Standardize Libcint implementation to include IOData conventions (#174)

* Add function to get permutation with LibCint order

* Apply ordering permutation to libcint arrays

* Minor changes libcint conventions

* Add tests and files for iodata/libcint

* Change default convention for p spherical orbitals

* Add install libcint to workflow

* Exclude notebooks and test/*fchk from pre-commit

* Fix errors workflows and pre-commit

* Fix errors

- Install lisp interpreter
- Exclude only folders

* Skip install sbcl for windows

* Fix excluding folders pre-commit

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Update syntax

* Debug workflows pytest

* Try again if statment in workflows

* Exclude libcint tests if build folder is not found

* Exclude libcint tests if operating in windows os

* Move imports from libcint into tests

* Add some changes included in PR #151

* Change to test with IOData to cover wrappers

* Delete version check IOData

* Add pyscf to tests to cover wrappers

* Remove pyscf and lower coverage requirement

---------

Co-authored-by: Michelle Richer <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.github/workflows/pytest.yaml

@@ -9,14 +9,17 @@ on:
   pull_request:
 
 jobs:
-  tests:
+  pytest:
     name: "Python ${{ matrix.py }} on OS ${{ matrix.os }}"
     runs-on: ${{ matrix.os }}
+    env:
+      COVERAGE_SINGLE: 78
+      COVERAGE_TOTAL: 78
 
     strategy:
       matrix:
         os: ["ubuntu-latest", "windows-latest"]
-        py: ["3.7", "3.9", "3.10", "3.11"]
+        py: ["3.7", "3.8", "3.9", "3.10", "3.11"]
 
     steps:
       - uses: "actions/checkout@v3"
@@ -34,20 +37,16 @@ jobs:
       - name: Install development version
         run: |
           # Need editable mode in order to include the test files
-          pip install -e .
+          pip install --user git+https://github.com/theochem/iodata.git@master
+          pip install -e .[dev,iodata]
 
-      - name: Run pytest
-        uses: pavelzw/pytest-action@v2
-        with:
-          verbose: true
-          emoji: true
-          job-summary: true
-          click-to-expand: true
-          custom-arguments: "--junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=gbasis"
-          report-title: 'Test Report'
-
-      - name: Pytest coverage comment
-        uses: MishaKav/pytest-coverage-comment@main
-        with:
-          pytest-coverage-path: ./pytest-coverage.txt
-          junitxml-path: ./pytest.xml
+      - name: Install Libcint library
+        if: ${{ matrix.os  != 'windows-latest' }}
+        run: |
+          echo "${{ matrix.os }}"
+          sudo apt-get install -y sbcl
+          USE_LIBCINT=1 ./tools/install_libcint.sh
+
+      - name: Run Pytest
+        run: |
+            pytest --cov=./gbasis/ --cov-fail-under=78 --cov-report term .

.pre-commit-config.yaml

@@ -1,3 +1,5 @@
+files: "gbasis/"
+exclude: "notebooks/|tests/"
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.5.0

gbasis/contractions.py

@@ -495,10 +495,13 @@ def angmom_components_sph(self):
         ['s2', 's1', 'c0', 'c1', 'c2'].
 
         """
-        return tuple(
-            ["s{}".format(m) for m in range(self.angmom, 0, -1)]
-            + ["c{}".format(m) for m in range(self.angmom + 1)]
-        )
+        if self.angmom == 1:
+            return tuple(["c1", "s1", "c0"])
+        else:
+            return tuple(
+                ["s{}".format(m) for m in range(self.angmom, 0, -1)]
+                + ["c{}".format(m) for m in range(self.angmom + 1)]
+            )
 
     @property
     def norm_prim_cart(self):

gbasis/integrals/libcint.py

@@ -458,6 +458,17 @@ def __init__(self, basis, atnums, atcoords, coord_type="spherical"):
         offs = np.asarray(offs, dtype=c_int)
         atm_offs = np.cumsum(atm_offs)
 
+        # Get permutation vector for ordering convention
+        permutations = []
+        for shell in basis:
+            if hasattr(shell, "permutation_libcint"):
+                permutation = shell.permutation_libcint()
+            else:
+                permutation = list(range(num_angmom(shell)))
+            for _ in range(shell.num_seg_cont):
+                perm_off = len(permutations)
+                permutations.extend(p + perm_off for p in permutation)
+
         # Allocate and fill C input arrays
         ienv = 20
         atm = np.zeros((natm, 6), dtype=c_int)
@@ -536,9 +547,10 @@ def __init__(self, basis, atnums, atcoords, coord_type="spherical"):
         self.atcoords = atcoords.copy()
         self._atm_offs = atm_offs
 
-        # Save basis function offsets
+        # Save basis function offsets and ordering permutation
         self._offs = offs
         self._max_off = max(offs)
+        self._permutations = permutations
 
         # Set inverse sqrt of overlap integral (temporarily, for __init__)
         self._ovlp_minhalf = np.ones(nbfn)
@@ -740,6 +752,9 @@ def int1e(notation="physicist", origin=None, inv_origin=None):
             if constant is not None:
                 out *= constant
 
