import numpy as np
from ase.structure import bulk, estimate_lattice_constant
from ase.atoms import Atoms, string2symbols
from ase.data.molecules import molecule
from ase.visualize import view
from ase.io import read, write
from ase.constraints import FixAtoms
from gpaw.utilities import devnull
from gpaw.utilities.bulk2 import EMTRunner, GPAWRunner
from gpaw.parameters import InputParameters
from gpaw.mpi import world
defaults = InputParameters()
def build_parser():
description = ('Run GPAW calculation for simple atoms, molecules or '
'bulk systems.')
epilog = 'GPAW options: --%s. ' % ', --'.join(defaults.keys())
parser = optparse.OptionParser(usage='%prog [options] formula or filename',
version='%prog 0.1',
description=description + ' ' + epilog)
struct = optparse.OptionGroup(parser, 'Structure')
struct.add_option('-i', '--identifier',
help='String identifier added to filenames.')
struct.add_option('-x', '--crystal-structure',
help='Crystal structure.',
choices=['sc', 'fcc', 'bcc', 'diamond', 'hcp',
# -------------------------------------------------------------------
from gpaw.test.ut_common import ase_svnversion, shapeopt, TestCase, \
TextTestRunner, CustomTextTestRunner, defaultTestLoader, \
initialTestLoader, create_random_atoms, create_parsize_maxbands
memstats = False
if memstats:
# Developer use of this feature requires ASE 3.1.0 svn.rev. 905 or later.
assert ase_svnversion >= 905 # wasn't bug-free untill 973!
from ase.utils.memory import MemorySingleton, MemoryStatistics
# -------------------------------------------------------------------
p = InputParameters(spinpol=False)
xc = XC(p.xc)
p.setups = dict([(symbol, SetupData(symbol, xc.name)) for symbol in 'HO'])
class UTBandParallelSetup(TestCase):
"""
Setup a simple band parallel calculation."""
# Number of bands
nbands = 36
# Spin-paired, single kpoint
nspins = 1
nibzkpts = 1
def main(argv):
defaults = InputParameters()
parser = build_parser()
populate_parser(parser, defaults)
opts, args = parser.parse_args(argv)
if opts.update is not None and opts.output is not None:
parser.error('Cannot both update and write to new file.')
if opts.update:
if not os.path.isfile(opts.update):
parser.error('No such file %s' % opts.update)
outfilename = opts.update
args = [outfilename] + args
elif opts.output:
outfilename = opts.output
else:
outfilename = None
parameters = {}
if opts.complete:
parameters.update(defaults)
for arg in args:
loaded_parameters = load(arg)
parameters.update(loaded_parameters)
# We have to use the newly loaded info (target file)
# to get new defaults!
#
# Rather ugly but hopefully it works
# We can probably avoid this somehow, think about it in the future
# (can one have different call formats like e.g. the 'du' man-page,
# and somehow detect which one is relevant?)
#parser2 = build_parser()
#populate_parser(parser2, loaded_parameters)
#opts, args2 = parser2.parse_args(argv)
cli_args = vars(opts)
cli_parameters = {}
keys = defaults.keys()
for key in defaults:
obj = eval(cli_args[key])
if defaults[key] != obj:
cli_parameters[key] = obj
parameters.update(cli_parameters)
# Remove keys which are not changed from defaults
if not opts.complete:
# must call keys() since dict cannot change size during iteration
for key in parameters.keys():
if defaults[key] == parameters[key]:
del parameters[key]
if opts.pop:
for kwarg in opts.pop.split(','):
parameters.pop(kwarg)
if outfilename is None:
out = sys.stdout
else:
out = open(outfilename, 'w')
print >> out, kwargs2str(**parameters)
# -------------------------------------------------------------------
from gpaw.test.ut_common import ase_svnversion, shapeopt, TestCase, \
TextTestRunner, CustomTextTestRunner, defaultTestLoader, \
initialTestLoader, create_random_atoms, create_parsize_maxbands
memstats = False
if memstats:
# Developer use of this feature requires ASE 3.1.0 svn.rev. 905 or later.
assert ase_svnversion >= 905 # wasn't bug-free untill 973!
from ase.utils.memory import MemorySingleton, MemoryStatistics
# -------------------------------------------------------------------
p = InputParameters(spinpol=False)
xc = XC(p.xc)
p.setups = dict([(symbol, SetupData(symbol, xc.name)) for symbol in 'HN'])
class UTBandParallelSetup(TestCase):
"""
Setup a simple band parallel calculation."""
