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Commit c6ebf6e2 authored by Peter Eastman's avatar Peter Eastman
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Removed the word "harmonic" from lots of places it didn't belong, including class and method names

parent 58b094ce
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plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceHarmonicBondForce.h → plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceBondForce.h
View file @ c6ebf6e2
...@@ -22,15 +22,15 @@ ...@@ -22,15 +22,15 @@
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/ */
#ifndef __AmoebaReferenceHarmonicBondForce_H__ #ifndef __AmoebaReferenceBondForce_H__
#define __AmoebaReferenceHarmonicBondForce_H__ #define __AmoebaReferenceBondForce_H__
#include "SimTKUtilities/RealVec.h" #include "SimTKUtilities/RealVec.h"
#include <vector> #include <vector>
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
class AmoebaReferenceHarmonicBondForce { class AmoebaReferenceBondForce {
public: public:
...@@ -40,7 +40,7 @@ public: ...@@ -40,7 +40,7 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
AmoebaReferenceHarmonicBondForce( ){}; AmoebaReferenceBondForce( ){};
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -48,12 +48,12 @@ public: ...@@ -48,12 +48,12 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
~AmoebaReferenceHarmonicBondForce( ){}; ~AmoebaReferenceBondForce( ){};
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Calculate Amoeba harmonic bond ixns (force and energy) Calculate Amoeba bond ixns (force and energy)
@param numBonds number of bonds @param numBonds number of bonds
@param posData particle positions @param posData particle positions
...@@ -81,7 +81,7 @@ private: ...@@ -81,7 +81,7 @@ private:
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Calculate Amoeba harmonic bond ixns (force and energy) Calculate Amoeba bond ixns (force and energy)
@param positionAtomA Cartesian coordinates of atom A @param positionAtomA Cartesian coordinates of atom A
@param positionAtomB Cartesian coordinates of atom B @param positionAtomB Cartesian coordinates of atom B
...@@ -104,4 +104,4 @@ private: ...@@ -104,4 +104,4 @@ private:
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
#endif // _AmoebaReferenceHarmonicBondForce___ #endif // _AmoebaReferenceBondForce___
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceHarmonicInPlaneAngleForce.cpp → plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceInPlaneAngleForce.cpp
View file @ c6ebf6e2
...@@ -23,7 +23,7 @@ ...@@ -23,7 +23,7 @@
*/ */
#include "AmoebaReferenceForce.h" #include "AmoebaReferenceForce.h"
#include "AmoebaReferenceHarmonicInPlaneAngleForce.h" #include "AmoebaReferenceInPlaneAngleForce.h"
using std::vector; using std::vector;
using OpenMM::RealVec; using OpenMM::RealVec;
...@@ -46,7 +46,7 @@ using OpenMM::RealVec; ...@@ -46,7 +46,7 @@ using OpenMM::RealVec;
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::getPrefactorsGivenAngleCosine( RealOpenMM cosine, RealOpenMM AmoebaReferenceInPlaneAngleForce::getPrefactorsGivenAngleCosine( RealOpenMM cosine,
RealOpenMM idealAngle, RealOpenMM angleK, RealOpenMM idealAngle, RealOpenMM angleK,
RealOpenMM angleCubic, RealOpenMM angleQuartic, RealOpenMM angleCubic, RealOpenMM angleQuartic,
RealOpenMM anglePentic, RealOpenMM angleSextic, RealOpenMM anglePentic, RealOpenMM angleSextic,
...@@ -62,7 +62,7 @@ RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::getPrefactorsGivenAngleCosi ...@@ -62,7 +62,7 @@ RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::getPrefactorsGivenAngleCosi
static const RealOpenMM five = 5.0; static const RealOpenMM five = 5.0;
static const RealOpenMM six = 6.0; static const RealOpenMM six = 6.0;
// static const std::string methodName = "AmoebaReferenceHarmonicInPlaneAngleForce::getPrefactorsGivenAngleCosine"; // static const std::string methodName = "AmoebaReferenceInPlaneAngleForce::getPrefactorsGivenAngleCosine";
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -96,7 +96,7 @@ RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::getPrefactorsGivenAngleCosi ...@@ -96,7 +96,7 @@ RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::getPrefactorsGivenAngleCosi
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Calculate Amoeba harmonic angle ixn (force and energy) Calculate Amoeba angle ixn (force and energy)
@param positionAtomA Cartesian coordinates of atom A @param positionAtomA Cartesian coordinates of atom A
@param positionAtomB Cartesian coordinates of atom B @param positionAtomB Cartesian coordinates of atom B
...@@ -114,7 +114,7 @@ RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::getPrefactorsGivenAngleCosi ...@@ -114,7 +114,7 @@ RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::getPrefactorsGivenAngleCosi
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::calculateAngleIxn( const RealVec& positionAtomA, const RealVec& positionAtomB, RealOpenMM AmoebaReferenceInPlaneAngleForce::calculateAngleIxn( const RealVec& positionAtomA, const RealVec& positionAtomB,
const RealVec& positionAtomC, const RealVec& positionAtomD, const RealVec& positionAtomC, const RealVec& positionAtomD,
RealOpenMM angle, RealOpenMM angleK, RealOpenMM angle, RealOpenMM angleK,
RealOpenMM angleCubic, RealOpenMM angleQuartic, RealOpenMM angleCubic, RealOpenMM angleQuartic,
...@@ -123,7 +123,7 @@ RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::calculateAngleIxn( const Re ...@@ -123,7 +123,7 @@ RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::calculateAngleIxn( const Re
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
//static const std::string methodName = "AmoebaReferenceHarmonicInPlaneAngleForce::calculateHarmonicForce"; //static const std::string methodName = "AmoebaReferenceInPlaneAngleForce::calculateAngleIxn";
static const RealOpenMM zero = 0.0; static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0; static const RealOpenMM one = 1.0;
...@@ -245,7 +245,7 @@ RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::calculateAngleIxn( const Re ...@@ -245,7 +245,7 @@ RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::calculateAngleIxn( const Re
} }
RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::calculateForceAndEnergy( int numAngles, vector<RealVec>& posData, RealOpenMM AmoebaReferenceInPlaneAngleForce::calculateForceAndEnergy( int numAngles, vector<RealVec>& posData,
const std::vector<int>& particle1, const std::vector<int>& particle1,
const std::vector<int>& particle2, const std::vector<int>& particle2,
const std::vector<int>& particle3, const std::vector<int>& particle3,
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceHarmonicInPlaneAngleForce.h → plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceInPlaneAngleForce.h
View file @ c6ebf6e2
...@@ -22,15 +22,15 @@ ...@@ -22,15 +22,15 @@
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/ */
#ifndef __AmoebaReferenceHarmonicInPlaneAngleForce_H__ #ifndef __AmoebaReferenceInPlaneAngleForce_H__
#define __AmoebaReferenceHarmonicInPlaneAngleForce_H__ #define __AmoebaReferenceInPlaneAngleForce_H__
#include "SimTKUtilities/RealVec.h" #include "SimTKUtilities/RealVec.h"
#include <vector> #include <vector>
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
class AmoebaReferenceHarmonicInPlaneAngleForce { class AmoebaReferenceInPlaneAngleForce {
public: public:
...@@ -40,7 +40,7 @@ public: ...@@ -40,7 +40,7 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
AmoebaReferenceHarmonicInPlaneAngleForce( ){}; AmoebaReferenceInPlaneAngleForce( ){};
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -48,11 +48,11 @@ public: ...@@ -48,11 +48,11 @@ public:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
~AmoebaReferenceHarmonicInPlaneAngleForce( ){}; ~AmoebaReferenceInPlaneAngleForce( ){};
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Calculate Amoeba harmonic in-plane angle ixns (force and energy) Calculate Amoeba in-plane angle ixns (force and energy)
@param numBonds number of angles @param numBonds number of angles
@param posData particle positions @param posData particle positions
...@@ -80,10 +80,10 @@ public: ...@@ -80,10 +80,10 @@ public:
const std::vector<int>& particle4, const std::vector<int>& particle4,
const std::vector<RealOpenMM>& angle, const std::vector<RealOpenMM>& angle,
const std::vector<RealOpenMM>& kQuadratic, const std::vector<RealOpenMM>& kQuadratic,
RealOpenMM globalHarmonicAngleCubic, RealOpenMM globalAngleCubic,
RealOpenMM globalHarmonicAngleQuartic, RealOpenMM globalAngleQuartic,
RealOpenMM globalHarmonicAnglePentic, RealOpenMM globalAnglePentic,
RealOpenMM globalHarmonicAngleSextic, RealOpenMM globalAngleSextic,
std::vector<OpenMM::RealVec>& forceData ) const; std::vector<OpenMM::RealVec>& forceData ) const;
private: private:
...@@ -113,7 +113,7 @@ private: ...@@ -113,7 +113,7 @@ private:
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Calculate Amoeba harmonic angle ixn (force and energy) Calculate Amoeba angle ixn (force and energy)
@param positionAtomA Cartesian coordinates of atom A @param positionAtomA Cartesian coordinates of atom A
@param positionAtomB Cartesian coordinates of atom B @param positionAtomB Cartesian coordinates of atom B
...@@ -142,4 +142,4 @@ private: ...@@ -142,4 +142,4 @@ private:
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
#endif // _AmoebaReferenceHarmonicInPlaneAngleForce___ #endif // _AmoebaReferenceInPlaneAngleForce___
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceOutOfPlaneBendForce.cpp
View file @ c6ebf6e2
...@@ -57,7 +57,7 @@ RealOpenMM AmoebaReferenceOutOfPlaneBendForce::calculateOutOfPlaneBendIxn( const ...@@ -57,7 +57,7 @@ RealOpenMM AmoebaReferenceOutOfPlaneBendForce::calculateOutOfPlaneBendIxn( const
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
//static const std::string methodName = "AmoebaReferenceOutOfPlaneBendForce::calculateHarmonicForce"; //static const std::string methodName = "AmoebaReferenceOutOfPlaneBendForce::calculateOutOfPlaneBendIxn";
static const RealOpenMM zero = 0.0; static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0; static const RealOpenMM one = 1.0;
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferencePiTorsionForce.cpp
View file @ c6ebf6e2
...@@ -53,7 +53,7 @@ RealOpenMM AmoebaReferencePiTorsionForce::calculatePiTorsionIxn( const RealVec& ...@@ -53,7 +53,7 @@ RealOpenMM AmoebaReferencePiTorsionForce::calculatePiTorsionIxn( const RealVec&
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
//static const std::string methodName = "AmoebaReferencePiTorsionForce::calculateHarmonicForce"; //static const std::string methodName = "AmoebaReferencePiTorsionForce::calculatePiTorsionIxn";
static const RealOpenMM zero = 0.0; static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0; static const RealOpenMM one = 1.0;
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceStretchBendForce.cpp
View file @ c6ebf6e2
...@@ -57,7 +57,7 @@ RealOpenMM AmoebaReferenceStretchBendForce::calculateStretchBendIxn( const RealV ...@@ -57,7 +57,7 @@ RealOpenMM AmoebaReferenceStretchBendForce::calculateStretchBendIxn( const RealV
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
//static const std::string methodName = "AmoebaReferenceStretchBendForce::calculateHarmonicForce"; //static const std::string methodName = "AmoebaReferenceStretchBendForce::calculateStretchBendIxn";
static const RealOpenMM zero = 0.0; static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0; static const RealOpenMM one = 1.0;
......
