Merge pull request #51 from TREX-CoE/basis_r_power

.github/workflows/test.yml

@@ -51,14 +51,28 @@ jobs:
           echo "=== Check TREXIO file converted from GAMESS ==="
           trexio check-mos -n 50 trexio_gamess.h5 > mos-res
           grep "Norm of the error" < mos-res | grep -Eo "([0-9]+\.[0-9]*|\.?[0-9]+)([eE][+-][0-9]+)?" > error-res
-          python -c 'with open("error-res") as f: error = f.readline().strip(); assert float(error) < 1.0'
+          cat error-res
+          python -c 'with open("error-res") as f: error = f.readline().strip(); assert float(error) < 0.12'
           echo "=== Check TREXIO file converted from PySCF ==="
-          trexio check-mos -n 50 trexio_pyscf_h2o.h5 > mos-res
+          trexio check-mos -n 100 trexio_pyscf_h2o.h5 > mos-res
           grep "Norm of the error" < mos-res | grep -Eo "([0-9]+\.[0-9]*|\.?[0-9]+)([eE][+-][0-9]+)?" > error-res
-          python -c 'with open("error-res") as f: error = f.readline().strip(); assert float(error) < 1.0'
+          cat error-res
+          python -c 'with open("error-res") as f: error = f.readline().strip(); assert float(error) < 0.00018'
           echo "=== Check TREXIO file converted from ORCA ==="
-          trexio check-mos -n 50 trexio_orca_h2o.h5 > mos-res
+          trexio check-mos -n 100 trexio_orca_h2o.h5 > mos-res
           grep "Norm of the error" < mos-res | grep -Eo "([0-9]+\.[0-9]*|\.?[0-9]+)([eE][+-][0-9]+)?" > error-res
-          python -c 'with open("error-res") as f: error = f.readline().strip(); assert float(error) < 1.0'
+          cat error-res
+          python -c 'with open("error-res") as f: error = f.readline().strip(); assert float(error) < 0.08'
           # benchmark helper converters
           trexio convert-to -t molden -o trexio_molden.h5 trexio_gamess.h5
+          echo "=== Check normalization in spherical file ==="
+          trexio check-mos -n 100 data/methane_sphe.hdf5  > mos-res
+          grep "Norm of the error" < mos-res | grep -Eo "([0-9]+\.[0-9]*|\.?[0-9]+)([eE][+-][0-9]+)?" > error-res
+          cat error-res
+          python -c 'with open("error-res") as f: error = f.readline().strip(); assert float(error) < 0.0017'
+          echo "=== Check normalization after transformation into cartesian file ==="
+          trexio convert-to -t cartesian data/methane_sphe.hdf5 -o methane_cart.hdf5
+          trexio check-mos -n 100 methane_cart.hdf5  > mos-res
+          grep "Norm of the error" < mos-res | grep -Eo "([0-9]+\.[0-9]*|\.?[0-9]+)([eE][+-][0-9]+)?" > error-res
+          cat error-res
+          python -c 'with open("error-res") as f: error = f.readline().strip(); assert float(error) < 0.0017'

src/trexio_tools/converters/convert_to.py

@@ -511,53 +511,30 @@ def run_cart_phe(inp, filename, to_cartesian):
     # Update MOs
     if trexio.has_mo_coefficient(inp):
       X = trexio.read_mo_coefficient(inp)
-      for i in range(R.shape[1]):
-         if normalization[i] != 1.:
-             X[i,:] /= normalization[i]
       Y = X @ R.T
       trexio.write_mo_coefficient(out, Y)
 
     # Update 1e Integrals
     if trexio.has_ao_1e_int_overlap(inp):
       X = trexio.read_ao_1e_int_overlap(inp)
-      for i in range(R.shape[1]):
-            X[:,i] /= normalization[i]
-      for i in range(R.shape[1]):
-            X[i,:] /= normalization[i]
       Y = R_norm_inv @ X @ R_norm_inv.T
       trexio.write_ao_1e_int_overlap(out, Y)
 
 
     if trexio.has_ao_1e_int_kinetic(inp):
       X = trexio.read_ao_1e_int_kinetic(inp)
-      for i in range(R.shape[1]):
-         if normalization[i] != 1.:
-            X[:,i] /= normalization[i]
-            X[i,:] /= normalization[i]
       trexio.write_ao_1e_int_kinetic(out, R_norm_inv @ X @ R_norm_inv.T)
 
     if trexio.has_ao_1e_int_potential_n_e(inp):
       X = trexio.read_ao_1e_int_potential_n_e(inp)
-      for i in range(R.shape[1]):
-         if normalization[i] != 1.:
-            X[:,i] /= normalization[i]
-            X[i,:] /= normalization[i]
       trexio.write_ao_1e_int_potential_n_e(out, R_norm_inv @ X @ R_norm_inv.T)
 
     if trexio.has_ao_1e_int_ecp(inp):
       X = trexio.read_ao_1e_int_ecp(inp)
-      for i in range(R.shape[1]):
-         if normalization[i] != 1.:
-            X[:,i] /= normalization[i]
-            X[i,:] /= normalization[i]
       trexio.write_ao_1e_int_ecp(out, R_norm_inv @ X @ R_norm_inv.T)
 
     if trexio.has_ao_1e_int_core_hamiltonian(inp):
       X = trexio.read_ao_1e_int_core_hamiltonian(inp)
-      for i in range(R.shape[1]):
-         if normalization[i] != 1.:
-            X[:,i] /= normalization[i]
-            X[i,:] /= normalization[i]
       trexio.write_ao_1e_int_core_hamiltonian(out, R_norm_inv @ X @ R_norm_inv.T)
 
     # Remove 2e integrals: too expensive to transform

src/trexio_tools/group_tools/check_basis.py

@@ -14,11 +14,6 @@ def run(trexio_file, n_points):
         the matrix stored in the file.
         """
 
-        if not trexio.has_ao_1e_int_overlap(trexio_file):
-          raise Exception(
-            "One-electron overlap integrals are missing in the TREXIO file. Required for check-basis."
-            )
-
         trexio_filename = trexio_file.filename
         context = qmckl.context_create()
         qmckl.trexio_read(context, trexio_filename)
@@ -56,7 +51,11 @@ def run(trexio_file, n_points):
         S = chi.T @ chi * dv
         print()
 
-        S_ex = trexio.read_ao_1e_int_overlap(trexio_file)
+        if trexio.has_ao_1e_int_overlap(trexio_file):
+            S_ex = trexio.read_ao_1e_int_overlap(trexio_file)
+        else:
+            S_ex = np.zeros((ao_num,ao_num))
+
 
         # This produces a lot of output for large molecules, maybe wrap up in ``if debug`` statement ?
         for i in range(ao_num):