def from_file(cls, *args, **kwargs):
"""Create a System object from a file.
A list of filenames may be provided, which will be loaded in that
order. Each file complements or overrides the information loaded
from a previous file in the list. Furthermore, keyword arguments
may be used to specify additional constructor arguments.
The ``lf`` optional argument is picked up from the kwargs list to
contstruct (when needed) arrays to store the results loaded from
file. When ``lf`` is not given, a DenseLinalgFactory is created by
default.
The filenames may also contain checkpoint files and open h5.File
objects of checkpoint files. The last such checkpoint file will
automatically be used as a checkpoint file for this class. If you
want to override this behavior, provide the ``chk`` keyword argument
(may be None).
"""
constructor_args = {}
lf = kwargs.get('lf')
if lf is None:
lf = DenseLinalgFactory()
for fn in args:
fn_args = load_system_args(fn, lf)
constructor_args.update(fn_args)
constructor_args.update(kwargs)
# If the basis comes from an external code and some operators are
# loaded, rows and columns may need to be reordered. Similar for the
# orbital coefficients and the density matrices.
permutation = constructor_args.get('permutation')
if permutation is not None:
cache = constructor_args.get('cache')
if cache is not None:
for value, tags in cache.itervalues():
if isinstance(value, LinalgObject):
value.apply_basis_permutation(permutation)
wfn = constructor_args.get('wfn')
if wfn is not None:
wfn.apply_basis_permutation(permutation)
del constructor_args['permutation']
# After the permutation, correct for different sign conventions of the
# orbitals
signs = constructor_args.get('signs')
if signs is not None:
cache = constructor_args.get('cache')
if cache is not None:
for value, tags in cache.itervalues():
if isinstance(value, LinalgObject):
value.apply_basis_signs(signs)
wfn = constructor_args.get('wfn')
if wfn is not None:
wfn.apply_basis_signs(signs)
del constructor_args['signs']
return cls(**constructor_args)
def test_dense_two_index():
from horton.matrix import DenseLinalgFactory, DenseTwoIndex
lf = DenseLinalgFactory()
c = Cache()
op1, new = c.load("egg", alloc=(lf.create_two_index, 10))
assert new
assert isinstance(op1, DenseTwoIndex)
assert op1.nbasis == 10
op2 = c.load("egg")
assert op1 is op2
op3, new = c.load("egg", alloc=(lf.create_two_index, 10))
assert not new
assert op1 is op3
# things that should not work
with assert_raises(TypeError):
op4, new = c.load("egg", alloc=(lf.create_two_index, 5))
with assert_raises(TypeError):
op4, new = c.load("egg", alloc=5)
# after clearing
op1.set_element(1, 2, 5.2)
c.clear()
assert op1._array[1, 2] == 0.0
with assert_raises(KeyError):
op4 = c.load("egg")
op4, new = c.load("egg", alloc=(lf.create_two_index, 10))
assert new
assert op1 is op4
op5 = c.load("egg")
assert op1 is op5
# default_nbasis
lf.default_nbasis = 5
with assert_raises(TypeError):
c.load("egg", alloc=lf.create_two_index)
c.clear()
op6, new = c.load("egg", alloc=lf.create_two_index)
assert new
assert not op5 is op6
assert op6.nbasis == 5
# the new method of the two-index object
op7, new = c.load("bork", alloc=op6.new)
assert new
assert not op5 is op7
assert op7.nbasis == 5
def test_dense_expansion():
from horton.matrix import DenseLinalgFactory, DenseExpansion
lf = DenseLinalgFactory()
c = Cache()
exp1, new = c.load("egg", alloc=(lf.create_expansion, 10, 9))
assert new
assert isinstance(exp1, DenseExpansion)
assert exp1.nbasis == 10
assert exp1.nfn == 9
exp2 = c.load("egg")
assert exp1 is exp2
exp3, new = c.load("egg", alloc=(lf.create_expansion, 10, 9))
assert not new
assert exp1 is exp3
# things that should not work
with assert_raises(TypeError):
exp4, new = c.load("egg", alloc=(lf.create_expansion, 5))
with assert_raises(TypeError):
exp4, new = c.load("egg", alloc=(lf.create_expansion, 10, 5))
with assert_raises(TypeError):
exp4, new = c.load("egg", alloc=5)
# after clearing
exp1.coeffs[1, 2] = 5.2
c.clear()
assert exp1.coeffs[1, 2] == 0.0
with assert_raises(KeyError):
exp4 = c.load("egg")
exp4, new = c.load("egg", alloc=(lf.create_expansion, 10, 9))
assert new
assert exp1 is exp4
exp5 = c.load("egg")
assert exp1 is exp5
# default_nbasis
lf.default_nbasis = 5
with assert_raises(TypeError):
c.load("egg", alloc=lf.create_expansion)
c.clear()
exp6, new = c.load("egg", alloc=lf.create_expansion)
assert new
assert not exp5 is exp6
assert exp6.nbasis == 5
assert exp6.nfn == 5
def test_dense_two_index():
from horton.matrix import DenseLinalgFactory, DenseTwoIndex
lf = DenseLinalgFactory()
c = Cache()
op1, new = c.load('egg', alloc=(lf.create_two_index, 10))
assert new