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaHarmonicAngleForce.cpp → plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaAngleForce.cpp
View file @ c6ebf6e2
...@@ -30,7 +30,7 @@ ...@@ -30,7 +30,7 @@
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
/** /**
* This tests the Cuda implementation of CudaAmoebaHarmonicAngleForce. * This tests the Cuda implementation of CudaAmoebaAngleForce.
*/ */
#include "openmm/internal/AssertionUtilities.h" #include "openmm/internal/AssertionUtilities.h"
...@@ -117,21 +117,21 @@ static void getPrefactorsGivenAngleCosine( double cosine, double idealAngle, dou ...@@ -117,21 +117,21 @@ static void getPrefactorsGivenAngleCosine( double cosine, double idealAngle, dou
return; return;
} }
static void computeAmoebaHarmonicAngleForce(int bondIndex, std::vector<Vec3>& positions, AmoebaHarmonicAngleForce& amoebaHarmonicAngleForce, static void computeAmoebaAngleForce(int bondIndex, std::vector<Vec3>& positions, AmoebaAngleForce& AmoebaAngleForce,
std::vector<Vec3>& forces, double* energy, FILE* log ) { std::vector<Vec3>& forces, double* energy, FILE* log ) {
int particle1, particle2, particle3; int particle1, particle2, particle3;
double idealAngle; double idealAngle;
double quadraticK; double quadraticK;
amoebaHarmonicAngleForce.getAngleParameters(bondIndex, particle1, particle2, particle3, idealAngle, quadraticK ); AmoebaAngleForce.getAngleParameters(bondIndex, particle1, particle2, particle3, idealAngle, quadraticK );
double cubicK = amoebaHarmonicAngleForce.getAmoebaGlobalHarmonicAngleCubic(); double cubicK = AmoebaAngleForce.getAmoebaGlobalAngleCubic();
double quarticK = amoebaHarmonicAngleForce.getAmoebaGlobalHarmonicAngleQuartic(); double quarticK = AmoebaAngleForce.getAmoebaGlobalAngleQuartic();
double penticK = amoebaHarmonicAngleForce.getAmoebaGlobalHarmonicAnglePentic(); double penticK = AmoebaAngleForce.getAmoebaGlobalAnglePentic();
double sexticK = amoebaHarmonicAngleForce.getAmoebaGlobalHarmonicAngleSextic(); double sexticK = AmoebaAngleForce.getAmoebaGlobalAngleSextic();
#ifdef AMOEBA_DEBUG #ifdef AMOEBA_DEBUG
if( log ){ if( log ){
(void) fprintf( log, "computeAmoebaHarmonicAngleForce: bond %d [%d %d %d] ang=%10.3f k=%10.3f [%10.3e %10.3e %10.3e %10.3e]\n", (void) fprintf( log, "computeAmoebaAngleForce: bond %d [%d %d %d] ang=%10.3f k=%10.3f [%10.3e %10.3e %10.3e %10.3e]\n",
bondIndex, particle1, particle2, particle3, idealAngle, quadraticK, cubicK, quarticK, penticK, sexticK ); bondIndex, particle1, particle2, particle3, idealAngle, quadraticK, cubicK, quarticK, penticK, sexticK );
(void) fflush( log ); (void) fflush( log );
} }
...@@ -198,7 +198,7 @@ static void computeAmoebaHarmonicAngleForce(int bondIndex, std::vector<Vec3>& p ...@@ -198,7 +198,7 @@ static void computeAmoebaHarmonicAngleForce(int bondIndex, std::vector<Vec3>& p
*energy += energyTerm; *energy += energyTerm;
} }
static void computeAmoebaHarmonicAngleForces( Context& context, AmoebaHarmonicAngleForce& amoebaHarmonicAngleForce, static void computeAmoebaAngleForces( Context& context, AmoebaAngleForce& AmoebaAngleForce,
std::vector<Vec3>& expectedForces, double* expectedEnergy, FILE* log ) { std::vector<Vec3>& expectedForces, double* expectedEnergy, FILE* log ) {
// get positions and zero forces // get positions and zero forces
...@@ -214,13 +214,13 @@ static void computeAmoebaHarmonicAngleForces( Context& context, AmoebaHarmonicAn ...@@ -214,13 +214,13 @@ static void computeAmoebaHarmonicAngleForces( Context& context, AmoebaHarmonicAn
// calculates forces/energy // calculates forces/energy
*expectedEnergy = 0.0; *expectedEnergy = 0.0;
for( int ii = 0; ii < amoebaHarmonicAngleForce.getNumAngles(); ii++ ){ for( int ii = 0; ii < AmoebaAngleForce.getNumAngles(); ii++ ){
computeAmoebaHarmonicAngleForce(ii, positions, amoebaHarmonicAngleForce, expectedForces, expectedEnergy, log ); computeAmoebaAngleForce(ii, positions, AmoebaAngleForce, expectedForces, expectedEnergy, log );
} }
#ifdef AMOEBA_DEBUG #ifdef AMOEBA_DEBUG
if( log ){ if( log ){
(void) fprintf( log, "computeAmoebaHarmonicAngleForces: expected energy=%14.7e\n", *expectedEnergy ); (void) fprintf( log, "computeAmoebaAngleForces: expected energy=%14.7e\n", *expectedEnergy );
for( unsigned int ii = 0; ii < positions.size(); ii++ ){ for( unsigned int ii = 0; ii < positions.size(); ii++ ){
(void) fprintf( log, "%6u [%14.7e %14.7e %14.7e]\n", ii, expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2] ); (void) fprintf( log, "%6u [%14.7e %14.7e %14.7e]\n", ii, expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2] );
} }
...@@ -231,19 +231,19 @@ static void computeAmoebaHarmonicAngleForces( Context& context, AmoebaHarmonicAn ...@@ -231,19 +231,19 @@ static void computeAmoebaHarmonicAngleForces( Context& context, AmoebaHarmonicAn
} }
void compareWithExpectedForceAndEnergy( Context& context, AmoebaHarmonicAngleForce& amoebaHarmonicAngleForce, void compareWithExpectedForceAndEnergy( Context& context, AmoebaAngleForce& AmoebaAngleForce,
double tolerance, const std::string& idString, FILE* log) { double tolerance, const std::string& idString, FILE* log) {
std::vector<Vec3> expectedForces; std::vector<Vec3> expectedForces;
double expectedEnergy; double expectedEnergy;
computeAmoebaHarmonicAngleForces( context, amoebaHarmonicAngleForce, expectedForces, &expectedEnergy, log ); computeAmoebaAngleForces( context, AmoebaAngleForce, expectedForces, &expectedEnergy, log );
State state = context.getState(State::Forces | State::Energy); State state = context.getState(State::Forces | State::Energy);
const std::vector<Vec3> forces = state.getForces(); const std::vector<Vec3> forces = state.getForces();
#ifdef AMOEBA_DEBUG #ifdef AMOEBA_DEBUG
if( log ){ if( log ){
(void) fprintf( log, "computeAmoebaHarmonicAngleForces: expected energy=%14.7e %14.7e\n", expectedEnergy, state.getPotentialEnergy() ); (void) fprintf( log, "computeAmoebaAngleForces: expected energy=%14.7e %14.7e\n", expectedEnergy, state.getPotentialEnergy() );
for( unsigned int ii = 0; ii < forces.size(); ii++ ){ for( unsigned int ii = 0; ii < forces.size(); ii++ ){
(void) fprintf( log, "%6u [%14.7e %14.7e %14.7e] [%14.7e %14.7e %14.7e]\n", ii, (void) fprintf( log, "%6u [%14.7e %14.7e %14.7e] [%14.7e %14.7e %14.7e]\n", ii,
expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2], forces[ii][0], forces[ii][1], forces[ii][2] ); expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2], forces[ii][0], forces[ii][1], forces[ii][2] );
...@@ -268,7 +268,7 @@ void testOneAngle( FILE* log ) { ...@@ -268,7 +268,7 @@ void testOneAngle( FILE* log ) {
LangevinIntegrator integrator(0.0, 0.1, 0.01); LangevinIntegrator integrator(0.0, 0.1, 0.01);
AmoebaHarmonicAngleForce* amoebaHarmonicAngleForce = new AmoebaHarmonicAngleForce(); AmoebaAngleForce* amoebaAngleForce = new AmoebaAngleForce();
double angle = 100.0; double angle = 100.0;
double quadraticK = 1.0; double quadraticK = 1.0;
...@@ -276,14 +276,14 @@ void testOneAngle( FILE* log ) { ...@@ -276,14 +276,14 @@ void testOneAngle( FILE* log ) {
double quarticK = 1.0e-02; double quarticK = 1.0e-02;
double penticK = 1.0e-03; double penticK = 1.0e-03;
double sexticK = 1.0e-04; double sexticK = 1.0e-04;
amoebaHarmonicAngleForce->addAngle(0, 1, 2, angle, quadraticK); amoebaAngleForce->addAngle(0, 1, 2, angle, quadraticK);
amoebaHarmonicAngleForce->setAmoebaGlobalHarmonicAngleCubic(cubicK); amoebaAngleForce->setAmoebaGlobalAngleCubic(cubicK);
amoebaHarmonicAngleForce->setAmoebaGlobalHarmonicAngleQuartic(quarticK); amoebaAngleForce->setAmoebaGlobalAngleQuartic(quarticK);
amoebaHarmonicAngleForce->setAmoebaGlobalHarmonicAnglePentic(penticK); amoebaAngleForce->setAmoebaGlobalAnglePentic(penticK);
amoebaHarmonicAngleForce->setAmoebaGlobalHarmonicAngleSextic(sexticK); amoebaAngleForce->setAmoebaGlobalAngleSextic(sexticK);
system.addForce(amoebaHarmonicAngleForce); system.addForce(amoebaAngleForce);
Context context(system, integrator, Platform::getPlatformByName( "Reference")); Context context(system, integrator, Platform::getPlatformByName( "Reference"));
std::vector<Vec3> positions(numberOfParticles); std::vector<Vec3> positions(numberOfParticles);
...@@ -293,16 +293,16 @@ void testOneAngle( FILE* log ) { ...@@ -293,16 +293,16 @@ void testOneAngle( FILE* log ) {
positions[2] = Vec3(0, 0, 1); positions[2] = Vec3(0, 0, 1);
context.setPositions(positions); context.setPositions(positions);
compareWithExpectedForceAndEnergy( context, *amoebaHarmonicAngleForce, TOL, "testOneAngle", log ); compareWithExpectedForceAndEnergy( context, *amoebaAngleForce, TOL, "testOneAngle", log );
} }
int main( int numberOfArguments, char* argv[] ) { int main( int numberOfArguments, char* argv[] ) {
try { try {
std::cout << "TestCudaAmoebaHarmonicAngleForce running test..." << std::endl; std::cout << "TestCudaAmoebaAngleForce running test..." << std::endl;
Platform::loadPluginsFromDirectory( Platform::getDefaultPluginsDirectory() ); Platform::loadPluginsFromDirectory( Platform::getDefaultPluginsDirectory() );
//FILE* log = fopen( "AmoebaHarmonicAngleForce.log", "w" );; //FILE* log = fopen( "AmoebaAngleForce.log", "w" );;
FILE* log = NULL; FILE* log = NULL;
//FILE* log = stderr; //FILE* log = stderr;
......
