
vmt = ViewmolTrajectory(s, vfname)
traj = PickleTrajectory(pfname, 'w', s)
#c.attach(vmt.add, 100000)
#sys.exit()

# Find the theoretical bond length:
dyn = QuasiNewton(s)
dyn.attach(traj.write)
dyn.attach(vmt.add)
dyn.run(fmax=0.05)

traj = PickleTrajectory(pfname, 'r')
vfname2='pickle.vmol'
write_viewmol(traj, vfname2)
Example #4
0
def run_molecule(adsorbate, geometry, xc, code):

    parameters = initialize_parameters(code, 0.01, h)
    parameters['xc'] = xc

    molecules = {
        'None': ('NO', 8),
        'N': ('N2', 8),
        'O': ('O2', 8),
    }

    for name, nbands in [molecules[adsorbate]]:
        if code != 'elk':
            parameters['nbands'] = nbands
        if geometry == 'fix':
            mol = read_trajectory(code + '_' + name + '.traj')
        else:
            mol = molecule(name)
        mol.center(vacuum=3.0 + add_vacuum)
        if name == 'NO':
            mol.translate((0, 0.1, 0))
        #
        if code == 'gpaw':
            from gpaw import GPAW as Calculator
            from gpaw.mpi import rank
            parameters['txt'] = code + '_' + name + '.txt'
            from gpaw.mixer import Mixer, MixerSum
            #if name == 'N2':
            #    parameters['mixer'] = Mixer(beta=0.1, nmaxold=5, metric='new', weight=100.0)
            #else:
            #    #parameters['eigensolver'] = 'cg'
            #    parameters['mixer'] = MixerSum(beta=0.2, nmaxold=5, metric='new', weight=100.0)
        if code == 'dacapo':
            from ase.calculators.dacapo import Dacapo as Calculator
            rank = 0
            parameters['txtout'] = code + '_' + name + '.txt'
        if code == 'abinit':
            from ase.calculators.abinit import Abinit as Calculator
            rank = 0
            parameters['label'] = code + '_' + name
        if code == 'elk':
            from ase.calculators.elk import ELK as Calculator
            rank = 0
            elk_dir = 'elk_' + str(parameters['rgkmax'])
            conv_param = 1.0
            parameters['dir'] = elk_dir + '_' + name
        #
        calc = Calculator(**parameters)
        #
        mol.set_calculator(calc)
        try:
            if geometry == 'fix':
                mol.get_potential_energy()
                traj = PickleTrajectory(code + '_' + name + '.traj', mode='w')
                traj.write(mol)
            else:
                opt = QuasiNewton(mol,
                                  logfile=code + '_' + name + '.qn',
                                  trajectory=code + '_' + name + '.traj')
                opt.run(fmax=fmax)
        except:
            raise