# Number of bands
nbands = 36
# Spin-paired, single kpoint
nspins = 1
nibzkpts = 1
# Strided or blocked groups
def __init__(self,
filename=None,
timer=None,
read_projections=True,
**kwargs):
"""ASE-calculator interface.
The following parameters can be used: nbands, xc, kpts,
spinpol, gpts, h, charge, symmetry, width, mixer,
hund, lmax, fixdensity, convergence, txt, parallel,
communicator, dtype, softgauss and stencils.
If you don't specify any parameters, you will get:
Defaults: neutrally charged, LDA, gamma-point calculation, a
reasonable grid-spacing, zero Kelvin electronic temperature,
and the number of bands will be equal to the number of atomic
orbitals present in the setups. Only occupied bands are used
in the convergence decision. The calculation will be
spin-polarized if and only if one or more of the atoms have
non-zero magnetic moments. Text output will be written to
standard output.
For a non-gamma point calculation, the electronic temperature
will be 0.1 eV (energies are extrapolated to zero Kelvin) and
all symmetries will be used to reduce the number of
**k**-points."""
PAWTextOutput.__init__(self)
self.grid_descriptor_class = GridDescriptor
self.input_parameters = InputParameters()
if timer is None:
self.timer = Timer()
else:
self.timer = timer
self.scf = None
self.forces = ForceCalculator(self.timer)
self.stress_vv = None
self.dipole_v = None
self.magmom_av = None
self.wfs = EmptyWaveFunctions()
self.occupations = None
self.density = None
self.hamiltonian = None
self.atoms = None
self.iter = 0
self.initialized = False
self.nbands_parallelization_adjustment = None # Somehow avoid this?
# Possibly read GPAW keyword arguments from file:
if filename is not None and filename.endswith('.gkw'):
from gpaw.utilities.kwargs import load
parameters = load(filename)
parameters.update(kwargs)
kwargs = parameters
filename = None # XXX
if filename is not None:
comm = kwargs.get('communicator', mpi.world)
reader = gpaw.io.open(filename, 'r', comm)
self.atoms = gpaw.io.read_atoms(reader)
par = self.input_parameters
par.read(reader)
# _changed_keywords contains those keywords that have been
# changed by set() since last time initialize() was called.
self._changed_keywords = set()
self.set(**kwargs)
# Here in the beginning, effectively every keyword has been changed.
self._changed_keywords.update(self.input_parameters)
if filename is not None:
# Setups are not saved in the file if the setups were not loaded
# *from* files in the first place
if par.setups is None:
if par.idiotproof:
raise RuntimeError('Setups not specified in file. Use '
'idiotproof=False to proceed anyway.')
else:
par.setups = {None: 'paw'}
if par.basis is None:
if par.idiotproof:
raise RuntimeError('Basis not specified in file. Use '
'idiotproof=False to proceed anyway.')
else:
par.basis = {}
self.initialize()
self.read(reader, read_projections)
if self.hamiltonian.xc.type == 'GLLB':
self.occupations.calculate(self.wfs)
self.print_cell_and_parameters()
self.observers = []
def main(argv):
defaults = InputParameters()
parser = build_parser()
populate_parser(parser, defaults)
opts, args = parser.parse_args(argv)
if opts.update is not None and opts.output is not None:
parser.error('Cannot both update and write to new file.')
if opts.update:
if not os.path.isfile(opts.update):
parser.error('No such file %s' % opts.update)
outfilename = opts.update
args = [outfilename] + args
elif opts.output:
outfilename = opts.output
else:
outfilename = None
parameters = {}
if opts.complete:
parameters.update(defaults)
for arg in args:
loaded_parameters = load(arg)
parameters.update(loaded_parameters)
# We have to use the newly loaded info (target file)
# to get new defaults!
#
# Rather ugly but hopefully it works
# We can probably avoid this somehow, think about it in the future
# (can one have different call formats like e.g. the 'du' man-page,
# and somehow detect which one is relevant?)
#parser2 = build_parser()
#populate_parser(parser2, loaded_parameters)
#opts, args2 = parser2.parse_args(argv)
cli_args = vars(opts)
cli_parameters = {}
keys = defaults.keys()
for key in defaults:
obj = eval(cli_args[key])
if defaults[key] != obj:
cli_parameters[key] = obj
parameters.update(cli_parameters)
# Remove keys which are not changed from defaults
if not opts.complete:
# must call keys() since dict cannot change size during iteration
for key in parameters.keys():
if defaults[key] == parameters[key]:
del parameters[key]
if opts.pop:
for kwarg in opts.pop.split(','):
parameters.pop(kwarg)
if outfilename is None:
out = sys.stdout
else:
out = open(outfilename, 'w')
print >> out, kwargs2str(**parameters)
