More

} else { -->
}
else {

However, these were not my additions originally, but rather part of the Amoeba
test cases that have been around for awhile. I figured while I was at it, I
might as well update these styles as well.

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaAngleForce.cpp

@@ -82,9 +82,11 @@ static void getPrefactorsGivenAngleCosine( double cosine, double idealAngle, dou
     double angle;
     if( cosine >= 1.0 ){
         angle = 0.0f;
-    } else if( cosine <= -1.0 ){
+    }
+    else if( cosine <= -1.0 ){
         angle = RADIAN*PI_M;
-    } else {
+    }
+    else {
         angle = RADIAN*acos(cosine);
     }
 #ifdef AMOEBA_DEBUG
@@ -157,7 +159,7 @@ static void computeAmoebaAngleForce(int bondIndex,  std::vector<Vec3>& positions
     double rp      = sqrt( pVector[0]*pVector[0] + pVector[1]*pVector[1] + pVector[2]*pVector[2] );
     if( rp < 1.0e-06 ){
        rp = 1.0e-06;
-    }   
+    }
     double dot    = deltaR[0][0]*deltaR[1][0] + deltaR[0][1]*deltaR[1][1] + deltaR[0][2]*deltaR[1][2];
     double cosine = dot/sqrt(r2_0*r2_1);
 

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaGeneralizedKirkwoodForce.cpp

@@ -8488,7 +8488,8 @@ int main( int numberOfArguments, char* argv[] ) {
         testGeneralizedKirkwoodVillinDirectPolarization( log );
         testGeneralizedKirkwoodVillinMutualPolarization( log );
-    } catch(const std::exception& e) {
+    }
+    catch(const std::exception& e) {
         std::cout << "exception: " << e.what() << std::endl;
         std::cout << "FAIL - ERROR.  Test failed." << std::endl;
         return 1;

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaInPlaneAngleForce.cpp

@@ -84,9 +84,11 @@ static void getPrefactorsGivenInPlaneAngleCosine( double cosine, double idealInP
     double angle;
     if( cosine >= 1.0 ){
         angle = 0.0f;
-    } else if( cosine <= -1.0 ){
+    }
+    else if( cosine <= -1.0 ){
         angle = RADIAN*PI_M;
-    } else {
+    }
+    else {
         angle = RADIAN*acos(cosine);
     }
 #ifdef AMOEBA_DEBUG
@@ -175,7 +177,7 @@ static void computeAmoebaInPlaneAngleForce(int bondIndex,  std::vector<Vec3>& po
        deltaR[P][ii]  = positions[particle2][ii] + deltaR[T][ii]*delta;
        deltaR[AP][ii] = positions[particle1][ii] - deltaR[P][ii];
        deltaR[CP][ii] = positions[particle3][ii] - deltaR[P][ii];
-    }   
+    }
  
     double rAp2 = dotVector3( deltaR[AP],  deltaR[AP] );
     double rCp2 = dotVector3( deltaR[CP],  deltaR[CP] );
@@ -245,7 +247,8 @@ static void computeAmoebaInPlaneAngleForce(int bondIndex,  std::vector<Vec3>& po
  
           forceTerm[dD][ii]  = -( forceTerm[dA][ii] + forceTerm[dB][ii] + forceTerm[dC][ii] );
        }
-    } else {
+    }
+    else {
        for( int ii = 0; ii < 3; ii++ ){
  
           forceTerm[dA][ii] += delta*deltaR[CDxdB][ii];

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaMultipoleForce.cpp

@@ -623,7 +623,7 @@ static void setupAndGetForcesEnergyMultipoleWater( AmoebaMultipoleForce::Nonbond
         covalentMap.push_back( jj+1 );
         amoebaMultipoleForce->setCovalentMap( jj+2, static_cast<OpenMM::AmoebaMultipoleForce::CovalentType>(1), covalentMap );
     
-    } 
+    }
  
     std::vector<Vec3> positions(numberOfParticles);
 
@@ -841,7 +841,8 @@ static void testQuadrupoleValidation( FILE* log ){
         std::stringstream buffer;        
         buffer << "Exception not thrown for quadrupole tensor w/ nonzero trace.";
         throw OpenMMException(buffer.str());
-    } catch(const std::exception& e) {
+    }
+    catch(const std::exception& e) {
     }
     oxygenMolecularQuadrupole[4] -= 0.1;
 
