Refactor FCIDump integration into qiskit_nature.second_q.formats (#799)

* Refactor FCIDump integration into qiskit_nature.second_q.formats * Update qiskit_nature/second_q/formats/fcidump/fcidump.py Co-authored-by: Max Rossmannek <[email protected]> * update translator * Update qiskit_nature/second_q/formats/fcidump/fcidump.py Co-authored-by: Max Rossmannek <[email protected]> * Update qiskit_nature/second_q/formats/fcidump/fcidump.py Co-authored-by: Max Rossmannek <[email protected]> * Update qiskit_nature/second_q/formats/fcidump/fcidump.py Co-authored-by: Max Rossmannek <[email protected]> * Update qiskit_nature/second_q/formats/fcidump/fcidump.py Co-authored-by: Max Rossmannek <[email protected]> * Update qiskit_nature/second_q/formats/fcidump/fcidump.py Co-authored-by: Max Rossmannek <[email protected]> * Update test/second_q/formats/fcidump/test_fcidump.py Co-authored-by: Max Rossmannek <[email protected]> * Update test/second_q/formats/fcidump/test_fcidump.py Co-authored-by: Max Rossmannek <[email protected]> * Update test/second_q/formats/fcidump/test_methods_fcidump.py Co-authored-by: Max Rossmannek <[email protected]> * Update test/second_q/formats/fcidump/test_methods_fcidump.py Co-authored-by: Max Rossmannek <[email protected]> * enable unit test * Apply suggestions from code review * fix energy name * Update qiskit_nature/second_q/formats/fcidump/fcidump.py Co-authored-by: Max Rossmannek <[email protected]> * Update qiskit_nature/second_q/formats/fcidump/fcidump.py Co-authored-by: Max Rossmannek <[email protected]> * Update qiskit_nature/second_q/formats/fcidump/fcidump.py Co-authored-by: Max Rossmannek <[email protected]> * Update qiskit_nature/second_q/formats/fcidump/fcidump.py Co-authored-by: Max Rossmannek <[email protected]> * change _parse to return FCIDump Co-authored-by: Max Rossmannek <[email protected]>
qiskit-community · Sep 14, 2022 · aaa41f7 · aaa41f7
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diff --git a/.gitignore b/.gitignore
@@ -71,6 +71,8 @@ test/**/*.log
 test/**/*.pdf
 test/**/*.prof
 test/**/*.npz
+#Allow
+!test/second_q/formats/fcidump/*.npz
 
 # Translations
 *.mo

diff --git a/docs/apidocs/qiskit_nature.second_q.formats.fcidump.rst b/docs/apidocs/qiskit_nature.second_q.formats.fcidump.rst
@@ -0,0 +1,7 @@
+FCIDump
+==============================
+
+.. automodule:: qiskit_nature.second_q.formats.fcidump
+   :no-members:
+   :no-inherited-members:
+   :no-special-members:
diff --git a/qiskit_nature/second_q/formats/__init__.py b/qiskit_nature/second_q/formats/__init__.py
@@ -23,6 +23,7 @@
 .. autosummary::
    :toctree:
 