assert isinstance(op1, DenseTwoIndex)
assert op1.nbasis == 10
op2 = c.load('egg')
assert op1 is op2
op3, new = c.load('egg', alloc=(lf.create_two_index, 10))
assert not new
assert op1 is op3
# things that should not work
with assert_raises(TypeError):
op4, new = c.load('egg', alloc=(lf.create_two_index, 5))
with assert_raises(TypeError):
op4, new = c.load('egg', alloc=5)
# after clearing
op1.set_element(1, 2, 5.2)
c.clear()
assert op1._array[1, 2] == 0.0
with assert_raises(KeyError):
op4 = c.load('egg')
op4, new = c.load('egg', alloc=(lf.create_two_index, 10))
assert new
assert op1 is op4
op5 = c.load('egg')
assert op1 is op5
# default_nbasis
lf.default_nbasis = 5
with assert_raises(TypeError):
c.load('egg', alloc=lf.create_two_index)
c.clear()
op6, new = c.load('egg', alloc=lf.create_two_index)
assert new
assert not op5 is op6
assert op6.nbasis == 5
# the new method of the two-index object
op7, new = c.load('bork', alloc=op6.new)
assert new
assert not op5 is op7
assert op7.nbasis == 5
def test_dense_expansion():
from horton.matrix import DenseLinalgFactory, DenseExpansion
lf = DenseLinalgFactory()
c = Cache()
exp1, new = c.load('egg', alloc=(lf.create_expansion, 10, 9))
assert new
assert isinstance(exp1, DenseExpansion)
assert exp1.nbasis == 10
assert exp1.nfn == 9
exp2 = c.load('egg')
assert exp1 is exp2
exp3, new = c.load('egg', alloc=(lf.create_expansion, 10, 9))
assert not new
assert exp1 is exp3
# things that should not work
with assert_raises(TypeError):
exp4, new = c.load('egg', alloc=(lf.create_expansion, 5))
with assert_raises(TypeError):
exp4, new = c.load('egg', alloc=(lf.create_expansion, 10, 5))
with assert_raises(TypeError):
exp4, new = c.load('egg', alloc=5)
# after clearing
exp1.coeffs[1, 2] = 5.2
c.clear()
assert exp1.coeffs[1, 2] == 0.0
with assert_raises(KeyError):
exp4 = c.load('egg')
exp4, new = c.load('egg', alloc=(lf.create_expansion, 10, 9))
assert new
assert exp1 is exp4
exp5 = c.load('egg')
assert exp1 is exp5
# default_nbasis
lf.set_default_nbasis(5)
with assert_raises(TypeError):
c.load('egg', alloc=lf.create_expansion)
c.clear()
exp6, new = c.load('egg', alloc=lf.create_expansion)
assert new
assert not exp5 is exp6
assert exp6.nbasis == 5
assert exp6.nfn == 5
def test_dense_two_body():
from horton.matrix import DenseLinalgFactory, DenseTwoBody
lf = DenseLinalgFactory()
c = Cache()
op1, new = c.load('egg', alloc=(lf.create_two_body, 10))
assert new
assert isinstance(op1, DenseTwoBody)
assert op1.nbasis == 10
op2 = c.load('egg')
assert op1 is op2
op3, new = c.load('egg', alloc=(lf.create_two_body, 10))
assert not new
assert op1 is op3
# things that should not work
with assert_raises(TypeError):
op4, new = c.load('egg', alloc=(lf.create_two_body, 5))
with assert_raises(TypeError):
op4, new = c.load('egg', alloc=5)
# after clearing
op1.set_element(1, 2, 1, 2, 5.2)
c.clear()
assert op1._array[1, 2, 1, 2] == 0.0
with assert_raises(KeyError):
op4 = c.load('egg')
op4, new = c.load('egg', alloc=(lf.create_two_body, 10))
assert new
assert op1 is op4
op5 = c.load('egg')
assert op1 is op5
# default_nbasis
lf.set_default_nbasis(5)
with assert_raises(TypeError):
c.load('egg', alloc=lf.create_two_body)
c.clear()
op6, new = c.load('egg', alloc=lf.create_one_body)
assert new
assert not op5 is op6
assert op6.nbasis == 5
def test_dense_two_body():
from horton.matrix import DenseLinalgFactory, DenseTwoBody
lf = DenseLinalgFactory()
c = Cache()
op1, new = c.load('egg', alloc=(lf.create_two_body, 10))
assert new
assert isinstance(op1, DenseTwoBody)
assert op1.nbasis == 10
op2 = c.load('egg')
assert op1 is op2
op3, new = c.load('egg', alloc=(lf.create_two_body, 10))
assert not new
assert op1 is op3
# things that should not work
with assert_raises(TypeError):
op4, new = c.load('egg', alloc=(lf.create_two_body, 5))
with assert_raises(TypeError):
op4, new = c.load('egg', alloc=5)
# after clearing
op1.set_element(1, 2, 1, 2, 5.2)
c.clear()
assert op1._array[1,2,1,2] == 0.0
with assert_raises(KeyError):
op4 = c.load('egg')
op4, new = c.load('egg', alloc=(lf.create_two_body, 10))
assert new
assert op1 is op4
op5 = c.load('egg')
assert op1 is op5
# default_nbasis
lf.set_default_nbasis(5)
with assert_raises(TypeError):
c.load('egg', alloc=lf.create_two_body)
c.clear()
op6, new = c.load('egg', alloc=lf.create_one_body)
assert new
assert not op5 is op6
assert op6.nbasis == 5
def __init__(self,
coordinates,
numbers,
obasis=None,
grid=None,
wfn=None,
lf=None,
cache=None,
extra=None,
cell=None,
pseudo_numbers=None,
chk=None):
"""
**Arguments:**
coordinates
A (N, 3) float numpy array with Cartesian coordinates of the
atoms.
numbers
A (N,) int numpy vector with the atomic numbers.