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaHarmonicBondForce.cpp → plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaBondForce.cpp
View file @ c6ebf6e2
...@@ -30,7 +30,7 @@ ...@@ -30,7 +30,7 @@
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
/** /**
* This tests the Reference implementation of HarmonicBondForce. * This tests the Reference implementation of AmoebaBondForce.
*/ */
#include "openmm/internal/AssertionUtilities.h" #include "openmm/internal/AssertionUtilities.h"
...@@ -45,15 +45,15 @@ using namespace OpenMM; ...@@ -45,15 +45,15 @@ using namespace OpenMM;
const double TOL = 1e-5; const double TOL = 1e-5;
static void computeAmoebaHarmonicBondForce(int bondIndex, std::vector<Vec3>& positions, AmoebaHarmonicBondForce& amoebaHarmonicBondForce, static void computeAmoebaBondForce(int bondIndex, std::vector<Vec3>& positions, AmoebaBondForce& AmoebaBondForce,
std::vector<Vec3>& forces, double* energy ) { std::vector<Vec3>& forces, double* energy ) {
int particle1, particle2; int particle1, particle2;
double bondLength; double bondLength;
double quadraticK; double quadraticK;
double cubicK = amoebaHarmonicBondForce.getAmoebaGlobalHarmonicBondCubic(); double cubicK = AmoebaBondForce.getAmoebaGlobalBondCubic();
double quarticK = amoebaHarmonicBondForce.getAmoebaGlobalHarmonicBondQuartic(); double quarticK = AmoebaBondForce.getAmoebaGlobalBondQuartic();
amoebaHarmonicBondForce.getBondParameters(bondIndex, particle1, particle2, bondLength, quadraticK ); AmoebaBondForce.getBondParameters(bondIndex, particle1, particle2, bondLength, quadraticK );
double deltaR[3]; double deltaR[3];
double r2 = 0.0; double r2 = 0.0;
...@@ -81,7 +81,7 @@ static void computeAmoebaHarmonicBondForce(int bondIndex, std::vector<Vec3>& po ...@@ -81,7 +81,7 @@ static void computeAmoebaHarmonicBondForce(int bondIndex, std::vector<Vec3>& po
} }
static void computeAmoebaHarmonicBondForces( Context& context, AmoebaHarmonicBondForce& amoebaHarmonicBondForce, static void computeAmoebaBondForces( Context& context, AmoebaBondForce& AmoebaBondForce,
std::vector<Vec3>& expectedForces, double* expectedEnergy, FILE* log ) { std::vector<Vec3>& expectedForces, double* expectedEnergy, FILE* log ) {
// get positions and zero forces // get positions and zero forces
...@@ -97,12 +97,12 @@ static void computeAmoebaHarmonicBondForces( Context& context, AmoebaHarmonicBon ...@@ -97,12 +97,12 @@ static void computeAmoebaHarmonicBondForces( Context& context, AmoebaHarmonicBon
// calculates forces/energy // calculates forces/energy
*expectedEnergy = 0.0; *expectedEnergy = 0.0;
for( int ii = 0; ii < amoebaHarmonicBondForce.getNumBonds(); ii++ ){ for( int ii = 0; ii < AmoebaBondForce.getNumBonds(); ii++ ){
computeAmoebaHarmonicBondForce(ii, positions, amoebaHarmonicBondForce, expectedForces, expectedEnergy ); computeAmoebaBondForce(ii, positions, AmoebaBondForce, expectedForces, expectedEnergy );
} }
#ifdef AMOEBA_DEBUG #ifdef AMOEBA_DEBUG
if( log ){ if( log ){
(void) fprintf( log, "computeAmoebaHarmonicBondForces: expected energy=%15.7e\n", *expectedEnergy ); (void) fprintf( log, "computeAmoebaBondForces: expected energy=%15.7e\n", *expectedEnergy );
for( unsigned int ii = 0; ii < positions.size(); ii++ ){ for( unsigned int ii = 0; ii < positions.size(); ii++ ){
(void) fprintf( log, "%6u [%15.7e %15.7e %15.7e]\n", ii, expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2] ); (void) fprintf( log, "%6u [%15.7e %15.7e %15.7e]\n", ii, expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2] );
} }
...@@ -113,17 +113,17 @@ static void computeAmoebaHarmonicBondForces( Context& context, AmoebaHarmonicBon ...@@ -113,17 +113,17 @@ static void computeAmoebaHarmonicBondForces( Context& context, AmoebaHarmonicBon
} }
void compareWithExpectedForceAndEnergy( Context& context, AmoebaHarmonicBondForce& amoebaHarmonicBondForce, double tolerance, const std::string& idString, FILE* log) { void compareWithExpectedForceAndEnergy( Context& context, AmoebaBondForce& AmoebaBondForce, double tolerance, const std::string& idString, FILE* log) {
std::vector<Vec3> expectedForces; std::vector<Vec3> expectedForces;
double expectedEnergy; double expectedEnergy;
computeAmoebaHarmonicBondForces( context, amoebaHarmonicBondForce, expectedForces, &expectedEnergy, NULL ); computeAmoebaBondForces( context, AmoebaBondForce, expectedForces, &expectedEnergy, NULL );
State state = context.getState(State::Forces | State::Energy); State state = context.getState(State::Forces | State::Energy);
const std::vector<Vec3> forces = state.getForces(); const std::vector<Vec3> forces = state.getForces();
#ifdef AMOEBA_DEBUG #ifdef AMOEBA_DEBUG
if( log ){ if( log ){
(void) fprintf( log, "computeAmoebaHarmonicBondForces: expected energy=%15.7e %15.7e\n", expectedEnergy, state.getPotentialEnergy() ); (void) fprintf( log, "computeAmoebaBondForces: expected energy=%15.7e %15.7e\n", expectedEnergy, state.getPotentialEnergy() );
for( unsigned int ii = 0; ii < forces.size(); ii++ ){ for( unsigned int ii = 0; ii < forces.size(); ii++ ){
(void) fprintf( log, "%6u [%15.7e %15.7e %15.7e] [%15.7e %15.7e %15.7e]\n", ii, (void) fprintf( log, "%6u [%15.7e %15.7e %15.7e] [%15.7e %15.7e %15.7e]\n", ii,
expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2], forces[ii][0], forces[ii][1], forces[ii][2] ); expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2], forces[ii][0], forces[ii][1], forces[ii][2] );
...@@ -147,17 +147,17 @@ void testOneBond( FILE* log ) { ...@@ -147,17 +147,17 @@ void testOneBond( FILE* log ) {
LangevinIntegrator integrator(0.0, 0.1, 0.01); LangevinIntegrator integrator(0.0, 0.1, 0.01);
AmoebaHarmonicBondForce* amoebaHarmonicBondForce = new AmoebaHarmonicBondForce(); AmoebaBondForce* amoebaBondForce = new AmoebaBondForce();
double bondLength = 1.5; double bondLength = 1.5;
double quadraticK = 1.0; double quadraticK = 1.0;
double cubicK = 2.0; double cubicK = 2.0;
double quarticicK = 3.0; double quarticicK = 3.0;
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondCubic( cubicK ); amoebaBondForce->setAmoebaGlobalBondCubic( cubicK );
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondQuartic( quarticicK ); amoebaBondForce->setAmoebaGlobalBondQuartic( quarticicK );
amoebaHarmonicBondForce->addBond(0, 1, bondLength, quadraticK); amoebaBondForce->addBond(0, 1, bondLength, quadraticK);
system.addForce(amoebaHarmonicBondForce); system.addForce(amoebaBondForce);
Context context(system, integrator, Platform::getPlatformByName( "Reference")); Context context(system, integrator, Platform::getPlatformByName( "Reference"));
std::vector<Vec3> positions(2); std::vector<Vec3> positions(2);
...@@ -165,7 +165,7 @@ void testOneBond( FILE* log ) { ...@@ -165,7 +165,7 @@ void testOneBond( FILE* log ) {
positions[1] = Vec3(0, 0, 0); positions[1] = Vec3(0, 0, 0);
context.setPositions(positions); context.setPositions(positions);
compareWithExpectedForceAndEnergy( context, *amoebaHarmonicBondForce, TOL, "testOneBond", log ); compareWithExpectedForceAndEnergy( context, *amoebaBondForce, TOL, "testOneBond", log );
} }
void testTwoBond( FILE* log ) { void testTwoBond( FILE* log ) {
...@@ -178,18 +178,18 @@ void testTwoBond( FILE* log ) { ...@@ -178,18 +178,18 @@ void testTwoBond( FILE* log ) {
LangevinIntegrator integrator(0.0, 0.1, 0.01); LangevinIntegrator integrator(0.0, 0.1, 0.01);
AmoebaHarmonicBondForce* amoebaHarmonicBondForce = new AmoebaHarmonicBondForce(); AmoebaBondForce* amoebaBondForce = new AmoebaBondForce();
double bondLength = 1.5; double bondLength = 1.5;
double quadraticK = 1.0; double quadraticK = 1.0;
double cubicK = 2.0; double cubicK = 2.0;
double quarticicK = 3.0; double quarticicK = 3.0;
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondCubic( cubicK ); amoebaBondForce->setAmoebaGlobalBondCubic( cubicK );
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondQuartic( quarticicK ); amoebaBondForce->setAmoebaGlobalBondQuartic( quarticicK );
amoebaHarmonicBondForce->addBond(0, 1, bondLength, quadraticK); amoebaBondForce->addBond(0, 1, bondLength, quadraticK);
amoebaHarmonicBondForce->addBond(1, 2, bondLength, quadraticK); amoebaBondForce->addBond(1, 2, bondLength, quadraticK);
system.addForce(amoebaHarmonicBondForce); system.addForce(amoebaBondForce);
Context context(system, integrator, Platform::getPlatformByName( "Reference")); Context context(system, integrator, Platform::getPlatformByName( "Reference"));
std::vector<Vec3> positions(3); std::vector<Vec3> positions(3);
...@@ -198,13 +198,13 @@ void testTwoBond( FILE* log ) { ...@@ -198,13 +198,13 @@ void testTwoBond( FILE* log ) {
positions[2] = Vec3(1, 0, 1); positions[2] = Vec3(1, 0, 1);
context.setPositions(positions); context.setPositions(positions);
compareWithExpectedForceAndEnergy( context, *amoebaHarmonicBondForce, TOL, "testTwoBond", log ); compareWithExpectedForceAndEnergy( context, *amoebaBondForce, TOL, "testTwoBond", log );
} }
int main( int numberOfArguments, char* argv[] ) { int main( int numberOfArguments, char* argv[] ) {
try { try {
std::cout << "TestReferenceAmoebaHarmonicBondForce running test..." << std::endl; std::cout << "TestReferenceAmoebaBondForce running test..." << std::endl;
Platform::loadPluginsFromDirectory( Platform::getDefaultPluginsDirectory() ); Platform::loadPluginsFromDirectory( Platform::getDefaultPluginsDirectory() );
FILE* log = NULL; FILE* log = NULL;
//FILE* log = stderr; //FILE* log = stderr;
......