+   fcidump
    qcschema
 
 """
diff --git a/qiskit_nature/second_q/formats/fcidump/__init__.py b/qiskit_nature/second_q/formats/fcidump/__init__.py
@@ -0,0 +1,32 @@
+# This code is part of Qiskit.
+#
+# (C) Copyright IBM 2020, 2022.
+#
+# This code is licensed under the Apache License, Version 2.0. You may
+# obtain a copy of this license in the LICENSE.txt file in the root directory
+# of this source tree or at http://www.apache.org/licenses/LICENSE-2.0.
+#
+# Any modifications or derivative works of this code must retain this
+# copyright notice, and modified files need to carry a notice indicating
+# that they have been altered from the originals.
+
+"""
+The FCIDump (:mod:`qiskit_nature.second_q.formats.fcidump`)
+=============================================================
+
+Contains tools to parse and dump FCIDump files.
+
+.. currentmodule:: qiskit_nature.second_q.formats.fcidump
+
+.. autosummary::
+   :toctree: ../stubs/
+   :nosignatures:
+
+
+   FCIDump
+
+"""
+
+from .fcidump import FCIDump
+
+__all__ = ["FCIDump"]
diff --git a/qiskit_nature/second_q/formats/fcidump/dumper.py b/qiskit_nature/second_q/formats/fcidump/dumper.py
@@ -0,0 +1,90 @@
+# This code is part of Qiskit.
+#
+# (C) Copyright IBM 2020, 2022.
+#
+# This code is licensed under the Apache License, Version 2.0. You may
+# obtain a copy of this license in the LICENSE.txt file in the root directory
+# of this source tree or at http://www.apache.org/licenses/LICENSE-2.0.
+#
+# Any modifications or derivative works of this code must retain this
+# copyright notice, and modified files need to carry a notice indicating
+# that they have been altered from the originals.
+
+"""FCIDump dumper."""
+
+from typing import List, Union, TextIO, Tuple, Iterator, Any
+import itertools
+import numpy as np
+
+
+def _dump_1e_ints(
+    hij: np.ndarray,
+    mos: Union[range, List[int]],
+    outfile: TextIO,
+    beta: bool = False,
+) -> None:
+    idx_offset = 1 if not beta else 1 + len(mos)
+    hij_elements = set()
+    for i, j in itertools.product(mos, repeat=2):
+        if i == j:
+            _write_to_outfile(outfile, hij[i][j], (i + idx_offset, j + idx_offset, 0, 0))
+            continue
+        if (j, i) in hij_elements and np.isclose(hij[i][j], hij[j][i]):
+            continue
+        _write_to_outfile(outfile, hij[i][j], (i + idx_offset, j + idx_offset, 0, 0))
+        hij_elements.add((i, j))
+
+
+def _dump_2e_ints(
+    hijkl: np.ndarray, mos: Union[range, List[int]], outfile: TextIO, beta: int = 0
+) -> None:
+    idx_offsets = [1, 1]
+    for b in range(beta):
+        idx_offsets[1 - b] += len(mos)
+    hijkl_elements = set()
+    for elem in itertools.product(mos, repeat=4):
+        if np.isclose(hijkl[elem], 0.0, atol=1e-14):
+            continue
+        if len(set(elem)) == 1:
+            _write_to_outfile(
+                outfile,
+                hijkl[elem],
+                (
+                    *[e + idx_offsets[0] for e in elem[:2]],
+                    *[e + idx_offsets[1] for e in elem[2:]],
+                ),
+            )
+            continue
+        if (
+            beta != 1
+            and elem[::-1] in hijkl_elements
+            and np.isclose(hijkl[elem], hijkl[elem[::-1]])
+        ):
+            continue
+        bra_perms = set(itertools.permutations(elem[:2]))
+        ket_perms = set(itertools.permutations(elem[2:]))
+        permutations: Iterator[Any]
+        if beta == 1:
+            permutations = itertools.product(bra_perms, ket_perms)
+        else:
+            permutations = itertools.chain(
+                itertools.product(bra_perms, ket_perms),
+                itertools.product(ket_perms, bra_perms),
+            )
+        for perm in {e1 + e2 for e1, e2 in permutations}:
+            if perm in hijkl_elements and np.isclose(hijkl[elem], hijkl[perm]):
+                break
+        else:
+            _write_to_outfile(
+                outfile,
+                hijkl[elem],
+                (
+                    *[e + idx_offsets[0] for e in elem[:2]],
+                    *[e + idx_offsets[1] for e in elem[2:]],
+                ),
+            )
+            hijkl_elements.add(elem)
+
+
+def _write_to_outfile(outfile: TextIO, value: float, indices: Tuple):
+    outfile.write(f"{value:23.16E}{indices[0]:4d}{indices[1]:4d}{indices[2]:4d}{indices[3]:4d}\n")
diff --git a/qiskit_nature/second_q/formats/fcidump/fcidump.py b/qiskit_nature/second_q/formats/fcidump/fcidump.py
@@ -0,0 +1,121 @@
+# This code is part of Qiskit.
+#
+# (C) Copyright IBM 2020, 2022.
+#
+# This code is licensed under the Apache License, Version 2.0. You may
