Merge pull request #762 from swails/is_periodic

Implements `usesPeriodicBoundaryConditions` on `Force`s and `System`

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

@@ -7176,6 +7176,8 @@ static void testGeneralizedKirkwoodAmmoniaMutualPolarizationWithCavityTerm( FILE
     System system;
     AmoebaGeneralizedKirkwoodForce* amoebaGeneralizedKirkwoodForce  = new AmoebaGeneralizedKirkwoodForce();
     setupMultipoleAmmonia(system, amoebaGeneralizedKirkwoodForce, AmoebaMultipoleForce::Mutual, 1);
+    ASSERT(!amoebaGeneralizedKirkwoodForce->usesPeriodicBoundaryConditions());
+    ASSERT(!system.usesPeriodicBoundaryConditions());
     LangevinIntegrator integrator(0.0, 0.1, 0.01);
     Context context(system, integrator, Platform::getPlatformByName("Reference"));
     getForcesEnergyMultipoleAmmonia(context, forces, energy, log );
@@ -8486,7 +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];
@@ -361,6 +364,8 @@ void testOneAngle( FILE* log ) {
     amoebaInPlaneAngleForce->setAmoebaGlobalInPlaneAngleSextic(sexticK);
 
     system.addForce(amoebaInPlaneAngleForce);
+    ASSERT(!amoebaInPlaneAngleForce->usesPeriodicBoundaryConditions());
+    ASSERT(!system.usesPeriodicBoundaryConditions());
     Context context(system, integrator, Platform::getPlatformByName( "Reference"));
 
     std::vector<Vec3> positions(numberOfParticles);

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

@@ -460,6 +460,8 @@ static void testMultipoleAmmoniaMutualPolarization( FILE* log ) {
     AmoebaMultipoleForce* amoebaMultipoleForce = new AmoebaMultipoleForce();;
     setupMultipoleAmmonia(system, amoebaMultipoleForce, AmoebaMultipoleForce::NoCutoff, AmoebaMultipoleForce::Mutual, 
                                              cutoff, inputPmeGridDimension);
+    ASSERT(!amoebaMultipoleForce->usesPeriodicBoundaryConditions());
+    ASSERT(!system.usesPeriodicBoundaryConditions());
     LangevinIntegrator integrator(0.0, 0.1, 0.01);
     Context context(system, integrator, Platform::getPlatformByName("Reference"));
     getForcesEnergyMultipoleAmmonia(context, forces, energy);
@@ -621,7 +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);
 
@@ -639,6 +641,8 @@ static void setupAndGetForcesEnergyMultipoleWater( AmoebaMultipoleForce::Nonbond
     positions[11]             = Vec3(   5.0590640e-01,   1.8880920e-01,   -6.8813470e-01 );
 
     system.addForce(amoebaMultipoleForce);
+    ASSERT(amoebaMultipoleForce->usesPeriodicBoundaryConditions());
+    ASSERT(system.usesPeriodicBoundaryConditions());
 
     std::string platformName;
     platformName = "Reference";
@@ -837,7 +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;
 
@@ -853,7 +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;
 
@@ -867,7 +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;
 
@@ -881,7 +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;
 
@@ -1039,7 +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);
 
@@ -1255,7 +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.
@@ -1919,9 +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();
@@ -2686,7 +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 ){
@@ -2850,7 +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 
@@ -321,6 +323,8 @@ void testOneOutOfPlaneBend( FILE* log ) {
     amoebaOutOfPlaneBendForce->addOutOfPlaneBend(0, 1, 2, 3, kOutOfPlaneBend );
 
     system.addForce(amoebaOutOfPlaneBendForce);
+    ASSERT(!amoebaOutOfPlaneBendForce->usesPeriodicBoundaryConditions());
+    ASSERT(!system.usesPeriodicBoundaryConditions());
     Context context(system, integrator, Platform::getPlatformByName( "Reference"));
 
     std::vector<Vec3> positions(numberOfParticles);
@@ -403,37 +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/TestReferenceAmoebaPiTorsionForce.cpp

@@ -285,6 +285,8 @@ void testOnePiTorsion( FILE* log ) {
     amoebaPiTorsionForce->addPiTorsion(0, 1, 2, 3, 4, 5, kTorsion );
 
     system.addForce(amoebaPiTorsionForce);
+    ASSERT(!amoebaPiTorsionForce->usesPeriodicBoundaryConditions());
+    ASSERT(!system.usesPeriodicBoundaryConditions());
     Context context(system, integrator, Platform::getPlatformByName( "Reference"));
 
     std::vector<Vec3> positions(numberOfParticles);

