Quadrupole tensors are now validated as being traceless and symmetric

Added tests for system of 2 ions and 2 water molecules;
Removed TestCudaAmoebaPME.cpp

plugins/amoeba/openmmapi/src/AmoebaMultipoleForceImpl.cpp

@@ -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

-/* -------------------------------------------------------------------------- *
- *                                   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;
-}
-