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Commit 2584685c authored by Mark Friedrichs's avatar Mark Friedrichs
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Amoeba Reference tests

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plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaHarmonicInPlaneAngleForce.cpp 0 → 100644
View file @ 2584685c
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the Reference implementation of ReferenceAmoebaHarmonicInPlaneAngleForce.
*/
#include "../../../tests/AssertionUtilities.h"
//#include "AmoebaTinkerParameterFile.h"
#include "openmm/Context.h"
#include "AmoebaOpenMM.h"
#include "openmm/System.h"
#include "openmm/LangevinIntegrator.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
const double TOL = 1e-5;
#define PI_M 3.141592653589
#define RADIAN 57.29577951308
/* ---------------------------------------------------------------------------------------
Compute cross product of two 3-vectors and place in 3rd vector
vectorZ = vectorX x vectorY
@param vectorX x-vector
@param vectorY y-vector
@param vectorZ z-vector
@return vector is vectorZ
--------------------------------------------------------------------------------------- */
static void crossProductVector3( double* vectorX, double* vectorY, double* vectorZ ){
vectorZ[0] = vectorX[1]*vectorY[2] - vectorX[2]*vectorY[1];
vectorZ[1] = vectorX[2]*vectorY[0] - vectorX[0]*vectorY[2];
vectorZ[2] = vectorX[0]*vectorY[1] - vectorX[1]*vectorY[0];
return;
}
static double dotVector3( double* vectorX, double* vectorY ){
return vectorX[0]*vectorY[0] + vectorX[1]*vectorY[1] + vectorX[2]*vectorY[2];
}
static void getPrefactorsGivenInPlaneAngleCosine( double cosine, double idealInPlaneAngle, double quadraticK, double cubicK,
double quarticK, double penticK, double sexticK,
double* dEdR, double* energyTerm, FILE* log ) {
double angle;
if( cosine >= 1.0 ){
angle = 0.0f;
} else if( cosine <= -1.0 ){
angle = RADIAN*PI_M;
} else {
angle = RADIAN*acos(cosine);
}
if( log ){
(void) fprintf( log, "getPrefactorsGivenInPlaneAngleCosine: cosine=%10.3e angle=%10.3e ideal=%10.3e\n", cosine, angle, idealInPlaneAngle );
(void) fflush( log );
}
double deltaIdeal = angle - idealInPlaneAngle;
double deltaIdeal2 = deltaIdeal*deltaIdeal;
double deltaIdeal3 = deltaIdeal*deltaIdeal2;
double deltaIdeal4 = deltaIdeal2*deltaIdeal2;
// deltaIdeal = r - r_0
*dEdR = ( 2.0 +
3.0*cubicK* deltaIdeal +
4.0*quarticK*deltaIdeal2 +
5.0*penticK* deltaIdeal3 +
6.0*sexticK* deltaIdeal4 );
*dEdR *= RADIAN*quadraticK*deltaIdeal;
*energyTerm = 1.0f + cubicK* deltaIdeal +
quarticK*deltaIdeal2 +
penticK* deltaIdeal3 +
sexticK* deltaIdeal4;
*energyTerm *= quadraticK*deltaIdeal2;
return;
}
static void computeAmoebaHarmonicInPlaneAngleForce(int bondIndex, std::vector<Vec3>& positions, AmoebaHarmonicInPlaneAngleForce& amoebaHarmonicInPlaneAngleForce,
std::vector<Vec3>& forces, double* energy, FILE* log ) {
int particle1, particle2, particle3, particle4;
double idealInPlaneAngle;
double quadraticK;
amoebaHarmonicInPlaneAngleForce.getAngleParameters(bondIndex, particle1, particle2, particle3, particle4, idealInPlaneAngle, quadraticK );
double cubicK = amoebaHarmonicInPlaneAngleForce.getAmoebaGlobalHarmonicInPlaneAngleCubic();
double quarticK = amoebaHarmonicInPlaneAngleForce.getAmoebaGlobalHarmonicInPlaneAngleQuartic();
double penticK = amoebaHarmonicInPlaneAngleForce.getAmoebaGlobalHarmonicInPlaneAnglePentic();
double sexticK = amoebaHarmonicInPlaneAngleForce.getAmoebaGlobalHarmonicInPlaneAngleSextic();
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",
bondIndex, particle1, particle2, particle3, particle4, idealInPlaneAngle, quadraticK, cubicK, quarticK, penticK, sexticK );
(void) fflush( log );
}
// T = AD x CD
// P = B + T*delta
// AP = A - P
// CP = A - P
// M = CP x AP
enum { AD, BD, CD, T, AP, P, CP, M, APxM, CPxM, ADxBD, BDxCD, TxCD, ADxT, dBxAD, CDxdB, LastDeltaAtomIndex };
// AD 0
// BD 1
// CD 2
// T 3
// AP 4
// P 5
// CP 6
// M 7
// APxM, CPxM, ADxBD, BDxCD, TxCD, ADxT, dBxAD, CDxdB, LastDeltaAtomIndex
double deltaR[LastDeltaAtomIndex][3];
for( int ii = 0; ii < 3; ii++ ){
deltaR[AD][ii] = positions[particle1][ii] - positions[particle4][ii];
deltaR[BD][ii] = positions[particle2][ii] - positions[particle4][ii];
deltaR[CD][ii] = positions[particle3][ii] - positions[particle4][ii];
}
crossProductVector3( deltaR[AD], deltaR[CD], deltaR[T] );
double rT2 = dotVector3( deltaR[T], deltaR[T] );
double delta = dotVector3( deltaR[T], deltaR[BD] );
delta *= -1.0/rT2;
for( int ii = 0; ii < 3; ii++ ){
deltaR[P][ii] = positions[particle2][ii] + deltaR[T][ii]*delta;