@@ -857,7 +858,8 @@ static void testQuadrupoleValidation( FILE* log ){
         std::stringstream buffer;        
         buffer << "Exception not thrown for quadrupole tensor w/ nonzero trace.";
         throw OpenMMException(buffer.str());
-    } catch(const std::exception& e) {
+    }
+    catch(const std::exception& e) {
     }
     oxygenMolecularQuadrupole[1] -= 0.1;
 
@@ -871,7 +873,8 @@ static void testQuadrupoleValidation( FILE* log ){
         std::stringstream buffer;        
         buffer << "Exception not thrown for quadrupole tensor w/ nonzero trace.";
         throw OpenMMException(buffer.str());
-    } catch(const std::exception& e) {
+    }
+    catch(const std::exception& e) {
     }
     oxygenMolecularQuadrupole[2] -= 0.1;
 
@@ -885,7 +888,8 @@ static void testQuadrupoleValidation( FILE* log ){
         std::stringstream buffer;        
         buffer << "Exception not thrown for quadrupole tensor w/ nonzero trace.";
         throw OpenMMException(buffer.str());
-    } catch(const std::exception& e) {
+    }
+    catch(const std::exception& e) {
     }
     oxygenMolecularQuadrupole[5] -= 0.1;
 
@@ -1043,7 +1047,7 @@ static void setupAndGetForcesEnergyMultipoleIonsAndWater( AmoebaMultipoleForce::
         covalentMap.push_back( jj+1 );
         amoebaMultipoleForce->setCovalentMap( jj+2, static_cast<OpenMM::AmoebaMultipoleForce::CovalentType>(1), covalentMap );
     
-    } 
+    }
  
     std::vector<Vec3> positions(numberOfParticles);
 
@@ -1259,7 +1263,7 @@ static void setupAndGetForcesEnergyMultipoleLargeWater( AmoebaMultipoleForce::No
         covalentMap.push_back( jj+1 );
         amoebaMultipoleForce->setCovalentMap( jj+2, static_cast<OpenMM::AmoebaMultipoleForce::CovalentType>(1), covalentMap );
     
-    } 
+    }
     system.addForce(amoebaMultipoleForce);
  
     static std::vector<Vec3> positions; // Static to work around bug in Visual Studio that makes compilation very very slow.
@@ -1923,9 +1927,11 @@ static void setupAndGetForcesEnergyMultipoleLargeWater( AmoebaMultipoleForce::No
 
     if( testName == "testSystemMultipoleMoments" ){
         amoebaMultipoleForce->getSystemMultipoleMoments( context, outputMultipoleMoments );
-    } else if( testName == "testMultipoleGridPotential" ){
+    }
+    else if( testName == "testMultipoleGridPotential" ){
         amoebaMultipoleForce->getElectrostaticPotential( inputGrid, context, outputGridPotential );
-    } else {
+    }
+    else {
 
         State state               = context.getState(State::Forces | State::Energy);
         forces                    = state.getForces();
@@ -2690,7 +2696,8 @@ static void testSystemMultipoleMoments( FILE* log ) {
         double difference;
         if( fabs( tinkerMoments[ii] ) > 0.0 ){
             difference = fabs( outputMultipoleMoments[ii] - tinkerMoments[ii] )/fabs( tinkerMoments[ii] );
-        } else {
+        }
+        else {
             difference = fabs( outputMultipoleMoments[ii] - tinkerMoments[ii] );
         }
         if( log ){
@@ -2854,7 +2861,8 @@ int main( int numberOfArguments, char* argv[] ) {
 
         testPMEMutualPolarizationLargeWater( log );
 
-    } catch(const std::exception& e) {
+    }
+    catch(const std::exception& e) {
         std::cout << "exception: " << e.what() << std::endl;
         std::cout << "FAIL - ERROR.  Test failed." << std::endl;
         return 1;

