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Commit b186314c authored by Mark Friedrichs's avatar Mark Friedrichs
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Quadrupole tensors are now validated as being traceless and symmetric 

Added tests for system of 2 ions and 2 water molecules;
Removed TestCudaAmoebaPME.cpp
parent 13c28cf0
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Showing with 630 additions and 191 deletions
plugins/amoeba/openmmapi/src/AmoebaMultipoleForceImpl.cpp
View file @ b186314c
......@@ -53,6 +53,7 @@ void AmoebaMultipoleForceImpl::initialize(ContextImpl& context) {
if (owner.getNumMultipoles() != system.getNumParticles())
throw OpenMMException("AmoebaMultipoleForce must have exactly as many particles as the System it belongs to.");
double quadrupoleValidationTolerance = 1.0e-05;
for( int ii = 0; ii < system.getNumParticles(); ii++ ){
int axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY;
......@@ -63,6 +64,39 @@ void AmoebaMultipoleForceImpl::initialize(ContextImpl& context) {
owner.getMultipoleParameters( ii, charge, molecularDipole, molecularQuadrupole, axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY,
thole, dampingFactor, polarity );
// check quadrupole is traceless and symmetric
double trace = fabs( molecularQuadrupole[0] + molecularQuadrupole[4] + molecularQuadrupole[8] );
if( trace > quadrupoleValidationTolerance ){
std::stringstream buffer;
buffer << "AmoebaMultipoleForce: qudarupole for particle=" << ii;
buffer << " has nonzero trace: " << trace << "; AMOEBA plugin assumes traceless quadrupole.";
throw OpenMMException(buffer.str());
}
if( fabs( molecularQuadrupole[1] - molecularQuadrupole[3] ) > quadrupoleValidationTolerance ){
std::stringstream buffer;
buffer << "AmoebaMultipoleForce: XY and YX components of quadrupole for particle=" << ii;
buffer << " are not equal: [" << molecularQuadrupole[1] << " " << molecularQuadrupole[3] << "];";
buffer << " AMOEBA plugin assumes symmetric quadrupole tensor.";
throw OpenMMException(buffer.str());
}
if( fabs( molecularQuadrupole[2] - molecularQuadrupole[6] ) > quadrupoleValidationTolerance ){
std::stringstream buffer;
buffer << "AmoebaMultipoleForce: XZ and ZX components of quadrupole for particle=" << ii;
buffer << " are not equal: [" << molecularQuadrupole[2] << " " << molecularQuadrupole[6] << "];";
buffer << " AMOEBA plugin assumes symmetric quadrupole tensor.";
throw OpenMMException(buffer.str());
}
if( fabs( molecularQuadrupole[5] - molecularQuadrupole[7] ) > quadrupoleValidationTolerance ){
std::stringstream buffer;
buffer << "AmoebaMultipoleForce: YZ and ZY components of quadrupole for particle=" << ii;
buffer << " are not equal: [" << molecularQuadrupole[5] << " " << molecularQuadrupole[7] << "];";
buffer << " AMOEBA plugin assumes symmetric quadrupole tensor.";
throw OpenMMException(buffer.str());
}
// only 'Z-then-X', 'Bisector', Z-Bisect, ThreeFold currently handled
if( axisType != AmoebaMultipoleForce::ZThenX && axisType != AmoebaMultipoleForce::Bisector &&
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaPME.cpp deleted 100644 → 0
View file @ 13c28cf0
/* -------------------------------------------------------------------------- *
* OpenMMAmoeba *
* -------------------------------------------------------------------------- *
* 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) 2008-2010 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 Ewald summation method cuda implementation of NonbondedForce.
*/
#include "openmm/internal/AssertionUtilities.h"
#include "AmoebaTinkerParameterFile.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/AmoebaMultipoleForce.h"
#include "openmm/System.h"
#include "openmm/VerletIntegrator.h"
#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
const double TOL = 1e-5;
void testPMEWater() {
Platform& platform = Platform::getPlatformByName("Cuda");
System system;
system.addParticle(16);
system.addParticle(1);
system.addParticle(1);
VerletIntegrator integrator(0.01);
AmoebaMultipoleForce* mp = new AmoebaMultipoleForce();
mp->setNonbondedMethod(AmoebaMultipoleForce::PME);
vector<double> dipole(3, 0.0);
dipole[2] = 7.556121361e-2;
vector<double> quadrupole(9, 0.0);
quadrupole[0] = 3.540307211e-2;
quadrupole[4] = -3.902570771e-2;
quadrupole[8] = 3.622635596e-3;
double damp = 9.707801995e-01*sqrt(0.1);
double polarity = 0.837*0.001;
mp->addParticle(-0.51966, dipole, quadrupole, 1, 1, 2, -1, 0.39, damp, polarity);
dipole[0] = -2.042094848e-2;
dipole[2] = -3.078753000e-2;
quadrupole[0] = -3.428482490e-3;
quadrupole[2] = -1.894859639e-4;
quadrupole[4] = -1.002408752e-2;
quadrupole[6] = -1.894859639e-4;
quadrupole[8] = 1.345257001e-2;
damp = 8.897068742e-01*sqrt(0.1);
polarity = 0.496*0.001;
mp->addParticle(0.25983, dipole, quadrupole, 0, 0, 2, -1, 0.39, damp, polarity);
mp->addParticle(0.25983, dipole, quadrupole, 0, 0, 1, -1, 0.39, damp, polarity);
mp->setCutoffDistance(1.0);
std::vector<int> intVector;
intVector.push_back( 0 );
intVector.push_back( 1 );
intVector.push_back( 2 );
mp->setCovalentMap( 0, AmoebaMultipoleForce::PolarizationCovalent11, intVector );
mp->setCovalentMap( 1, AmoebaMultipoleForce::PolarizationCovalent11, intVector );
mp->setCovalentMap( 2, AmoebaMultipoleForce::PolarizationCovalent11, intVector );
intVector.resize(0); intVector.push_back( 1 ); intVector.push_back( 2 );
mp->setCovalentMap( 0, AmoebaMultipoleForce::Covalent12, intVector );
intVector.resize(0); intVector.push_back( 0 ); intVector.push_back( 2 );
mp->setCovalentMap( 1, AmoebaMultipoleForce::Covalent12, intVector );
intVector.resize(0); intVector.push_back( 0 ); intVector.push_back( 1 );
mp->setCovalentMap( 2, AmoebaMultipoleForce::Covalent12, intVector );
mp->setEwaldErrorTolerance(TOL);
system.setDefaultPeriodicBoxVectors(Vec3(2, 0, 0), Vec3(0, 2, 0), Vec3(0, 0, 2));
system.addForce(mp);
Context context(system, integrator, platform);
vector<Vec3> positions(3);
const double angle = 109.47*M_PI/180;
const double dOH = 0.1;
positions[0] = Vec3();
positions[1] = Vec3(dOH, 0, 0);
positions[2] = Vec3(dOH*std::cos(angle), dOH*std::sin(angle), 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
#ifdef AMOEBA_DEBUG
(void) fprintf( stderr, "PME forces\n" );
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
(void) fprintf( stderr, "%6u [%14.7e %14.7e %14.7e]\n", ii,
forces[ii][0], forces[ii][1], forces[ii][2] );
}
(void) fflush( stderr );
#endif
}
int main() {
try {
registerAmoebaCudaKernelFactories();
testPMEWater();
} catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
std::cout << "Done" << std::endl;
return 0;
}
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