Commit bf381d1d authored by Ask Hjorth Larsen's avatar Ask Hjorth Larsen
Browse files

clean up extraneous code which is not used for parsing

parent ee8dfe6b
# coding=utf-8
"""ASE-interface to Octopus.
"""This is based on a fork of the ASE-interface to Octopus.
The Octopus ASE interface is written by
......@@ -22,7 +22,6 @@ import numpy as np
from ase import Atoms
from ase.calculators.calculator import FileIOCalculator
# XXX raise ReadError upon bad read
from ase.data import atomic_numbers
from ase.io import read
from ase.io.xsf import read_xsf
......@@ -203,21 +202,6 @@ def unpad(pbc, arr):
return np.ascontiguousarray(arr)
def unpad_smarter(pbc, arr):
# 'Smarter' but less easy to understand version of the above.
# (untested I think)
slices = []
for c, is_periodic in enumerate(pbc):
if is_periodic:
left = np.take(arr, [0], axis=c)
right = np.take(arr, [-1], axis=c)
assert np.all(left == right)
slices.append(slice(0, -1))
else:
slices.append(slice(None))
return np.ascontiguousarray(arr[slices])
# Parse value as written in input file *or* something that one would be
# passing to the ASE interface, i.e., this might already be a boolean
def octbool2bool(value):
......@@ -392,303 +376,6 @@ def parse_input_file(fd):
return namespace.names
def boxshape_is_ase_compatible(kwargs):
pdims = int(kwargs.get('periodicdimensions', 0))
default_boxshape = 'parallelepiped' if pdims > 0 else 'minimum'
boxshape = kwargs.get('boxshape', default_boxshape).lower()
# XXX add support for experimental keyword 'latticevectors'
return boxshape == 'parallelepiped'
def kwargs2atoms(kwargs, directory=None):
"""Extract atoms object from keywords and return remaining keywords.
Some keyword arguments may refer to files. The directory keyword
may be necessary to resolve the paths correctly, and is used for
example when running 'ase-gui somedir/inp'."""
kwargs = normalize_keywords(kwargs)
# Only input units accepted nowadays are 'atomic'.
# But if we are loading an old file, and it specifies something else,
# we can be sure that the user wanted that back then.
units = get_input_units(kwargs)
atomic_units = (units == 'atomic')
if atomic_units:
length_unit = Bohr
else:
length_unit = Angstrom
coord_keywords = ['coordinates',
'xyzcoordinates',
'pdbcoordinates',
'reducedcoordinates',
'xsfcoordinates',
'xsfcoordinatesanimstep']
nkeywords = 0
for keyword in coord_keywords:
if keyword in kwargs:
nkeywords += 1
if nkeywords == 0:
raise OctopusParseError('No coordinates')
elif nkeywords > 1:
raise OctopusParseError('Multiple coordinate specifications present. '
'This may be okay in Octopus, but we do not '
'implement it.')
def get_positions_from_block(keyword):
# %Coordinates or %ReducedCoordinates -> atomic numbers, positions.
block = kwargs.pop(keyword)
positions = []
numbers = []
for row in block:
assert len(row) in [ndims + 1, ndims + 2]
row = row[:ndims + 1]
sym = row[0]
assert sym.startswith('"') or sym.startswith("'")
assert sym[0] == sym[-1]
sym = sym[1:-1]
pos0 = np.zeros(3)
ndim = int(kwargs.get('dimensions', 3))
pos0[:ndim] = [float(element) for element in row[1:]]
number = atomic_numbers[sym] # Use 0 ~ 'X' for unknown?
numbers.append(number)
positions.append(pos0)
positions = np.array(positions)
return numbers, positions
def read_atoms_from_file(fname, fmt):
assert fname.startswith('"') or fname.startswith("'")
assert fname[0] == fname[-1]
fname = fname[1:-1]
if directory is not None:
fname = os.path.join(directory, fname)
# XXX test xyz, pbd and xsf
if fmt == 'xsf' and 'xsfcoordinatesanimstep' in kwargs:
anim_step = kwargs.pop('xsfcoordinatesanimstep')
theslice = slice(anim_step, anim_step + 1, 1)
# XXX test animstep
else:
theslice = slice(None, None, 1)
images = read(fname, theslice, fmt)
if len(images) != 1:
raise OctopusParseError('Expected only one image. Don\'t know '
'what to do with %d images.' % len(images))
return images[0]