**Optional arguments:**
obasis
A string or an instance of either the basis set or basis set
description classes, e.g. 'STO-3G', GOBasisDesc('STO-3G'), ...
for the orbitals.
grid
A grid object used for molecular integration.
wfn
A wavefunction object.
lf
A LinalgFactory instance. When not given, a DenseLinalgFactory
is used by default.
cache
A cache object with computed results that depend on other
attributes of the system class. Cached items should be tagged
according to the attributes they depend on:
- ``o``: obasis
- ``c``: coordinates
- ``g``: grid
When given as a dictionary, each value must consist of two
items: the object to be cached and the tags.
extra
A dictionary with additional information about the system. The
keys must be strings.
cell
A Cell object that describes the (generally triclinic) periodic
boundary conditions. So far, this is nearly nowhere supported in
Horton, so don't get too excited.
pseudo_numbers
The core charges of the pseudo potential, if applicable
chk
A filename for the checkpoint file or an open h5.File object.
If the file does not exist yet, it will be created. If the file
already exists, it must be an HDF5 file that is structured
such that it adheres to the format that Horton creates itself.
If chk is an open h5.File object, it will not be closed when the
System instance is deleted.
"""
# A) Assign all attributes
self._coordinates = np.array(coordinates, dtype=float, copy=False)
self._numbers = np.array(numbers, dtype=int, copy=False)
# some checks
if len(self._coordinates.shape
) != 2 or self._coordinates.shape[1] != 3:
raise TypeError(
'coordinates argument must be a 2D array with three columns')
if len(self._numbers.shape) != 1:
raise TypeError('numbers must a vector of integers.')
if self._numbers.shape[0] != self._coordinates.shape[0]:
raise TypeError(
'numbers and coordinates must have compatible array shapes.')
#
self._grid = grid
#
self._wfn = wfn
#
if cache is None:
self._cache = Cache()
elif isinstance(cache, Cache):
self._cache = cache
elif isinstance(cache, dict):
self._cache = Cache()
for key, (value, tags) in cache.iteritems():
self._cache.dump(key, value, tags=tags)
else:
raise TypeError('Could not interpret the cache argument.')
#
if lf is None:
self._lf = DenseLinalgFactory()
else:
self._lf = lf
#
if extra is None:
self._extra = {}
else:
self._extra = extra
#
self._obasis = None
self._obasis_desc = None
if obasis is not None:
self.update_obasis(obasis)
self._cell = cell
self._pseudo_numbers = pseudo_numbers
# The checkpoint file
self._chk = None
self._close_chk = False
self.assign_chk(chk)
self._log_init()
class System(object):
def __init__(self,
coordinates,
numbers,
obasis=None,
grid=None,
wfn=None,
lf=None,
cache=None,
extra=None,
cell=None,
pseudo_numbers=None,
chk=None):
"""
**Arguments:**
coordinates
A (N, 3) float numpy array with Cartesian coordinates of the
atoms.
numbers
A (N,) int numpy vector with the atomic numbers.
**Optional arguments:**
obasis
A string or an instance of either the basis set or basis set
description classes, e.g. 'STO-3G', GOBasisDesc('STO-3G'), ...
for the orbitals.
grid
A grid object used for molecular integration.
wfn
A wavefunction object.
lf
A LinalgFactory instance. When not given, a DenseLinalgFactory
is used by default.
cache
A cache object with computed results that depend on other
attributes of the system class. Cached items should be tagged
according to the attributes they depend on:
- ``o``: obasis
- ``c``: coordinates
- ``g``: grid
When given as a dictionary, each value must consist of two
items: the object to be cached and the tags.
extra
A dictionary with additional information about the system. The
keys must be strings.
cell
A Cell object that describes the (generally triclinic) periodic
boundary conditions. So far, this is nearly nowhere supported in
Horton, so don't get too excited.
pseudo_numbers
The core charges of the pseudo potential, if applicable
chk
A filename for the checkpoint file or an open h5.File object.
If the file does not exist yet, it will be created. If the file
already exists, it must be an HDF5 file that is structured
such that it adheres to the format that Horton creates itself.
If chk is an open h5.File object, it will not be closed when the
System instance is deleted.
"""
# A) Assign all attributes
self._coordinates = np.array(coordinates, dtype=float, copy=False)
self._numbers = np.array(numbers, dtype=int, copy=False)
# some checks
if len(self._coordinates.shape
) != 2 or self._coordinates.shape[1] != 3:
raise TypeError(
'coordinates argument must be a 2D array with three columns')
if len(self._numbers.shape) != 1:
raise TypeError('numbers must a vector of integers.')
if self._numbers.shape[0] != self._coordinates.shape[0]:
raise TypeError(
'numbers and coordinates must have compatible array shapes.')
