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Commit 495a43c6 authored by Mark Friedrichs's avatar Mark Friedrichs
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platforms/brook/tests/TestBrookAngleBondForce.cpp 0 → 100644
View file @ 495a43c6
/* -------------------------------------------------------------------------- *
* 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: Mark Friedrichs *
* 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 Brook harmonic angle bond force/energy
*/
#include "../../../tests/AssertionUtilities.h"
#include "BrookPlatform.h"
#include "OpenMMContext.h"
#include "HarmonicAngleForce.h"
#include "System.h"
#include "LangevinIntegrator.h"
#include <vector>
#define PI_M 3.141592653589
using namespace OpenMM;
using namespace std;
const double TOL = 1e-5;
void testBrookAngles( FILE* log ){
// ---------------------------------------------------------------------------------------
static const std::string methodName = "testBrookAngles";
static const int debug = 1;
int PrintOn = 0;
int numberOfParticles = 4;
double mass = 2.0;
// ---------------------------------------------------------------------------------------
PrintOn = log ? PrintOn : 0;
if( PrintOn ){
(void) fprintf( log, "%s\n", methodName.c_str() ); (void) fflush( log );
}
BrookPlatform platform( 32, "cal", log );
System system( numberOfParticles, 0 );
LangevinIntegrator integrator( 0, 0.1, 0.01 );
// int numParticles, int numBonds, int numAngles, int numPeriodicTorsions, int numRBTorsions
HarmonicAngleForce* forceField = new HarmonicAngleForce(2);
// int index, int atom1, int atom2, int atom3, double angle, double k
forceField->setAngleParameters(0, 0, 1, 2, PI_M/3, 1.1);
forceField->setAngleParameters(1, 1, 2, 3, PI_M/2, 1.2);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(numberOfParticles);
positions[0] = Vec3(0, 1, 0);
positions[1] = Vec3(0, 0, 0);
positions[2] = Vec3(1, 0, 0);
positions[3] = Vec3(2, 1, 0);
context.setPositions(positions);
State state = context.getState( State::Forces | State::Energy );
const vector<Vec3>& forces = state.getForces();
if( PrintOn ){
(void) fprintf( log, "Angle bond forces\n");
for( int ii = 0; ii < numberOfParticles; ii++ ){
(void) fprintf( log, "%d [%.5e %.5e %.5e]\n", ii, forces[ii][0], forces[ii][1], forces[ii][2] );
}
(void) fflush( log );
}
double tolerance = 1.0e-03;
double torque1 = 1.1*PI_M/6;
double torque2 = 1.2*PI_M/4;
ASSERT_EQUAL_VEC(Vec3(torque1, 0, 0), forces[0], tolerance);
ASSERT_EQUAL_VEC(Vec3(-0.5*torque2, 0.5*torque2, 0), forces[3], tolerance); // reduced by sqrt(2) due to the bond length, another sqrt(2) due to the angle
ASSERT_EQUAL_VEC(Vec3(forces[0][0]+forces[1][0]+forces[2][0]+forces[3][0],
forces[0][1]+forces[1][1]+forces[2][1]+forces[3][1],
forces[0][2]+forces[1][2]+forces[2][2]+forces[3][2]),
Vec3(0, 0, 0), tolerance);
ASSERT_EQUAL_TOL(0.5*1.1*(PI_M/6)*(PI_M/6) + 0.5*1.2*(PI_M/4)*(PI_M/4), state.getPotentialEnergy(), tolerance);
if( PrintOn ){
(void) fprintf( log, "Angle bond forces ok tolerance=%.2e\n", tolerance ); (void) fflush( log );
}
}
int main( ){
// ---------------------------------------------------------------------------------------
static const std::string methodName = "testBrookAngles";
FILE* log = stdout;
// ---------------------------------------------------------------------------------------
(void) fflush( stdout );
(void) fflush( stderr );
try {
testBrookAngles( log );
} catch( const exception& e ){
