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Commit b587b396 authored by Peter Eastman's avatar Peter Eastman
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Continuing to convert AmoebaGeneralizedKirkwoodForce to new CUDA platform

parent 222378c6
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Showing with 491 additions and 20 deletions
plugins/amoeba/platforms/cuda2/src/AmoebaCudaKernels.cpp
View file @ b587b396
...@@ -1342,22 +1342,11 @@ double CudaCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool in ...@@ -1342,22 +1342,11 @@ double CudaCalcAmoebaMultipoleForceKernel::execute(ContextImpl& context, bool in
&gkKernel->getBornRadii()->getDevicePointer(), &gkKernel->getField()->getDevicePointer(), &gkKernel->getBornRadii()->getDevicePointer(), &gkKernel->getField()->getDevicePointer(),
&labFrameDipoles->getDevicePointer(), &labFrameQuadrupoles->getDevicePointer(), &dampingAndThole->getDevicePointer()}; &labFrameDipoles->getDevicePointer(), &labFrameQuadrupoles->getDevicePointer(), &dampingAndThole->getDevicePointer()};
cu.executeKernel(computeFixedFieldKernel, computeFixedFieldArgs, numForceThreadBlocks*forceThreadBlockSize, forceThreadBlockSize); cu.executeKernel(computeFixedFieldKernel, computeFixedFieldArgs, numForceThreadBlocks*forceThreadBlockSize, forceThreadBlockSize);
vector<long long> f;
gkKernel->getField()->download(f);
printf("field\n");
for (int i = 0; i < 3*cu.getNumAtoms(); i++)
printf("%d %g\n", i, f[i]/(double) 0xFFFFFFFF);
void* recordInducedDipolesArgs[] = {&field->getDevicePointer(), &fieldPolar->getDevicePointer(), void* recordInducedDipolesArgs[] = {&field->getDevicePointer(), &fieldPolar->getDevicePointer(),
&gkKernel->getField()->getDevicePointer(), &gkKernel->getInducedDipoles()->getDevicePointer(), &gkKernel->getField()->getDevicePointer(), &gkKernel->getInducedDipoles()->getDevicePointer(),
&gkKernel->getInducedDipolesPolar()->getDevicePointer(), &inducedDipole->getDevicePointer(), &gkKernel->getInducedDipolesPolar()->getDevicePointer(), &inducedDipole->getDevicePointer(),
&inducedDipolePolar->getDevicePointer(), &polarizability->getDevicePointer()}; &inducedDipolePolar->getDevicePointer(), &polarizability->getDevicePointer()};
cu.executeKernel(recordInducedDipolesKernel, recordInducedDipolesArgs, cu.getNumAtoms()); cu.executeKernel(recordInducedDipolesKernel, recordInducedDipolesArgs, cu.getNumAtoms());
vector<float> d, dp;
gkKernel->getInducedDipoles()->download(d);
gkKernel->getInducedDipolesPolar()->download(dp);
printf("dipoles\n");
for (int i = 0; i < cu.getNumAtoms(); i++)
printf("%d %g %g %g, %g %g %g\n", i, d[3*i], d[3*i+1], d[3*i+2], dp[3*i], dp[3*i+1], dp[3*i+2]);
} }
// Iterate until the dipoles converge. // Iterate until the dipoles converge.