deltaR[AP][ii] = positions[particle1][ii] - deltaR[P][ii];
deltaR[CP][ii] = positions[particle3][ii] - deltaR[P][ii];
}
double rAp2 = dotVector3( deltaR[AP], deltaR[AP] );
double rCp2 = dotVector3( deltaR[CP], deltaR[CP] );
if( rAp2 <= 0.0 && rCp2 <= 0.0 ){
if( log ){
(void) fprintf( log, "computeAmoebaHarmonicInPlaneAngleForce: rAp2 or rCp2 <= 0.0\n" );
(void) fflush( log );
}
return;
}
crossProductVector3( deltaR[CP], deltaR[AP], deltaR[M] );
double rm = dotVector3( deltaR[M], deltaR[M] );
rm = sqrt( rm );
if( rm < 0.000001 ){
rm = 0.000001;
}
double dot = dotVector3( deltaR[AP], deltaR[CP] );
double cosine = dot/sqrt( rAp2*rCp2 );
double dEdR;
double energyTerm;
getPrefactorsGivenInPlaneAngleCosine( cosine, idealInPlaneAngle, quadraticK, cubicK,
quarticK, penticK, sexticK, &dEdR, &energyTerm, log );
double termA = -dEdR/(rAp2*rm);
double termC = dEdR/(rCp2*rm);
crossProductVector3( deltaR[AP], deltaR[M], deltaR[APxM] );
crossProductVector3( deltaR[CP], deltaR[M], deltaR[CPxM] );
// forces will be gathered here
enum { dA, dB, dC, dD, LastDIndex };
double forceTerm[LastDIndex][3];
for( int ii = 0; ii < 3; ii++ ){
forceTerm[dA][ii] = deltaR[APxM][ii]*termA;
forceTerm[dC][ii] = deltaR[CPxM][ii]*termC;
forceTerm[dB][ii] = -1.0*( forceTerm[dA][ii] + forceTerm[dC][ii] );
}
double pTrT2 = dotVector3( forceTerm[dB], deltaR[T] );
pTrT2 /= rT2;
crossProductVector3( deltaR[CD], forceTerm[dB], deltaR[CDxdB] );
crossProductVector3( forceTerm[dB], deltaR[AD], deltaR[dBxAD] );
if( fabs( pTrT2 ) > 1.0e-08 ){
double delta2 = delta*2.0;
crossProductVector3( deltaR[BD], deltaR[CD], deltaR[BDxCD] );
crossProductVector3( deltaR[T], deltaR[CD], deltaR[TxCD] );
crossProductVector3( deltaR[AD], deltaR[BD], deltaR[ADxBD] );
crossProductVector3( deltaR[AD], deltaR[T], deltaR[ADxT] );
for( int ii = 0; ii < 3; ii++ ){
double term = deltaR[BDxCD][ii] + delta2*deltaR[TxCD][ii];
forceTerm[dA][ii] += delta*deltaR[CDxdB][ii] + term*pTrT2;
term = deltaR[ADxBD][ii] + delta2*deltaR[ADxT][ii];
forceTerm[dC][ii] += delta*deltaR[dBxAD][ii] + term*pTrT2;
forceTerm[dD][ii] = -( forceTerm[dA][ii] + forceTerm[dB][ii] + forceTerm[dC][ii] );
}
} else {
for( int ii = 0; ii < 3; ii++ ){
forceTerm[dA][ii] += delta*deltaR[CDxdB][ii];
forceTerm[dC][ii] += delta*deltaR[dBxAD][ii];
forceTerm[dD][ii] = -( forceTerm[dA][ii] + forceTerm[dB][ii] + forceTerm[dC][ii] );
}
}
// accumulate forces and energy
*energy += energyTerm;
forces[particle1][0] -= forceTerm[0][0];
forces[particle1][1] -= forceTerm[0][1];
forces[particle1][2] -= forceTerm[0][2];
forces[particle2][0] -= forceTerm[1][0];
forces[particle2][1] -= forceTerm[1][1];
forces[particle2][2] -= forceTerm[1][2];
forces[particle3][0] -= forceTerm[2][0];
forces[particle3][1] -= forceTerm[2][1];
forces[particle3][2] -= forceTerm[2][2];
forces[particle4][0] -= forceTerm[3][0];
forces[particle4][1] -= forceTerm[3][1];
forces[particle4][2] -= forceTerm[3][2];
}
static void computeAmoebaHarmonicInPlaneAngleForces( Context& context, AmoebaHarmonicInPlaneAngleForce& amoebaHarmonicInPlaneAngleForce,
std::vector<Vec3>& expectedForces, double* expectedEnergy, FILE* log ) {
// get positions and zero forces
State state = context.getState(State::Positions);
std::vector<Vec3> positions = state.getPositions();
expectedForces.resize( positions.size() );
for( unsigned int ii = 0; ii < expectedForces.size(); ii++ ){
expectedForces[ii][0] = expectedForces[ii][1] = expectedForces[ii][2] = 0.0;
}
// calculates forces/energy
*expectedEnergy = 0.0;
for( int ii = 0; ii < amoebaHarmonicInPlaneAngleForce.getNumAngles(); ii++ ){
computeAmoebaHarmonicInPlaneAngleForce(ii, positions, amoebaHarmonicInPlaneAngleForce, expectedForces, expectedEnergy, log );
}
if( log ){
(void) fprintf( log, "computeAmoebaHarmonicInPlaneAngleForces: expected energy=%14.7e\n", *expectedEnergy );
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) fflush( log );
}
return;
}
void compareWithExpectedForceAndEnergy( Context& context, AmoebaHarmonicInPlaneAngleForce& amoebaHarmonicInPlaneAngleForce,
double tolerance, const std::string& idString, FILE* log) {
std::vector<Vec3> expectedForces;
double expectedEnergy;
computeAmoebaHarmonicInPlaneAngleForces( context, amoebaHarmonicInPlaneAngleForce, expectedForces, &expectedEnergy, log );
State state = context.getState(State::Forces | State::Energy);
const std::vector<Vec3> forces = state.getForces();
if( log ){
(void) fprintf( log, "computeAmoebaHarmonicInPlaneAngleForces: expected energy=%14.7e %14.7e\n", expectedEnergy, state.getPotentialEnergy() );