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaHarmonicInPlaneAngleForce.cpp → plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaInPlaneAngleForce.cpp
View file @ c6ebf6e2
...@@ -30,7 +30,7 @@ ...@@ -30,7 +30,7 @@
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
/** /**
* This tests the Reference implementation of ReferenceAmoebaHarmonicInPlaneAngleForce. * This tests the Reference implementation of ReferenceAmoebaInPlaneAngleForce.
*/ */
#include "openmm/internal/AssertionUtilities.h" #include "openmm/internal/AssertionUtilities.h"
...@@ -119,21 +119,21 @@ static void getPrefactorsGivenInPlaneAngleCosine( double cosine, double idealInP ...@@ -119,21 +119,21 @@ static void getPrefactorsGivenInPlaneAngleCosine( double cosine, double idealInP
return; return;
} }
static void computeAmoebaHarmonicInPlaneAngleForce(int bondIndex, std::vector<Vec3>& positions, AmoebaHarmonicInPlaneAngleForce& amoebaHarmonicInPlaneAngleForce, static void computeAmoebaInPlaneAngleForce(int bondIndex, std::vector<Vec3>& positions, AmoebaInPlaneAngleForce& AmoebaInPlaneAngleForce,
std::vector<Vec3>& forces, double* energy, FILE* log ) { std::vector<Vec3>& forces, double* energy, FILE* log ) {
int particle1, particle2, particle3, particle4; int particle1, particle2, particle3, particle4;
double idealInPlaneAngle; double idealInPlaneAngle;
double quadraticK; double quadraticK;
amoebaHarmonicInPlaneAngleForce.getAngleParameters(bondIndex, particle1, particle2, particle3, particle4, idealInPlaneAngle, quadraticK ); AmoebaInPlaneAngleForce.getAngleParameters(bondIndex, particle1, particle2, particle3, particle4, idealInPlaneAngle, quadraticK );
double cubicK = amoebaHarmonicInPlaneAngleForce.getAmoebaGlobalHarmonicInPlaneAngleCubic(); double cubicK = AmoebaInPlaneAngleForce.getAmoebaGlobalInPlaneAngleCubic();
double quarticK = amoebaHarmonicInPlaneAngleForce.getAmoebaGlobalHarmonicInPlaneAngleQuartic(); double quarticK = AmoebaInPlaneAngleForce.getAmoebaGlobalInPlaneAngleQuartic();
double penticK = amoebaHarmonicInPlaneAngleForce.getAmoebaGlobalHarmonicInPlaneAnglePentic(); double penticK = AmoebaInPlaneAngleForce.getAmoebaGlobalInPlaneAnglePentic();
double sexticK = amoebaHarmonicInPlaneAngleForce.getAmoebaGlobalHarmonicInPlaneAngleSextic(); double sexticK = AmoebaInPlaneAngleForce.getAmoebaGlobalInPlaneAngleSextic();
#ifdef AMOEBA_DEBUG #ifdef AMOEBA_DEBUG
if( log ){ if( log ){
(void) fprintf( log, "computeAmoebaHarmonicInPlaneAngleForce: bond %d [%d %d %d %d] ang=%10.3f k=%10.3f [%10.3e %10.3e %10.3e %10.3e]\n", (void) fprintf( log, "computeAmoebaInPlaneAngleForce: bond %d [%d %d %d %d] ang=%10.3f k=%10.3f [%10.3e %10.3e %10.3e %10.3e]\n",
bondIndex, particle1, particle2, particle3, particle4, idealInPlaneAngle, quadraticK, cubicK, quarticK, penticK, sexticK ); bondIndex, particle1, particle2, particle3, particle4, idealInPlaneAngle, quadraticK, cubicK, quarticK, penticK, sexticK );
(void) fflush( log ); (void) fflush( log );
} }
...@@ -180,7 +180,7 @@ static void computeAmoebaHarmonicInPlaneAngleForce(int bondIndex, std::vector<V ...@@ -180,7 +180,7 @@ static void computeAmoebaHarmonicInPlaneAngleForce(int bondIndex, std::vector<V
if( rAp2 <= 0.0 && rCp2 <= 0.0 ){ if( rAp2 <= 0.0 && rCp2 <= 0.0 ){
#ifdef AMOEBA_DEBUG #ifdef AMOEBA_DEBUG
if( log ){ if( log ){
(void) fprintf( log, "computeAmoebaHarmonicInPlaneAngleForce: rAp2 or rCp2 <= 0.0\n" ); (void) fprintf( log, "computeAmoebaInPlaneAngleForce: rAp2 or rCp2 <= 0.0\n" );
(void) fflush( log ); (void) fflush( log );
} }
#endif #endif
...@@ -275,7 +275,7 @@ static void computeAmoebaHarmonicInPlaneAngleForce(int bondIndex, std::vector<V ...@@ -275,7 +275,7 @@ static void computeAmoebaHarmonicInPlaneAngleForce(int bondIndex, std::vector<V
} }
static void computeAmoebaHarmonicInPlaneAngleForces( Context& context, AmoebaHarmonicInPlaneAngleForce& amoebaHarmonicInPlaneAngleForce, static void computeAmoebaInPlaneAngleForces( Context& context, AmoebaInPlaneAngleForce& AmoebaInPlaneAngleForce,
std::vector<Vec3>& expectedForces, double* expectedEnergy, FILE* log ) { std::vector<Vec3>& expectedForces, double* expectedEnergy, FILE* log ) {
// get positions and zero forces // get positions and zero forces
...@@ -291,12 +291,12 @@ static void computeAmoebaHarmonicInPlaneAngleForces( Context& context, AmoebaHar ...@@ -291,12 +291,12 @@ static void computeAmoebaHarmonicInPlaneAngleForces( Context& context, AmoebaHar
// calculates forces/energy // calculates forces/energy
*expectedEnergy = 0.0; *expectedEnergy = 0.0;
for( int ii = 0; ii < amoebaHarmonicInPlaneAngleForce.getNumAngles(); ii++ ){ for( int ii = 0; ii < AmoebaInPlaneAngleForce.getNumAngles(); ii++ ){
computeAmoebaHarmonicInPlaneAngleForce(ii, positions, amoebaHarmonicInPlaneAngleForce, expectedForces, expectedEnergy, log ); computeAmoebaInPlaneAngleForce(ii, positions, AmoebaInPlaneAngleForce, expectedForces, expectedEnergy, log );
} }
#ifdef AMOEBA_DEBUG #ifdef AMOEBA_DEBUG
if( log ){ if( log ){
(void) fprintf( log, "computeAmoebaHarmonicInPlaneAngleForces: expected energy=%14.7e\n", *expectedEnergy ); (void) fprintf( log, "computeAmoebaInPlaneAngleForces: expected energy=%14.7e\n", *expectedEnergy );
for( unsigned int ii = 0; ii < positions.size(); ii++ ){ for( unsigned int ii = 0; ii < positions.size(); ii++ ){
(void) fprintf( log, "%6u [%14.7e %14.7e %14.7e]\n", ii, expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2] ); (void) fprintf( log, "%6u [%14.7e %14.7e %14.7e]\n", ii, expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2] );
} }
...@@ -307,18 +307,18 @@ static void computeAmoebaHarmonicInPlaneAngleForces( Context& context, AmoebaHar ...@@ -307,18 +307,18 @@ static void computeAmoebaHarmonicInPlaneAngleForces( Context& context, AmoebaHar
} }
void compareWithExpectedForceAndEnergy( Context& context, AmoebaHarmonicInPlaneAngleForce& amoebaHarmonicInPlaneAngleForce, void compareWithExpectedForceAndEnergy( Context& context, AmoebaInPlaneAngleForce& AmoebaInPlaneAngleForce,
double tolerance, const std::string& idString, FILE* log) { double tolerance, const std::string& idString, FILE* log) {
std::vector<Vec3> expectedForces; std::vector<Vec3> expectedForces;
double expectedEnergy; double expectedEnergy;
computeAmoebaHarmonicInPlaneAngleForces( context, amoebaHarmonicInPlaneAngleForce, expectedForces, &expectedEnergy, log ); computeAmoebaInPlaneAngleForces( context, AmoebaInPlaneAngleForce, expectedForces, &expectedEnergy, log );
State state = context.getState(State::Forces | State::Energy); State state = context.getState(State::Forces | State::Energy);
const std::vector<Vec3> forces = state.getForces(); const std::vector<Vec3> forces = state.getForces();
#ifdef AMOEBA_DEBUG #ifdef AMOEBA_DEBUG
if( log ){ if( log ){
(void) fprintf( log, "computeAmoebaHarmonicInPlaneAngleForces: expected energy=%14.7e %14.7e\n", expectedEnergy, state.getPotentialEnergy() ); (void) fprintf( log, "computeAmoebaInPlaneAngleForces: expected energy=%14.7e %14.7e\n", expectedEnergy, state.getPotentialEnergy() );
for( unsigned int ii = 0; ii < forces.size(); ii++ ){ for( unsigned int ii = 0; ii < forces.size(); ii++ ){