# We will attempt to extract cell and pbc from kwargs if 'lacking'.
# But they might have been left unspecified on purpose.
#
# We need to keep track of these two variables "externally"
# because the Atoms object assigns values when they are not given.
cell = None
pbc = None
adjust_positions_by_half_cell = False
atoms = None
xsfcoords = kwargs.pop('xsfcoordinates', None)
if xsfcoords is not None:
atoms = read_atoms_from_file(xsfcoords, 'xsf')
atoms.positions *= length_unit
atoms.cell *= length_unit
# As it turns out, non-periodic xsf is not supported by octopus.
# Also, it only supports fully periodic or fully non-periodic....
# So the only thing that we can test here is 3D fully periodic.
if sum(atoms.pbc) != 3:
raise NotImplementedError('XSF not fully periodic with Octopus')
cell = atoms.cell
pbc = atoms.pbc
# Position adjustment doesn't actually matter but this should work
# most 'nicely':
adjust_positions_by_half_cell = False
xyzcoords = kwargs.pop('xyzcoordinates', None)
if xyzcoords is not None:
atoms = read_atoms_from_file(xyzcoords, 'xyz')
atoms.positions *= length_unit
adjust_positions_by_half_cell = True
pdbcoords = kwargs.pop('pdbcoordinates', None)
if pdbcoords is not None:
atoms = read_atoms_from_file(pdbcoords, 'pdb')
pbc = atoms.pbc
adjust_positions_by_half_cell = True
# Due to an error in ASE pdb, we can only test the nonperiodic case.
# atoms.cell *= length_unit # XXX cell? Not in nonperiodic case...
atoms.positions *= length_unit
if sum(atoms.pbc) != 0:
raise NotImplementedError('Periodic pdb not supported by ASE.')
#if cell is None:
# cell could not be established from the file, so we set it on the
# Atoms now if possible:
# cell, kwargs = kwargs2cell(kwargs)
# if cell is not None:
# cell *= length_unit
# if cell is not None and atoms is not None:
# atoms.cell = cell
# In case of boxshape = sphere and similar, we still do not have
# a cell.
ndims = int(kwargs.get('dimensions', 3))
if ndims != 3:
raise NotImplementedError('Only 3D calculations supported.')
coords = kwargs.get('coordinates')
if coords is not None:
numbers, positions = get_positions_from_block('coordinates')
positions *= length_unit
adjust_positions_by_half_cell = True
atoms = Atoms(cell=cell, numbers=numbers, positions=positions)
rcoords = kwargs.get('reducedcoordinates')
if rcoords is not None:
numbers, rpositions = get_positions_from_block('reducedcoordinates')
#if cell is None:
# raise ValueError('Cannot figure out what the cell is, '
# 'and thus cannot interpret reduced coordinates.')
atoms = Atoms(cell=cell, numbers=numbers, positions=rpositions)
# Very invalid, but we get (scaled) positions from elsewhere anyway
if atoms is None:
raise OctopusParseError('Apparently there are no atoms.')
# Either we have non-periodic BCs or the atoms object already
# got its BCs from reading the file. In the latter case
# we shall override only if PeriodicDimensions was given specifically:
if pbc is None:
pdims = int(kwargs.pop('periodicdimensions', 0))
pbc = np.zeros(3, dtype=bool)
pbc[:pdims] = True
atoms.pbc = pbc
if (cell is not None and cell.shape == (3,)
and adjust_positions_by_half_cell):
nonpbc = (atoms.pbc == 0)
atoms.positions[:, nonpbc] += np.array(cell)[None, nonpbc] / 2.0
return atoms, kwargs
def atoms2kwargs(atoms, use_ase_cell):
kwargs = {}
positions = atoms.positions / Bohr
# TODO LatticeVectors parameter for non-orthogonal cells
if use_ase_cell:
cell = atoms.cell / Bohr
if is_orthorhombic(cell):
Lsize = 0.5 * np.diag(cell)
kwargs['lsize'] = [[repr(size) for size in Lsize]]
# ASE uses (0...cell) while Octopus uses -L/2...L/2.
# Lsize is really cell / 2, and we have to adjust our
# positions by subtracting Lsize (see construction of the coords
# block) in non-periodic directions.
nonpbc = (atoms.pbc == 0)
positions[:, nonpbc] -= Lsize[None, nonpbc]
else:
kwargs['latticevectors'] = cell.tolist()
coord_block = [[repr(sym)] + list(map(repr, pos))
for sym, pos in zip(atoms.get_chemical_symbols(),
positions)]
kwargs['coordinates'] = coord_block
npbc = sum(atoms.pbc)
for c in range(npbc):
if not atoms.pbc[c]:
msg = ('Boundary conditions of Atoms object inconsistent '
'with requirements of Octopus. pbc must be either '
'000, 100, 110, or 111.')
raise ValueError(msg)
kwargs['periodicdimensions'] = npbc
# TODO InitialSpins
#
# TODO can use maximumiterations + output/outputformat to extract
# things from restart file into output files without trouble.
#
# Velocities etc.?
return kwargs
def generate_input(atoms, kwargs, normalized2pretty):
"""Convert atoms and keyword arguments to Octopus input file."""
