Merge pull request #221 from timcallow/enforce_log_grid

Enforce log grid

atoMEC/postprocess/conductivity.py

@@ -44,6 +44,12 @@ def __init__(self, Atom, model, orbitals, valence_orbs=[], nmax=0, lmax=0):
                 "Kubo-Greenwood is not yet set-up for spin-polarized calculations. \
 Please run again with spin-unpolarized input."
             )
+
+        if orbitals.grid_type != "log":
+            sys.exit(
+                "Sqrt grid is not yet supported for Kubo-Greenwood calculations."
+                "Please switch to log grid."
+            )
         if nmax == 0:
             self._nmax = nmax_default
         else:

atoMEC/staticKS.py

@@ -1669,10 +1669,17 @@ def calc_entropy(self, orbs):
 class GramSchmidt:
     """Class holding Gram-Schmidt orthoganalization process."""
 
-    def __init__(self, eigfuncs, xgrid):
+    def __init__(self, eigfuncs, xgrid, grid_type):
         self._eigfuncs = eigfuncs
         self._xgrid = xgrid
 
+        # check grid is logarithmic
+        if grid_type != "log":
+            raise check_inputs.InputError.grid_error(
+                "Sqrt grid is not yet supported for Gram-Schmidt procedure."
+                "Please switch to log grid."
+            )
+
     def make_ortho(self):
         """
         Make eigenfunctions orthonormal using Gram-Schmidt orthoganalization.

tests/gramschmidt_test.py

@@ -6,7 +6,7 @@
 integrals and perform Gram-Schmidt orthonormalization.
 """
 
-from atoMEC import Atom, models, staticKS
+from atoMEC import Atom, models, staticKS, config
 import pytest
 from pytest_lazyfixture import lazy_fixture
 import numpy as np
@@ -34,6 +34,7 @@ def SCF_output(self):
     )
     def test_overlap(self, input_SCF, case, expected):
         """Run overlap integral after orthonormalizatation."""
+        config.grid_type = "log"
         assert np.isclose(
             self._run_overlap(input_SCF, case),
             expected,
@@ -88,7 +89,7 @@ def _run_overlap(input_SCF, case):
 
         """
         xgrid = input_SCF["orbitals"]._xgrid
-        GS = staticKS.GramSchmidt(input_SCF["orbitals"].eigfuncs, xgrid)
+        GS = staticKS.GramSchmidt(input_SCF["orbitals"].eigfuncs, xgrid, "log")
         ortho = GS.make_ortho()
         if case == "self":
             norm = GS.prod_eigfuncs(ortho[0, 0, 0, 1], ortho[0, 0, 0, 1], xgrid)
@@ -99,6 +100,7 @@ def _run_overlap(input_SCF, case):
 
 
 if __name__ == "__main__":
+    config.grid_type = "log"
     SCF_out = TestGS._run_SCF()
     print("self_overlap_expected =", TestGS._run_overlap(SCF_out, "self"))
     print("overlap_expected =", TestGS._run_overlap(SCF_out, "other"))