#
self._grid = grid
#
self._wfn = wfn
#
if cache is None:
self._cache = Cache()
elif isinstance(cache, Cache):
self._cache = cache
elif isinstance(cache, dict):
self._cache = Cache()
for key, (value, tags) in cache.iteritems():
self._cache.dump(key, value, tags=tags)
else:
raise TypeError('Could not interpret the cache argument.')
#
if lf is None:
self._lf = DenseLinalgFactory()
else:
self._lf = lf
#
if extra is None:
self._extra = {}
else:
self._extra = extra
#
self._obasis = None
self._obasis_desc = None
if obasis is not None:
self.update_obasis(obasis)
self._cell = cell
self._pseudo_numbers = pseudo_numbers
# The checkpoint file
self._chk = None
self._close_chk = False
self.assign_chk(chk)
self._log_init()
def __del__(self):
# Close the HD5 checkpoint file. This must be done carefully to avoid
# spurious error messages when an unrelated exception occurs.
if hasattr(self, '_chk') and self.chk is not None and self._close_chk:
self.chk.close()
def _get_natom(self):
'''The number of atoms'''
return len(self.numbers)
natom = property(_get_natom)
def _get_coordinates(self):
'''The positions of the nuclei'''
return self._coordinates.view()
coordinates = property(_get_coordinates)
def _get_numbers(self):
'''An array with the atomic numbers'''
return self._numbers.view()
numbers = property(_get_numbers)
def _get_obasis(self):
'''The orbital basis'''
return self._obasis
obasis = property(_get_obasis)
def _get_obasis_desc(self):
'''The orbital basis description'''
return self._obasis_desc
obasis_desc = property(_get_obasis_desc)
def _get_grid(self):
'''The integration grid'''
return self._grid
grid = property(_get_grid)
def _get_wfn(self):
'''The wavefunction'''
return self._wfn
wfn = property(_get_wfn)
def _get_lf(self):
'''The LinalgFactory for this system'''
return self._lf
lf = property(_get_lf)
def _get_cache(self):
'''A cache of intermediate results that depend on the coordinates'''
return self._cache
cache = property(_get_cache)
def _get_extra(self):
'''A dictionary with extra properties of the system.'''
return self._extra
extra = property(_get_extra)
def _get_cell(self):
'''A Cell object describing the periodic boundary conditions.'''
return self._cell
cell = property(_get_cell)
def _get_pseudo_numbers(self):
result = self._pseudo_numbers
if result is None:
result = self._numbers
return result
pseudo_numbers = property(_get_pseudo_numbers)
def _get_chk(self):
'''A ``h5.File`` instance used as checkpoint file or ``None``'''
return self._chk
chk = property(_get_chk)
@classmethod
def from_file(cls, *args, **kwargs):
"""Create a System object from a file.
A list of filenames may be provided, which will be loaded in that
order. Each file complements or overrides the information loaded
from a previous file in the list. Furthermore, keyword arguments
may be used to specify additional constructor arguments.
The ``lf`` optional argument is picked up from the kwargs list to
contstruct (when needed) arrays to store the results loaded from
file. When ``lf`` is not given, a DenseLinalgFactory is created by
default.
The filenames may also contain checkpoint files and open h5.File
objects of checkpoint files. The last such checkpoint file will
automatically be used as a checkpoint file for this class. If you
want to override this behavior, provide the ``chk`` keyword argument
(may be None).
"""
constructor_args = {}
lf = kwargs.get('lf')
if lf is None:
lf = DenseLinalgFactory()
for fn in args:
fn_args = load_system_args(fn, lf)
constructor_args.update(fn_args)
constructor_args.update(kwargs)
# If the basis comes from an external code and some operators are
# loaded, rows and columns may need to be reordered. Similar for the
# orbital coefficients and the density matrices.
permutation = constructor_args.get('permutation')
if permutation is not None:
cache = constructor_args.get('cache')
if cache is not None:
for value, tags in cache.itervalues():
if isinstance(value, LinalgObject):
value.apply_basis_permutation(permutation)
wfn = constructor_args.get('wfn')
if wfn is not None:
wfn.apply_basis_permutation(permutation)
del constructor_args['permutation']
# After the permutation, correct for different sign conventions of the
# orbitals
signs = constructor_args.get('signs')
if signs is not None:
cache = constructor_args.get('cache')
if cache is not None:
for value, tags in cache.itervalues():
if isinstance(value, LinalgObject):
value.apply_basis_signs(signs)
wfn = constructor_args.get('wfn')
if wfn is not None:
wfn.apply_basis_signs(signs)
del constructor_args['signs']
return cls(**constructor_args)
def _log_init(self):
'''Write some basic information about the system to the screen logger.'''
