#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, version 3.
#
# Psi4 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License along
# with Psi4; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
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# @END LICENSE
#
import sys
import numpy as np
from psi4 import core
from .exceptions import *
### Matrix and Vector properties
# The next three functions make me angry
def translate_interface(interface):
"""
This is extra stupid with unicode
"""
if sys.version_info[0] > 2:
return interface
nouni_interface = {}
for k, v in interface.items():
if k == 'typestr':
nouni_interface[k.encode('ascii', 'ignore')] = v.encode('ascii', 'ignore')
else:
nouni_interface[k.encode('ascii', 'ignore')] = v
return nouni_interface
class numpy_holder(object):
"""
Blank object, stupid. Apparently you cannot create a view directly from a dictionary
"""
def __init__(self, interface):
self.__array_interface__ = translate_interface(interface)
def _get_raw_views(self, copy=False):
"""
Gets simple raw view of the passed in object.
"""
ret = []
for data in self.array_interface():
# Yet another hack
if isinstance(data["shape"], list):
data["shape"] = tuple(data["shape"])
if 0 in data["shape"]:
ret.append(np.empty(shape=data["shape"]))
else:
ret.append(np.array(numpy_holder(data), copy=copy))
return ret
def _find_dim(arr, ndim):
"""
Helper function to help deal with zero or sized arrays
"""
# Zero arrays
if (arr is None) or (arr is False):
return [0] * ndim
# Make sure this is a numpy array like thing
try:
arr.shape
except:
raise ValidationError("Expected numpy array, found object of type '%s'", type(arr))
if len(arr.shape) == ndim:
return [arr.shape[x] for x in range(ndim)]
else:
raise ValidationError("Input array does not have a valid shape.")
[docs]def array_to_matrix(self, arr, name="New Matrix", dim1=None, dim2=None):
"""
Converts a numpy array or list of numpy arrays into a Psi4 Matrix (irreped if list).
Parameters
----------
arr : array or list of arrays
Numpy array or list of arrays to use as the data for a new core.Matrix
name : str
Name to give the new core.Matrix
dim1 : list, tuple, or core.Dimension (optional)
If a single dense numpy array is given, a dimension can be supplied to
apply irreps to this array. Note that this discards all extra information
given in the matrix besides the diagonal blocks determined by the passed
dimension.
dim2 :
Same as dim1 only if using a Psi4.Dimension object.
Returns
-------
matrix : :py:class:`~psi4.core.Matrix` or :py:class:`~psi4.core.Vector`
Returns the given Psi4 object
Notes
-----
This is a generalized function to convert a NumPy array to a Psi4 object
Examples
--------
>>> data = np.random.rand(20)
>>> vector = array_to_matrix(data)
>>> irrep_data = [np.random.rand(2, 2), np.empty(shape=(0,3)), np.random.rand(4, 4)]
>>> matrix = array_to_matrix(irrep_data)
>>> print matrix.rowspi().to_tuple()
(2, 0, 4)
"""
# What type is it? MRO can help.
arr_type = self.__mro__[0]
# Irreped case
if isinstance(arr, (list, tuple)):
if (dim1 is not None) or (dim2 is not None):
raise ValidationError("Array_to_Matrix: If passed input is list of arrays dimension cannot be specified.")
irreps = len(arr)
if arr_type == core.Matrix:
sdim1 = core.Dimension(irreps)
sdim2 = core.Dimension(irreps)
for i in range(irreps):
d1, d2 = _find_dim(arr[i], 2)
sdim1[i] = d1
sdim2[i] = d2
ret = self(name, sdim1, sdim2)
elif arr_type == core.Vector:
sdim1 = core.Dimension(irreps)
for i in range(irreps):
d1 = _find_dim(arr[i], 1)
sdim1[i] = d1[0]
ret = self(name, sdim1)
else:
raise ValidationError("Array_to_Matrix: type '%s' is not recognized." % str(arr_type))
for view, vals in zip(ret.nph, arr):
if 0 in view.shape: continue
view[:] = vals
return ret
# No irreps implied by list
else:
if arr_type == core.Matrix:
# Build an irreped array back out
if dim1 is not None:
if dim2 is None:
raise ValidationError ("Array_to_Matrix: If dim1 is supplied must supply dim2 also")
dim1 = core.Dimension.from_list(dim1)
dim2 = core.Dimension.from_list(dim2)
if dim1.n() != dim2.n():
raise ValidationError("Array_to_Matrix: Length of passed dim1 must equal length of dim2.")
ret = self(name, dim1, dim2)
start1 = 0
start2 = 0
for num, interface in enumerate(ret.nph):
d1 = dim1[num]
d2 = dim2[num]
if (d1 == 0) or (d2 == 0):
continue
view = np.asarray(interface)
view[:] = arr[start1:start1 + d1, start2:start2 + d2]
start1 += d1
start2 += d2
return ret
# Simple case without irreps
else:
ret = self(name, arr.shape[0], arr.shape[1])
view = _get_raw_views(ret)[0]
view[:] = arr
return ret
elif arr_type == core.Vector:
# Build an irreped array back out
if dim1 is not None:
if dim2 is not None:
raise ValidationError ("Array_to_Matrix: If dim2 should not be supplied for 1D vectors.")