_lines = []
def append(line):
_lines.append(line)
def extend(lines):
_lines.extend(lines)
append('')
def setvar(key, var):
prettykey = normalized2pretty[key]
append('%s = %s' % (prettykey, var))
for kw in ['lsize', 'latticevectors', 'latticeparameters']:
assert kw not in kwargs
defaultboxshape = 'parallelepiped' if atoms.pbc.any() else 'minimum'
boxshape = kwargs.get('boxshape', defaultboxshape).lower()
use_ase_cell = (boxshape == 'parallelepiped')
atomskwargs = atoms2kwargs(atoms, use_ase_cell)
if use_ase_cell:
if 'lsize' in atomskwargs:
block = list2block('LSize', atomskwargs['lsize'])
elif 'latticevectors' in atomskwargs:
extend(list2block('LatticeParameters', [[1., 1., 1.]]))
block = list2block('LatticeVectors', atomskwargs['latticevectors'])
extend(block)
# Allow override or issue errors?
pdim = 'periodicdimensions'
if pdim in kwargs:
if int(kwargs[pdim]) != int(atomskwargs[pdim]):
raise ValueError('Cannot reconcile periodicity in input '
'with that of Atoms object')
setvar('periodicdimensions', atomskwargs[pdim])
# We like to output forces
if 'output' in kwargs:
output_string = kwargs.pop('output')
output_tokens = [token.strip()
for token in output_string.lower().split('+')]
else:
output_tokens = []
if 'forces' not in output_tokens:
output_tokens.append('forces')
setvar('output', ' + '.join(output_tokens))
# It is illegal to have output forces without any OutputFormat.
# Even though the forces are written in the same format no matter
# OutputFormat. Thus we have to make one up:
# Old Octopus has 'OutputHow' but new Octopus has 'OutputFormat'.
# We have to write the right one.
outputkw = 'outputformat'
if outputkw not in normalized2pretty:
outputkw = 'outputhow'
assert outputkw in normalized2pretty
if outputkw not in kwargs:
setvar(outputkw, 'xcrysden')
for key, val in kwargs.items():
# Most datatypes are straightforward but blocks require some attention.
if isinstance(val, list):
append('')
dict_data = list2block(normalized2pretty[key], val)
extend(dict_data)
else:
setvar(key, str(val))
append('')
coord_block = list2block('Coordinates', atomskwargs['coordinates'])
extend(coord_block)
return '\n'.join(_lines)
def read_static_info_kpoints(fd):
for line in fd:
if line.startswith('List of k-points'):
......@@ -862,63 +549,10 @@ class Octopus(FileIOCalculator):
special_ase_keywords = set(['kpts'])
def __init__(self,
restart=None,
label=None,
atoms=None,
command='octopus',
ignore_troublesome_keywords=None,
check_keywords=True,
_autofix_outputformats=False,
**kwargs):
"""Create Octopus calculator.
Label is always taken as a subdirectory.
Restart is taken to be a label."""
# XXX support the specially defined ASE parameters,
# "smear" etc.
# We run oct-help to get a list of all keywords.
# This makes us able to robustly construct the input file
# in the face of changing octopus versions, and also of
# early partial verification of user input.
if check_keywords:
try:
octopus_keywords = get_octopus_keywords()
except OSError as err:
msg = ('Could not obtain Octopus keyword list from '
'command oct-help: %s. Octopus not installed in '
'accordance with expectations. '
'Use check_octopus_keywords=False to override.' % err)
raise OSError(msg)
else:
octopus_keywords = None
self.octopus_keywords = octopus_keywords
self._autofix_outputformats = _autofix_outputformats
if restart is not None:
if label is not None and restart != label:
raise ValueError('restart and label are mutually exclusive '
'or must at the very least coincide.')
label = restart
if label is None:
label = 'ink-pool'
if ignore_troublesome_keywords:
trouble = set(self.troublesome_keywords)
for keyword in ignore_troublesome_keywords:
trouble.remove(keyword)
self.troublesome_keywords = trouble
def __init__(self, restart):
self.kwargs = {}
FileIOCalculator.__init__(self, restart=restart,
ignore_bad_restart_file=False,
label=label,
atoms=atoms,
command=command, **kwargs)
FileIOCalculator.__init__(self, restart=restart, label=restart)
# The above call triggers set() so we can update self.kwargs.
def set_label(self, label):
......@@ -931,8 +565,6 @@ class Octopus(FileIOCalculator):
def set(self, **kwargs):
"""Set octopus input file parameters."""
