Merge pull request #762 from swails/is_periodic

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

platforms/reference/tests/TestReferenceHarmonicBondForce.cpp

@@ -59,6 +59,8 @@ void testBonds() {
     forceField->addBond(0, 1, 1.5, 0.8);
     forceField->addBond(1, 2, 1.2, 0.7);
     system.addForce(forceField);
+    ASSERT(!forceField->usesPeriodicBoundaryConditions());
+    ASSERT(!system.usesPeriodicBoundaryConditions());
     Context context(system, integrator, platform);
     vector<Vec3> positions(3);
     positions[0] = Vec3(0, 2, 0);

platforms/reference/tests/TestReferenceMonteCarloAnisotropicBarostat.cpp

@@ -75,6 +75,8 @@ void testIdealGas() {
     }
     MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], true, true, true, frequency);
     system.addForce(barostat);
+    ASSERT(barostat->usesPeriodicBoundaryConditions());
+    ASSERT(system.usesPeriodicBoundaryConditions());
     
     // Test it for three different temperatures.
     
@@ -134,6 +136,8 @@ void testIdealGasAxis(int axis) {
     }
     MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp[0], scaleX, scaleY, scaleZ, frequency);
     system.addForce(barostat);
+    ASSERT(barostat->usesPeriodicBoundaryConditions());
+    ASSERT(system.usesPeriodicBoundaryConditions());
     
     // Test it for three different temperatures.
     
@@ -191,6 +195,8 @@ void testRandomSeed() {
     system.addForce(forceField);
     MonteCarloAnisotropicBarostat* barostat = new MonteCarloAnisotropicBarostat(Vec3(pressure, pressure, pressure), temp, true, true, true, 1);
     system.addForce(barostat);
+    ASSERT(barostat->usesPeriodicBoundaryConditions());
+    ASSERT(system.usesPeriodicBoundaryConditions());
     vector<Vec3> positions(numParticles);
     vector<Vec3> velocities(numParticles);
     for (int i = 0; i < numParticles; ++i) {

platforms/reference/tests/TestReferenceMonteCarloBarostat.cpp

@@ -112,6 +112,8 @@ void testIdealGas() {
     }
     MonteCarloBarostat* barostat = new MonteCarloBarostat(pressure, temp[0], frequency);
     system.addForce(barostat);
+    ASSERT(barostat->usesPeriodicBoundaryConditions());
+    ASSERT(system.usesPeriodicBoundaryConditions());
 
     // Test it for three different temperatures.
 
@@ -159,6 +161,8 @@ void testRandomSeed() {
     system.addForce(forceField);
     MonteCarloBarostat* barostat = new MonteCarloBarostat(pressure, temp, 1);
     system.addForce(barostat);
+    ASSERT(barostat->usesPeriodicBoundaryConditions());
+    ASSERT(system.usesPeriodicBoundaryConditions());
     vector<Vec3> positions(numParticles);
     vector<Vec3> velocities(numParticles);
     for (int i = 0; i < numParticles; ++i) {

platforms/reference/tests/TestReferenceMonteCarloMembraneBarostat.cpp

@@ -75,6 +75,8 @@ void testIdealGas(MonteCarloMembraneBarostat::XYMode xymode, MonteCarloMembraneB
     }
     MonteCarloMembraneBarostat* barostat = new MonteCarloMembraneBarostat(pressure, tension, temp[0], xymode, zmode, frequency);
     system.addForce(barostat);
+    ASSERT(barostat->usesPeriodicBoundaryConditions());
+    ASSERT(system.usesPeriodicBoundaryConditions());
 
     // Test it for three different temperatures.
 
@@ -132,6 +134,8 @@ void testRandomSeed() {
     system.addForce(forceField);
     MonteCarloMembraneBarostat* barostat = new MonteCarloMembraneBarostat(pressure, tension, temp, MonteCarloMembraneBarostat::XYAnisotropic, MonteCarloMembraneBarostat::ZFree, 1);
     system.addForce(barostat);
+    ASSERT(barostat->usesPeriodicBoundaryConditions());
+    ASSERT(system.usesPeriodicBoundaryConditions());
     vector<Vec3> positions(numParticles);
     vector<Vec3> velocities(numParticles);
     for (int i = 0; i < numParticles; ++i) {

