Make zero LJ sigma check consistent with Sire.

OpenBioSim · Jun 4, 2024 · 7326023 · 7326023
1 parent 9326a91
commit 7326023
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/src/somd2/runner/_somd1.py b/src/somd2/runner/_somd1.py
@@ -70,16 +70,16 @@ def _make_compatible(system):
         # First fix zero LJ sigmas values.
         ##################################
 
-        # Create a null LJParameter.
-        null_lj = _SireMM.LJParameter()
+        # Tolerance for zero sigma values.
+        null_lj_sigma = 1e-9
 
         for atom in mol.atoms():
             # Get the end state LJ sigma values.
             lj0 = atom.property("LJ0")
             lj1 = atom.property("LJ1")
 
             # Lambda = 0 state has a zero sigma value.
-            if lj0.sigma() == null_lj.sigma():
+            if abs(lj0.sigma().value()) <= null_lj_sigma:
                 # Use the sigma value from the lambda = 1 state.
                 edit_mol = (
                     edit_mol.atom(atom.index())
@@ -90,7 +90,7 @@ def _make_compatible(system):
                 )
 
             # Lambda = 1 state has a zero sigma value.
-            if lj1.sigma() == null_lj.sigma():
+            if abs(lj1.sigma().value()) <= null_lj_sigma:
                 # Use the sigma value from the lambda = 0 state.
                 edit_mol = (
                     edit_mol.atom(atom.index())