if log.do_medium:
log('Initialized: %s' % self)
log.deflist([('Number of atoms', self.natom)] +
[('Number of %s' % periodic[n].symbol,
(self.numbers == n).sum())
for n in sorted(np.unique(self.numbers))] + [
('Linalg Factory', self._lf),
('Orbital basis', self._obasis),
('Wavefunction', self._wfn),
('Checkpoint file', self._chk),
])
if len(self._cache) > 0:
log('The following cached items are present: %s' %
(', '.join(self._cache.iterkeys())))
if len(self._extra) > 0:
log('The following extra attributes are present: %s' %
(', '.join(self._extra.iterkeys())))
log.blank()
def assign_chk(self, chk):
if self.chk is not None and self._close_chk:
self.chk.close()
if isinstance(chk, basestring):
# Suppose a filename is given. Create or open an HDF5 file.
self._chk = h5.File(chk)
self._close_chk = True
elif isinstance(chk, h5.Group) or chk is None:
self._chk = chk
self._close_chk = False
else:
raise TypeError(
'The chk argument, when not None, must be a filename or an open h5.Group object.'
)
self.update_chk()
def update_chk(self, field_name=None):
"""Write (a part of) the system to the checkpoint file.
**Optional Argument:**
field
A field string that specifies which part must be written to the
checkpoint file. When not given, all possible fields are
written. The latter is only useful in specific cases, e.g. upon
initialization of the system. The available field names are
specified in the attribute register dictionary in the
module ``horton.checkpoint``.
"""
if self._chk is not None:
from horton.checkpoint import attribute_register
if field_name is None:
for field_name, field in attribute_register.iteritems():
field.write(self._chk, self)
else:
field = attribute_register[field_name]
field.write(self._chk, self)
def to_file(self, filename):
'''Write the system to a file
**Arguments:**
filename
The name of the file to write to. The extension of the file
is used to determine the file format.
'''
dump_system(filename, self)
def _get_charge(self):
return self.pseudo_numbers.sum() - self.wfn.nel
charge = property(_get_charge)
def update_coordinates(self, coordinates=None):
'''Update all attributes that depend on coodinates and clear related parts of cache
**Optional arguments:**
coordinates
The new atomic coordinates
When one wants to set new coordintes, one may also edit the
system.coordinates array in-place and then call this method without
any arguments.
'''
if coordinates is not None:
self._coordinates[:] = coordinates
if self._obasis is not None:
self._obasis.centers[:] = self._coordinates
if self._grid is not None:
self._grid.update_centers(self)
self.cache.clear(tags='cog')
self._extra = {}
def update_grid(self, grid=None):
'''Define a new integration grid and clear related parts of the cache
**Optional arguments:**
grid
The new integration grid. When not given, it is assumed that
the grid was modified in-place and that only derived results in
the cache need to be pruned.
'''
if grid is not None:
self._grid = grid
self.cache.clear(tags='g')
def update_obasis(self, obasis=None):
'''Regenerate the orbital basis and clear all attributes that depend on it.
**Optional arguments:**
obasis
The new basis. This may be a string or an instance of GOBasis or
GOBasisDesc. When not given, the orbital basis description
stored in the system object (_obasis_desc attribute) will be
used.
'''
# Get the orbital basis and if possible the orbital basis description.
from horton.gbasis import GOBasisDesc, GOBasis
if isinstance(obasis, str):
obasis_desc = GOBasisDesc(obasis)
elif isinstance(obasis, GOBasisDesc):
obasis_desc = obasis
elif isinstance(obasis, GOBasis):
obasis_desc = None
elif obasis is None:
if self.obasis_desc is None:
raise TypeError(
'No orbital basis description (obasis_desc) available to update obasis.'
)
obasis_desc = self.obasis_desc
else:
raise TypeError('Could not interpret the obasis argument.')
if obasis_desc is not None:
obasis = obasis_desc.apply_to(self)
# Discard or reset results that depend on orbital basis
if self.obasis is not None:
self._cache.clear(tags='o')
# Ideally, the user of the system object does some sort of
# projection of the wavefunction on the new basis. This should be
# done outside the system class as their are too many different ways
# to handle this. Here, we set the wfn to None, just to force the
# user to do something.
self._wfn = None
self._extra = {}
# Assign new obasis
self._lf.set_default_nbasis(obasis.nbasis)
self._obasis = obasis
self._obasis_desc = obasis_desc
# Some consistency checks. These are needed when the initial value of
# obasis was None. This may occur when the system object is initialized.
if self._wfn is not None and self._obasis.nbasis != self._wfn.nbasis:
raise TypeError(
'The nbasis attribute of obasis and wfn are inconsistent.')
for key, value in self._cache.iteritems():
if isinstance(
value,
LinalgObject) and value.nbasis != self._obasis.nbasis:
raise TypeError(
'The nbasis attribute of the cached object \'%s\' and obasis are inconsistent.'