platforms/reference/tests/TestReferenceNonbondedForce.cpp

@@ -59,6 +59,8 @@ void testCoulomb() {
     forceField->addParticle(0.5, 1, 0);
     forceField->addParticle(-1.5, 1, 0);
     system.addForce(forceField);
+    ASSERT(!forceField->usesPeriodicBoundaryConditions());
+    ASSERT(!system.usesPeriodicBoundaryConditions());
     Context context(system, integrator, platform);
     vector<Vec3> positions(2);
     positions[0] = Vec3(0, 0, 0);
@@ -82,6 +84,8 @@ void testLJ() {
     forceField->addParticle(0, 1.2, 1);
     forceField->addParticle(0, 1.4, 2);
     system.addForce(forceField);
+    ASSERT(!forceField->usesPeriodicBoundaryConditions());
+    ASSERT(!system.usesPeriodicBoundaryConditions());
     Context context(system, integrator, platform);
     vector<Vec3> positions(2);
     positions[0] = Vec3(0, 0, 0);
@@ -201,6 +205,8 @@ void testCutoff() {
     const double eps = 50.0;
     forceField->setReactionFieldDielectric(eps);
     system.addForce(forceField);
+    ASSERT(!forceField->usesPeriodicBoundaryConditions());
+    ASSERT(!system.usesPeriodicBoundaryConditions());
     Context context(system, integrator, platform);
     vector<Vec3> positions(3);
     positions[0] = Vec3(0, 0, 0);
@@ -252,6 +258,8 @@ void testCutoff14() {
             second14 = i;
     }
     system.addForce(nonbonded);
+    ASSERT(!nonbonded->usesPeriodicBoundaryConditions());
+    ASSERT(!system.usesPeriodicBoundaryConditions());
     Context context(system, integrator, platform);
     vector<Vec3> positions(5);
     positions[0] = Vec3(0, 0, 0);
@@ -333,6 +341,8 @@ void testPeriodic() {
     nonbonded->setCutoffDistance(cutoff);
     system.setDefaultPeriodicBoxVectors(Vec3(4, 0, 0), Vec3(0, 4, 0), Vec3(0, 0, 4));
     system.addForce(nonbonded);
+    ASSERT(nonbonded->usesPeriodicBoundaryConditions());
+    ASSERT(system.usesPeriodicBoundaryConditions());
     Context context(system, integrator, platform);
     vector<Vec3> positions(3);
     positions[0] = Vec3(0, 0, 0);
@@ -376,6 +386,8 @@ void testDispersionCorrection() {
     nonbonded->setCutoffDistance(cutoff);
     system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
     system.addForce(nonbonded);
+    ASSERT(nonbonded->usesPeriodicBoundaryConditions());
+    ASSERT(system.usesPeriodicBoundaryConditions());
 
     // See if the correction has the correct value.
 
@@ -435,6 +447,14 @@ void testSwitchingFunction(NonbondedForce::NonbondedMethod method) {
     nonbonded->setSwitchingDistance(1.5);
     nonbonded->setUseDispersionCorrection(false);
     system.addForce(nonbonded);
+    if (method == NonbondedForce::PME) {
+        ASSERT(nonbonded->usesPeriodicBoundaryConditions());
+        ASSERT(system.usesPeriodicBoundaryConditions());
+    }
+    else {
+        ASSERT(!nonbonded->usesPeriodicBoundaryConditions());
+        ASSERT(!system.usesPeriodicBoundaryConditions());
+    }
     Context context(system, integrator, platform);
     vector<Vec3> positions(2);
     positions[0] = Vec3(0, 0, 0);

platforms/reference/tests/TestReferencePeriodicTorsionForce.cpp

@@ -59,6 +59,8 @@ void testPeriodicTorsions() {
     PeriodicTorsionForce* forceField = new PeriodicTorsionForce();
     forceField->addTorsion(0, 1, 2, 3, 2, PI_M/3, 1.1);
     system.addForce(forceField);
+    ASSERT(!forceField->usesPeriodicBoundaryConditions());
+    ASSERT(!system.usesPeriodicBoundaryConditions());
     Context context(system, integrator, platform);
     vector<Vec3> positions(4);
     positions[0] = Vec3(0, 1, 0);

platforms/reference/tests/TestReferenceRBTorsionForce.cpp

@@ -59,6 +59,8 @@ void testRBTorsions() {
     RBTorsionForce* forceField = new RBTorsionForce();
     forceField->addTorsion(0, 1, 2, 3, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6);
     system.addForce(forceField);
+    ASSERT(!forceField->usesPeriodicBoundaryConditions());
+    ASSERT(!system.usesPeriodicBoundaryConditions());
     Context context(system, integrator, platform);
     vector<Vec3> positions(4);
     positions[0] = Vec3(0, 1, 0);