(void) fprintf( log, "Exception %s %.s\n", methodName.c_str(), e.what() ); (void) fflush( log );
return 1;
}
(void) fprintf( log, "\n%s done\n", methodName.c_str() ); (void) fflush( log );
return 0;
}
platforms/brook/tests/TestBrookHarmonicBondForce.cpp 0 → 100644
View file @ 495a43c6
/* -------------------------------------------------------------------------- *
* 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: Mark Friedrichs *
* 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 Brook Harmonic bond force/energy
*/
#include "../../../tests/AssertionUtilities.h"
#include "BrookPlatform.h"
#include "OpenMMContext.h"
#include "HarmonicBondForce.h"
#include "System.h"
#include "LangevinIntegrator.h"
#include <vector>
using namespace OpenMM;
using namespace std;
const double TOL = 1e-5;
void testBrookBonds( FILE* log ){
// ---------------------------------------------------------------------------------------
static const std::string methodName = "testBrookBonds";
int PrintOn = 0;
int numberOfParticles = 3;
double mass = 2.0;
// ---------------------------------------------------------------------------------------
PrintOn = log ? PrintOn : 0;
if( PrintOn ){
(void) fprintf( log, "%s\n", methodName.c_str() ); (void) fflush( log );
}
BrookPlatform platform( 32, "cal", log );
System system( numberOfParticles, 0 );
LangevinIntegrator integrator(0, 0.1, 0.01);
// int numParticles, int numBonds, int numAngles, int numPeriodicTorsions, int numRBTorsions
HarmonicBondForce* forceField = new HarmonicBondForce( 2 );
// ( index, atom1, atom2, length, k )
forceField->setBondParameters(0, 0, 1, 1.5, 0.8);
forceField->setBondParameters(1, 1, 2, 1.2, 0.7);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(3);
positions[0] = Vec3(0, 2, 0);
positions[1] = Vec3(0, 0, 0);
positions[2] = Vec3(1, 0, 0);
context.setPositions(positions);
//(void) fprintf( log, "testBrookBonds:Calling getState\n");
//(void) fflush( log );
State state = context.getState( State::Forces | State::Energy );
const vector<Vec3>& forces = state.getForces();
if( PrintOn ){
(void) fprintf( log, "Harmonic bond forces\n");
for( int ii = 0; ii < numberOfParticles; ii++ ){
(void) fprintf( log, "%d [%.5e %.5e %.5e]\n", ii, forces[ii][0], forces[ii][1], forces[ii][2] );
}
(void) fflush( log );
}
ASSERT_EQUAL_VEC(Vec3(0, -0.8*0.5, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0.7*0.2, 0, 0), forces[2], TOL);
ASSERT_EQUAL_VEC(Vec3(-forces[0][0]-forces[2][0], -forces[0][1]-forces[2][1], -forces[0][2]-forces[2][2]), forces[1], TOL);
if( PrintOn ){
(void) fprintf( log, "Harmonic bond forces ok -- checking energy\n"); (void) fflush( log );
}
ASSERT_EQUAL_TOL( 0.5*0.8*0.5*0.5 + 0.5*0.7*0.2*0.2, state.getPotentialEnergy(), TOL);
if( PrintOn ){
(void) fprintf( log, "Harmonic bond energy ok\n"); (void) fflush( log );
}
}
int main( ){
// ---------------------------------------------------------------------------------------
static const std::string methodName = "testBrookBonds";
FILE* log = stdout;
// ---------------------------------------------------------------------------------------
(void) fflush( stdout );
(void) fflush( stderr );
try {
testBrookBonds( log );
} catch( const exception& e ){
(void) fprintf( log, "Exception %s %.s\n", methodName.c_str(), e.what() ); (void) fflush( log );
return 1;
}
(void) fprintf( log, "\n%s done\n", methodName.c_str() ); (void) fflush( log );
return 0;
}
platforms/brook/tests/TestBrookRBTorsionForce.cpp 0 → 100644
