One of loops in reference GBSA/OBC code was missing tests for periodic bndy conditions, cutoff, ...

b292cfcd · Mark Friedrichs · e1656dcb · b292cfcd
Commit b292cfcd authored Jun 19, 2009 by Mark Friedrichs
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Showing with 26 additions and 13 deletions

platforms/reference/src/gbsa/CpuObc.cpp platforms/reference/src/gbsa/CpuObc.cpp +26 -13

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--- a/platforms/reference/src/gbsa/CpuObc.cpp
+++ b/platforms/reference/src/gbsa/CpuObc.cpp
@@ -527,12 +527,18 @@ int CpuObc::computeBornEnergyForces( RealOpenMM* bornRadii, RealOpenMM** atomCoo

         if( atomJ != atomI ){

-            RealOpenMM deltaX             = atomCoordinates[atomJ][0] - atomCoordinates[atomI][0];
-            RealOpenMM deltaY             = atomCoordinates[atomJ][1] - atomCoordinates[atomI][1];
-            RealOpenMM deltaZ             = atomCoordinates[atomJ][2] - atomCoordinates[atomI][2];
-    
-            RealOpenMM r2                 = deltaX*deltaX + deltaY*deltaY + deltaZ*deltaZ;
-            RealOpenMM r                  = SQRT( r2 );
+            RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
+            if (_obcParameters->getPeriodic())
+               ReferenceForce::getDeltaRPeriodic( atomCoordinates[atomI], atomCoordinates[atomJ], _obcParameters->getPeriodicBox(), deltaR );
+            else 
+               ReferenceForce::getDeltaR( atomCoordinates[atomI], atomCoordinates[atomJ], deltaR );
+            if (_obcParameters->getUseCutoff() && deltaR[ReferenceForce::RIndex] > _obcParameters->getCutoffDistance())
+                   continue;
+   
+            RealOpenMM deltaX             = deltaR[ReferenceForce::XIndex];
+            RealOpenMM deltaY             = deltaR[ReferenceForce::YIndex];
+            RealOpenMM deltaZ             = deltaR[ReferenceForce::ZIndex];
+            RealOpenMM r                  = deltaR[ReferenceForce::RIndex];
 
            // radius w/ dielectric offset applied

@@ -969,6 +975,7 @@ FILE* logFile = NULL;
             ReferenceForce::getDeltaR( atomCoordinates[atomI], atomCoordinates[atomJ], deltaR );
         if (_obcParameters->getUseCutoff() && deltaR[ReferenceForce::RIndex] > _obcParameters->getCutoffDistance())
             continue;
+
         RealOpenMM r2                 = deltaR[ReferenceForce::R2Index];
         RealOpenMM deltaX             = deltaR[ReferenceForce::XIndex];
         RealOpenMM deltaY             = deltaR[ReferenceForce::YIndex];
@@ -1131,13 +1138,19 @@ for( int atomI = 0; atomI < numberOfAtoms; atomI++ ){

         if( atomJ != atomI ){

-            RealOpenMM deltaX             = atomCoordinates[atomJ][0] - atomCoordinates[atomI][0];
-            RealOpenMM deltaY             = atomCoordinates[atomJ][1] - atomCoordinates[atomI][1];
-            RealOpenMM deltaZ             = atomCoordinates[atomJ][2] - atomCoordinates[atomI][2];
-    
-            RealOpenMM r2                 = deltaX*deltaX + deltaY*deltaY + deltaZ*deltaZ;
-            RealOpenMM r                  = SQRT( r2 );
- 
+            RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
+            if (_obcParameters->getPeriodic())
+               ReferenceForce::getDeltaRPeriodic( atomCoordinates[atomI], atomCoordinates[atomJ], _obcParameters->getPeriodicBox(), deltaR );
+            else 
+               ReferenceForce::getDeltaR( atomCoordinates[atomI], atomCoordinates[atomJ], deltaR );
+            if (_obcParameters->getUseCutoff() && deltaR[ReferenceForce::RIndex] > _obcParameters->getCutoffDistance())
+                   continue;
+   
+            RealOpenMM deltaX             = deltaR[ReferenceForce::XIndex];
+            RealOpenMM deltaY             = deltaR[ReferenceForce::YIndex];
+            RealOpenMM deltaZ             = deltaR[ReferenceForce::ZIndex];
+            RealOpenMM r                  = deltaR[ReferenceForce::RIndex];
+
            // radius w/ dielectric offset applied

            RealOpenMM radiusJ            = atomicRadii[atomJ] - dielectricOffset;