plugins/amoeba/openmmapi/include/openmm/AmoebaAngleForce.h

@@ -166,7 +166,15 @@ public:
      * in an angle cannot be changed, nor can new angles be added.
      */
     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;
     double _globalCubicK, _globalQuarticK, _globalPenticK, _globalSexticK;

plugins/amoeba/openmmapi/include/openmm/AmoebaBondForce.h

@@ -138,7 +138,15 @@ public:
      * in a bond cannot be changed, nor can new bonds be added.
      */
     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:
     double _globalQuarticK, _globalCubicK;
     ForceImpl* createImpl() const;

plugins/amoeba/openmmapi/include/openmm/AmoebaGeneralizedKirkwoodForce.h

@@ -163,7 +163,15 @@ public:
      * (the probe radius, the surface area factor, etc.) are unaffected and can only be changed by reinitializing the Context.
      */
     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/amoeba/openmmapi/include/openmm/AmoebaInPlaneAngleForce.h

@@ -171,7 +171,15 @@ public:
      * in an angle cannot be changed, nor can new angles be added.
      */
     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;
     double _globalCubicK, _globalQuarticK, _globalPenticK, _globalSexticK;

plugins/amoeba/openmmapi/include/openmm/AmoebaMultipoleForce.h

@@ -349,7 +349,15 @@ public:
      * 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 nonbondedMethod == AmoebaMultipoleForce::PME;
+    }
 protected:
     ForceImpl* createImpl() const;
 private:

plugins/amoeba/openmmapi/include/openmm/AmoebaOutOfPlaneBendForce.h

@@ -163,7 +163,15 @@ public:
      * in a term cannot be changed, nor can new terms be added.
      */
     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;
     double _globalCubicK, _globalQuarticK, _globalPenticK, _globalSexticK;

plugins/amoeba/openmmapi/include/openmm/AmoebaPiTorsionForce.h

@@ -113,7 +113,15 @@ public:
      * in a torsion cannot be changed, nor can new torsions be added.
      */
     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/amoeba/openmmapi/include/openmm/AmoebaStretchBendForce.h

@@ -116,7 +116,15 @@ public:
      * in a term cannot be changed, nor can new terms be added.
      */
     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/amoeba/openmmapi/include/openmm/AmoebaTorsionTorsionForce.h

@@ -137,7 +137,15 @@ public:
      *                         grid[x][y][5] = dEd(xy) value
      */
     void setTorsionTorsionGrid(int index, const std::vector<std::vector<std::vector<double> > >& grid);
-
+    /**
+     * 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/amoeba/openmmapi/include/openmm/AmoebaVdwForce.h

@@ -212,7 +212,15 @@ public:
      * (the nonbonded method, the cutoff distance, etc.) are unaffected and can only be changed by reinitializing the Context.
      */
     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 nonbondedMethod == AmoebaVdwForce::CutoffPeriodic;
+    }
 protected:
     ForceImpl* createImpl() const;
 private:

plugins/amoeba/openmmapi/include/openmm/AmoebaWcaDispersionForce.h

@@ -121,7 +121,15 @@ public:
     void setShctd(double inputValue);
     void setDispoff(double inputValue);
     void setSlevy(double inputValue);
-
+    /**
+     * 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/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);
 
@@ -286,6 +288,8 @@ void testOneAngle( FILE* log ) {
     amoebaAngleForce->setAmoebaGlobalAngleSextic(sexticK);
 
     system.addForce(amoebaAngleForce);
+    ASSERT(!amoebaAngleForce->usesPeriodicBoundaryConditions());
+    ASSERT(!system.usesPeriodicBoundaryConditions());
     Context context(system, integrator, Platform::getPlatformByName( "Reference"));
 
     std::vector<Vec3> positions(numberOfParticles);

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

@@ -193,6 +193,8 @@ void testTwoBond( FILE* log ) {
     amoebaBondForce->addBond(1, 2, bondLength, quadraticK);
 
     system.addForce(amoebaBondForce);
+    ASSERT(!amoebaBondForce->usesPeriodicBoundaryConditions());
+    ASSERT(!system.usesPeriodicBoundaryConditions());
     Context context(system, integrator, Platform::getPlatformByName( "Reference"));
     std::vector<Vec3> positions(3);