separate test file

Author: hatemhelal

pyscf_ipu/experimental/interop.py

@@ -12,11 +12,9 @@
 def to_pyscf(
     structure: Structure, basis_name: str = "sto-3g", unit: str = "Bohr"
 ) -> "gto.Mole":
+    position = np.asarray(structure.position)
     mol = gto.Mole(unit=unit, spin=structure.num_electrons % 2, cart=True)
-    mol.atom = [
-        (symbol, pos)
-        for symbol, pos in zip(structure.atomic_symbol, structure.position)
-    ]
+    mol.atom = [(symbol, pos) for symbol, pos in zip(structure.atomic_symbol, position)]
     mol.basis = basis_name
     mol.build(unit=unit)
     return mol

pyscf_ipu/experimental/nuclear_gradients.py

@@ -35,7 +35,6 @@ def grad_primitive_integral(
     Returns:
         Float3: Gradient of the integral with respect to cartesian axes.
     """
-
     t1 = [primitive_op(a.offset_lmn(ax, 1), b) for ax in range(3)]
     t2 = [primitive_op(a.offset_lmn(ax, -1), b) for ax in range(3)]
     grad_out = 2 * a.alpha * jnp.stack(t1) - a.lmn * jnp.stack(t2)

pyscf_ipu/experimental/types.py

@@ -5,6 +5,7 @@
 
 Float3 = Float[Array, "3"]
 Float3xNxN = Float[Array, "3 N N"]
+Float3xNxNxNxN = Float[Array, "3 N N N N"]
 FloatNx3 = Float[Array, "N 3"]
 FloatN = Float[Array, "N"]
 FloatNxN = Float[Array, "N N"]

test/test_integrals.py

@@ -2,11 +2,9 @@
 import jax.numpy as jnp
 import numpy as np
 import pytest
-from jax import tree_map, vmap
 from numpy.testing import assert_allclose
 
 from pyscf_ipu.experimental.basis import basisset
-from pyscf_ipu.experimental.device import has_ipu, ipu_func
 from pyscf_ipu.experimental.integrals import (
     eri_basis,
     eri_basis_sparse,
@@ -19,51 +17,10 @@
     overlap_primitives,
 )
 from pyscf_ipu.experimental.interop import to_pyscf
-from pyscf_ipu.experimental.nuclear_gradients import (
-    grad_kinetic_basis,
-    grad_nuclear_basis,
-    grad_overlap_basis,
-)
 from pyscf_ipu.experimental.primitive import Primitive
 from pyscf_ipu.experimental.structure import molecule
 
 
-@pytest.mark.parametrize("basis_name", ["sto-3g", "6-31g**"])
-def test_to_pyscf(basis_name):
-    mol = molecule("water")
-    basis = basisset(mol, basis_name)
-    pyscf_mol = to_pyscf(mol, basis_name)
-    assert basis.num_orbitals == pyscf_mol.nao
-
-
-@pytest.mark.parametrize("basis_name", ["sto-3g", "6-31+g"])
-def test_gto(basis_name):
-    from pyscf.dft.numint import eval_rho
-
-    # Atomic orbitals
-    structure = molecule("water")
-    basis = basisset(structure, basis_name)
-    mesh, _ = uniform_mesh()
-    actual = basis(mesh)
-
-    mol = to_pyscf(structure, basis_name)
-    expect_ao = mol.eval_gto("GTOval_cart", np.asarray(mesh))
-    assert_allclose(actual, expect_ao, atol=1e-6)
-
-    # Molecular orbitals
-    mf = mol.KS()
-    mf.kernel()
-    C = jnp.array(mf.mo_coeff, dtype=jnp.float32)
-    actual = basis.occupancy * C @ C.T
-    expect = jnp.array(mf.make_rdm1(), dtype=jnp.float32)
-    assert_allclose(actual, expect, atol=1e-6)
-
-    # Electron density
-    actual = electron_density(basis, mesh, C)
-    expect = eval_rho(mol, expect_ao, mf.make_rdm1(), "lda")
-    assert_allclose(actual, expect, atol=1e-6)
-
-
 def test_overlap():
     # Exercise 3.21 of "Modern quantum chemistry: introduction to advanced
     # electronic structure theory."" by Szabo and Ostlund
@@ -151,19 +108,6 @@ def test_water_nuclear():
     assert_allclose(actual, expect, atol=1e-4)
 
 
-def eri_orbitals(orbitals):
-    def take(orbital, index):
-        p = tree_map(lambda *xs: jnp.stack(xs), *orbital.primitives)
-        p = tree_map(lambda x: jnp.take(x, index, axis=0), p)
-        c = jnp.take(orbital.coefficients, index)
-        return p, c
-
-    indices = [jnp.arange(o.num_primitives) for o in orbitals]
-    indices = [i.reshape(-1) for i in jnp.meshgrid(*indices)]
-    prim, coef = zip(*[take(o, i) for o, i in zip(orbitals, indices)])
-    return jnp.sum(jnp.prod(jnp.stack(coef), axis=0) * vmap(eri_primitives)(*prim))
-
-
 def test_eri():
     # PyQuante test cases for ERI
     a, b, c, d = [Primitive()] * 4
@@ -172,18 +116,6 @@ def test_eri():
     c, d = [Primitive(lmn=jnp.array([1, 0, 0]))] * 2
     assert_allclose(eri_primitives(a, b, c, d), 0.940316, atol=1e-5)
 