...@@ -1837,11 +1826,6 @@ void CudaCalcAmoebaGeneralizedKirkwoodForceKernel::computeBornRadii() { ...@@ -1837,11 +1826,6 @@ void CudaCalcAmoebaGeneralizedKirkwoodForceKernel::computeBornRadii() {
cu.executeKernel(computeBornSumKernel, computeBornSumArgs, numForceThreadBlocks*forceThreadBlockSize, forceThreadBlockSize); cu.executeKernel(computeBornSumKernel, computeBornSumArgs, numForceThreadBlocks*forceThreadBlockSize, forceThreadBlockSize);
void* reduceBornSumArgs[] = {&bornSum->getDevicePointer(), &params->getDevicePointer(), &bornRadii->getDevicePointer()}; void* reduceBornSumArgs[] = {&bornSum->getDevicePointer(), &params->getDevicePointer(), &bornRadii->getDevicePointer()};
cu.executeKernel(reduceBornSumKernel, reduceBornSumArgs, cu.getNumAtoms()); cu.executeKernel(reduceBornSumKernel, reduceBornSumArgs, cu.getNumAtoms());
vector<float> r;
bornRadii->download(r);
printf("radii\n");
for (int i = 0; i < cu.getNumAtoms(); i++)
printf("%d %g\n", i, r[i]);
} }
void CudaCalcAmoebaGeneralizedKirkwoodForceKernel::finishComputation(CudaArray& torque, CudaArray& labFrameDipoles, CudaArray& labFrameQuadrupoles, void CudaCalcAmoebaGeneralizedKirkwoodForceKernel::finishComputation(CudaArray& torque, CudaArray& labFrameDipoles, CudaArray& labFrameQuadrupoles,
...@@ -1856,6 +1840,11 @@ void CudaCalcAmoebaGeneralizedKirkwoodForceKernel::finishComputation(CudaArray& ...@@ -1856,6 +1840,11 @@ void CudaCalcAmoebaGeneralizedKirkwoodForceKernel::finishComputation(CudaArray&
&labFrameQuadrupoles.getDevicePointer(), &inducedDipole.getDevicePointer(), &inducedDipolePolar.getDevicePointer(), &labFrameQuadrupoles.getDevicePointer(), &inducedDipole.getDevicePointer(), &inducedDipolePolar.getDevicePointer(),
&bornRadii->getDevicePointer(), &bornForce->getDevicePointer()}; &bornRadii->getDevicePointer(), &bornForce->getDevicePointer()};
cu.executeKernel(gkForceKernel, gkForceArgs, numForceThreadBlocks*forceThreadBlockSize, forceThreadBlockSize); cu.executeKernel(gkForceKernel, gkForceArgs, numForceThreadBlocks*forceThreadBlockSize, forceThreadBlockSize);
printf("bornForce\n");
vector<long long> f;
bornForce->download(f);
for (int i = 0; i < cu.getNumAtoms(); i++)
printf("%d %g\n", i, f[i]/(double) 0xFFFFFFFF);
// Compute cavity term... // Compute cavity term...
......
plugins/amoeba/platforms/cuda2/src/kernels/amoebaGk.cu
View file @ b587b396
...@@ -275,12 +275,12 @@ extern "C" __global__ void computeGKForces( ...@@ -275,12 +275,12 @@ extern "C" __global__ void computeGKForces(
atomicAdd(&torqueBuffers[atom1+PADDED_NUM_ATOMS], static_cast<unsigned long long>((long long) (data.force.y*0xFFFFFFFF))); atomicAdd(&torqueBuffers[atom1+PADDED_NUM_ATOMS], static_cast<unsigned long long>((long long) (data.force.y*0xFFFFFFFF)));
atomicAdd(&torqueBuffers[atom1+2*PADDED_NUM_ATOMS], static_cast<unsigned long long>((long long) (data.force.z*0xFFFFFFFF))); atomicAdd(&torqueBuffers[atom1+2*PADDED_NUM_ATOMS], static_cast<unsigned long long>((long long) (data.force.z*0xFFFFFFFF)));
// Chain rule terms? // Compute chain rule terms.