% key)
@timer.with_section('OLP integrals')
def get_overlap(self):
overlap, new = self.cache.load('olp',
alloc=self.lf.create_one_body,
tags='o')
if new:
self.obasis.compute_overlap(overlap)
self.update_chk('cache.olp')
return overlap
@timer.with_section('KIN integrals')
def get_kinetic(self):
kinetic, new = self.cache.load('kin',
alloc=self.lf.create_one_body,
tags='o')
if new:
self.obasis.compute_kinetic(kinetic)
self.update_chk('cache.kin')
return kinetic
@timer.with_section('NAI integrals')
def get_nuclear_attraction(self):
nuclear_attraction, new = self.cache.load(
'na', alloc=self.lf.create_one_body, tags='o')
if new:
# TODO: ghost atoms and extra charges
self.obasis.compute_nuclear_attraction(self.numbers.astype(float),
self.coordinates,
nuclear_attraction)
self.update_chk('cache.na')
return nuclear_attraction
@timer.with_section('ER integrals')
def get_electron_repulsion(self):
electron_repulsion, new = self.cache.load(
'er', alloc=self.lf.create_two_body, tags='o')
if new:
self.obasis.compute_electron_repulsion(electron_repulsion)
# ER integrals are not checkpointed by default because they are too heavy.
# Can be done manually by user if needed: ``system.update_chk('cache.er')``
#self.update_chk('cache.er')
return electron_repulsion
@timer.with_section('Orbitals grid')
def compute_grid_orbitals(self,
points,
iorbs=None,
orbs=None,
select='alpha'):
'''Compute the electron density on a grid using self.wfn as input
**Arguments:**
points
A Numpy array with grid points, shape (npoint,3)
**Optional arguments:**
iorbs
The indexes of the orbitals to be computed. If not given, the
orbitals with a non-zero occupation number are computed
orbs
An output array, shape (npoint, len(iorbs)). The results are
added to this array.
select
'alpha', 'beta'
**Returns:**
orbs
The array with the result. This is the same as the output
argument, in case it was provided.
'''
exp = self.wfn.get_exp(select)
if iorbs is None:
iorbs = (exp.occupations > 0).nonzero()[0]
shape = (len(points), len(iorbs))
if orbs is None:
orbs = np.zeros(shape, float)
elif orbs.shape != shape:
raise TypeError('The shape of the output array is wrong')
self.obasis.compute_grid_orbitals_exp(exp, points, iorbs, orbs)
return orbs
@timer.with_section('Density grid')
def compute_grid_density(self,
points,
rhos=None,
select='full',
epsilon=0):
'''Compute the electron density on a grid using self.wfn as input
**Arguments:**
points
A Numpy array with grid points, shape (npoint,3)
**Optional arguments:**
rhos
An output array, shape (npoint,). The results are added to this
array.
select
'alpha', 'beta', 'full' or 'spin'. ('full' is the default.)
epsilon
Allow errors on the density of this magnitude for the sake of
efficiency.
**Returns:**
rhos
The array with the result. This is the same as the output
argument, in case it was provided.
'''
if rhos is None:
rhos = np.zeros(len(points), float)
elif rhos.shape != (points.shape[0], ):
raise TypeError('The shape of the output array is wrong')
dm = self.wfn.get_dm(select)
self.obasis.compute_grid_density_dm(dm, points, rhos, epsilon)
return rhos
@timer.with_section('Gradient grid')
def compute_grid_gradient(self, points, gradrhos=None, select='full'):
'''Compute the electron density on a grid using self.wfn as input
**Arguments:**
points
A Numpy array with grid points, shape (npoint,3)
**Optional arguments:**
gradrhos
An output array, shape (npoint, 3). The results are added to
this array.
select
'alpha', 'beta', 'full' or 'spin'. ('full' is the default.)
**Returns:**
gradrhos
The array with the result. This is the same as the output
argument, in case it was provided.
'''
if gradrhos is None:
gradrhos = np.zeros((len(points), 3), float)
elif gradrhos.shape != (points.shape[0], 3):
raise TypeError('The shape of the output array is wrong')
dm = self.wfn.get_dm(select)
self.obasis.compute_grid_gradient_dm(dm, points, gradrhos)
return gradrhos
@timer.with_section('Hartree grid')
def compute_grid_hartree(self, points, hartree=None, select='full'):
'''Compute the hartree potential on a grid using self.wfn as input
**Arguments:**
points
A Numpy array with grid points, shape (npoint,3)
**Optional arguments:**
hartree
An output array, shape (npoint,). The results are added to this
array.
select
'alpha', 'beta', 'full' or 'spin'. ('full' is the default.)
**Returns:**
hartree
The array with the result. This is the same as the output
argument, in case it was provided.
'''
if hartree is None:
hartree = np.zeros(len(points), float)
elif hartree.shape != (points.shape[0], ):
raise TypeError('The shape of the output array is wrong')
dm = self.wfn.get_dm(select)
self.obasis.compute_grid_hartree_dm(dm, points, hartree)
return hartree
@timer.with_section('ESP grid')
def compute_grid_esp(self, points, esp=None, select='full'):
'''Compute the esp on a grid using self.wfn as input
**Arguments:**
points
A Numpy array with grid points, shape (npoint,3)
**Optional arguments:**
esp
An output array, shape (npoint,). The results are added to this
array.
select
'alpha', 'beta', 'full' or 'spin'. ('full' is the default.)
**Returns:**
esp
The array with the result. This is the same as the output
argument, in case it was provided.