-    # H2 molecule in sto-3g: See equation 3.235 of Szabo and Ostlund
-    h2 = molecule("h2")
-    basis = basisset(h2, "sto-3g")
-    indices = [(0, 0, 0, 0), (0, 0, 1, 1), (1, 0, 0, 0), (1, 0, 1, 0)]
-    expected = [0.7746, 0.5697, 0.4441, 0.2970]
-
-    for ijkl, expect in zip(indices, expected):
-        actual = eri_orbitals([basis.orbitals[aoid] for aoid in ijkl])
-        assert_allclose(actual, expect, atol=1e-4)
-
-
-def test_eri_basis():
     # H2 molecule in sto-3g: See equation 3.235 of Szabo and Ostlund
     h2 = molecule("h2")
     basis = basisset(h2, "sto-3g")
@@ -219,63 +151,3 @@ def test_water_eri(sparse):
     aosym = "s8" if sparse else "s1"
     expect = to_pyscf(h2o, basis_name=basis_name).intor("int2e_cart", aosym=aosym)
     assert_allclose(actual, expect, atol=1e-4)
-
-
-@pytest.mark.skipif(not has_ipu(), reason="Skipping ipu test!")
-def test_ipu_overlap():
-    from pyscf_ipu.experimental.integrals import _overlap_primitives
-
-    a, b = [Primitive()] * 2
-    actual = ipu_func(_overlap_primitives)(a, b)
-    assert_allclose(actual, overlap_primitives(a, b))
-
-
-@pytest.mark.skipif(not has_ipu(), reason="Skipping ipu test!")
-def test_ipu_kinetic():
-    from pyscf_ipu.experimental.integrals import _kinetic_primitives
-
-    a, b = [Primitive()] * 2
-    actual = ipu_func(_kinetic_primitives)(a, b)
-    assert_allclose(actual, kinetic_primitives(a, b))
-
-
-@pytest.mark.skipif(not has_ipu(), reason="Skipping ipu test!")
-def test_ipu_nuclear():
-    from pyscf_ipu.experimental.integrals import _nuclear_primitives
-
-    # PyQuante test case for nuclear attraction integral
-    a, b = [Primitive()] * 2
-    c = jnp.zeros(3)
-    actual = ipu_func(_nuclear_primitives)(a, b, c)
-    assert_allclose(actual, -1.595769, atol=1e-5)
-
-
-@pytest.mark.skipif(not has_ipu(), reason="Skipping ipu test!")
-def test_ipu_eri():
-    from pyscf_ipu.experimental.integrals import _eri_primitives
-
-    # PyQuante test cases for ERI
-    a, b, c, d = [Primitive()] * 4
-    actual = ipu_func(_eri_primitives)(a, b, c, d)
-    assert_allclose(actual, 1.128379, atol=1e-5)
-
-
-@pytest.mark.parametrize("basis_name", ["sto-3g", "6-31+g"])
-def test_nuclear_gradients(basis_name):
-    h2 = molecule("h2")
-    scfmol = to_pyscf(h2, basis_name)
-    basis = basisset(h2, basis_name)
-
-    actual = grad_overlap_basis(basis)
-    expect = scfmol.intor("int1e_ipovlp_cart", comp=3)
-    assert_allclose(actual, expect, atol=1e-6)
-
-    actual = grad_kinetic_basis(basis)
-    expect = scfmol.intor("int1e_ipkin_cart", comp=3)
-    assert_allclose(actual, expect, atol=1e-6)
-
-    # TODO: investigate possible inconsistency in libcint outputs?
-    actual = grad_nuclear_basis(basis)
-    expect = scfmol.intor("int1e_ipnuc_cart", comp=3)
-    expect = -np.moveaxis(expect, 1, 2)
-    assert_allclose(actual, expect, atol=1e-6)

test/test_nuclear_gradients.py

@@ -0,0 +1,33 @@
+# Copyright (c) 2023 Graphcore Ltd. All rights reserved.
+import numpy as np
+from numpy.testing import assert_allclose
+
+from pyscf_ipu.experimental.basis import basisset
+from pyscf_ipu.experimental.interop import to_pyscf
+from pyscf_ipu.experimental.nuclear_gradients import (
+    grad_kinetic_basis,
+    grad_nuclear_basis,
+    grad_overlap_basis,
+)
+from pyscf_ipu.experimental.structure import molecule
+
+
+def test_nuclear_gradients():
+    basis_name = "sto-3g"
+    h2 = molecule("h2")
+    scfmol = to_pyscf(h2, basis_name)
+    basis = basisset(h2, basis_name)
+
+    actual = grad_overlap_basis(basis)
+    expect = scfmol.intor("int1e_ipovlp_cart", comp=3)
+    assert_allclose(actual, expect, atol=1e-6)
+
+    actual = grad_kinetic_basis(basis)
+    expect = scfmol.intor("int1e_ipkin_cart", comp=3)
+    assert_allclose(actual, expect, atol=1e-6)
+
+    # TODO: investigate possible inconsistency in libcint outputs?
+    actual = grad_nuclear_basis(basis)
+    expect = scfmol.intor("int1e_ipnuc_cart", comp=3)
+    expect = -np.moveaxis(expect, 1, 2)
+    assert_allclose(actual, expect, atol=1e-6)