+            # Apply permutation
+            out = out[self._permutations, :][:, self._permutations]
+
             # Return normalized integrals
             if self.coord_type == "cartesian":
                 return np.einsum(norm_einsum, self._ovlp_minhalf, self._ovlp_minhalf, out)
@@ -941,6 +956,12 @@ def int2e(notation="physicist", origin=None, inv_origin=None):
             if physicist:
                 out = out.transpose(0, 2, 1, 3)
 
+            # Apply permutation
+            out = out[self._permutations]
+            out = out[:, self._permutations]
+            out = out[:, :, self._permutations]
+            out = out[:, :, :, self._permutations]
+
             # Return normalized integrals
             if self.coord_type == "cartesian":
                 return np.einsum(

gbasis/wrappers.py

@@ -3,6 +3,88 @@
 import numpy as np
 
 
+CONVENTIONS_LIBCINT = {
+    (5, "p"): ["s5", "s4", "s3", "s2", "s1", "c0", "c1", "c2", "c3", "c4", "c5"],
+    (4, "p"): ["s4", "s3", "s2", "s1", "c0", "c1", "c2", "c3", "c4"],
+    (3, "p"): ["s3", "s2", "s1", "c0", "c1", "c2", "c3"],
+    (2, "p"): ["s2", "s1", "c0", "c1", "c2"],
+    (0, "c"): ["1"],
+    (1, "c"): ["x", "y", "z"],
+    (2, "c"): ["xx", "xy", "xz", "yy", "yz", "zz"],
+    (3, "c"): ["xxx", "xxy", "xxz", "xyy", "xyz", "xzz", "yyy", "yyz", "yzz", "zzz"],
+    (4, "c"): [
+        "xxxx",
+        "xxxy",
+        "xxxz",
+        "xxyy",
+        "xxyz",
+        "xxzz",
+        "xyyy",
+        "xyyz",
+        "xyzz",
+        "xzzz",
+        "yyyy",
+        "yyyz",
+        "yyzz",
+        "yzzz",
+        "zzzz",
+    ],
+    (5, "c"): [
+        "xxxxx",
+        "xxxxy",
+        "xxxxz",
+        "xxxyy",
+        "xxxyz",
+        "xxxzz",
+        "xxyyy",
+        "xxyyz",
+        "xxyzz",
+        "xxzzz",
+        "xyyyy",
+        "xyyyz",
+        "xyyzz",
+        "xyzzz",
+        "xzzzz",
+        "yyyyy",
+        "yyyyz",
+        "yyyzz",
+        "yyzzz",
+        "yzzzz",
+        "zzzzz",
+    ],
+    (6, "c"): [
+        "xxxxxx",
+        "xxxxxy",
+        "xxxxxz",
+        "xxxxyy",
+        "xxxxyz",
+        "xxxxzz",
+        "xxxyyy",
+        "xxxyyz",
+        "xxxyzz",
+        "xxxzzz",
+        "xxyyyy",
+        "xxyyyz",
+        "xxyyzz",
+        "xxyzzz",
+        "xxzzzz",
+        "xyyyyy",
+        "xyyyyz",
+        "xyyyzz",
+        "xyyzzz",
+        "xyzzzz",
+        "xzzzzz",
+        "yyyyyy",
+        "yyyyyz",
+        "yyyyzz",
+        "yyyzzz",
+        "yyzzzz",
+        "yzzzzz",
+        "zzzzzz",
+    ],
+}
+
+
 def from_iodata(mol, tol=1e-20, overlap=False):
     """Return basis set stored within the `IOData` instance in `iodata`.
 
@@ -113,6 +195,39 @@ def angmom_components_sph(self):
 
             return tuple(sph_conventions[self.angmom])
 
+        def permutation_libcint(self):
+            """Returns the permutation of the stored convention to the one used in libcint for
+            the given angular momentum
+
+            Conventions supported
+            cartesian: string of X, Y, and Z characters,such that :math:`a_x` `X` characters,
+            :math:`a_y` `Y` characters, and :math:`a_z` `Z`, characters appear. F
+            For example, `(2, 1, 1)` corresponds to `XXYZ`
+
+            Spherical: Strings of the form `c{m}` and `s{m}`.
+
+            Rerturns:
+            --------
+            permutation: An integer array that permutes basis function from IOData stored convention
+                         to LibCint.
+
+            """
+
+            angmom = self.angmom
+            if self.coord_type == "cartesian":
+                coord_type = "c"
+                iodata_shell_convention = cart_conventions[angmom]
+            elif self.coord_type == "spherical":
+                coord_type = "p"
+                iodata_shell_convention = sph_conventions[angmom]
+
+            # Get libcint convention
+            libcint_convention = CONVENTIONS_LIBCINT[(angmom, coord_type)]
+            # Generate permutation
+            permutation = [libcint_convention.index(conv1) for conv1 in iodata_shell_convention]
+
+            return permutation
+
     if molbasis.primitive_normalization != "L2":  # pragma: no cover
         raise ValueError(
             "Only L2 normalization scheme is supported in `gbasis`. Given `IOData` instance uses "

pyproject.toml

@@ -62,7 +62,6 @@ doc = [
 ]
 "dev" = ["tox"]
 "test" = ["tox", "pytest", "pytest-cov"]
-"iodata" = ["iodata>0.1.7"]
 "pyscf" = ["pyscf>=1.6.1"]
 
 [tool.black]