View file @ 495a43c6
/* -------------------------------------------------------------------------- *
* 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: Mark Friedrichs *
* 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 Brook RB torsion bond force/energy
*/
#include "../../../tests/AssertionUtilities.h"
#include "BrookPlatform.h"
#include "ReferencePlatform.h"
#include "OpenMMContext.h"
#include "RBTorsionForce.h"
#include "System.h"
#include "LangevinIntegrator.h"
#include <vector>
#define PI_M 3.141592653589
using namespace OpenMM;
using namespace std;
const double TOL = 1e-5;
void testBrookRBTorsions( FILE* log ){
// ---------------------------------------------------------------------------------------
static const std::string methodName = "RBTorsions";
int PrintOn = 0;
int numberOfParticles = 4;
double mass = 2.0;
// ---------------------------------------------------------------------------------------
PrintOn = log ? PrintOn : 0;
if( PrintOn ){
(void) fprintf( log, "%s\n", methodName.c_str() ); (void) fflush( log );
}
BrookPlatform platform( 32, "cal", log );
//ReferencePlatform platform;
System system( numberOfParticles, 0 );
LangevinIntegrator integrator( 0, 0.1, 0.01 );
RBTorsionForce* forceField = new RBTorsionForce( 1 );
forceField->setTorsionParameters(0, 0, 1, 2, 3, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(numberOfParticles);
positions[0] = Vec3(0, 1, 0);
positions[1] = Vec3(0, 0, 0);
positions[2] = Vec3(1, 0, 0);
positions[3] = Vec3(1, 1, 1);
context.setPositions(positions);
State state = context.getState( State::Forces | State::Energy );
const vector<Vec3>& forces = state.getForces();
if( PrintOn ){
(void) fprintf( log, "RB torsion bond forces\n");
for( int ii = 0; ii < numberOfParticles; ii++ ){
(void) fprintf( log, "%d [%.5e %.5e %.5e]\n", ii, forces[ii][0], forces[ii][1], forces[ii][2] );
}
(void) fflush( log );
}
double psi = 0.25*PI_M - PI_M;
double torque = 0.0;
for (int i = 1; i < 6; ++i) {
double c = 0.1*(i+1);
torque += -c*i*std::pow(std::cos(psi), i-1)*std::sin(psi);
}
if( PrintOn ){
(void) fprintf( log, "RB torsion bond expected forces\n");
(void) fprintf( log, "0 [0.0 0.0 %.5e]\n", torque );
(void) fprintf( log, "3 [0.0 %.5e %.5e]\n", 0.5*torque, -0.5*torque );
(void) fflush( log );
}
double tolerance = 0.001;
ASSERT_EQUAL_VEC(Vec3(0, 0, torque), forces[0], tolerance );
ASSERT_EQUAL_VEC(Vec3(0, 0.5*torque, -0.5*torque), forces[3], tolerance );
ASSERT_EQUAL_VEC(Vec3(forces[0][0]+forces[1][0]+forces[2][0]+forces[3][0],
forces[0][1]+forces[1][1]+forces[2][1]+forces[3][1],
forces[0][2]+forces[1][2]+forces[2][2]+forces[3][2]),
Vec3(0, 0, 0), tolerance);
double energy = 0.0;
for (int i = 0; i < 6; ++i) {
double c = 0.1*(i+1);
energy += c*std::pow(std::cos(psi), i);
}
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), tolerance );
if( PrintOn ){
(void) fprintf( log, "RB torsion bond forces ok tolerance=%.2e\n", tolerance); fflush( log );
}
}
int main( ){
// ---------------------------------------------------------------------------------------
static const std::string methodName = "testBrookRbTorsion";
FILE* log = stdout;
// ---------------------------------------------------------------------------------------
(void) fflush( stdout );
(void) fflush( stderr );
try {
testBrookRBTorsions( log );
} catch( const exception& e ){
(void) fprintf( log, "Exception %s %.s\n", methodName.c_str(), e.what() ); (void) fflush( log );
return 1;
}