(void) fprintf( log, "%6u [%14.7e %14.7e %14.7e] [%14.7e %14.7e %14.7e]\n", ii, (void) fprintf( log, "%6u [%14.7e %14.7e %14.7e] [%14.7e %14.7e %14.7e]\n", ii,
expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2], forces[ii][0], forces[ii][1], forces[ii][2] ); expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2], forces[ii][0], forces[ii][1], forces[ii][2] );
...@@ -343,7 +343,7 @@ void testOneAngle( FILE* log ) { ...@@ -343,7 +343,7 @@ void testOneAngle( FILE* log ) {
LangevinIntegrator integrator(0.0, 0.1, 0.01); LangevinIntegrator integrator(0.0, 0.1, 0.01);
AmoebaHarmonicInPlaneAngleForce* amoebaHarmonicInPlaneAngleForce = new AmoebaHarmonicInPlaneAngleForce(); AmoebaInPlaneAngleForce* amoebaInPlaneAngleForce = new AmoebaInPlaneAngleForce();
double angle = 65.0; double angle = 65.0;
double quadraticK = 1.0; double quadraticK = 1.0;
...@@ -351,14 +351,14 @@ void testOneAngle( FILE* log ) { ...@@ -351,14 +351,14 @@ void testOneAngle( FILE* log ) {
double quarticK = 0.0e-02; double quarticK = 0.0e-02;
double penticK = 0.0e-03; double penticK = 0.0e-03;
double sexticK = 0.0e-04; double sexticK = 0.0e-04;
amoebaHarmonicInPlaneAngleForce->addAngle(0, 1, 2, 3, angle, quadraticK); amoebaInPlaneAngleForce->addAngle(0, 1, 2, 3, angle, quadraticK);
amoebaHarmonicInPlaneAngleForce->setAmoebaGlobalHarmonicInPlaneAngleCubic(cubicK); amoebaInPlaneAngleForce->setAmoebaGlobalInPlaneAngleCubic(cubicK);
amoebaHarmonicInPlaneAngleForce->setAmoebaGlobalHarmonicInPlaneAngleQuartic(quarticK); amoebaInPlaneAngleForce->setAmoebaGlobalInPlaneAngleQuartic(quarticK);
amoebaHarmonicInPlaneAngleForce->setAmoebaGlobalHarmonicInPlaneAnglePentic(penticK); amoebaInPlaneAngleForce->setAmoebaGlobalInPlaneAnglePentic(penticK);
amoebaHarmonicInPlaneAngleForce->setAmoebaGlobalHarmonicInPlaneAngleSextic(sexticK); amoebaInPlaneAngleForce->setAmoebaGlobalInPlaneAngleSextic(sexticK);
system.addForce(amoebaHarmonicInPlaneAngleForce); system.addForce(amoebaInPlaneAngleForce);
Context context(system, integrator, Platform::getPlatformByName( "Reference")); Context context(system, integrator, Platform::getPlatformByName( "Reference"));
std::vector<Vec3> positions(numberOfParticles); std::vector<Vec3> positions(numberOfParticles);
...@@ -369,18 +369,18 @@ void testOneAngle( FILE* log ) { ...@@ -369,18 +369,18 @@ void testOneAngle( FILE* log ) {
positions[3] = Vec3(1, 1, 1); positions[3] = Vec3(1, 1, 1);
context.setPositions(positions); context.setPositions(positions);
compareWithExpectedForceAndEnergy( context, *amoebaHarmonicInPlaneAngleForce, TOL, "testOneInPlaneAngle", log ); compareWithExpectedForceAndEnergy( context, *amoebaInPlaneAngleForce, TOL, "testOneInPlaneAngle", log );
} }
int main( int numberOfArguments, char* argv[] ) { int main( int numberOfArguments, char* argv[] ) {
try { try {
std::cout << "TestReferenceAmoebaHarmonicInPlaneAngleForce running test..." << std::endl; std::cout << "TestReferenceAmoebaInPlaneAngleForce running test..." << std::endl;
Platform::loadPluginsFromDirectory( Platform::getDefaultPluginsDirectory() ); Platform::loadPluginsFromDirectory( Platform::getDefaultPluginsDirectory() );
FILE* log = NULL; FILE* log = NULL;
//FILE* log = stderr; //FILE* log = stderr;
//FILE* log = fopen( "AmoebaHarmonicInPlaneAngleForce.log", "w" );; //FILE* log = fopen( "AmoebaInPlaneAngleForce.log", "w" );;
testOneAngle( NULL ); testOneAngle( NULL );
#ifdef AMOEBA_DEBUG #ifdef AMOEBA_DEBUG
......
plugins/amoeba/serialization/include/openmm/serialization/AmoebaHarmonicAngleForceProxy.h → plugins/amoeba/serialization/include/openmm/serialization/AmoebaAngleForceProxy.h
View file @ c6ebf6e2
#ifndef OPENMM_AMOEBA_HARMONIC_ANGLE_FORCE_PROXY_H_ #ifndef OPENMM_AMOEBA_ANGLE_FORCE_PROXY_H_
#define OPENMM_AMOEBA_HARMONIC_ANGLE_FORCE_PROXY_H_ #define OPENMM_AMOEBA_ANGLE_FORCE_PROXY_H_
/* -------------------------------------------------------------------------- * /* -------------------------------------------------------------------------- *
* OpenMMAmoeba * * OpenMMAmoeba *
...@@ -38,16 +38,16 @@ ...@@ -38,16 +38,16 @@
namespace OpenMM { namespace OpenMM {
/** /**
* This is a proxy for serializing AmoebaHarmonicAngleForce objects. * This is a proxy for serializing AmoebaAngleForce objects.
*/ */
class OPENMM_EXPORT AmoebaHarmonicAngleForceProxy : public SerializationProxy { class OPENMM_EXPORT AmoebaAngleForceProxy : public SerializationProxy {
public: public:
AmoebaHarmonicAngleForceProxy(); AmoebaAngleForceProxy();
void serialize(const void* object, SerializationNode& node) const; void serialize(const void* object, SerializationNode& node) const;
void* deserialize(const SerializationNode& node) const; void* deserialize(const SerializationNode& node) const;
}; };
} // namespace OpenMM } // namespace OpenMM
#endif /*OPENMM_AMOEBA_HARMONIC_ANGLE_FORCE_PROXY_H_*/ #endif /*OPENMM_AMOEBA_ANGLE_FORCE_PROXY_H_*/
plugins/amoeba/serialization/include/openmm/serialization/AmoebaHarmonicInPlaneAngleForceProxy.h → plugins/amoeba/serialization/include/openmm/serialization/AmoebaBondForceProxy.h
View file @ c6ebf6e2
#ifndef OPENMM_AMOEBA_HARMONIC_IN_PLANE_ANGLE_FORCE_PROXY_H_ #ifndef OPENMM_AMOEBA_BOND_FORCE_PROXY_H_
#define OPENMM_AMOEBA_HARMONIC_IN_PLANE_ANGLE_FORCE_PROXY_H_ #define OPENMM_AMOEBA_BOND_FORCE_PROXY_H_
/* -------------------------------------------------------------------------- * /* -------------------------------------------------------------------------- *
* OpenMMAmoeba * * OpenMMAmoeba *
...@@ -38,16 +38,16 @@ ...@@ -38,16 +38,16 @@
namespace OpenMM { namespace OpenMM {
/** /**
* This is a proxy for serializing AmoebaHarmonicInPlaneAngleForce objects. * This is a proxy for serializing AmoebaBondForce objects.
*/ */
class OPENMM_EXPORT AmoebaHarmonicInPlaneAngleForceProxy : public SerializationProxy { class OPENMM_EXPORT AmoebaBondForceProxy : public SerializationProxy {
public: public:
AmoebaHarmonicInPlaneAngleForceProxy(); AmoebaBondForceProxy();
void serialize(const void* object, SerializationNode& node) const; void serialize(const void* object, SerializationNode& node) const;
void* deserialize(const SerializationNode& node) const; void* deserialize(const SerializationNode& node) const;
}; };
} // namespace OpenMM } // namespace OpenMM
#endif /*OPENMM_AMOEBA_HARMONIC_IN_PLANE_ANGLE_FORCE_PROXY_H_*/ #endif /*OPENMM_AMOEBA_BOND_FORCE_PROXY_H_*/
plugins/amoeba/serialization/include/openmm/serialization/AmoebaHarmonicBondForceProxy.h → plugins/amoeba/serialization/include/openmm/serialization/AmoebaInPlaneAngleForceProxy.h
View file @ c6ebf6e2
#ifndef OPENMM_AMOEBA_HARMONIC_BOND_FORCE_PROXY_H_ #ifndef OPENMM_AMOEBA_IN_PLANE_ANGLE_FORCE_PROXY_H_
#define OPENMM_AMOEBA_HARMONIC_BOND_FORCE_PROXY_H_ #define OPENMM_AMOEBA_IN_PLANE_ANGLE_FORCE_PROXY_H_
/* -------------------------------------------------------------------------- * /* -------------------------------------------------------------------------- *
* OpenMMAmoeba * * OpenMMAmoeba *
...@@ -38,16 +38,16 @@ ...@@ -38,16 +38,16 @@
namespace OpenMM { namespace OpenMM {
/** /**
* This is a proxy for serializing AmoebaHarmonicBondForce objects. * This is a proxy for serializing AmoebaInPlaneAngleForce objects.