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaOutOfPlaneBendForce.cpp

@@ -114,7 +114,7 @@ static void computeAmoebaOutOfPlaneBendForce(int bondIndex,  std::vector<Vec3>&
          deltaR[DB][ii] = positions[particle4][ii] - positions[particle2][ii];
          deltaR[AD][ii] = positions[particle1][ii] - positions[particle4][ii];
          deltaR[CD][ii] = positions[particle3][ii] - positions[particle4][ii];
-    }   
+    }
 
     double rDB2  = dotVector3( deltaR[DB], deltaR[DB] );
     double rAD2  = dotVector3( deltaR[AD], deltaR[AD] );
@@ -134,9 +134,11 @@ static void computeAmoebaOutOfPlaneBendForce(int bondIndex,  std::vector<Vec3>&
     double angle;
     if( cosine >= 1.0 ){
         angle = 0.0;
-    } else if( cosine <= -1.0 ){
+    }
+    else if( cosine <= -1.0 ){
         angle = PI_M;
-    } else {
+    }
+    else {
         angle = RADIAN*acos(cosine);
     }
 #ifdef AMOEBA_DEBUG 
@@ -405,37 +407,43 @@ void testOneOutOfPlaneBend2( FILE* log, int setId ) {
         particleIndices.push_back( 443 ); 
         particleIndices.push_back( 444 ); 
         kOutOfPlaneBend = 0.328682196E-01;
-    } else if( setId == 2 ){
+    }
+    else if( setId == 2 ){
         particleIndices.push_back( 441 ); 
         particleIndices.push_back( 442 ); 
         particleIndices.push_back( 444 ); 
         particleIndices.push_back( 443 ); 
         kOutOfPlaneBend = 0.164493407E-01;
-    } else if( setId == 3 ){
+    }
+    else if( setId == 3 ){
         particleIndices.push_back( 443 ); 
         particleIndices.push_back( 442 ); 
         particleIndices.push_back( 444 ); 
         particleIndices.push_back( 441 ); 
         kOutOfPlaneBend = 0.636650407E-02;
-    } else if( setId == 4 ){
+    }
+    else if( setId == 4 ){
         particleIndices.push_back( 442 ); 
         particleIndices.push_back( 444 ); 
         particleIndices.push_back( 447 ); 
         particleIndices.push_back( 448 ); 
         kOutOfPlaneBend = 0.392956472E-02;
-    } else if( setId == 5 ){
+    }
+    else if( setId == 5 ){
         particleIndices.push_back( 442 ); 
         particleIndices.push_back( 444 ); 
         particleIndices.push_back( 448 ); 
         particleIndices.push_back( 447 ); 
         kOutOfPlaneBend = 0.392956472E-02;
-    } else if( setId == 6 ){
+    }
+    else if( setId == 6 ){
         particleIndices.push_back( 447 ); 
         particleIndices.push_back( 444 ); 
         particleIndices.push_back( 448 ); 
         particleIndices.push_back( 442 ); 
         kOutOfPlaneBend = 0.214755281E-01;
-    } else {
+    }
+    else {
 #ifdef AMOEBA_DEBUG
         if( log ){
             (void) fprintf( log, "Set id %d not recognized.\n", setId );

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaStretchBendForce.cpp

@@ -129,9 +129,11 @@ static void computeAmoebaStretchBendForce(int bondIndex,  std::vector<Vec3>& pos
     double angle;
     if( cosine >= 1.0 ){
        angle = 0.0;
-    } else if( cosine <= -1.0 ){
+    }
+    else if( cosine <= -1.0 ){
        angle = PI_M;
-    } else {
+    }
+    else {
        angle = RADIAN*acos(cosine);
     }
  

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaTorsionTorsionForce.cpp

@@ -2620,7 +2620,8 @@ void testTorsionTorsion(int systemId, bool includeDerivs) {
 
         expectedEnergy        = -2.699654759E+00;
 
-    } else if( systemId == 1 ){
+    }
+    else if( systemId == 1 ){
 
         // villin: 158    176    177    178    183     -1      0
         chiralCheckAtomIndex  = -1;
@@ -2676,7 +2677,8 @@ int main( int numberOfArguments, char* argv[] ) {
         registerAmoebaReferenceKernelFactories();
         testTorsionTorsion(1, true);
         testTorsionTorsion(1, false);
-    } catch(const std::exception& e) {
+    }
+    catch(const std::exception& e) {
         std::cout << "exception: " << e.what() << std::endl;
         std::cout << "FAIL - ERROR.  Test failed." << std::endl;
         return 1;