'''
if esp is None:
esp = np.zeros(len(points), float)
elif esp.shape != (points.shape[0], ):
raise TypeError('The shape of the output array is wrong')
dm = self.wfn.get_dm(select)
self.obasis.compute_grid_hartree_dm(dm, points, esp)
esp *= -1
compute_grid_nucpot(self.numbers, self.coordinates, points, esp)
return esp
@timer.with_section('Fock grid dens')
def compute_grid_density_fock(self, points, weights, pots, fock):
'''See documentation self.obasis.compute_grid_density_fock'''
self.obasis.compute_grid_density_fock(points, weights, pots, fock)
@timer.with_section('Fock grid grad')
def compute_grid_gradient_fock(self, points, weights, pots, fock):
'''See documentation self.obasis.compute_grid_gradient_fock'''
self.obasis.compute_grid_gradient_fock(points, weights, pots, fock)
def compute_nucnuc(self):
'''Compute interaction energy of the nuclei'''
# TODO: move this to low-level code one day.
result = 0.0
for i in xrange(self.natom):
for j in xrange(i):
distance = np.linalg.norm(self.coordinates[i] -
self.coordinates[j])
result += self.numbers[i] * self.numbers[j] / distance
self._extra['energy_nn'] = result
return result
def project_orbitals_mgs_low(obasis0, obasis1, exp0, exp1, eps=1e-10):
'''Project the orbitals in ``exp0`` (wrt ``obasis0``) on ``obasis1`` and store in ``exp1`` with the modified Gram-Schmidt algorithm.
**Arguments:**
obasis0
The orbital basis for the original wavefunction expansion.
obasis1
The new orbital basis for the projected wavefunction expansion.
exp0
The expansion of the original orbitals.
exp1 (output)
An output argument in which the projected orbitals will be stored.
**Optional arguments:**
eps
A threshold for the renormalization in the Gram-Schmidt procedure
The projection is based on the Modified Gram-Schmidt (MGS) process. In
each iteration of the MGS, a renormalization is carried out. If the norm
in this step is smaller than ``eps``, an error is raised.
Note that ``exp1`` will be incomplete in several ways. The orbital
energies are not copied. Only the occupied orbitals in ``exp0`` are
projected. Coefficients of higher orbitals are set to zero. The orbital
occupations are simply copied. This should be sufficient to construct
an initial guess in a new orbital basis set based on a previous solution.
If the number of orbitals in ``exp1`` is too small to store all projected
orbitals, an error is raised.
'''
# Compute the overlap matrix of the combined orbital basis
obasis_both = GOBasis.concatenate(obasis0, obasis1)
lf = DenseLinalgFactory(obasis_both.nbasis)
olp_both = lf.create_one_body()
obasis_both.compute_overlap(olp_both)
# Select the blocks of interest from the big overlap matrix
olp_21 = olp_both._array[obasis0.nbasis:, :obasis0.nbasis]
olp_22 = olp_both._array[obasis0.nbasis:, obasis0.nbasis:]
# construct the projector
projector = np.dot(np.linalg.pinv(olp_22), olp_21)
# project occupied orbitals
i1 = 0
for i0 in xrange(exp0.nfn):
if exp0.occupations[i0] == 0.0:
continue
if i1 > exp1.nfn:
raise ProjectionError('Not enough functions available in exp1 to store the projected orbitals.')
exp1.coeffs[:,i1] = np.dot(projector, exp0.coeffs[:,i0])
exp1.occupations[i1] = exp0.occupations[i0]
i1 += 1
# clear all parts of exp1 that were not touched by the projection loop
ntrans = i1
del i1
exp1.coeffs[:,ntrans:] = 0.0
exp1.occupations[ntrans:] = 0.0
exp1.energies[:] = 0.0
# auxiliary function for the MGS algo
def dot22(a, b):
return np.dot(np.dot(a, olp_22), b)
# Apply the MGS algorithm to orthogonalize the orbitals
for i1 in xrange(ntrans):
orb = exp1.coeffs[:,i1]
# Subtract overlap with previous orbitals
for j1 in xrange(i1):
other = exp1.coeffs[:,j1]
orb -= other*dot22(other, orb)/np.sqrt(dot22(orb, orb))
# Renormalize
norm = np.sqrt(dot22(orb, orb))
if norm < eps:
raise ProjectionError('The norm of a vector in the MGS algorithm becomes too small. Orbitals are redundant in new basis.')
orb /= norm
def project_orbitals_mgs_low(obasis0, obasis1, exp0, exp1, eps=1e-10):
'''Project the orbitals in ``exp0`` (wrt ``obasis0``) on ``obasis1`` and store in ``exp1`` with the modified Gram-Schmidt algorithm.
**Arguments:**
obasis0
The orbital basis for the original wavefunction expansion.
obasis1
The new orbital basis for the projected wavefunction expansion.
exp0
The expansion of the original orbitals.
exp1 (output)
An output argument in which the projected orbitals will be stored.
**Optional arguments:**
eps
A threshold for the renormalization in the Gram-Schmidt procedure
The projection is based on the Modified Gram-Schmidt (MGS) process. In
each iteration of the MGS, a renormalization is carried out. If the norm
in this step is smaller than ``eps``, an error is raised.
Note that ``exp1`` will be incomplete in several ways. The orbital
energies are not copied. Only the occupied orbitals in ``exp0`` are
projected. Coefficients of higher orbitals are set to zero. The orbital
occupations are simply copied. This should be sufficient to construct
an initial guess in a new orbital basis set based on a previous solution.