dim1 = core.Dimension.from_list(dim1)
ret = self(name, dim1)
start1 = 0
for num, interface in enumerate(ret.nph):
d1 = dim1[num]
if (d1 == 0):
continue
view = np.asarray(interface)
view[:] = arr[start1:start1 + d1]
start1 += d1
return ret
# Simple case without irreps
else:
ret = self(name, arr.shape[0])
ret.np[:] = arr
return ret
else:
raise ValidationError("Array_to_Matrix: type '%s' is not recognized." % str(arr_type))
[docs]def _to_array(matrix, copy=True, dense=False):
"""
Converts a Psi4 Matrix or Vector to a numpy array. Either copies the data or simply
consturcts a view.
Parameters
----------
matrix : :py:class:`~psi4.core.Matrix` or :py:class:`~psi4.core.Vector`
Pointers to which Psi4 core class should be used in the construction.
copy : bool
Copy the data if True, return a view otherwise
dense : bool
Converts irreped Psi4 objects to diagonally blocked dense arrays. Returns a list of arrays otherwise.
Returns
-------
array : np.array or list of of np.array
Returns either a list of np.array's or the base array depending on options.
Notes
-----
This is a generalized function to convert a Psi4 object to a NumPy array
Examples
--------
>>> data = psi4.Matrix(3, 3)
>>> data._to_array()
[[ 0. 0. 0.]
[ 0. 0. 0.]
[ 0. 0. 0.]]
"""
if matrix.nirrep() > 1:
# We will copy when we make a large matrix
if dense:
copy = False
ret = _get_raw_views(matrix, copy=copy)
# Return the list of arrays
if dense is False:
return ret
# Build the dense matrix
if isinstance(matrix, core.Vector):
ret_type = '1D'
elif isinstance(matrix, core.Matrix):
ret_type = '2D'
else:
raise ValidationError("Array_to_Matrix: type '%s' is not recognized." % type(matrix))
dim1 = []
dim2 = []
for h in ret:
# Ignore zero dim irreps
if 0 in h.shape:
dim1.append(0)
dim2.append(0)
else:
dim1.append(h.shape[0])
if ret_type == '2D':
dim2.append(h.shape[1])
ndim1 = np.sum(dim1)
ndim2 = np.sum(dim2)
if ret_type == '1D':
dense_ret = np.zeros(shape=(ndim1))
start = 0
for d1, arr in zip(dim1, ret):
if d1 == 0: continue
dense_ret[start: start + d1] = arr
start += d1
else:
dense_ret = np.zeros(shape=(ndim1, ndim2))
start1 = 0
start2 = 0
for d1, d2, arr in zip(dim1, dim2, ret):
if d1 == 0: continue
dense_ret[start1: start1 + d1, start2: start2 + d2] = arr
start1 += d1
start2 += d2
return dense_ret
else:
return _get_raw_views(matrix, copy=copy)[0]
def _build_view(matrix):
"""
Builds a view of the vector or matrix
"""
views = _to_array(matrix, copy=False, dense=False)
if matrix.nirrep() > 1:
return tuple(views)
else:
return views
def get_view(self):
if hasattr(self, '_np_view_data'):
return self._np_view_data
else:
self._np_view_data = _build_view(self)
return self._np_view_data
@property
def _np_shape(self):
"""
Shape of the Psi4 data object
"""
view_data = get_view(self)
if self.nirrep() > 1:
return tuple(view_data[x].shape for x in range(self.nirrep()))
else:
return view_data.shape
@property
def _np_view(self):
"""
View without only one irrep
"""
if self.nirrep() > 1:
raise ValidationError("Attempted to call .np on a Psi4 data object with multiple irreps. Please use .nph for objects with irreps.")
return get_view(self)
@property
def _nph_view(self):
"""
View with irreps.
"""
if self.nirrep() > 1:
return get_view(self)
else:
return get_view(self),
@property
def _array_conversion(self):
if self.nirrep() > 1:
raise ValidationError("__array__interface__ can only be called on Psi4 data object with only one irrep!")