*/ */
class OPENMM_EXPORT AmoebaHarmonicBondForceProxy : public SerializationProxy { class OPENMM_EXPORT AmoebaInPlaneAngleForceProxy : public SerializationProxy {
public: public:
AmoebaHarmonicBondForceProxy(); AmoebaInPlaneAngleForceProxy();
void serialize(const void* object, SerializationNode& node) const; void serialize(const void* object, SerializationNode& node) const;
void* deserialize(const SerializationNode& node) const; void* deserialize(const SerializationNode& node) const;
}; };
} // namespace OpenMM } // namespace OpenMM
#endif /*OPENMM_AMOEBA_HARMONIC_BOND_FORCE_PROXY_H_*/ #endif /*OPENMM_AMOEBA_IN_PLANE_ANGLE_FORCE_PROXY_H_*/
plugins/amoeba/serialization/src/AmoebaHarmonicAngleForceProxy.cpp → plugins/amoeba/serialization/src/AmoebaAngleForceProxy.cpp
View file @ c6ebf6e2
...@@ -29,27 +29,27 @@ ...@@ -29,27 +29,27 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. * * USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
#include "openmm/serialization/AmoebaHarmonicAngleForceProxy.h" #include "openmm/serialization/AmoebaAngleForceProxy.h"
#include "openmm/serialization/SerializationNode.h" #include "openmm/serialization/SerializationNode.h"
#include "openmm/Force.h" #include "openmm/Force.h"
#include "openmm/AmoebaHarmonicAngleForce.h" #include "openmm/AmoebaAngleForce.h"
#include <sstream> #include <sstream>
using namespace OpenMM; using namespace OpenMM;
using namespace std; using namespace std;
AmoebaHarmonicAngleForceProxy::AmoebaHarmonicAngleForceProxy() : SerializationProxy("AmoebaHarmonicAngleForce") { AmoebaAngleForceProxy::AmoebaAngleForceProxy() : SerializationProxy("AmoebaAngleForce") {
} }
void AmoebaHarmonicAngleForceProxy::serialize(const void* object, SerializationNode& node) const { void AmoebaAngleForceProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 1); node.setIntProperty("version", 1);
const AmoebaHarmonicAngleForce& force = *reinterpret_cast<const AmoebaHarmonicAngleForce*>(object); const AmoebaAngleForce& force = *reinterpret_cast<const AmoebaAngleForce*>(object);
node.setDoubleProperty("HarmonicAngleCubic", force.getAmoebaGlobalHarmonicAngleCubic()); node.setDoubleProperty("cubic", force.getAmoebaGlobalAngleCubic());
node.setDoubleProperty("HarmonicAngleQuartic", force.getAmoebaGlobalHarmonicAngleQuartic()); node.setDoubleProperty("quartic", force.getAmoebaGlobalAngleQuartic());
node.setDoubleProperty("HarmonicAnglePentic", force.getAmoebaGlobalHarmonicAnglePentic()); node.setDoubleProperty("pentic", force.getAmoebaGlobalAnglePentic());
node.setDoubleProperty("HarmonicAngleSextic", force.getAmoebaGlobalHarmonicAngleSextic()); node.setDoubleProperty("sextic", force.getAmoebaGlobalAngleSextic());
SerializationNode& bonds = node.createChildNode("Angles").setIntProperty( "size", force.getNumAngles() ); SerializationNode& bonds = node.createChildNode("Angles").setIntProperty( "size", force.getNumAngles() );
for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumAngles()); ii++) { for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumAngles()); ii++) {
...@@ -60,16 +60,16 @@ void AmoebaHarmonicAngleForceProxy::serialize(const void* object, SerializationN ...@@ -60,16 +60,16 @@ void AmoebaHarmonicAngleForceProxy::serialize(const void* object, SerializationN
} }
} }
void* AmoebaHarmonicAngleForceProxy::deserialize(const SerializationNode& node) const { void* AmoebaAngleForceProxy::deserialize(const SerializationNode& node) const {
if (node.getIntProperty("version") != 1) if (node.getIntProperty("version") != 1)
throw OpenMMException("Unsupported version number"); throw OpenMMException("Unsupported version number");
AmoebaHarmonicAngleForce* force = new AmoebaHarmonicAngleForce(); AmoebaAngleForce* force = new AmoebaAngleForce();
try { try {
force->setAmoebaGlobalHarmonicAngleCubic(node.getDoubleProperty( "HarmonicAngleCubic")); force->setAmoebaGlobalAngleCubic(node.getDoubleProperty( "cubic"));
force->setAmoebaGlobalHarmonicAngleQuartic(node.getDoubleProperty("HarmonicAngleQuartic")); force->setAmoebaGlobalAngleQuartic(node.getDoubleProperty("quartic"));
force->setAmoebaGlobalHarmonicAnglePentic(node.getDoubleProperty( "HarmonicAnglePentic")); force->setAmoebaGlobalAnglePentic(node.getDoubleProperty( "pentic"));
force->setAmoebaGlobalHarmonicAngleSextic(node.getDoubleProperty( "HarmonicAngleSextic")); force->setAmoebaGlobalAngleSextic(node.getDoubleProperty( "sextic"));
const SerializationNode& bonds = node.getChildNode("Angles"); const SerializationNode& bonds = node.getChildNode("Angles");
for ( unsigned int ii = 0; ii < bonds.getChildren().size(); ii++) { for ( unsigned int ii = 0; ii < bonds.getChildren().size(); ii++) {
......
plugins/amoeba/serialization/src/AmoebaHarmonicBondForceProxy.cpp → plugins/amoeba/serialization/src/AmoebaBondForceProxy.cpp
View file @ c6ebf6e2
...@@ -29,24 +29,24 @@ ...@@ -29,24 +29,24 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. * * USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
#include "openmm/serialization/AmoebaHarmonicBondForceProxy.h" #include "openmm/serialization/AmoebaBondForceProxy.h"
#include "openmm/serialization/SerializationNode.h" #include "openmm/serialization/SerializationNode.h"
#include "openmm/Force.h" #include "openmm/Force.h"
#include "openmm/AmoebaHarmonicBondForce.h" #include "openmm/AmoebaBondForce.h"
#include <sstream> #include <sstream>
using namespace OpenMM; using namespace OpenMM;
using namespace std; using namespace std;
AmoebaHarmonicBondForceProxy::AmoebaHarmonicBondForceProxy() : SerializationProxy("AmoebaHarmonicBondForce") { AmoebaBondForceProxy::AmoebaBondForceProxy() : SerializationProxy("AmoebaBondForce") {
} }
void AmoebaHarmonicBondForceProxy::serialize(const void* object, SerializationNode& node) const { void AmoebaBondForceProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 1); node.setIntProperty("version", 1);
const AmoebaHarmonicBondForce& force = *reinterpret_cast<const AmoebaHarmonicBondForce*>(object); const AmoebaBondForce& force = *reinterpret_cast<const AmoebaBondForce*>(object);
node.setDoubleProperty("HarmonicBondCubic", force.getAmoebaGlobalHarmonicBondCubic()); node.setDoubleProperty("cubic", force.getAmoebaGlobalBondCubic());
node.setDoubleProperty("HarmonicBondQuartic", force.getAmoebaGlobalHarmonicBondQuartic()); node.setDoubleProperty("quartic", force.getAmoebaGlobalBondQuartic());
SerializationNode& bonds = node.createChildNode("Bonds").setIntProperty( "size", force.getNumBonds() ); SerializationNode& bonds = node.createChildNode("Bonds").setIntProperty( "size", force.getNumBonds() );
for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumBonds()); ii++) { for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumBonds()); ii++) {
...@@ -57,13 +57,13 @@ void AmoebaHarmonicBondForceProxy::serialize(const void* object, SerializationNo ...@@ -57,13 +57,13 @@ void AmoebaHarmonicBondForceProxy::serialize(const void* object, SerializationNo
} }
} }
void* AmoebaHarmonicBondForceProxy::deserialize(const SerializationNode& node) const { void* AmoebaBondForceProxy::deserialize(const SerializationNode& node) const {
if (node.getIntProperty("version") != 1) if (node.getIntProperty("version") != 1)
throw OpenMMException("Unsupported version number"); throw OpenMMException("Unsupported version number");
AmoebaHarmonicBondForce* force = new AmoebaHarmonicBondForce(); AmoebaBondForce* force = new AmoebaBondForce();
try { try {
force->setAmoebaGlobalHarmonicBondCubic(node.getDoubleProperty("HarmonicBondCubic")); force->setAmoebaGlobalBondCubic(node.getDoubleProperty("condCubic"));
force->setAmoebaGlobalHarmonicBondQuartic(node.getDoubleProperty("HarmonicBondQuartic")); force->setAmoebaGlobalBondQuartic(node.getDoubleProperty("quartic"));
const SerializationNode& bonds = node.getChildNode("Bonds"); const SerializationNode& bonds = node.getChildNode("Bonds");
for ( unsigned int ii = 0; ii < (int) bonds.getChildren().size(); ii++) { for ( unsigned int ii = 0; ii < (int) bonds.getChildren().size(); ii++) {
const SerializationNode& bond = bonds.getChildren()[ii]; const SerializationNode& bond = bonds.getChildren()[ii];
......
plugins/amoeba/serialization/src/AmoebaHarmonicInPlaneAngleForceProxy.cpp → plugins/amoeba/serialization/src/AmoebaInPlaneAngleForceProxy.cpp
View file @ c6ebf6e2
...@@ -29,27 +29,27 @@ ...@@ -29,27 +29,27 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. * * USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
#include "openmm/serialization/AmoebaHarmonicInPlaneAngleForceProxy.h" #include "openmm/serialization/AmoebaInPlaneAngleForceProxy.h"
#include "openmm/serialization/SerializationNode.h" #include "openmm/serialization/SerializationNode.h"
#include "openmm/Force.h" #include "openmm/Force.h"
#include "openmm/AmoebaHarmonicInPlaneAngleForce.h" #include "openmm/AmoebaInPlaneAngleForce.h"
#include <sstream> #include <sstream>
using namespace OpenMM; using namespace OpenMM;
using namespace std; using namespace std;
AmoebaHarmonicInPlaneAngleForceProxy::AmoebaHarmonicInPlaneAngleForceProxy() : SerializationProxy("AmoebaHarmonicInPlaneAngleForce") { AmoebaInPlaneAngleForceProxy::AmoebaInPlaneAngleForceProxy() : SerializationProxy("AmoebaInPlaneAngleForce") {
} }
void AmoebaHarmonicInPlaneAngleForceProxy::serialize(const void* object, SerializationNode& node) const { void AmoebaInPlaneAngleForceProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 1); node.setIntProperty("version", 1);
const AmoebaHarmonicInPlaneAngleForce& force = *reinterpret_cast<const AmoebaHarmonicInPlaneAngleForce*>(object); const AmoebaInPlaneAngleForce& force = *reinterpret_cast<const AmoebaInPlaneAngleForce*>(object);
node.setDoubleProperty("HarmonicInPlaneAngleCubic", force.getAmoebaGlobalHarmonicInPlaneAngleCubic()); node.setDoubleProperty("cubic", force.getAmoebaGlobalInPlaneAngleCubic());
node.setDoubleProperty("HarmonicInPlaneAngleQuartic", force.getAmoebaGlobalHarmonicInPlaneAngleQuartic()); node.setDoubleProperty("quartic", force.getAmoebaGlobalInPlaneAngleQuartic());
node.setDoubleProperty("HarmonicInPlaneAnglePentic", force.getAmoebaGlobalHarmonicInPlaneAnglePentic()); node.setDoubleProperty("pentic", force.getAmoebaGlobalInPlaneAnglePentic());
node.setDoubleProperty("HarmonicInPlaneAngleSextic", force.getAmoebaGlobalHarmonicInPlaneAngleSextic()); node.setDoubleProperty("sextic", force.getAmoebaGlobalInPlaneAngleSextic());
SerializationNode& bonds = node.createChildNode("InPlaneAngles").setIntProperty( "size", force.getNumAngles() ); SerializationNode& bonds = node.createChildNode("InPlaneAngles").setIntProperty( "size", force.getNumAngles() );
for ( unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumAngles()); ii++) { for ( unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumAngles()); ii++) {
...@@ -60,16 +60,16 @@ void AmoebaHarmonicInPlaneAngleForceProxy::serialize(const void* object, Seriali ...@@ -60,16 +60,16 @@ void AmoebaHarmonicInPlaneAngleForceProxy::serialize(const void* object, Seriali
} }
} }
void* AmoebaHarmonicInPlaneAngleForceProxy::deserialize(const SerializationNode& node) const { void* AmoebaInPlaneAngleForceProxy::deserialize(const SerializationNode& node) const {
if (node.getIntProperty("version") != 1) if (node.getIntProperty("version") != 1)
throw OpenMMException("Unsupported version number"); throw OpenMMException("Unsupported version number");
AmoebaHarmonicInPlaneAngleForce* force = new AmoebaHarmonicInPlaneAngleForce(); AmoebaInPlaneAngleForce* force = new AmoebaInPlaneAngleForce();
try { try {
force->setAmoebaGlobalHarmonicInPlaneAngleCubic( node.getDoubleProperty("HarmonicInPlaneAngleCubic")); force->setAmoebaGlobalInPlaneAngleCubic( node.getDoubleProperty("cubic"));
force->setAmoebaGlobalHarmonicInPlaneAngleQuartic(node.getDoubleProperty("HarmonicInPlaneAngleQuartic")); force->setAmoebaGlobalInPlaneAngleQuartic(node.getDoubleProperty("quartic"));
force->setAmoebaGlobalHarmonicInPlaneAnglePentic( node.getDoubleProperty("HarmonicInPlaneAnglePentic")); force->setAmoebaGlobalInPlaneAnglePentic( node.getDoubleProperty("pentic"));
force->setAmoebaGlobalHarmonicInPlaneAngleSextic( node.getDoubleProperty("HarmonicInPlaneAngleSextic")); force->setAmoebaGlobalInPlaneAngleSextic( node.getDoubleProperty("sextic"));
const SerializationNode& bonds = node.getChildNode("InPlaneAngles"); const SerializationNode& bonds = node.getChildNode("InPlaneAngles");
for (unsigned int ii = 0; ii < bonds.getChildren().size(); ii++) { for (unsigned int ii = 0; ii < bonds.getChildren().size(); ii++) {
......