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,
expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2], forces[ii][0], forces[ii][1], forces[ii][2] );
}
(void) fflush( log );
}
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
ASSERT_EQUAL_VEC( expectedForces[ii], forces[ii], tolerance );
}
ASSERT_EQUAL_TOL( expectedEnergy, state.getPotentialEnergy(), tolerance );
}
void testOneAngle( FILE* log ) {
System system;
int numberOfParticles = 4;
for( int ii = 0; ii < numberOfParticles; ii++ ){
system.addParticle(1.0);
}
LangevinIntegrator integrator(0.0, 0.1, 0.01);
AmoebaHarmonicInPlaneAngleForce* amoebaHarmonicInPlaneAngleForce = new AmoebaHarmonicInPlaneAngleForce();
double angle = 65.0;
double quadraticK = 1.0;
double cubicK = 0.0e-01;
double quarticK = 0.0e-02;
double penticK = 0.0e-03;
double sexticK = 0.0e-04;
amoebaHarmonicInPlaneAngleForce->addAngle(0, 1, 2, 3, angle, quadraticK);
amoebaHarmonicInPlaneAngleForce->setAmoebaGlobalHarmonicInPlaneAngleCubic(cubicK);
amoebaHarmonicInPlaneAngleForce->setAmoebaGlobalHarmonicInPlaneAngleQuartic(quarticK);
amoebaHarmonicInPlaneAngleForce->setAmoebaGlobalHarmonicInPlaneAnglePentic(penticK);
amoebaHarmonicInPlaneAngleForce->setAmoebaGlobalHarmonicInPlaneAngleSextic(sexticK);
system.addForce(amoebaHarmonicInPlaneAngleForce);
Context context(system, integrator, Platform::getPlatformByName( "Reference"));
std::vector<Vec3> positions(numberOfParticles);
positions[0] = Vec3(0, 1, 0);
positions[1] = Vec3(0, 0, 0);
positions[2] = Vec3(0, 0, 1);
positions[3] = Vec3(1, 1, 1);
context.setPositions(positions);
compareWithExpectedForceAndEnergy( context, *amoebaHarmonicInPlaneAngleForce, TOL, "testOneInPlaneAngle", log );
}
int main( int numberOfArguments, char* argv[] ) {
try {
std::cout << "TestReferenceAmoebaHarmonicInPlaneAngleForce running test..." << std::endl;
Platform::loadPluginsFromDirectory( Platform::getDefaultPluginsDirectory() );
//FILE* log = NULL;
FILE* log = stderr;
//FILE* log = fopen( "AmoebaHarmonicInPlaneAngleForce.log", "w" );;
testOneAngle( NULL );
if( log && log != stderr )
(void) fclose( log );
}
catch(const std::exception& e) {
std::cout << "exception: " << e.what() << std::endl;
std::cout << "FAIL - ERROR. Test failed." << std::endl;
return 1;
}
std::cout << "PASS - Test succeeded." << std::endl;
return 0;
}
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaOutOfPlaneBendForce.cpp 0 → 100644
View file @ 2584685c
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the Reference implementation of ReferenceAmoebaOutOfPlaneBendForce.
*/
#include "../../../tests/AssertionUtilities.h"
//#include "AmoebaTinkerParameterFile.h"
#include "openmm/Context.h"
#include "AmoebaOpenMM.h"
#include "openmm/System.h"
#include "openmm/LangevinIntegrator.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
const double TOL = 1e-3;
#define PI_M 3.141592653589
#define RADIAN 57.29577951308
/* ---------------------------------------------------------------------------------------
Compute cross product of two 3-vectors and place in 3rd vector
vectorZ = vectorX x vectorY
@param vectorX x-vector
@param vectorY y-vector
@param vectorZ z-vector
@return vector is vectorZ
--------------------------------------------------------------------------------------- */
static void crossProductVector3( double* vectorX, double* vectorY, double* vectorZ ){
vectorZ[0] = vectorX[1]*vectorY[2] - vectorX[2]*vectorY[1];
vectorZ[1] = vectorX[2]*vectorY[0] - vectorX[0]*vectorY[2];
vectorZ[2] = vectorX[0]*vectorY[1] - vectorX[1]*vectorY[0];
return;
}
static double dotVector3( double* vectorX, double* vectorY ){
return vectorX[0]*vectorY[0] + vectorX[1]*vectorY[1] + vectorX[2]*vectorY[2];
}
static void computeAmoebaOutOfPlaneBendForce(int bondIndex, std::vector<Vec3>& positions, AmoebaOutOfPlaneBendForce& amoebaOutOfPlaneBendForce,
std::vector<Vec3>& forces, double* energy, FILE* log ) {
double kAngleCubic = amoebaOutOfPlaneBendForce.getAmoebaGlobalOutOfPlaneBendCubic();
double kAngleQuartic = amoebaOutOfPlaneBendForce.getAmoebaGlobalOutOfPlaneBendQuartic();
double kAnglePentic = amoebaOutOfPlaneBendForce.getAmoebaGlobalOutOfPlaneBendPentic();
double kAngleSextic = amoebaOutOfPlaneBendForce.getAmoebaGlobalOutOfPlaneBendSextic();
int particle1, particle2, particle3, particle4;
double kAngleQuadratic;
amoebaOutOfPlaneBendForce.getOutOfPlaneBendParameters(bondIndex, particle1, particle2, particle3, particle4, kAngleQuadratic );
if( log ){
(void) fprintf( log, "computeAmoebaOutOfPlaneBendForce: bond %d [%d %d %d %d] k=[%10.3e %10.3e %10.3e %10.3e %10.3e]\n",