zeroAtomData(data); zeroAtomData(data);
for (unsigned int j = 0; j < TILE_SIZE; j++) { for (unsigned int j = 0; j < TILE_SIZE; j++) {
int atom2 = y*TILE_SIZE+j; int atom2 = y*TILE_SIZE+j;
if (atom1 != atom2 && atom1 < NUM_ATOMS && atom2 < NUM_ATOMS) if (atom1 < NUM_ATOMS && atom2 < NUM_ATOMS)
computeOneInteractionB1B2(data, localData[tbx+j]); computeOneInteractionB1B2(data, localData[tbx+j]);
} }
atomicAdd(&bornForce[atom1], static_cast<unsigned long long>((long long) (data.bornForce*0xFFFFFFFF))); atomicAdd(&bornForce[atom1], static_cast<unsigned long long>((long long) (data.bornForce*0xFFFFFFFF)));
...@@ -346,7 +346,7 @@ extern "C" __global__ void computeGKForces( ...@@ -346,7 +346,7 @@ extern "C" __global__ void computeGKForces(
atomicAdd(&torqueBuffers[offset+2*PADDED_NUM_ATOMS], static_cast<unsigned long long>((long long) (localData[threadIdx.x].force.z*0xFFFFFFFF))); atomicAdd(&torqueBuffers[offset+2*PADDED_NUM_ATOMS], static_cast<unsigned long long>((long long) (localData[threadIdx.x].force.z*0xFFFFFFFF)));
} }
// Chain rule terms? // Compute chain rule terms.
zeroAtomData(data); zeroAtomData(data);
zeroAtomData(localData[threadIdx.x]); zeroAtomData(localData[threadIdx.x]);
......
plugins/amoeba/platforms/cuda2/src/kernels/multipoleFixedField.cu
View file @ b587b396
...@@ -432,6 +432,9 @@ extern "C" __global__ void computeFixedField( ...@@ -432,6 +432,9 @@ extern "C" __global__ void computeFixedField(
AtomData data; AtomData data;
data.field = make_real3(0); data.field = make_real3(0);
data.fieldPolar = make_real3(0); data.fieldPolar = make_real3(0);
#ifdef USE_GK
data.gkField = make_real3(0);
#endif
if (pos < end) { if (pos < end) {
#ifdef USE_CUTOFF #ifdef USE_CUTOFF
if (numTiles <= maxTiles) { if (numTiles <= maxTiles) {
...@@ -501,11 +504,14 @@ extern "C" __global__ void computeFixedField( ...@@ -501,11 +504,14 @@ extern "C" __global__ void computeFixedField(
computeOneInteraction(data, localData[tbx+j], delta, d, p, fields); computeOneInteraction(data, localData[tbx+j], delta, d, p, fields);
data.field += fields[0]; data.field += fields[0];
data.fieldPolar += fields[1]; data.fieldPolar += fields[1];
}
#ifdef USE_GK #ifdef USE_GK
if (atom1 < NUM_ATOMS && atom2 < NUM_ATOMS) {
real3 fields[2];
computeOneGkInteraction(data, localData[tbx+j], delta, fields); computeOneGkInteraction(data, localData[tbx+j], delta, fields);
data.gkField += fields[0]; data.gkField += fields[0];
#endif
} }
#endif
covalent.x >>= 1; covalent.x >>= 1;
covalent.y >>= 1; covalent.y >>= 1;
polarizationGroup >>= 1; polarizationGroup >>= 1;
......
plugins/amoeba/platforms/cuda2/tests/TestCudaAmoebaGeneralizedKirkwoodForce.cpp 0 → 100644
View file @ b587b396
/* -------------------------------------------------------------------------- *
* 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) 2008-2012 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 CUDA implementation of CudaAmoebaMultipoleForce.