plugins/amoeba/serialization/src/AmoebaSerializationProxyRegistration.cpp
View file @ c6ebf6e2
...@@ -41,9 +41,9 @@ ...@@ -41,9 +41,9 @@
#include "openmm/OpenMMException.h" #include "openmm/OpenMMException.h"
#include "openmm/AmoebaGeneralizedKirkwoodForce.h" #include "openmm/AmoebaGeneralizedKirkwoodForce.h"
#include "openmm/AmoebaHarmonicBondForce.h" #include "openmm/AmoebaBondForce.h"
#include "openmm/AmoebaHarmonicAngleForce.h" #include "openmm/AmoebaAngleForce.h"
#include "openmm/AmoebaHarmonicInPlaneAngleForce.h" #include "openmm/AmoebaInPlaneAngleForce.h"
#include "openmm/AmoebaMultipoleForce.h" #include "openmm/AmoebaMultipoleForce.h"
#include "openmm/AmoebaOutOfPlaneBendForce.h" #include "openmm/AmoebaOutOfPlaneBendForce.h"
#include "openmm/AmoebaPiTorsionForce.h" #include "openmm/AmoebaPiTorsionForce.h"
...@@ -55,9 +55,9 @@ ...@@ -55,9 +55,9 @@
#include "openmm/serialization/SerializationProxy.h" #include "openmm/serialization/SerializationProxy.h"
#include "openmm/serialization/AmoebaGeneralizedKirkwoodForceProxy.h" #include "openmm/serialization/AmoebaGeneralizedKirkwoodForceProxy.h"
#include "openmm/serialization/AmoebaHarmonicBondForceProxy.h" #include "openmm/serialization/AmoebaBondForceProxy.h"
#include "openmm/serialization/AmoebaHarmonicAngleForceProxy.h" #include "openmm/serialization/AmoebaAngleForceProxy.h"
#include "openmm/serialization/AmoebaHarmonicInPlaneAngleForceProxy.h" #include "openmm/serialization/AmoebaInPlaneAngleForceProxy.h"
#include "openmm/serialization/AmoebaMultipoleForceProxy.h" #include "openmm/serialization/AmoebaMultipoleForceProxy.h"
#include "openmm/serialization/AmoebaOutOfPlaneBendForceProxy.h" #include "openmm/serialization/AmoebaOutOfPlaneBendForceProxy.h"
#include "openmm/serialization/AmoebaPiTorsionForceProxy.h" #include "openmm/serialization/AmoebaPiTorsionForceProxy.h"
...@@ -82,9 +82,9 @@ using namespace OpenMM; ...@@ -82,9 +82,9 @@ using namespace OpenMM;
extern "C" void registerAmoebaSerializationProxies() { extern "C" void registerAmoebaSerializationProxies() {
SerializationProxy::registerProxy(typeid(AmoebaGeneralizedKirkwoodForce), new AmoebaGeneralizedKirkwoodForceProxy()); SerializationProxy::registerProxy(typeid(AmoebaGeneralizedKirkwoodForce), new AmoebaGeneralizedKirkwoodForceProxy());
SerializationProxy::registerProxy(typeid(AmoebaHarmonicBondForce), new AmoebaHarmonicBondForceProxy()); SerializationProxy::registerProxy(typeid(AmoebaBondForce), new AmoebaBondForceProxy());
SerializationProxy::registerProxy(typeid(AmoebaHarmonicAngleForce), new AmoebaHarmonicAngleForceProxy()); SerializationProxy::registerProxy(typeid(AmoebaAngleForce), new AmoebaAngleForceProxy());
SerializationProxy::registerProxy(typeid(AmoebaHarmonicInPlaneAngleForce), new AmoebaHarmonicInPlaneAngleForceProxy()); SerializationProxy::registerProxy(typeid(AmoebaInPlaneAngleForce), new AmoebaInPlaneAngleForceProxy());
SerializationProxy::registerProxy(typeid(AmoebaMultipoleForce), new AmoebaMultipoleForceProxy()); SerializationProxy::registerProxy(typeid(AmoebaMultipoleForce), new AmoebaMultipoleForceProxy());
SerializationProxy::registerProxy(typeid(AmoebaOutOfPlaneBendForce), new AmoebaOutOfPlaneBendForceProxy()); SerializationProxy::registerProxy(typeid(AmoebaOutOfPlaneBendForce), new AmoebaOutOfPlaneBendForceProxy());
SerializationProxy::registerProxy(typeid(AmoebaPiTorsionForce), new AmoebaPiTorsionForceProxy()); SerializationProxy::registerProxy(typeid(AmoebaPiTorsionForce), new AmoebaPiTorsionForceProxy());
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaHarmonicAngleForce.cpp → plugins/amoeba/serialization/tests/TestSerializeAmoebaAngleForce.cpp
View file @ c6ebf6e2
...@@ -30,7 +30,7 @@ ...@@ -30,7 +30,7 @@
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
#include "openmm/internal/AssertionUtilities.h" #include "openmm/internal/AssertionUtilities.h"
#include "openmm/AmoebaHarmonicAngleForce.h" #include "openmm/AmoebaAngleForce.h"
#include "openmm/serialization/XmlSerializer.h" #include "openmm/serialization/XmlSerializer.h"
#include <iostream> #include <iostream>
#include <sstream> #include <sstream>
...@@ -41,11 +41,11 @@ using namespace std; ...@@ -41,11 +41,11 @@ using namespace std;
void testSerialization() { void testSerialization() {
// Create a Force. // Create a Force.
AmoebaHarmonicAngleForce force1; AmoebaAngleForce force1;
force1.setAmoebaGlobalHarmonicAngleCubic( 12.3 ); force1.setAmoebaGlobalAngleCubic( 12.3 );
force1.setAmoebaGlobalHarmonicAngleQuartic( 98.7 ); force1.setAmoebaGlobalAngleQuartic( 98.7 );
force1.setAmoebaGlobalHarmonicAnglePentic( 91.7 ); force1.setAmoebaGlobalAnglePentic( 91.7 );
force1.setAmoebaGlobalHarmonicAngleSextic( 93.7 ); force1.setAmoebaGlobalAngleSextic( 93.7 );
force1.addAngle(0, 1, 3, 1.0, 2.0); force1.addAngle(0, 1, 3, 1.0, 2.0);
force1.addAngle(0, 2, 3, 2.0, 2.1); force1.addAngle(0, 2, 3, 2.0, 2.1);
force1.addAngle(2, 3, 5, 3.0, 2.2); force1.addAngle(2, 3, 5, 3.0, 2.2);
...@@ -54,15 +54,15 @@ void testSerialization() { ...@@ -54,15 +54,15 @@ void testSerialization() {
// Serialize and then deserialize it. // Serialize and then deserialize it.
stringstream buffer; stringstream buffer;
XmlSerializer::serialize<AmoebaHarmonicAngleForce>(&force1, "Force", buffer); XmlSerializer::serialize<AmoebaAngleForce>(&force1, "Force", buffer);
AmoebaHarmonicAngleForce* copy = XmlSerializer::deserialize<AmoebaHarmonicAngleForce>(buffer); AmoebaAngleForce* copy = XmlSerializer::deserialize<AmoebaAngleForce>(buffer);
// Compare the two forces to see if they are identical. // Compare the two forces to see if they are identical.
AmoebaHarmonicAngleForce& force2 = *copy; AmoebaAngleForce& force2 = *copy;
ASSERT_EQUAL(force1.getAmoebaGlobalHarmonicAngleCubic(), force2.getAmoebaGlobalHarmonicAngleCubic()); ASSERT_EQUAL(force1.getAmoebaGlobalAngleCubic(), force2.getAmoebaGlobalAngleCubic());
ASSERT_EQUAL(force1.getAmoebaGlobalHarmonicAngleQuartic(), force2.getAmoebaGlobalHarmonicAngleQuartic()); ASSERT_EQUAL(force1.getAmoebaGlobalAngleQuartic(), force2.getAmoebaGlobalAngleQuartic());
ASSERT_EQUAL(force1.getAmoebaGlobalHarmonicAnglePentic(), force2.getAmoebaGlobalHarmonicAnglePentic()); ASSERT_EQUAL(force1.getAmoebaGlobalAnglePentic(), force2.getAmoebaGlobalAnglePentic());
ASSERT_EQUAL(force1.getAmoebaGlobalHarmonicAngleSextic(), force2.getAmoebaGlobalHarmonicAngleSextic()); ASSERT_EQUAL(force1.getAmoebaGlobalAngleSextic(), force2.getAmoebaGlobalAngleSextic());
ASSERT_EQUAL(force1.getNumAngles(), force2.getNumAngles()); ASSERT_EQUAL(force1.getNumAngles(), force2.getNumAngles());
for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumAngles()); ii++) { for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumAngles()); ii++) {
int a1, a2, a3, b1, b2, b3; int a1, a2, a3, b1, b2, b3;
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaHarmonicBondForce.cpp → plugins/amoeba/serialization/tests/TestSerializeAmoebaBondForce.cpp
View file @ c6ebf6e2
...@@ -30,7 +30,7 @@ ...@@ -30,7 +30,7 @@
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
#include "openmm/internal/AssertionUtilities.h" #include "openmm/internal/AssertionUtilities.h"
#include "openmm/AmoebaHarmonicBondForce.h" #include "openmm/AmoebaBondForce.h"
#include "openmm/serialization/XmlSerializer.h" #include "openmm/serialization/XmlSerializer.h"
#include <iostream> #include <iostream>
#include <sstream> #include <sstream>
...@@ -41,9 +41,9 @@ using namespace std; ...@@ -41,9 +41,9 @@ using namespace std;
void testSerialization() { void testSerialization() {
// Create a Force. // Create a Force.
