Merge remote-tracking branch 'origin/main' into dev

pyscfad/_src/scipy/linalg.py

@@ -0,0 +1,93 @@
+import numpy
+import scipy
+
+def logm(A, disp=True, real=False):
+    """Compute matrix logarithm.
+
+    Compute the matrix logarithm ensuring that it is real
+    when `A` is nonsingular and each Jordan block of `A` belonging
+    to negative eigenvalue occurs an even number of times.
+
+    Parameters
+    ----------
+    A : (N, N) array_like
+        Matrix whose logarithm to evaluate
+    real : bool, default=False
+        If `True`, compute a real logarithm of a real matrix if it exists.
+        Otherwise, call `scipy.linalg.logm`.
+
+    See Also
+    --------
+    scipy.linalg.logm
+    """
+    if real and numpy.isreal(A).all():
+        A = numpy.real(A)
+        # perform the real Schur decomposition
+        t, q = scipy.linalg.schur(A)
+
+        n = A.shape[0]
+        idx = 0
+        real_output = True
+        while idx < n:
+            # final block reached for an odd number of orbitals
+            if idx == n - 1:
+                # single positive block
+                if t[idx,idx] > 0:
+                    t[idx,idx] = numpy.log(t[idx,idx])
+                # single negative block
+                else:
+                    real_output = False
+                    break
+            else:
+                diag = numpy.isclose(t[idx,idx+1], 0) and numpy.isclose(t[idx+1,idx], 0)
+                # single positive block
+                if t[idx,idx] > 0 and diag:
+                    t[idx,idx] = numpy.log(t[idx,idx])
+                # pair of two negative blocks
+                elif (
+                    t[idx,idx] < 0
+                    and diag
+                    and numpy.isclose(t[idx,idx], t[idx + 1,idx + 1])
+                ):
+                    log_lambda = numpy.log(-t[idx,idx])
+                    t[idx:idx+2,idx:idx+2] = numpy.array(
+                        [[log_lambda, numpy.pi], [-numpy.pi, log_lambda]]
+                    )
+                    idx += 1
+                # antisymmetric 2x2 block
+                elif (
+                    numpy.isclose(t[idx,idx], t[idx + 1,idx + 1])
+                    and numpy.isclose(t[idx + 1,idx], -t[idx,idx + 1])
+                ):
+                    log_comp = numpy.log(complex(t[idx,idx], t[idx,idx + 1]))
+                    t[idx:idx+2,idx:idx+2] = numpy.array(
+                        [
+                            [numpy.real(log_comp), numpy.imag(log_comp)],
+                            [-numpy.imag(log_comp), numpy.real(log_comp)],
+                        ],
+                    )
+                    idx += 1
+                else:
+                    real_output = False
+                    break
+            idx += 1
+
+        if not real_output:
+            return scipy.linalg.logm(A, disp=disp)
+
+        F = q @ t @ q.T
+
+        # NOTE copied from scipy
+        errtol = 1000 * numpy.finfo("d").eps
+        # TODO use a better error approximation
+        errest = scipy.linalg.norm(scipy.linalg.expm(F) - A, 1) / scipy.linalg.norm(A, 1)
+        if disp:
+            if not numpy.isfinite(errest) or errest >= errtol:
+                print("logm result may be inaccurate, approximate err =", errest)
+            return F
+        else:
+            return F, errest
+
+    else:
+        return scipy.linalg.logm(A, disp=disp)
+

pyscfad/lo/boys.py

@@ -1,5 +1,4 @@
 import numpy
-import scipy
 import jax
 from pyscf.lib import logger
 from pyscf.lo import boys as pyscf_boys
@@ -11,6 +10,7 @@
     pack_uniq_var,
 )
 from pyscfad.tools.linear_solver import gen_gmres
+from pyscfad.scipy.linalg import logm
 
 # modified from pyscf v2.6
 def kernel(localizer, mo_coeff=None, callback=None, verbose=None,
@@ -133,12 +133,11 @@ def _extract_x0(loc, u):
                     'Saddle point reached in orbital localization.'
                     f'\n{h_diag}')
 
-    #TODO ensure real solution of logm
-    mat = scipy.linalg.logm(u)
-    if not numpy.allclose(mat.imag, 0, atol=1e-6):
+    mat = logm(u, real=True)
+    if not numpy.isreal(mat).all():
         raise RuntimeError('Complex solutions are not supported for '
                            'differentiating the Boys localiztion.')
-    x = pack_uniq_var(mat.real)
+    x = pack_uniq_var(numpy.real(mat))
     return x
 
 def _boys(x, mol, mo_coeff, *,

pyscfad/scipy/linalg.py

@@ -4,3 +4,7 @@
     eigh as eigh,
     svd as svd,
 )
+
+from pyscfad._src.scipy.linalg import (
+    logm as logm,
+)

pyscfad/scipy/test/test_linalg.py

@@ -1,8 +1,10 @@
 from functools import partial
+import numpy as np
+import scipy
 import jax
 from jax import numpy as jnp
 from jax import scipy as jsp
-from pyscfad.scipy.linalg import eigh, svd
+from pyscfad.scipy.linalg import eigh, svd, logm
 
 def test_eigh():
     a = jnp.ones((2,2))
@@ -41,3 +43,15 @@ def test_svd():
     assert abs(jac0[1] - jac1[1]).max() < 1e-7
     assert abs(jac0[2] - jac1[2]).max() < 1e-7
 
+def test_logm():
+    theta = 2 * np.pi / 3
+    a = np.array([[np.cos(theta), -np.sin(theta)],
+                  [np.sin(theta),  np.cos(theta)]])
+    A = scipy.linalg.block_diag(np.diag(np.array([-1, -1, 1])), a)
+
+    X = logm(A, real=True)
+    assert np.isreal(X).all()
+    assert scipy.linalg.norm(scipy.linalg.expm(X) - A, 1) < 1e-12
+
+    assert np.allclose(logm(A), scipy.linalg.logm(A))
+