If the number of orbitals in ``exp1`` is too small to store all projected
orbitals, an error is raised.
'''
# Compute the overlap matrix of the combined orbital basis
obasis_both = GOBasis.concatenate(obasis0, obasis1)
lf = DenseLinalgFactory(obasis_both.nbasis)
olp_both = lf.create_one_body()
obasis_both.compute_overlap(olp_both)
# Select the blocks of interest from the big overlap matrix
olp_21 = olp_both._array[obasis0.nbasis:, :obasis0.nbasis]
olp_22 = olp_both._array[obasis0.nbasis:, obasis0.nbasis:]
# construct the projector
projector = np.dot(np.linalg.pinv(olp_22), olp_21)
# project occupied orbitals
i1 = 0
for i0 in xrange(exp0.nfn):
if exp0.occupations[i0] == 0.0:
continue
if i1 > exp1.nfn:
raise ProjectionError(
'Not enough functions available in exp1 to store the projected orbitals.'
)
exp1.coeffs[:, i1] = np.dot(projector, exp0.coeffs[:, i0])
exp1.occupations[i1] = exp0.occupations[i0]
i1 += 1
# clear all parts of exp1 that were not touched by the projection loop
ntrans = i1
del i1
exp1.coeffs[:, ntrans:] = 0.0
exp1.occupations[ntrans:] = 0.0
exp1.energies[:] = 0.0
# auxiliary function for the MGS algo
def dot22(a, b):
return np.dot(np.dot(a, olp_22), b)
# Apply the MGS algorithm to orthogonalize the orbitals
for i1 in xrange(ntrans):
orb = exp1.coeffs[:, i1]
# Subtract overlap with previous orbitals
for j1 in xrange(i1):
other = exp1.coeffs[:, j1]
orb -= other * dot22(other, orb) / np.sqrt(dot22(orb, orb))
# Renormalize
norm = np.sqrt(dot22(orb, orb))
if norm < eps:
raise ProjectionError(
'The norm of a vector in the MGS algorithm becomes too small. Orbitals are redundant in new basis.'
)
orb /= norm
def from_file(cls, *filenames, **kwargs):
'''Load data from a file.
**Arguments:**
filename1, filename2, ...
The files to load data from. When multiple files are given, data
from the first file is overwritten by data from the second, etc.
When one file contains sign and permutation changes for the
orbital basis, these changes will be applied to data from all
other files.
**Optional arguments:**
lf
A LinalgFactory instance. DenseLinalgFactory is used as default.
This routine uses the extension or prefix of the filename to
determine the file format. It returns a dictionary with data loaded
from the file.
For each file format, a specialized function is called that returns a
dictionary with data from the file.
'''
result = {}
lf = kwargs.pop('lf', None)
if lf is None:
lf = DenseLinalgFactory()
if len(kwargs) > 0:
raise TypeError('Keyword argument(s) not supported: %s' %
kwargs.keys())
for filename in filenames:
if isinstance(filename, h5.Group) or filename.endswith('.h5'):
from horton.io.internal import load_h5
result.update(load_h5(filename))
elif filename.endswith('.xyz'):
from horton.io.xyz import load_xyz
result.update(load_xyz(filename))
elif filename.endswith('.fchk'):
from horton.io.gaussian import load_fchk
result.update(load_fchk(filename, lf))
elif filename.endswith('.log'):
from horton.io.gaussian import load_operators_g09
result.update(load_operators_g09(filename, lf))
elif filename.endswith('.mkl'):
from horton.io.molekel import load_mkl
result.update(load_mkl(filename, lf))
elif filename.endswith('.molden.input') or filename.endswith(
'.molden'):
from horton.io.molden import load_molden
result.update(load_molden(filename, lf))
elif filename.endswith('.cube'):
from horton.io.cube import load_cube
result.update(load_cube(filename))
elif filename.endswith('.wfn'):
from horton.io.wfn import load_wfn
result.update(load_wfn(filename, lf))
elif os.path.basename(filename).startswith('POSCAR'):
from horton.io.vasp import load_poscar
result.update(load_poscar(filename))
elif os.path.basename(filename)[:6] in ['CHGCAR', 'AECCAR']:
from horton.io.vasp import load_chgcar
result.update(load_chgcar(filename))
elif os.path.basename(filename).startswith('LOCPOT'):
from horton.io.vasp import load_locpot
result.update(load_locpot(filename))
elif filename.endswith('.cp2k.out'):
from horton.io.cp2k import load_atom_cp2k
result.update(load_atom_cp2k(filename, lf))
elif filename.endswith('.cif'):
from horton.io.cif import load_cif
result.update(load_cif(filename, lf))
elif 'FCIDUMP' in os.path.basename(filename):
from horton.io.molpro import load_fcidump
result.update(load_fcidump(filename, lf))
else:
raise ValueError('Unknown file format for reading: %s' %
filename)
# Apply changes in orbital order and sign conventions
if 'permutation' in result:
for key, value in result.iteritems():
if isinstance(value, LinalgObject):
value.permute_basis(result['permutation'])
del result['permutation']
if 'signs' in result:
for key, value in result.iteritems():
if isinstance(value, LinalgObject):
value.change_basis_signs(result['signs'])
del result['signs']
return cls(**result)
