fix

ash/interfaces/interface_OpenMM.py

@@ -1911,6 +1911,32 @@ def delete_exceptions(self, atomlist):
     #     print_time_rel(timeA, modulename="zero_nonbondedforce")
     #     # self.create_simulation()
 
+    # Updating LJ interactions in OpenMM object. Used to set LJ sites to zero e.g. so that they do not contribute
+    # Can be used to get QM-MM LJ interaction energy
+    def update_LJ_epsilons(self, atomlist, epsilons):
+        import openmm
+        timeA = time.time()
+        print("Updating LJ interaction strengths in OpenMM object.")
+        assert len(atomlist) == len(epsilons)
+        for atomindex, newepsilon in zip(atomlist, epsilons):
+            print("atomindex:", atomindex)
+            print("newepsilon:", newepsilon)
+            charge, sigma, oldepsilon = self.nonbonded_force.getParticleParameters(atomindex)
+            print("charge:", charge)
+            print("oldepsilon", oldepsilon)
+            # Different depending on type of NonbondedForce
+            if isinstance(self.nonbonded_force, openmm.CustomNonbondedForce):
+                self.nonbonded_force.setParticleParameters(atomindex, [charge, sigma, newepsilon])
+                # bla1,bla2,bla3 = self.nonbonded_force.getParticleParameters(i)
+                # print("bla1,bla2,bla3", bla1,bla2,bla3)
+            elif isinstance(self.nonbonded_force, openmm.NonbondedForce):
+                self.nonbonded_force.setParticleParameters(atomindex, charge, sigma, newepsilon)
+                bla1,bla2,bla3 = self.nonbonded_force.getParticleParameters(atomindex)
+                print("bla1,bla2,bla3", bla1,bla2,bla3)
+
+        printdebug("done here")
+        print_time_rel(timeA, modulename="update_LJ_epsilons")
+
     # Updating charges in OpenMM object. Used to set QM charges to 0 for example
     # Taking list of atom-indices and list of charges (usually zero) and setting new charge
     # Note: Exceptions also needs to be dealt with (see delete_exceptions)

ash/tests/test_QM_MM_openmm.py

@@ -6,7 +6,7 @@
 def test_qm_mm_pyscf_nonbondedtheory_MeOH_H2O():
 
     # H2O...MeOH fragment defined. Reading XYZ file
-    H2O_MeOH = Fragment(xyzfile=f"{ashpath}/tests/xyzfile/h2o_MeOH.xyz")
+    H2O_MeOH = Fragment(xyzfile=f"{ashpath}/tests/xyzfiles/h2o_MeOH.xyz")
 
     # Specifying the QM atoms (3-8) by atom indices (MeOH). The other atoms (0,1,2) is the H2O and MM.
     # IMPORTANT: atom indices begin at 0.
@@ -56,7 +56,7 @@ def test_qm_mm_pyscf_nonbondedtheory_MeOH_H2O():
 def test_qm_mm_pyscf_openmm_MeOH_H2O():
 
     # H2O...MeOH fragment defined. Reading XYZ file
-    H2O_MeOH = Fragment(xyzfile=f"{ashpath}/tests/xyzfile/h2o_MeOH.xyz")
+    H2O_MeOH = Fragment(xyzfile=f"{ashpath}/tests/xyzfiles/h2o_MeOH.xyz")
 
     # Write PDB-file for OpenMM (used for topology)
     H2O_MeOH.write_pdbfile_openmm(filename="h2o_MeOH.pdb", skip_connectivity=True)