*/
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "OpenMMAmoeba.h"
#include "AmoebaTinkerParameterFile.h"
#include "openmm/System.h"
#include "openmm/AmoebaMultipoleForce.h"
#include "openmm/LangevinIntegrator.h"
#include <iostream>
#include <vector>
#include <stdlib.h>
#include <stdio.h>
#define ASSERT_EQUAL_TOL_MOD(expected, found, tol, testname) {double _scale_ = std::abs(expected) > 1.0 ? std::abs(expected) : 1.0; if (!(std::abs((expected)-(found))/_scale_ <= (tol))) {std::stringstream details; details << testname << " Expected "<<(expected)<<", found "<<(found); throwException(__FILE__, __LINE__, details.str());}};
#define ASSERT_EQUAL_VEC_MOD(expected, found, tol,testname) {ASSERT_EQUAL_TOL_MOD((expected)[0], (found)[0], (tol),(testname)); ASSERT_EQUAL_TOL_MOD((expected)[1], (found)[1], (tol),(testname)); ASSERT_EQUAL_TOL_MOD((expected)[2], (found)[2], (tol),(testname));};
using namespace OpenMM;
const double TOL = 1e-4;
// setup for 2 ammonia molecules
static void setupAndGetForcesEnergyMultipoleAmmonia( AmoebaMultipoleForce::AmoebaPolarizationType polarizationType,
int includeCavityTerm, std::vector<Vec3>& forces, double& energy, FILE* log ){
// beginning of Multipole setup
System system;
AmoebaMultipoleForce* amoebaMultipoleForce = new AmoebaMultipoleForce();;
int numberOfParticles = 8;
amoebaMultipoleForce->setNonbondedMethod( AmoebaMultipoleForce::NoCutoff );
amoebaMultipoleForce->setPolarizationType( polarizationType );
amoebaMultipoleForce->setMutualInducedTargetEpsilon( 1.0e-06 );
amoebaMultipoleForce->setMutualInducedMaxIterations( 500 );
std::vector<double> nitrogenMolecularDipole(3);
std::vector<double> nitrogenMolecularQuadrupole(9);
nitrogenMolecularDipole[0] = 8.3832254e-03;
nitrogenMolecularDipole[1] = 0.0000000e+00;
nitrogenMolecularDipole[2] = 3.4232474e-03;
nitrogenMolecularQuadrupole[0] = -4.0406249e-04;
nitrogenMolecularQuadrupole[1] = 0.0000000e+00;
nitrogenMolecularQuadrupole[2] = -2.6883671e-04;
nitrogenMolecularQuadrupole[3] = 0.0000000e+00;
nitrogenMolecularQuadrupole[4] = 2.5463927e-04;
nitrogenMolecularQuadrupole[5] = 0.0000000e+00;
nitrogenMolecularQuadrupole[6] = -2.6883671e-04;
nitrogenMolecularQuadrupole[7] = 0.0000000e+00;
nitrogenMolecularQuadrupole[8] = 1.4942322e-04;
// first N
system.addParticle( 1.4007000e+01 );
amoebaMultipoleForce->addParticle( -5.7960000e-01, nitrogenMolecularDipole, nitrogenMolecularQuadrupole, 2, 1, 2, 3, 3.9000000e-01, 3.1996314e-01, 1.0730000e-03 );
// 3 H attached to first N
std::vector<double> hydrogenMolecularDipole(3);
std::vector<double> hydrogenMolecularQuadrupole(9);
hydrogenMolecularDipole[0] = -1.7388763e-03;
hydrogenMolecularDipole[1] = 0.0000000e+00;
hydrogenMolecularDipole[2] = -4.6837475e-03;
hydrogenMolecularQuadrupole[0] = -4.4253841e-05;
hydrogenMolecularQuadrupole[1] = 0.0000000e+00;
hydrogenMolecularQuadrupole[2] = 1.5429571e-05;
hydrogenMolecularQuadrupole[3] = 0.0000000e+00;
hydrogenMolecularQuadrupole[4] = 4.1798924e-05;
hydrogenMolecularQuadrupole[5] = 0.0000000e+00;
hydrogenMolecularQuadrupole[6] = 1.5429571e-05;
hydrogenMolecularQuadrupole[7] = 0.0000000e+00;
hydrogenMolecularQuadrupole[8] = 2.4549167e-06;
system.addParticle( 1.0080000e+00 );
system.addParticle( 1.0080000e+00 );
system.addParticle( 1.0080000e+00 );