else:
return self.np.__array_interface__
def _np_write(self, filename=None, prefix=""):
ret = {}
ret[prefix + "Irreps"] = self.nirrep()
ret[prefix + "Name"] = self.name
for h, v in enumerate(self.nph):
ret[prefix + "IrrepData" + str(h)] = v
if isinstance(self, core.Matrix):
ret[prefix + "Dim1"] = self.rowdim().to_tuple()
ret[prefix + "Dim2"] = self.coldim().to_tuple()
if isinstance(self, core.Vector):
ret[prefix + "Dim"] = [self.dim(x) for x in range(self.nirrep())]
if filename is None:
return ret
np.savez(filename, **ret)
def _np_read(self, filename, prefix=""):
if isinstance(filename, np.lib.npyio.NpzFile):
data = filename
elif (sys.version_info[0] == 2) and isinstance(filename, (str, unicode)):
if not filename.endswith('.npz'):
filename = filename + '.npz'
data = np.load(filename)
elif (sys.version_info[0] > 2) and isinstance(filename, str):
if not filename.endswith('.npz'):
filename = filename + '.npz'
data = np.load(filename)
else:
raise Exception("Filename not understood: %s" % filename)
ret_data = []
if ((prefix + "Irreps") not in data.keys()) or ((prefix + "Name") not in data.keys()):
raise ValidationError("File %s does not appear to be a numpyz save" % filename)
for h in range(data[prefix + "Irreps"]):
ret_data.append(data[prefix + "IrrepData" + str(h)])
arr_type = self.__mro__[0]
if arr_type == core.Matrix:
dim1 = core.Dimension.from_list(data[prefix + "Dim1"])
dim2 = core.Dimension.from_list(data[prefix + "Dim2"])
ret = self(str(data[prefix + "Name"]), dim1, dim2)
elif arr_type == core.Vector:
dim1 = core.Dimension.from_list(data[prefix + "Dim"])
ret = self(str(data[prefix + "Name"]), dim1)
for h in range(data[prefix + "Irreps"]):
ret.nph[h][:] = ret_data[h]
return ret
def _to_serial(data):
"""
Converts an object with a .nph accessor to a serialized dictionary
"""
json_data = {}
json_data["shape"] = []
json_data["data"] = []
for view in data.nph:
json_data["shape"].append(view.shape)
json_data["data"].append(view.tostring())
if len(json_data["shape"][0]) == 1:
json_data["type"] = "vector"
elif len(json_data["shape"][0]) == 2:
json_data["type"] = "matrix"
else:
raise ValidationError("_to_json is only used for vector and matrix objects.")
return json_data
def _from_serial(self, json_data):
"""
Converts serialized data to the correct Psi4 data type
"""
if json_data["type"] == "vector":
dim1 = core.Dimension.from_list([x[0] for x in json_data["shape"]])
ret = self("Vector from JSON", dim1)
elif json_data["type"] == "matrix":
dim1 = core.Dimension.from_list([x[0] for x in json_data["shape"]])
dim2 = core.Dimension.from_list([x[1] for x in json_data["shape"]])
ret = self("Matrix from JSON", dim1, dim2)
else:
raise ValidationError("_from_json did not recognize type option of %s." % str(json_data["type"]))
for n in range(len(ret.nph)):
ret.nph[n].flat[:] = np.fromstring(json_data["data"][n], dtype=np.double)
return ret
# Matrix attributes
core.Matrix.from_array = classmethod(array_to_matrix)
core.Matrix.to_array = _to_array
core.Matrix.shape = _np_shape
core.Matrix.np = _np_view
core.Matrix.nph = _nph_view
core.Matrix.__array_interface__ = _array_conversion
core.Matrix.np_write = _np_write
core.Matrix.np_read = classmethod(_np_read)
core.Matrix.to_serial = _to_serial
core.Matrix.from_serial = classmethod(_from_serial)
# Vector attributes
core.Vector.from_array = classmethod(array_to_matrix)
core.Vector.to_array = _to_array
core.Vector.shape = _np_shape
core.Vector.np = _np_view
core.Vector.nph = _nph_view
core.Vector.__array_interface__ = _array_conversion
core.Vector.np_write = _np_write
core.Vector.np_read = classmethod(_np_read)
core.Vector.to_serial = _to_serial
core.Vector.from_serial = classmethod(_from_serial)
### CIVector properties
@property
def _civec_view(self):
"Returns a view of the CIVector's buffer"
return np.asarray(self)
core.CIVector.np = _civec_view
### Dimension properties
@classmethod
def _dimension_from_list(self, dims, name="New Dimension"):
"""
Builds a core.Dimension object from a python list or tuple. If a dimension
object is passed a copy will be returned.
"""
if isinstance(dims, (tuple, list, np.ndarray)):
irreps = len(dims)
elif isinstance(dims, core.Dimension):
irreps = dims.n()
else:
raise ValidationError("Dimension from list: Type '%s' not understood" % type(dims))
ret = core.Dimension(irreps, name)
for i in range(irreps):
ret[i] = dims[i]
return ret
def _dimension_to_tuple(dim):
"""
Converts a core.Dimension object to a tuple.
"""
if isinstance(dim, (tuple, list)):
return tuple(dim)
irreps = dim.n()
ret = []
for i in range(irreps):
ret.append(dim[i])
return tuple(ret)
def _dimension_iter(dim):
"""
Provides an iterator class for the Dimension object.
Allows:
dim = psi4.core.Dimension(...)
list(dim)
"""
for i in range(dim.n()):
yield dim[i]
# Dimension attributes
core.Dimension.from_list = _dimension_from_list
core.Dimension.to_tuple = _dimension_to_tuple
core.Dimension.__iter__ = _dimension_iter