bondIndex, particle1, particle2, particle3, particle4, kAngleQuadratic, kAngleCubic, kAngleQuartic, kAnglePentic, kAngleSextic );
(void) fflush( log );
}
enum { A, B, C, D, LastAtomIndex };
enum { AB, CB, DB, AD, CD, LastDeltaIndex };
// ---------------------------------------------------------------------------------------
// get deltaR between various combinations of the 4 atoms
// and various intermediate terms
double deltaR[LastDeltaIndex][6];
for( int ii = 0; ii < 3; ii++ ){
deltaR[AB][ii] = positions[particle1][ii] - positions[particle2][ii];
deltaR[CB][ii] = positions[particle3][ii] - positions[particle2][ii];
deltaR[DB][ii] = positions[particle4][ii] - positions[particle2][ii];
deltaR[AD][ii] = positions[particle1][ii] - positions[particle4][ii];
deltaR[CD][ii] = positions[particle3][ii] - positions[particle4][ii];
}
double rDB2 = dotVector3( deltaR[DB], deltaR[DB] );
double rAD2 = dotVector3( deltaR[AD], deltaR[AD] );
double rCD2 = dotVector3( deltaR[CD], deltaR[CD] );
double tempVector[3];
crossProductVector3( deltaR[CB], deltaR[DB], tempVector );
double eE = dotVector3( deltaR[AB], tempVector );
double dot = dotVector3( deltaR[AD], deltaR[CD] );
double cc = rAD2*rCD2 - dot*dot;
if( rDB2 <= 0.0 || cc == 0.0 ){
return;
}
double bkk2 = rDB2 - eE*eE/cc;
double cosine = sqrt(bkk2/rDB2);
double angle;
if( cosine >= 1.0 ){
angle = 0.0;
} else if( cosine <= -1.0 ){
angle = PI_M;
} else {
angle = RADIAN*acos(cosine);
}
if( log ){
(void) fprintf( log, "computeAmoebaOutOfPlaneBendForce: bkk2=%14.7e rDB2=%14.7e cos=%14.7e dt=%14.7e]\n",
bkk2, rDB2, cosine, angle );
(void) fflush( log );
}
// chain rule
double dt = angle;
double dt2 = dt*dt;
double dt3 = dt2*dt;
double dt4 = dt2*dt2;
double dEdDt = 2.0 + 3.0*kAngleCubic*dt + 4.0*kAngleQuartic*dt2 + 5.0*kAnglePentic *dt3 + 6.0*kAngleSextic *dt4;
dEdDt *= kAngleQuadratic*dt*RADIAN;
double dEdCos;
dEdCos = dEdDt/sqrt(cc*bkk2);
if( eE > 0.0 ){
dEdCos *= -1.0;
}
double term = eE/cc;
double dccd[LastAtomIndex][3];
for( int ii = 0; ii < 3; ii++ ){
dccd[A][ii] = (deltaR[AD][ii]*rCD2 - deltaR[CD][ii]*dot)*term;
dccd[C][ii] = (deltaR[CD][ii]*rAD2 - deltaR[AD][ii]*dot)*term;
dccd[D][ii] = -1.0*(dccd[A][ii] + dccd[C][ii]);
}
double deed[LastAtomIndex][3];
crossProductVector3( deltaR[DB], deltaR[CB], deed[A] );
crossProductVector3( deltaR[AB], deltaR[DB], deed[C] );
crossProductVector3( deltaR[CB], deltaR[AB], deed[D] );
term = eE/rDB2;
deed[D][0] += deltaR[DB][0]*term;
deed[D][1] += deltaR[DB][1]*term;
deed[D][2] += deltaR[DB][2]*term;
// ---------------------------------------------------------------------------------------
// forces
// calculate forces for atoms a, c, d
// the force for b is then -( a+ c + d)
double subForce[LastAtomIndex][3];
for( int jj = 0; jj < LastAtomIndex; jj++ ){
// A, C, D
for( int ii = 0; ii < 3; ii++ ){
subForce[jj][ii] = dEdCos*( dccd[jj][ii] + deed[jj][ii] );
}
if( jj == 0 )jj++; // skip B
// now compute B
if( jj == 3 ){
for( int ii = 0; ii < 3; ii++ ){
subForce[1][ii] = -1.0*(subForce[0][ii] + subForce[2][ii] + subForce[3][ii]);
}
}
}
// accumulate forces and energy
forces[particle1][0] -= subForce[0][0];
forces[particle1][1] -= subForce[0][1];
forces[particle1][2] -= subForce[0][2];
forces[particle2][0] -= subForce[1][0];
forces[particle2][1] -= subForce[1][1];
forces[particle2][2] -= subForce[1][2];
forces[particle3][0] -= subForce[2][0];
forces[particle3][1] -= subForce[2][1];
forces[particle3][2] -= subForce[2][2];
forces[particle4][0] -= subForce[3][0];
forces[particle4][1] -= subForce[3][1];
forces[particle4][2] -= subForce[3][2];
// ---------------------------------------------------------------------------------------
// calculate energy if 'energy' is set
double energyTerm = 1.0 + kAngleCubic *dt +
kAngleQuartic*dt2 +
kAnglePentic *dt3 +
kAngleSextic *dt4;
energyTerm *= kAngleQuadratic*dt2;
*energy += energyTerm;
return;
}
static void computeAmoebaOutOfPlaneBendForces( Context& context, AmoebaOutOfPlaneBendForce& amoebaOutOfPlaneBendForce,
std::vector<Vec3>& expectedForces, double* expectedEnergy, FILE* log ) {
// get positions and zero forces
State state = context.getState(State::Positions);
std::vector<Vec3> positions = state.getPositions();
expectedForces.resize( positions.size() );
for( unsigned int ii = 0; ii < expectedForces.size(); ii++ ){
expectedForces[ii][0] = expectedForces[ii][1] = expectedForces[ii][2] = 0.0;
}
// calculates forces/energy
*expectedEnergy = 0.0;
for( int ii = 0; ii < amoebaOutOfPlaneBendForce.getNumOutOfPlaneBends(); ii++ ){
computeAmoebaOutOfPlaneBendForce(ii, positions, amoebaOutOfPlaneBendForce, expectedForces, expectedEnergy, log );