amoebaMultipoleForce->addParticle( 1.9320000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 0, 2, 3, 3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
amoebaMultipoleForce->addParticle( 1.9320000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 0, 1, 3, 3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
amoebaMultipoleForce->addParticle( 1.9320000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 0, 1, 2, 3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
// second N
system.addParticle( 1.4007000e+01 );
amoebaMultipoleForce->addParticle( -5.7960000e-01, nitrogenMolecularDipole, nitrogenMolecularQuadrupole, 2, 5, 6, 7, 3.9000000e-01, 3.1996314e-01, 1.0730000e-03 );
// 3 H attached to second N
system.addParticle( 1.0080000e+00 );
system.addParticle( 1.0080000e+00 );
system.addParticle( 1.0080000e+00 );
amoebaMultipoleForce->addParticle( 1.9320000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 4, 6, 7, 3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
amoebaMultipoleForce->addParticle( 1.9320000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 4, 5, 7, 3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
amoebaMultipoleForce->addParticle( 1.9320000e-01, hydrogenMolecularDipole, hydrogenMolecularQuadrupole, 2, 4, 5, 6, 3.9000000e-01, 2.8135002e-01, 4.9600000e-04 );
// covalent maps
std::vector< int > covalentMap;
covalentMap.resize(0);
covalentMap.push_back( 1 );
covalentMap.push_back( 2 );
covalentMap.push_back( 3 );
amoebaMultipoleForce->setCovalentMap( 0, static_cast<OpenMM::AmoebaMultipoleForce::CovalentType>(0), covalentMap );
covalentMap.resize(0);
covalentMap.push_back( 0 );
covalentMap.push_back( 1 );
covalentMap.push_back( 2 );
covalentMap.push_back( 3 );
amoebaMultipoleForce->setCovalentMap( 0, static_cast<OpenMM::AmoebaMultipoleForce::CovalentType>(4), covalentMap );
covalentMap.resize(0);
covalentMap.push_back( 0 );
amoebaMultipoleForce->setCovalentMap( 1, static_cast<OpenMM::AmoebaMultipoleForce::CovalentType>(0), covalentMap );
covalentMap.resize(0);
covalentMap.push_back( 2 );
covalentMap.push_back( 3 );
amoebaMultipoleForce->setCovalentMap( 1, static_cast<OpenMM::AmoebaMultipoleForce::CovalentType>(1), covalentMap );
covalentMap.resize(0);
covalentMap.push_back( 0 );
covalentMap.push_back( 1 );
covalentMap.push_back( 2 );
covalentMap.push_back( 3 );
amoebaMultipoleForce->setCovalentMap( 1, static_cast<OpenMM::AmoebaMultipoleForce::CovalentType>(4), covalentMap );
covalentMap.resize(0);
covalentMap.push_back( 0 );
amoebaMultipoleForce->setCovalentMap( 2, static_cast<OpenMM::AmoebaMultipoleForce::CovalentType>(0), covalentMap );
covalentMap.resize(0);
covalentMap.push_back( 1 );
covalentMap.push_back( 3 );
amoebaMultipoleForce->setCovalentMap( 2, static_cast<OpenMM::AmoebaMultipoleForce::CovalentType>(1), covalentMap );
covalentMap.resize(0);
covalentMap.push_back( 0 );
covalentMap.push_back( 1 );
covalentMap.push_back( 2 );
covalentMap.push_back( 3 );
amoebaMultipoleForce->setCovalentMap( 2, static_cast<OpenMM::AmoebaMultipoleForce::CovalentType>(4), covalentMap );
covalentMap.resize(0);
covalentMap.push_back( 0 );
amoebaMultipoleForce->setCovalentMap( 3, static_cast<OpenMM::AmoebaMultipoleForce::CovalentType>(0), covalentMap );
covalentMap.resize(0);
covalentMap.push_back( 1 );
covalentMap.push_back( 2 );
amoebaMultipoleForce->setCovalentMap( 3, static_cast<OpenMM::AmoebaMultipoleForce::CovalentType>(1), covalentMap );
