Source code for psi4.driver.p4util.numpy_helper

# Psi4: an open-source quantum chemistry software package
# Copyright (c) 2007-2019 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
# GNU Lesser General Public License for more details.
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# with Psi4; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.

import sys

import numpy as np

from psi4 import core
from .exceptions import ValidationError

### Matrix and Vector properties

def _get_raw_views(self, copy=False):
    Gets simple raw view of the passed in object.
    if copy:
        return tuple([np.array(x) for x in self.array_interface()])
        return tuple(self.array_interface())

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
    if not hasattr(arr, 'shape'):
        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)]
        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.core.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])[:] = 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])[:] = 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 constructs 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, optional Copy the data if `True`, return a view otherwise dense : bool, optional Converts irreped Psi4 objects to diagonally blocked dense arrays if `True`. Returns a list of arrays otherwise. Returns ------- array : ndarray or list of ndarray 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 matrix_views = _get_raw_views(matrix, copy=copy) # Return the list of arrays if dense is False: return matrix_views # 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 matrix_views: # 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, matrix_views): 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, matrix_views): if (d1 == 0) or (d2 == 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]
@property def _np_shape(self): """ Shape of the Psi4 data object """ view_data = _get_raw_views(self) if self.nirrep() > 1: return tuple(view_data[x].shape for x in range(self.nirrep())) else: return view_data[0].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_raw_views(self)[0] @property def _nph_view(self): """ View with irreps. """ return _get_raw_views(self) @property def _array_conversion(self): """ Provides the array interface to simply classes so that np.array(core.Matrix(5, 5)) works flawlessly. """ if self.nirrep() > 1: raise ValidationError("__array__interface__ can only be called on Psi4 data object with only one irrep!") else: return def _np_write(self, filename=None, prefix=""): """ Writes the irreped matrix to a NumPy zipped file. Can return the packed data for saving many matrices into the same file. """ ret = {} ret[prefix + "Irreps"] = self.nirrep() ret[prefix + "Name"] = for h, v in enumerate(self.nph): # If returning arrays to user, we want to return copies (snapshot), not # views of the core.Matrix's memory. if filename is None and not v.flags['OWNDATA']: v = np.copy(v) 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=""): """ Reads the data from a NumPy compress file. """ if isinstance(filename, np.lib.npyio.NpzFile): data = filename elif 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.frombuffer(json_data["data"][n], dtype=np.double) return ret def _chain_dot(*args, **kwargs): """ Chains dot products together from a series of Psi4 Matrix classes. By default there is no transposes, an optional vector of booleans can be passed in. """ trans = kwargs.pop("trans", None) if trans is None: trans = [False for x in range(len(args))] else: if len(trans) != len(args): raise ValidationError( "Chain dot: The length of the transpose arguements is not equal to the length of args.") # Setup chain ret = args[0] if trans[0]: ret = ret.transpose() # Run through for n, mat in enumerate(args[1:]): ret = core.doublet(ret, mat, False, trans[n + 1]) return ret def _irrep_access(self, *args, **kwargs): """ Warns user when iterating/accessing an irreped object. """ raise ValidationError("Attempted to access by index/iteration a Psi4 data object that supports multiple" "irreps. Please use .np or .nph explicitly.") # Matrix attributes core.Matrix.from_array = classmethod(array_to_matrix) core.Matrix.from_list = classmethod(lambda self, x: array_to_matrix(self, np.array(x))) core.Matrix.to_array = _to_array core.Matrix.shape = _np_shape = _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) core.Matrix.chain_dot = _chain_dot core.Matrix.__iter__ = _irrep_access core.Matrix.__getitem__ = _irrep_access # Vector attributes core.Vector.from_array = classmethod(array_to_matrix) core.Vector.from_list = classmethod(lambda self, x: array_to_matrix(self, np.array(x))) core.Vector.to_array = _to_array core.Vector.shape = _np_shape = _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) core.Vector.__iter__ = _irrep_access core.Vector.__getitem__ = _irrep_access ### CIVector properties @property def _civec_view(self): """ Returns a view of the CIVector's buffer """ return np.asarray(self) = _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 # General functions for NumPy array manipulation def block_diagonal_array(*args): """ Convert square NumPy array to a single block diagonal array. Mimic of SciPy's block_diag. """ # Validate the input matrices. dim = 0 for matrix in args: try: shape = matrix.shape dim += shape[0] except (AttributeError, TypeError): raise ValidationError("Cannot construct block diagonal from non-arrays.") if len(shape) != 2: raise ValidationError("Cannot construct block diagonal from non-2D arrays.") if shape[0] != shape[1]: raise ValidationError("Cannot construct block diagonal from non-square arrays.") # If this is too slow, try a sparse matrix? block_diag = np.zeros((dim, dim)) start = 0 for matrix in args: next_block = slice(start, start + matrix.shape[0]) block_diag[next_block, next_block] = matrix start += matrix.shape[0] return block_diag