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);
     }
  
@@ -275,6 +277,8 @@ void testOneStretchBend( FILE* log ) {
     amoebaStretchBendForce->addStretchBend(0, 1, 2, abLength, cbLength, angleStretchBend, kStretchBend );
 
     system.addForce(amoebaStretchBendForce);
+    ASSERT(!amoebaStretchBendForce->usesPeriodicBoundaryConditions());
+    ASSERT(!system.usesPeriodicBoundaryConditions());
     Context context(system, integrator, Platform::getPlatformByName( "Reference"));
 
     std::vector<Vec3> positions(numberOfParticles);

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;
@@ -2646,6 +2647,8 @@ void testTorsionTorsion(int systemId, bool includeDerivs) {
     amoebaTorsionTorsionForce->setTorsionTorsionGrid(0, getTorsionGrid(gridIndex, includeDerivs));
     
     system.addForce(amoebaTorsionTorsionForce);
+    ASSERT(!amoebaTorsionTorsionForce->usesPeriodicBoundaryConditions());
+    ASSERT(!system.usesPeriodicBoundaryConditions());
     Context context(system, integrator, Platform::getPlatformByName("Reference"));
 
     context.setPositions(positions);
@@ -2674,7 +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 );
     }
@@ -328,6 +331,13 @@ void setupAndGetForcesEnergyVdwAmmonia( const std::string& sigmaCombiningRule, c
 
     system.addForce(amoebaVdwForce);
 
+    if( boxDimension > 0.0 ){
+        ASSERT(amoebaVdwForce->usesPeriodicBoundaryConditions());
+    }
+    else {
+        ASSERT(!amoebaVdwForce->usesPeriodicBoundaryConditions());
+    }
+
     std::string platformName;
     platformName = "Reference";
     LangevinIntegrator integrator(0.0, 0.1, 0.01);
@@ -567,7 +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 );
     }
@@ -1275,7 +1286,8 @@ void testVdwWater( int includeVdwDispersionCorrection, FILE* log ) {
     std::string testName;
     if( includeVdwDispersionCorrection ){
         testName      = "testVdwWaterWithDispersionCorrection";
-    } else {
+    }
+    else {
         testName      = "testVdwWater";
     }
 
@@ -1293,7 +1305,8 @@ void testVdwWater( int includeVdwDispersionCorrection, FILE* log ) {
     double expectedEnergy;
     if( includeVdwDispersionCorrection ){
         expectedEnergy     = 4.0108819792e+03;
-    } else {
+    }
+    else {
         expectedEnergy     = 4.0349101e+03;
     }
 
@@ -2030,7 +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

@@ -116,6 +116,8 @@ void testWcaDispersionAmmonia( FILE* log ) {
     positions[7]              = Vec3(  -2.0426290e-01,  -8.1231400e-02,    4.1033500e-02 );
 
     system.addForce(amoebaWcaDispersionForce);
+    ASSERT(!amoebaWcaDispersionForce->usesPeriodicBoundaryConditions());
+    ASSERT(!system.usesPeriodicBoundaryConditions());
 
     std::string platformName;
     platformName = "Reference";
@@ -183,7 +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;

plugins/drude/openmmapi/include/openmm/DrudeForce.h

@@ -162,6 +162,15 @@ public:
      * be used to add new particles or screenedPairs, only to change the parameters of existing ones.
      */
     void updateParametersInContext(Context& context);
+    /**
+     * Returns whether or not this force makes use of periodic boundary
+     * conditions.
+     *
+     * @returns true if nonbondedMethod uses PBC and false otherwise
+     */
+    bool usesPeriodicBoundaryConditions() const {
+        return false;
+    }
 protected:
     ForceImpl* createImpl() const;
 private:

plugins/drude/platforms/reference/tests/TestReferenceDrudeForce.cpp

@@ -85,6 +85,8 @@ void testSingleParticle() {
     DrudeForce* drude = new DrudeForce();
     drude->addParticle(1, 0, -1, -1, -1, charge, alpha, 1, 1);
     system.addForce(drude);
+    ASSERT(!drude->usesPeriodicBoundaryConditions());
+    ASSERT(!system.usesPeriodicBoundaryConditions());
     vector<Vec3> positions(2);
     positions[0] = Vec3(-1, 0, 0);
     positions[1] = Vec3(2, 0, 0);