covalentMap.resize(0);
covalentMap.push_back( 0 );
covalentMap.push_back( 1 );
covalentMap.push_back( 2 );
covalentMap.push_back( 3 );
amoebaMultipoleForce->setCovalentMap( 3, static_cast<OpenMM::AmoebaMultipoleForce::CovalentType>(4), covalentMap );
covalentMap.resize(0);
covalentMap.push_back( 5 );
covalentMap.push_back( 6 );
covalentMap.push_back( 7 );
amoebaMultipoleForce->setCovalentMap( 4, static_cast<OpenMM::AmoebaMultipoleForce::CovalentType>(0), covalentMap );
covalentMap.resize(0);
covalentMap.push_back( 4 );
covalentMap.push_back( 5 );
covalentMap.push_back( 6 );
covalentMap.push_back( 7 );
amoebaMultipoleForce->setCovalentMap( 4, static_cast<OpenMM::AmoebaMultipoleForce::CovalentType>(4), covalentMap );
covalentMap.resize(0);
covalentMap.push_back( 4 );
amoebaMultipoleForce->setCovalentMap( 5, static_cast<OpenMM::AmoebaMultipoleForce::CovalentType>(0), covalentMap );
covalentMap.resize(0);
covalentMap.push_back( 6 );
covalentMap.push_back( 7 );
amoebaMultipoleForce->setCovalentMap( 5, static_cast<OpenMM::AmoebaMultipoleForce::CovalentType>(1), covalentMap );
covalentMap.resize(0);
covalentMap.push_back( 4 );
covalentMap.push_back( 5 );
covalentMap.push_back( 6 );
covalentMap.push_back( 7 );
amoebaMultipoleForce->setCovalentMap( 5, static_cast<OpenMM::AmoebaMultipoleForce::CovalentType>(4), covalentMap );
covalentMap.resize(0);
covalentMap.push_back( 4 );
amoebaMultipoleForce->setCovalentMap( 6, static_cast<OpenMM::AmoebaMultipoleForce::CovalentType>(0), covalentMap );
covalentMap.resize(0);
covalentMap.push_back( 5 );
covalentMap.push_back( 7 );
amoebaMultipoleForce->setCovalentMap( 6, static_cast<OpenMM::AmoebaMultipoleForce::CovalentType>(1), covalentMap );
covalentMap.resize(0);
covalentMap.push_back( 4 );
covalentMap.push_back( 5 );
covalentMap.push_back( 6 );
covalentMap.push_back( 7 );
amoebaMultipoleForce->setCovalentMap( 6, static_cast<OpenMM::AmoebaMultipoleForce::CovalentType>(4), covalentMap );
covalentMap.resize(0);
covalentMap.push_back( 4 );
amoebaMultipoleForce->setCovalentMap( 7, static_cast<OpenMM::AmoebaMultipoleForce::CovalentType>(0), covalentMap );
covalentMap.resize(0);
covalentMap.push_back( 5 );
covalentMap.push_back( 6 );
amoebaMultipoleForce->setCovalentMap( 7, static_cast<OpenMM::AmoebaMultipoleForce::CovalentType>(1), covalentMap );
covalentMap.resize(0);
covalentMap.push_back( 4 );
covalentMap.push_back( 5 );
covalentMap.push_back( 6 );
covalentMap.push_back( 7 );
amoebaMultipoleForce->setCovalentMap( 7, static_cast<OpenMM::AmoebaMultipoleForce::CovalentType>(4), covalentMap );
system.addForce(amoebaMultipoleForce);
// GK force
AmoebaGeneralizedKirkwoodForce* amoebaGeneralizedKirkwoodForce = new AmoebaGeneralizedKirkwoodForce();
amoebaGeneralizedKirkwoodForce->setSolventDielectric( 7.8300000e+01 );
amoebaGeneralizedKirkwoodForce->setSoluteDielectric( 1.0000000e+00 );
amoebaGeneralizedKirkwoodForce->setIncludeCavityTerm( includeCavityTerm );
// addParticle: charge, radius, scalingFactor
for( unsigned int ii = 0; ii < 2; ii++ ){
amoebaGeneralizedKirkwoodForce->addParticle( -5.7960000e-01, 1.5965000e-01, 6.9000000e-01 );
amoebaGeneralizedKirkwoodForce->addParticle( 1.9320000e-01, 1.2360000e-01, 6.9000000e-01 );
amoebaGeneralizedKirkwoodForce->addParticle( 1.9320000e-01, 1.2360000e-01, 6.9000000e-01 );
