Merge pull request #49 from WangXinyan940/wangxy/xmlholder

fix(unittest): fix classical UTs and remove double check of cutoff distance in potential calculation.
deepmodeling · Jul 5, 2022 · cfa4eac · cfa4eac
2 parents 28642bb + e75620e
commit cfa4eac
Show file tree

Hide file tree

Showing 4 changed files with 3 additions and 5 deletions.
diff --git a/dmff/classical/inter.py b/dmff/classical/inter.py
@@ -198,8 +198,6 @@ def get_rf_energy(dr_vec, chrgprod, box):
             if self.ifPBC:
                 dr_vec = v_pbc_shift(dr_vec, box, jnp.linalg.inv(box))
             dr_norm = jnp.linalg.norm(dr_vec, axis=1)
-            chrgprod = chrgprod[dr_norm <= self.r_cut]
-            dr_norm = dr_norm[dr_norm <= self.r_cut]
 
             dr_inv = 1.0 / dr_norm
             E = (

diff --git a/tests/data/impr1.xml b/tests/data/impr1.xml
@@ -16,7 +16,7 @@
             <Bond atomName1="N1" atomName2="N4"/>
         </Residue>
     </Residues>
-    <PeriodicTorsionForce>
+    <PeriodicTorsionForce ordering="amber">
         <Improper type1="n1" type2="n2" type3="n3" type4="n4" periodicity1="1" phase1="0.0" k1="2.092"/>
     </PeriodicTorsionForce>
 </ForceField>
diff --git a/tests/data/wild1.xml b/tests/data/wild1.xml
@@ -16,7 +16,7 @@
             <Bond atomName1="N3" atomName2="N4"/>
         </Residue>
     </Residues>
-    <PeriodicTorsionForce>
+    <PeriodicTorsionForce ordering="amber">
         <Proper type1="" type2="n2" type3="n3" type4="" periodicity1="1" phase1="0.0" k1="2.092" periodicity2="2" phase2="0.0" k2="2.092" periodicity3="3" phase3="0.0" k3="2.092" periodicity4="4" phase4="0.0" k4="2.092"/>
     </PeriodicTorsionForce>
 </ForceField>
diff --git a/tests/data/wild2.xml b/tests/data/wild2.xml
@@ -16,7 +16,7 @@
             <Bond atomName1="N1" atomName2="N4"/>
         </Residue>
     </Residues>
-    <PeriodicTorsionForce>
+    <PeriodicTorsionForce ordering="amber">
         <Improper type1="n1" type2="" type3="" type4="n4" periodicity1="1" phase1="0.0" k1="2.092"/>
     </PeriodicTorsionForce>
 </ForceField>