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaVdwForce.cpp

@@ -75,7 +75,8 @@ void testVdw( FILE* log ) {
             sigma       = 1.70250E+00;
             epsilon     = 1.10000E-01;
             reduction   = 0.0;
-        } else {
+        }
+        else {
             mass        = 1.0;
             indexIV     = ii < 3 ? 0 : 3;
             sigma       = 1.32750E+00;
@@ -89,7 +90,8 @@ void testVdw( FILE* log ) {
             exclusions.push_back ( 0 );
             exclusions.push_back ( 1 );
             exclusions.push_back ( 2 );
-        } else {
+        }
+        else {
             exclusions.push_back ( 3 );
             exclusions.push_back ( 4 );
             exclusions.push_back ( 5 );
@@ -155,7 +157,7 @@ void testVdw( FILE* log ) {
         forces[ii][0] *= conversion;
         forces[ii][1] *= conversion;
         forces[ii][2] *= conversion;
-    }    
+    }
     expectedEnergy *= CalToJoule;
 
 #ifdef AMOEBA_DEBUG
@@ -223,7 +225,8 @@ void setupAndGetForcesEnergyVdwAmmonia( const std::string& sigmaCombiningRule, c
         system.setDefaultPeriodicBoxVectors( a, b, c );
         amoebaVdwForce->setNonbondedMethod(AmoebaVdwForce::CutoffPeriodic);
         amoebaVdwForce->setUseDispersionCorrection( 1 );
-    } else {
+    }
+    else {
         amoebaVdwForce->setNonbondedMethod(AmoebaVdwForce::NoCutoff);
         amoebaVdwForce->setUseDispersionCorrection( 0 );
     }
@@ -330,7 +333,8 @@ void setupAndGetForcesEnergyVdwAmmonia( const std::string& sigmaCombiningRule, c
 
     if( boxDimension > 0.0 ){
         ASSERT(amoebaVdwForce->usesPeriodicBoundaryConditions());
-    } else {
+    }
+    else {
         ASSERT(!amoebaVdwForce->usesPeriodicBoundaryConditions());
     }
 
@@ -573,7 +577,8 @@ void setupAndGetForcesEnergyVdwWater( const std::string& sigmaCombiningRule, con
         system.setDefaultPeriodicBoxVectors( a, b, c );
         amoebaVdwForce->setNonbondedMethod(AmoebaVdwForce::CutoffPeriodic);
         amoebaVdwForce->setUseDispersionCorrection( includeVdwDispersionCorrection );
-    } else {
+    }
+    else {
         amoebaVdwForce->setNonbondedMethod(AmoebaVdwForce::NoCutoff);
         amoebaVdwForce->setUseDispersionCorrection( 0 );
     }
@@ -1281,7 +1286,8 @@ void testVdwWater( int includeVdwDispersionCorrection, FILE* log ) {
     std::string testName;
     if( includeVdwDispersionCorrection ){
         testName      = "testVdwWaterWithDispersionCorrection";
-    } else {
+    }
+    else {
         testName      = "testVdwWater";
     }
 
@@ -1299,7 +1305,8 @@ void testVdwWater( int includeVdwDispersionCorrection, FILE* log ) {
     double expectedEnergy;
     if( includeVdwDispersionCorrection ){
         expectedEnergy     = 4.0108819792e+03;
-    } else {
+    }
+    else {
         expectedEnergy     = 4.0349101e+03;
     }
 
@@ -2036,7 +2043,8 @@ int main( int numberOfArguments, char* argv[] ) {
         includeVdwDispersionCorrection     = 1;
         testVdwWater( includeVdwDispersionCorrection, log );
 
-    } catch(const std::exception& e) {
+    }
+    catch(const std::exception& e) {
         std::cout << "exception: " << e.what() << std::endl;
         std::cout << "FAIL - ERROR.  Test failed." << std::endl;
         return 1;

plugins/amoeba/platforms/reference/tests/TestReferenceWcaDispersionForce.cpp

@@ -185,7 +185,8 @@ int main( int numberOfArguments, char* argv[] ) {
         testWcaDispersionAmmonia( log );
 
 
-    } catch(const std::exception& e) {
+    }
+    catch(const std::exception& e) {
         std::cout << "exception: " << e.what() << std::endl;
         std::cout << "FAIL - ERROR.  Test failed." << std::endl;
         return 1;