}
if( log ){
(void) fprintf( log, "computeAmoebaOutOfPlaneBendForces: expected energy=%14.7e\n", *expectedEnergy );
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) fflush( log );
}
return;
}
void compareWithExpectedForceAndEnergy( Context& context, AmoebaOutOfPlaneBendForce& amoebaOutOfPlaneBendForce,
double tolerance, const std::string& idString, FILE* log) {
std::vector<Vec3> expectedForces;
double expectedEnergy;
computeAmoebaOutOfPlaneBendForces( context, amoebaOutOfPlaneBendForce, expectedForces, &expectedEnergy, log );
State state = context.getState(State::Forces | State::Energy);
const std::vector<Vec3> forces = state.getForces();
if( log ){
(void) fprintf( log, "computeAmoebaOutOfPlaneBendForces: expected energy=%14.7e %14.7e\n", expectedEnergy, state.getPotentialEnergy() );
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,
expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2], forces[ii][0], forces[ii][1], forces[ii][2] );
}
(void) fflush( log );
}
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
ASSERT_EQUAL_VEC( expectedForces[ii], forces[ii], tolerance );
}
ASSERT_EQUAL_TOL( expectedEnergy, state.getPotentialEnergy(), tolerance );
}
void testOneOutOfPlaneBend( FILE* log ) {
System system;
int numberOfParticles = 4;
for( int ii = 0; ii < numberOfParticles; ii++ ){
system.addParticle(1.0);
}
LangevinIntegrator integrator(0.0, 0.1, 0.01);
AmoebaOutOfPlaneBendForce* amoebaOutOfPlaneBendForce = new AmoebaOutOfPlaneBendForce();
amoebaOutOfPlaneBendForce->setAmoebaGlobalOutOfPlaneBendCubic( -0.1400000E-01 );
amoebaOutOfPlaneBendForce->setAmoebaGlobalOutOfPlaneBendQuartic( 0.5600000E-04 );
amoebaOutOfPlaneBendForce->setAmoebaGlobalOutOfPlaneBendPentic( -0.7000000E-06 );
amoebaOutOfPlaneBendForce->setAmoebaGlobalOutOfPlaneBendSextic( 0.2200000E-07 );
double kOutOfPlaneBend = 0.328682196E-01;
amoebaOutOfPlaneBendForce->addOutOfPlaneBend(0, 1, 2, 3, kOutOfPlaneBend );
system.addForce(amoebaOutOfPlaneBendForce);
Context context(system, integrator, Platform::getPlatformByName( "Reference"));
std::vector<Vec3> positions(numberOfParticles);
positions[0] = Vec3( 0.262660000E+02, 0.254130000E+02, 0.284200000E+01 );
positions[1] = Vec3( 0.269130000E+02, 0.266390000E+02, 0.353100000E+01 );
positions[2] = Vec3( 0.278860000E+02, 0.264630000E+02, 0.426300000E+01 );
positions[3] = Vec3( 0.245568230E+02, 0.250215290E+02, 0.796852800E+01 );
context.setPositions(positions);
compareWithExpectedForceAndEnergy( context, *amoebaOutOfPlaneBendForce, TOL, "testOneOutOfPlaneBend", log );
}
void testOneOutOfPlaneBend2( FILE* log, int setId ) {
System system;
int numberOfParticles = 4;
for( int ii = 0; ii < numberOfParticles; ii++ ){
system.addParticle(1.0);
}
LangevinIntegrator integrator(0.0, 0.1, 0.01);
AmoebaOutOfPlaneBendForce* amoebaOutOfPlaneBendForce = new AmoebaOutOfPlaneBendForce();
amoebaOutOfPlaneBendForce->setAmoebaGlobalOutOfPlaneBendCubic( -0.1400000E-01 );
amoebaOutOfPlaneBendForce->setAmoebaGlobalOutOfPlaneBendQuartic( 0.5600000E-04 );
amoebaOutOfPlaneBendForce->setAmoebaGlobalOutOfPlaneBendPentic( -0.7000000E-06 );
amoebaOutOfPlaneBendForce->setAmoebaGlobalOutOfPlaneBendSextic( 0.2200000E-07 );
/*
285 441 442 443 444 0.328682196E-01
286 441 442 444 443 0.164493407E-01
287 443 442 444 441 0.636650407E-02
288 442 444 447 448 0.392956472E-02
289 442 444 448 447 0.392956472E-02
290 447 444 448 442 0.214755281E-01
441 0.893800000E+01 0.439800000E+01 0.343100000E+01
442 0.779100000E+01 0.614600000E+01 0.390100000E+01
443 0.915400000E+01 0.683900000E+01 0.389400000E+01
444 0.101770000E+02 0.619000000E+01 0.379900000E+01
445 0.921000000E+01 0.813800000E+01 0.398600000E+01
446 0.708500000E+01 0.672900000E+01 0.332700000E+01
447 0.744300000E+01 0.605200000E+01 0.491900000E+01
448 0.100820000E+02 0.859300000E+01 0.398200000E+01
449 0.838000000E+01 0.866100000E+01 0.406000000E+01
*/
std::map<int,Vec3> coordinates;
coordinates[440] = Vec3( 0.893800000E+01, 0.439800000E+01, 0.343100000E+01 );
coordinates[441] = Vec3( 0.779100000E+01, 0.614600000E+01, 0.390100000E+01 );
coordinates[442] = Vec3( 0.915400000E+01, 0.683900000E+01, 0.389400000E+01 );
coordinates[443] = Vec3( 0.101770000E+02, 0.619000000E+01, 0.379900000E+01 );
coordinates[444] = Vec3( 0.921000000E+01, 0.813800000E+01, 0.398600000E+01 );
coordinates[445] = Vec3( 0.708500000E+01, 0.672900000E+01, 0.332700000E+01 );
coordinates[446] = Vec3( 0.744300000E+01, 0.605200000E+01, 0.491900000E+01 );
coordinates[447] = Vec3( 0.100820000E+02, 0.859300000E+01, 0.398200000E+01 );