(void) fprintf( log, "\n%s done\n", methodName.c_str() ); (void) fflush( log );
return 0;
}
platforms/brook/tests/testBrookPeriodicTorsionForce.cpp 0 → 100644
View file @ 495a43c6
/* -------------------------------------------------------------------------- *
* 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: Mark Friedrichs *
* 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 Brook periodic torsion bond force/energy
*/
#include "../../../tests/AssertionUtilities.h"
#include "BrookPlatform.h"
#include "OpenMMContext.h"
#include "PeriodicTorsionForce.h"
#include "System.h"
#include "LangevinIntegrator.h"
#include <vector>
#define PI_M 3.141592653589
using namespace OpenMM;
using namespace std;
const double TOL = 1e-5;
void testBrookPeriodicTorsions( FILE* log ){
// ---------------------------------------------------------------------------------------
static const std::string methodName = "PeriodicTorsions";
int PrintOn = 0;
int numberOfParticles = 4;
double mass = 2.0;
// ---------------------------------------------------------------------------------------
PrintOn = log ? PrintOn : 0;
if( PrintOn ){
(void) fprintf( log, "%s\n", methodName.c_str() ); (void) fflush( log );
}
BrookPlatform platform( 32, "cal", log );
System system( numberOfParticles, 0 );
LangevinIntegrator integrator( 0, 0.1, 0.01 );
// int numParticles, int numBonds, int numAngles, int numPeriodicTorsions, int numRBTorsions
PeriodicTorsionForce* forceField = new PeriodicTorsionForce( 1 );
// int index, int atom1, int atom2, int atom3, double angle, double k
forceField->setTorsionParameters(0, 0, 1, 2, 3, 2, PI_M/3, 1.1);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(numberOfParticles);
positions[0] = Vec3(0, 1, 0);
positions[1] = Vec3(0, 0, 0);
positions[2] = Vec3(1, 0, 0);
positions[3] = Vec3(1, 0, 2);
context.setPositions(positions);
State state = context.getState( State::Forces | State::Energy );
const vector<Vec3>& forces = state.getForces();
if( PrintOn ){
(void) fprintf( log, "Periodic torsion bond forces\n");
for( int ii = 0; ii < numberOfParticles; ii++ ){
(void) fprintf( log, "%d [%.5e %.5e %.5e]\n", ii, forces[ii][0], forces[ii][1], forces[ii][2] );
}
(void) fflush( log );
}
double torque = -2*1.1*std::sin(2*PI_M/3);
double tolerance = 1.0e-03;
ASSERT_EQUAL_VEC(Vec3(0, 0, torque), forces[0], tolerance );
ASSERT_EQUAL_VEC(Vec3(0, 0.5*torque, 0), forces[3], tolerance );
ASSERT_EQUAL_VEC(Vec3(forces[0][0]+forces[1][0]+forces[2][0]+forces[3][0],
forces[0][1]+forces[1][1]+forces[2][1]+forces[3][1],
forces[0][2]+forces[1][2]+forces[2][2]+forces[3][2]),
Vec3(0, 0, 0), tolerance );
ASSERT_EQUAL_TOL(1.1*(1+std::cos(2*PI_M/3)), state.getPotentialEnergy(), tolerance );
if( PrintOn ){
(void) fprintf( log, "Periodic torsion bond forces ok -- tolerance=%.2e\n", tolerance); (void) fflush( log );
}
}
int main( ){
// ---------------------------------------------------------------------------------------
static const std::string methodName = "testBrookPeriodicTorsions";
FILE* log = stdout;
// ---------------------------------------------------------------------------------------
(void) fflush( stdout );
(void) fflush( stderr );
try {
testBrookPeriodicTorsions( log );
} catch( const exception& e ){
(void) fprintf( log, "Exception %s %.s\n", methodName.c_str(), e.what() ); (void) fflush( log );
return 1;
}
(void) fprintf( log, "\n%s done\n", methodName.c_str() ); (void) fflush( log );
return 0;
}
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