AmoebaHarmonicBondForce force1; AmoebaBondForce force1;
force1.setAmoebaGlobalHarmonicBondCubic( 12.3 ); force1.setAmoebaGlobalBondCubic( 12.3 );
force1.setAmoebaGlobalHarmonicBondQuartic( 98.7 ); force1.setAmoebaGlobalBondQuartic( 98.7 );
force1.addBond(0, 1, 1.0, 2.0); force1.addBond(0, 1, 1.0, 2.0);
force1.addBond(0, 2, 2.0, 2.1); force1.addBond(0, 2, 2.0, 2.1);
force1.addBond(2, 3, 3.0, 2.2); force1.addBond(2, 3, 3.0, 2.2);
...@@ -52,13 +52,13 @@ void testSerialization() { ...@@ -52,13 +52,13 @@ void testSerialization() {
// Serialize and then deserialize it. // Serialize and then deserialize it.
stringstream buffer; stringstream buffer;
XmlSerializer::serialize<AmoebaHarmonicBondForce>(&force1, "Force", buffer); XmlSerializer::serialize<AmoebaBondForce>(&force1, "Force", buffer);
AmoebaHarmonicBondForce* copy = XmlSerializer::deserialize<AmoebaHarmonicBondForce>(buffer); AmoebaBondForce* copy = XmlSerializer::deserialize<AmoebaBondForce>(buffer);
// Compare the two forces to see if they are identical. // Compare the two forces to see if they are identical.
AmoebaHarmonicBondForce& force2 = *copy; AmoebaBondForce& force2 = *copy;
ASSERT_EQUAL(force1.getAmoebaGlobalHarmonicBondCubic(), force2.getAmoebaGlobalHarmonicBondCubic()); ASSERT_EQUAL(force1.getAmoebaGlobalBondCubic(), force2.getAmoebaGlobalBondCubic());
ASSERT_EQUAL(force1.getAmoebaGlobalHarmonicBondQuartic(), force2.getAmoebaGlobalHarmonicBondQuartic()); ASSERT_EQUAL(force1.getAmoebaGlobalBondQuartic(), force2.getAmoebaGlobalBondQuartic());
ASSERT_EQUAL(force1.getNumBonds(), force2.getNumBonds()); ASSERT_EQUAL(force1.getNumBonds(), force2.getNumBonds());
for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumBonds()); ii++) { for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumBonds()); ii++) {
int a1, a2, b1, b2; int a1, a2, b1, b2;
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaHarmonicInPlaneAngleForce.cpp → plugins/amoeba/serialization/tests/TestSerializeAmoebaInPlaneAngleForce.cpp
View file @ c6ebf6e2
...@@ -30,7 +30,7 @@ ...@@ -30,7 +30,7 @@
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
#include "openmm/internal/AssertionUtilities.h" #include "openmm/internal/AssertionUtilities.h"
#include "openmm/AmoebaHarmonicInPlaneAngleForce.h" #include "openmm/AmoebaInPlaneAngleForce.h"
#include "openmm/serialization/XmlSerializer.h" #include "openmm/serialization/XmlSerializer.h"
#include <iostream> #include <iostream>
#include <sstream> #include <sstream>
...@@ -41,12 +41,12 @@ using namespace std; ...@@ -41,12 +41,12 @@ using namespace std;
void testSerialization() { void testSerialization() {
// Create a Force. // Create a Force.
AmoebaHarmonicInPlaneAngleForce force1; AmoebaInPlaneAngleForce force1;
force1.setAmoebaGlobalHarmonicInPlaneAngleCubic( 12.3 ); force1.setAmoebaGlobalInPlaneAngleCubic( 12.3 );
force1.setAmoebaGlobalHarmonicInPlaneAngleQuartic( 98.7 ); force1.setAmoebaGlobalInPlaneAngleQuartic( 98.7 );
force1.setAmoebaGlobalHarmonicInPlaneAnglePentic( 91.7 ); force1.setAmoebaGlobalInPlaneAnglePentic( 91.7 );
force1.setAmoebaGlobalHarmonicInPlaneAngleSextic( 93.7 ); force1.setAmoebaGlobalInPlaneAngleSextic( 93.7 );
force1.addAngle(0, 1, 3, 4, 1.0, 2.0); force1.addAngle(0, 1, 3, 4, 1.0, 2.0);
force1.addAngle(0, 2, 3, 5, 2.0, 2.1); force1.addAngle(0, 2, 3, 5, 2.0, 2.1);
...@@ -56,16 +56,16 @@ void testSerialization() { ...@@ -56,16 +56,16 @@ void testSerialization() {
// Serialize and then deserialize it. // Serialize and then deserialize it.
stringstream buffer; stringstream buffer;
XmlSerializer::serialize<AmoebaHarmonicInPlaneAngleForce>(&force1, "Force", buffer); XmlSerializer::serialize<AmoebaInPlaneAngleForce>(&force1, "Force", buffer);
AmoebaHarmonicInPlaneAngleForce* copy = XmlSerializer::deserialize<AmoebaHarmonicInPlaneAngleForce>(buffer); AmoebaInPlaneAngleForce* copy = XmlSerializer::deserialize<AmoebaInPlaneAngleForce>(buffer);
// Compare the two forces to see if they are identical. // Compare the two forces to see if they are identical.
AmoebaHarmonicInPlaneAngleForce& force2 = *copy; AmoebaInPlaneAngleForce& force2 = *copy;
ASSERT_EQUAL(force1.getAmoebaGlobalHarmonicInPlaneAngleCubic(), force2.getAmoebaGlobalHarmonicInPlaneAngleCubic()); ASSERT_EQUAL(force1.getAmoebaGlobalInPlaneAngleCubic(), force2.getAmoebaGlobalInPlaneAngleCubic());
ASSERT_EQUAL(force1.getAmoebaGlobalHarmonicInPlaneAngleQuartic(), force2.getAmoebaGlobalHarmonicInPlaneAngleQuartic()); ASSERT_EQUAL(force1.getAmoebaGlobalInPlaneAngleQuartic(), force2.getAmoebaGlobalInPlaneAngleQuartic());
ASSERT_EQUAL(force1.getAmoebaGlobalHarmonicInPlaneAnglePentic(), force2.getAmoebaGlobalHarmonicInPlaneAnglePentic()); ASSERT_EQUAL(force1.getAmoebaGlobalInPlaneAnglePentic(), force2.getAmoebaGlobalInPlaneAnglePentic());
ASSERT_EQUAL(force1.getAmoebaGlobalHarmonicInPlaneAngleSextic(), force2.getAmoebaGlobalHarmonicInPlaneAngleSextic()); ASSERT_EQUAL(force1.getAmoebaGlobalInPlaneAngleSextic(), force2.getAmoebaGlobalInPlaneAngleSextic());
ASSERT_EQUAL(force1.getNumAngles(), force2.getNumAngles()); ASSERT_EQUAL(force1.getNumAngles(), force2.getNumAngles());
for ( unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumAngles()); ii++) { for ( unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumAngles()); ii++) {
......
wrappers/python/simtk/openmm/app/data/amoeba2009.xml
View file @ c6ebf6e2
...@@ -3543,7 +3543,7 @@ ...@@ -3543,7 +3543,7 @@
<Atom name="LI" type="382"/> <Atom name="LI" type="382"/>
</Residue> </Residue>
</Residues> </Residues>
<AmoebaHarmonicBondForce bond-cubic="-25.5" bond-quartic="379.3125"> <AmoebaBondForce bond-cubic="-25.5" bond-quartic="379.3125">
<Bond class1="1" class2="2" length="0.1437" k="156900.0"/> <Bond class1="1" class2="2" length="0.1437" k="156900.0"/>
<Bond class1="1" class2="3" length="0.1345" k="201668.8"/> <Bond class1="1" class2="3" length="0.1345" k="201668.8"/>
<Bond class1="1" class2="4" length="0.1028" k="203760.8"/> <Bond class1="1" class2="4" length="0.1028" k="203760.8"/>
...@@ -3664,8 +3664,8 @@ ...@@ -3664,8 +3664,8 @@
<Bond class1="69" class2="69" length="0.1513" k="133929.84"/> <Bond class1="69" class2="69" length="0.1513" k="133929.84"/>
<Bond class1="70" class2="71" length="0.148" k="325054.96"/> <Bond class1="70" class2="71" length="0.148" k="325054.96"/>
<Bond class1="73" class2="74" length="0.09572" k="221584.64"/> <Bond class1="73" class2="74" length="0.09572" k="221584.64"/>
</AmoebaHarmonicBondForce> </AmoebaBondForce>
<AmoebaHarmonicAngleForce angle-cubic="-0.014" angle-quartic="5.6e-05" angle-pentic="-7e-07" angle-sextic="2.2e-08"> <AmoebaAngleForce angle-cubic="-0.014" angle-quartic="5.6e-05" angle-pentic="-7e-07" angle-sextic="2.2e-08">
<Angle class1="2" class2="1" class3="3" k="0.0637259642196" angle1="122.00" /> <Angle class1="2" class2="1" class3="3" k="0.0637259642196" angle1="122.00" />
<Angle class1="2" class2="1" class3="4" k="0.0407846171005" angle1="117.00" /> <Angle class1="2" class2="1" class3="4" k="0.0407846171005" angle1="117.00" />
<Angle class1="3" class2="1" class3="4" k="0.0458826942381" angle1="121.00" /> <Angle class1="3" class2="1" class3="4" k="0.0458826942381" angle1="121.00" />
...@@ -3962,7 +3962,7 @@ ...@@ -3962,7 +3962,7 @@
<Angle class1="62" class2="70" class3="71" k="0.0966850329139" angle1="110.00" /> <Angle class1="62" class2="70" class3="71" k="0.0966850329139" angle1="110.00" />
<Angle class1="71" class2="70" class3="71" k="0.114553793281" angle1="121.20" /> <Angle class1="71" class2="70" class3="71" k="0.114553793281" angle1="121.20" />
<Angle class1="74" class2="73" class3="74" k="0.0433973816335" angle1="108.50" /> <Angle class1="74" class2="73" class3="74" k="0.0433973816335" angle1="108.50" />
</AmoebaHarmonicAngleForce> </AmoebaAngleForce>
<AmoebaOutOfPlaneBendForce type="ALLINGER" opbend-cubic="-0.014" opbend-quartic="5.6e-05" opbend-pentic="-7e-07" opbend-sextic="2.2e-08"> <AmoebaOutOfPlaneBendForce type="ALLINGER" opbend-cubic="-0.014" opbend-quartic="5.6e-05" opbend-pentic="-7e-07" opbend-sextic="2.2e-08">
<Angle class1="2" class2="1" class3="0" class4="0" k="0.0531474541591"/> <Angle class1="2" class2="1" class3="0" class4="0" k="0.0531474541591"/>
<Angle class1="3" class2="1" class3="0" class4="0" k="0.0898536095496"/> <Angle class1="3" class2="1" class3="0" class4="0" k="0.0898536095496"/>
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