coordinates[448] = Vec3( 0.838000000E+01, 0.866100000E+01, 0.406000000E+01 );
double kOutOfPlaneBend = 0.328682196E-01;
std::vector<int> particleIndices;
if( setId == 1 ){
particleIndices.push_back( 441 );
particleIndices.push_back( 442 );
particleIndices.push_back( 443 );
particleIndices.push_back( 444 );
kOutOfPlaneBend = 0.328682196E-01;
} else if( setId == 2 ){
particleIndices.push_back( 441 );
particleIndices.push_back( 442 );
particleIndices.push_back( 444 );
particleIndices.push_back( 443 );
kOutOfPlaneBend = 0.164493407E-01;
} else if( setId == 3 ){
particleIndices.push_back( 443 );
particleIndices.push_back( 442 );
particleIndices.push_back( 444 );
particleIndices.push_back( 441 );
kOutOfPlaneBend = 0.636650407E-02;
} else if( setId == 4 ){
particleIndices.push_back( 442 );
particleIndices.push_back( 444 );
particleIndices.push_back( 447 );
particleIndices.push_back( 448 );
kOutOfPlaneBend = 0.392956472E-02;
} else if( setId == 5 ){
particleIndices.push_back( 442 );
particleIndices.push_back( 444 );
particleIndices.push_back( 448 );
particleIndices.push_back( 447 );
kOutOfPlaneBend = 0.392956472E-02;
} else if( setId == 6 ){
particleIndices.push_back( 447 );
particleIndices.push_back( 444 );
particleIndices.push_back( 448 );
particleIndices.push_back( 442 );
kOutOfPlaneBend = 0.214755281E-01;
} else {
if( log ){
(void) fprintf( log, "Set id %d not recognized.\n", setId );
}
char buffer[1024];
(void) sprintf( buffer, "Set id %d not recognized.", setId );
throw OpenMMException( buffer );
}
if( log ){
(void) fprintf( log, "Set id %d.\n", setId );
}
amoebaOutOfPlaneBendForce->addOutOfPlaneBend(0, 1, 2, 3, kOutOfPlaneBend );
system.addForce(amoebaOutOfPlaneBendForce);
Context context(system, integrator, Platform::getPlatformByName( "Reference"));
std::vector<Vec3> positions(numberOfParticles);
for( unsigned int ii = 0; ii < numberOfParticles; ii++ ){
if( coordinates.find( particleIndices[ii] ) == coordinates.end() ){
if( log ){
(void) fprintf( log, "Coordinates %d not loaded.", particleIndices[ii] );
}
char buffer[1024];
(void) sprintf( buffer, "Coordinates %d not loaded.", particleIndices[ii] );
throw OpenMMException( buffer );
}
positions[ii] = coordinates[particleIndices[ii]];
}
context.setPositions(positions);
compareWithExpectedForceAndEnergy( context, *amoebaOutOfPlaneBendForce, TOL, "testOneOutOfPlaneBend", log );
static int iter = 0;
static std::map<int,Vec3> totalForces;
static double totalEnergy;
if( iter == 0 ){
totalForces[441] = Vec3( 0.0, 0.0, 0.0 );
totalForces[442] = Vec3( 0.0, 0.0, 0.0 );
totalForces[443] = Vec3( 0.0, 0.0, 0.0 );
totalForces[444] = Vec3( 0.0, 0.0, 0.0 );
totalForces[445] = Vec3( 0.0, 0.0, 0.0 );
totalForces[446] = Vec3( 0.0, 0.0, 0.0 );
totalForces[447] = Vec3( 0.0, 0.0, 0.0 );
totalForces[448] = Vec3( 0.0, 0.0, 0.0 );
totalForces[449] = Vec3( 0.0, 0.0, 0.0 );
totalEnergy = 0.0;
}
iter++;
std::vector<Vec3> forces;
forces.resize( numberOfParticles );
double energy;
computeAmoebaOutOfPlaneBendForce( 0, positions, *amoebaOutOfPlaneBendForce, forces, &energy, log );
totalEnergy += energy;
for( unsigned int ii = 0; ii < numberOfParticles; ii++ ){
for( unsigned int jj = 0; jj < 3; jj++ ){
totalForces[particleIndices[ii]][jj] += forces[ii][jj];
}
}
if( iter == 6 ){
if( log ){
(void) fprintf( log, "computeAmoebaOutOfPlaneBendForces: energy=%14.7e\n", totalEnergy);
for( std::map<int,Vec3>::iterator ii = totalForces.begin(); ii != totalForces.end(); ii++ ){
int particleIndex = ii->first;
Vec3 forces = ii->second;
(void) fprintf( log, "%6d [%14.7e %14.7e %14.7e] \n", particleIndex,
forces[0], forces[1], forces[2] );
}
(void) fflush( log );
}
}
}
int main( int numberOfArguments, char* argv[] ) {
try {
std::cout << "TestReferenceAmoebaOutOfPlaneBendForce running test..." << std::endl;
Platform::loadPluginsFromDirectory( Platform::getDefaultPluginsDirectory() );
FILE* log = stderr;
//FILE* log = NULL;
//FILE* log = fopen( "AmoebaOutOfPlaneBendForce.log", "w" );;
testOneOutOfPlaneBend( log );
//testOneOutOfPlaneBend2( log, atoi( argv[1] ) );
//for( int ii = 1; ii <= 6; ii++ ){
// testOneOutOfPlaneBend2( log, ii );
//}
if( log && log != stderr )
(void) fclose( log );
}
catch(const std::exception& e) {
std::cout << "exception: " << e.what() << std::endl;
std::cout << "FAIL - ERROR. Test failed." << std::endl;
return 1;
}
std::cout << "PASS - Test succeeded." << std::endl;
return 0;
}
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaStretchBendForce.cpp 0 → 100644
View file @ 2584685c
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the Reference implementation of ReferenceAmoebaStretchBendForce.