kwargs = normalize_keywords(kwargs)
if self.octopus_keywords is not None:
self.check_keywords_exist(kwargs)
for keyword in kwargs:
if keyword in self.troublesome_keywords:
......@@ -948,45 +580,14 @@ class Octopus(FileIOCalculator):
self.kwargs.update(kwargs)
# XXX should use 'Parameters' but don't know how
def check_keywords_exist(self, kwargs):
keywords = list(kwargs.keys())
for keyword in keywords:
if (keyword not in self.octopus_keywords
and keyword not in self.special_ase_keywords):
if self._autofix_outputformats:
if (keyword == 'outputhow' and 'outputformat'
in self.octopus_keywords):
kwargs['outputformat'] = kwargs.pop('outputhow')
if (keyword == 'outputformat' and 'outputhow'
in self.octopus_keywords):
kwargs['outputhow'] = kwargs.pop('outputformat')
continue
msg = ('Unknown Octopus keyword %s. Use oct-help to list '
'available keywords.') % keyword
raise OctopusKeywordError(msg)
def get_xc_functional(self):
"""Return the XC-functional identifier.
'LDA', 'PBE', ..."""
return self.kwargs.get('xcfunctional', 'LDA')
def get_bz_k_points(self):
"""Return all the k-points in the 1. Brillouin zone.
The coordinates are relative to reciprocal latice vectors."""
# Have not found nice way of extracting this information
# from Octopus. Thus unimplemented. -askhl
raise NotImplementedError
def get_charges(self, atoms=None):
raise NotImplementedError
def get_fermi_level(self):
return self.results['efermi']
def get_potential_energies(self):
raise NotImplementedError
def get_dipole_moment(self, atoms=None):
if 'dipole' not in self.results:
msg = ('Dipole moment not calculated.\n'
......@@ -994,9 +595,6 @@ class Octopus(FileIOCalculator):
raise OctopusIOError(msg)
return self.results['dipole']
def get_stresses(self):
raise NotImplementedError
def _read_array(self, fname, outputkeyword=None):
path = self._getpath('static/%s' % fname)
if not os.path.exists(path):
......@@ -1180,19 +778,6 @@ class Octopus(FileIOCalculator):
ibz_k_points=kpts,
k_point_weights=kpt_weights)
def write_input(self, atoms, properties=None, system_changes=None):
FileIOCalculator.write_input(self, atoms, properties=properties,
system_changes=system_changes)
octopus_keywords = self.octopus_keywords
if octopus_keywords is None:
# Will not do automatic pretty capitalization
octopus_keywords = self.kwargs
txt = generate_input(atoms, process_special_kwargs(atoms, self.kwargs),
octopus_keywords)
fd = open(self._getpath('inp'), 'w')
fd.write(txt)
fd.close()
def read(self, label):
# XXX label of restart file may not be the same as actual label!
# This makes things rather tricky. We first set the label to
......@@ -1204,35 +789,9 @@ class Octopus(FileIOCalculator):
inp_path = self._getpath('inp')
fd = open(inp_path)
kwargs = parse_input_file(fd)
if self.octopus_keywords is not None:
self.check_keywords_exist(kwargs)
#self.atoms, kwargs = kwargs2atoms(kwargs)
self.kwargs.update(kwargs)
fd.close()
self.read_results()
def main():
from ase.build import bulk
from ase.calculators.interfacechecker import check_interface
system = bulk('Si', 'diamond', orthorhombic=True)
calc = Octopus(Spacing=0.275,
KPointsGrid=[[2, 2, 2]],
KPointsUseSymmetries=True,
Smearing=0.1,
SmearingFunction='fermi_dirac',
ExtraStates=2,
stdout='"stdout.log"',
stderr='"stderr.log"',
Output='density + potential + wfs',
OutputFormat='xcrysden')
system.set_calculator(calc)
system.get_potential_energy()
check_interface(calc)
if __name__ == '__main__':
main()
......@@ -391,7 +391,7 @@ def parse(fname, fd):
kwargs = override_keywords(kwargs, parser_log_kwargs, fd)
print('Read as ASE calculator', file=fd)
calc = Octopus(dirname, check_keywords=False)
calc = Octopus(dirname)
with open_section('section_basis_set_cell_dependent') as basis_set_cell_dependent_gid:
pew.addValue('basis_set_cell_dependent_kind', 'realspace_grids')
......
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