+# obtain a copy of this license in the LICENSE.txt file in the root directory
+# of this source tree or at http://www.apache.org/licenses/LICENSE-2.0.
+#
+# Any modifications or derivative works of this code must retain this
+# copyright notice, and modified files need to carry a notice indicating
+# that they have been altered from the originals.
+
+"""FCIDump"""
+
+from __future__ import annotations
+
+from typing import List
+from dataclasses import dataclass
+from pathlib import Path
+import numpy as np
+
+from qiskit_nature import QiskitNatureError
+
+
+from .dumper import _dump_1e_ints, _dump_2e_ints, _write_to_outfile
+
+
+@dataclass
+class FCIDump:
+    """
+    Qiskit Nature dataclass for representing the FCIDump format.
+
+    The FCIDump format is partially defined in Knowles1989.
+
+    References:
+        Knowles1989: Peter J. Knowles, Nicholas C. Handy,
+            A determinant based full configuration interaction program,
+            Computer Physics Communications, Volume 54, Issue 1, 1989, Pages 75-83,
+            ISSN 0010-4655, https://doi.org/10.1016/0010-4655(89)90033-7.
+    """
+
+    hij: np.ndarray
+    """The alpha 1-electron integrals."""
+    hijkl: np.ndarray
+    """The alpha/alpha 2-electron integrals."""
+    hij_b: np.ndarray | None
+    """The beta 1-electron integrals."""
+    hijkl_ba: np.ndarray | None
+    """The beta/alpha 2-electron integrals."""
+    hijkl_bb: np.ndarray | None
+    """The beta/beta 2-electron integrals."""
+    multiplicity: int
+    """The multiplicity."""
+    num_electrons: int
+    """The number of electrons."""
+    num_orbitals: int
+    """The number of orbitals."""
+    constant_energy: float | None
+    """The constant energy comprising (for example) the nuclear repulsion energy
+    and inactive energies."""
+    orbsym: List[str] | None
+    """A list of spatial symmetries of the orbitals."""
+    isym: int
+    """The spatial symmetry of the wave function."""
+
+    @classmethod
+    def from_file(cls, fcidump: str | Path) -> FCIDump:
+        """Constructs an FCIDump object from a file."""
+        # pylint: disable=cyclic-import
+        from .parser import _parse
+
+        return _parse(fcidump if isinstance(fcidump, Path) else Path(fcidump))
+
+    def to_file(self, fcidump: str | Path) -> None:
+        """Dumps an FCIDump object to a file.
+
+        Args:
+            fcidump: Path to the output file.
+        Raises:
+            QiskitNatureError: invalid number of orbitals.
+            QiskitNatureError: not all beta-spin related matrices are either None or not None.
+        """
+        outpath = fcidump if isinstance(fcidump, Path) else Path(fcidump)
+        # either all beta variables are None or all of them are not
+        if not all(h is None for h in [self.hij_b, self.hijkl_ba, self.hijkl_bb]) and not all(
+            h is not None for h in [self.hij_b, self.hijkl_ba, self.hijkl_bb]
+        ):
+            raise QiskitNatureError("Invalid beta variables.")
+        norb = self.num_orbitals
+        nelec = self.num_electrons
+        einact = self.constant_energy
+        ms2 = self.multiplicity - 1
+        if norb != self.hij.shape[0] or norb != self.hijkl.shape[0]:
+            raise QiskitNatureError(
+                f"Invalid number of orbitals {norb} {self.hij.shape[0]} {self.hijkl.shape[0]}"
+            )
+
+        mos = range(norb)
+        with outpath.open("w", encoding="utf8") as outfile:
+            # print header
+            outfile.write(f"&FCI NORB={norb:4d},NELEC={nelec:4d},MS2={ms2:4d}\n")
+            if self.orbsym is None:
+                outfile.write(" ORBSYM=" + "1," * norb + "\n")
+            else:
+                if len(self.orbsym) != norb:
+                    raise QiskitNatureError(f"Invalid number of orbitals {norb} {len(self.orbsym)}")
+                outfile.write(" ORBSYM=" + ",".join(self.orbsym) + "\n")
+            outfile.write(f" ISYM={self.isym:d},\n&END\n")
+            # append 2e integrals
+            _dump_2e_ints(self.hijkl, mos, outfile)
+            if self.hijkl_ba is not None:
+                _dump_2e_ints(self.hijkl_ba.transpose(), mos, outfile)
+            if self.hijkl_bb is not None:
+                _dump_2e_ints(self.hijkl_bb, mos, outfile)
+            # append 1e integrals
+            _dump_1e_ints(self.hij, mos, outfile)
+            if self.hij_b is not None:
+                _dump_1e_ints(self.hij_b, mos, outfile)
+            # TODO append MO energies (last three indices are 0)
+            # append inactive energy
+            _write_to_outfile(outfile, einact, (0, 0, 0, 0))