*/
#include "../../../tests/AssertionUtilities.h"
//#include "AmoebaTinkerParameterFile.h"
const double DegreesToRadians = 3.14159265/180.0;
#include "openmm/Context.h"
#include "AmoebaOpenMM.h"
#include "openmm/System.h"
#include "openmm/LangevinIntegrator.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
const double TOL = 1e-4;
#define PI_M 3.141592653589
#define RADIAN 57.29577951308
/* ---------------------------------------------------------------------------------------
Compute cross product of two 3-vectors and place in 3rd vector
vectorZ = vectorX x vectorY
@param vectorX x-vector
@param vectorY y-vector
@param vectorZ z-vector
@return vector is vectorZ
--------------------------------------------------------------------------------------- */
static void crossProductVector3( double* vectorX, double* vectorY, double* vectorZ ){
vectorZ[0] = vectorX[1]*vectorY[2] - vectorX[2]*vectorY[1];
vectorZ[1] = vectorX[2]*vectorY[0] - vectorX[0]*vectorY[2];
vectorZ[2] = vectorX[0]*vectorY[1] - vectorX[1]*vectorY[0];
return;
}
static double dotVector3( double* vectorX, double* vectorY ){
return vectorX[0]*vectorY[0] + vectorX[1]*vectorY[1] + vectorX[2]*vectorY[2];
}
static void computeAmoebaStretchBendForce(int bondIndex, std::vector<Vec3>& positions, AmoebaStretchBendForce& amoebaStretchBendForce,
std::vector<Vec3>& forces, double* energy, FILE* log ) {
int particle1, particle2, particle3;
double abBondLength, cbBondLength, angleStretchBend, kStretchBend;
amoebaStretchBendForce.getStretchBendParameters(bondIndex, particle1, particle2, particle3, abBondLength, cbBondLength, angleStretchBend, kStretchBend);
angleStretchBend *= RADIAN;
if( log ){
(void) fprintf( log, "computeAmoebaStretchBendForce: bond %d [%d %d %d] ab=%10.3e cb=%10.3e angle=%10.3e k=%10.3e\n",
bondIndex, particle1, particle2, particle3, abBondLength, cbBondLength, angleStretchBend, kStretchBend );
(void) fflush( log );
}
enum { A, B, C, LastAtomIndex };
enum { AB, CB, CBxAB, ABxP, CBxP, LastDeltaIndex };
// ---------------------------------------------------------------------------------------
// get deltaR between various combinations of the 3 atoms
// and various intermediate terms
double deltaR[LastDeltaIndex][3];
double rAB2 = 0.0;
double rCB2 = 0.0;
for( int ii = 0; ii < 3; ii++ ){
deltaR[AB][ii] = positions[particle1][ii] - positions[particle2][ii];
rAB2 += deltaR[AB][ii]*deltaR[AB][ii];
deltaR[CB][ii] = positions[particle3][ii] - positions[particle2][ii];
rCB2 += deltaR[CB][ii]*deltaR[CB][ii];
}
double rAB = sqrt( rAB2 );
double rCB = sqrt( rCB2 );
crossProductVector3( deltaR[CB], deltaR[AB], deltaR[CBxAB] );
double rP = dotVector3( deltaR[CBxAB], deltaR[CBxAB] );
rP = sqrt( rP );
if( rP <= 0.0 ){
return;
}
double dot = dotVector3( deltaR[CB], deltaR[AB] );
double cosine = dot/(rAB*rCB);
double angle;
if( cosine >= 1.0 ){
angle = 0.0;
} else if( cosine <= -1.0 ){
angle = PI_M;
} else {
angle = RADIAN*acos(cosine);
}
double termA = -RADIAN/(rAB2*rP);
double termC = RADIAN/(rCB2*rP);
// P = CBxAB
crossProductVector3( deltaR[AB], deltaR[CBxAB], deltaR[ABxP] );
crossProductVector3( deltaR[CB], deltaR[CBxAB], deltaR[CBxP] );
for( int ii = 0; ii < 3; ii++ ){
deltaR[ABxP][ii] *= termA;
deltaR[CBxP][ii] *= termC;
}
double dr = rAB - abBondLength + rCB - cbBondLength;
termA = 1.0/rAB;
termC = 1.0/rCB;
double term = kStretchBend;
// ---------------------------------------------------------------------------------------
// forces
// calculate forces for atoms a, b, c
// the force for b is then -( a + c)
double subForce[LastAtomIndex][3];
double dt = angle - angleStretchBend;
for( int jj = 0; jj < 3; jj++ ){
subForce[A][jj] = term*(dt*termA*deltaR[AB][jj] + dr*deltaR[ABxP][jj] );
subForce[C][jj] = term*(dt*termC*deltaR[CB][jj] + dr*deltaR[CBxP][jj] );
subForce[B][jj] = -( subForce[A][jj] + subForce[C][jj] );
}
// ---------------------------------------------------------------------------------------
// accumulate forces and energy
forces[particle1][0] -= subForce[0][0];
forces[particle1][1] -= subForce[0][1];
forces[particle1][2] -= subForce[0][2];
forces[particle2][0] -= subForce[1][0];
forces[particle2][1] -= subForce[1][1];
forces[particle2][2] -= subForce[1][2];
forces[particle3][0] -= subForce[2][0];
forces[particle3][1] -= subForce[2][1];
forces[particle3][2] -= subForce[2][2];
*energy += term*dt*dr;
if( log ){
(void) fprintf( log, "computeAmoebaStretchBendForce: angle=%10.3e dt=%10.3e dr=%10.3e\n", angle, dt, dr );
(void) fflush( log );
}
return;
}
static void computeAmoebaStretchBendForces( Context& context, AmoebaStretchBendForce& amoebaStretchBendForce,
std::vector<Vec3>& expectedForces, double* expectedEnergy, FILE* log ) {
// get positions and zero forces
State state = context.getState(State::Positions);
std::vector<Vec3> positions = state.getPositions();
expectedForces.resize( positions.size() );
for( unsigned int ii = 0; ii < expectedForces.size(); ii++ ){
expectedForces[ii][0] = expectedForces[ii][1] = expectedForces[ii][2] = 0.0;
}
// calculates forces/energy
*expectedEnergy = 0.0;
for( int ii = 0; ii < amoebaStretchBendForce.getNumStretchBends(); ii++ ){
computeAmoebaStretchBendForce(ii, positions, amoebaStretchBendForce, expectedForces, expectedEnergy, log );
}
if( log ){
(void) fprintf( log, "computeAmoebaStretchBendForces: expected energy=%14.7e\n", *expectedEnergy );
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) fflush( log );
}
return;
}
void compareWithExpectedForceAndEnergy( Context& context, AmoebaStretchBendForce& amoebaStretchBendForce,
double tolerance, const std::string& idString, FILE* log) {
std::vector<Vec3> expectedForces;
double expectedEnergy;
computeAmoebaStretchBendForces( context, amoebaStretchBendForce, expectedForces, &expectedEnergy, log );
State state = context.getState(State::Forces | State::Energy);
const std::vector<Vec3> forces = state.getForces();
if( log ){
(void) fprintf( log, "computeAmoebaStretchBendForces: expected energy=%14.7e %14.7e\n", expectedEnergy, state.getPotentialEnergy() );
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,
expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2], forces[ii][0], forces[ii][1], forces[ii][2] );
}
(void) fflush( log );
}
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
ASSERT_EQUAL_VEC( expectedForces[ii], forces[ii], tolerance );
}
ASSERT_EQUAL_TOL( expectedEnergy, state.getPotentialEnergy(), tolerance );
}
void testOneStretchBend( FILE* log ) {
System system;
int numberOfParticles = 3;
for( int ii = 0; ii < numberOfParticles; ii++ ){
system.addParticle(1.0);
}
LangevinIntegrator integrator(0.0, 0.1, 0.01);
AmoebaStretchBendForce* amoebaStretchBendForce = new AmoebaStretchBendForce();
double abLength = 0.144800000E+01;
double cbLength = 0.101500000E+01;
double angleStretchBend = 0.108500000E+03*DegreesToRadians;
//double kStretchBend = 0.750491578E-01;
double kStretchBend = 1.0;
amoebaStretchBendForce->addStretchBend(0, 1, 2, abLength, cbLength, angleStretchBend, kStretchBend );
system.addForce(amoebaStretchBendForce);
Context context(system, integrator, Platform::getPlatformByName( "Reference"));
std::vector<Vec3> positions(numberOfParticles);
positions[0] = Vec3( 0.262660000E+02, 0.254130000E+02, 0.284200000E+01 );
positions[1] = Vec3( 0.273400000E+02, 0.244300000E+02, 0.261400000E+01 );
positions[2] = Vec3( 0.269573220E+02, 0.236108860E+02, 0.216376800E+01 );
context.setPositions(positions);
compareWithExpectedForceAndEnergy( context, *amoebaStretchBendForce, TOL, "testOneStretchBend", log );
}
int main( int numberOfArguments, char* argv[] ) {
try {
std::cout << "TestReferenceAmoebaStretchBendForce running test..." << std::endl;
Platform::loadPluginsFromDirectory( Platform::getDefaultPluginsDirectory() );
//FILE* log = NULL;
FILE* log = stderr;
//FILE* log = fopen( "AmoebaStretchBendForce1.log", "w" );;
testOneStretchBend( log );
if( log && log != stderr )
(void) fclose( log );
}
catch(const std::exception& e) {
std::cout << "exception: " << e.what() << std::endl;
std::cout << "FAIL - ERROR. Test failed." << std::endl;
return 1;
}
std::cout << "PASS - Test succeeded." << std::endl;
return 0;
}
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