amoebaGeneralizedKirkwoodForce->addParticle( 1.9320000e-01, 1.2360000e-01, 6.9000000e-01 );
}
system.addForce(amoebaGeneralizedKirkwoodForce);
// 1-2 bonds needed
/*
AmoebaHarmonicBondForce* amoebaHarmonicBondForce = new AmoebaHarmonicBondForce();
// addBond: particle1, particle2, length, quadraticK
amoebaHarmonicBondForce->addBond( 0, 1, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->addBond( 0, 2, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->addBond( 0, 3, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->addBond( 4, 5, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->addBond( 4, 6, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->addBond( 4, 7, 0.0000000e+00, 0.0000000e+00 );
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondCubic( -2.5500000e+01 );
amoebaHarmonicBondForce->setAmoebaGlobalHarmonicBondQuartic( 3.7931250e+02 );
system.addForce(amoebaHarmonicBondForce);
*/
std::vector<Vec3> positions(numberOfParticles);
positions[0] = Vec3( 1.5927280e-01, 1.7000000e-06, 1.6491000e-03 );
positions[1] = Vec3( 2.0805540e-01, -8.1258800e-02, 3.7282500e-02 );
positions[2] = Vec3( 2.0843610e-01, 8.0953200e-02, 3.7462200e-02 );
positions[3] = Vec3( 1.7280780e-01, 2.0730000e-04, -9.8741700e-02 );
positions[4] = Vec3( -1.6743680e-01, 1.5900000e-05, -6.6149000e-03 );
positions[5] = Vec3( -2.0428260e-01, 8.1071500e-02, 4.1343900e-02 );
positions[6] = Vec3( -6.7308300e-02, 1.2800000e-05, 1.0623300e-02 );
positions[7] = Vec3( -2.0426290e-01, -8.1231400e-02, 4.1033500e-02 );
std::string platformName;
platformName = "CUDA";
LangevinIntegrator integrator(0.0, 0.1, 0.01);
Context context(system, integrator, Platform::getPlatformByName( platformName ) );
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
forces = state.getForces();
energy = state.getPotentialEnergy();
}
// compare forces and energies
static void compareForcesEnergy( std::string& testName, double expectedEnergy, double energy,
std::vector<Vec3>& expectedForces,
std::vector<Vec3>& forces, double tolerance, FILE* log ) {
//#define AMOEBA_DEBUG
#ifdef AMOEBA_DEBUG
if( log ){
double conversion = 1.0/4.184;
double energyAbsDiff = fabs( expectedEnergy - energy );
double energyRelDiff = 2.0*energyAbsDiff/( fabs( expectedEnergy ) + fabs( energy ) + 1.0e-08 );
(void) fprintf( log, "%s: expected energy=%14.7e %14.7e absDiff=%15.7e relDiff=%15.7e\n", testName.c_str(), conversion*expectedEnergy, conversion*energy,
conversion*energyAbsDiff, conversion*energyRelDiff );
if( conversion != 1.0 )conversion *= -0.1;
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
double expectedNorm = sqrt( expectedForces[ii][0]*expectedForces[ii][0] +
expectedForces[ii][1]*expectedForces[ii][1] +
expectedForces[ii][2]*expectedForces[ii][2] );
double norm = sqrt( forces[ii][0]*forces[ii][0] + forces[ii][1]*forces[ii][1] + forces[ii][2]*forces[ii][2] );
double absDiff = fabs( norm - expectedNorm );
double relDiff = 2.0*absDiff/(fabs( norm ) + fabs( expectedNorm ) + 1.0e-08);
(void) fprintf( log, "%6u %15.7e %15.7e [%14.7e %14.7e %14.7e] [%14.7e %14.7e %14.7e]\n", ii,
conversion*absDiff, conversion*relDiff,
conversion*expectedForces[ii][0], conversion*expectedForces[ii][1], conversion*expectedForces[ii][2],
conversion*forces[ii][0], conversion*forces[ii][1], conversion*forces[ii][2], conversion*expectedNorm, conversion*norm );
}
(void) fflush( log );
conversion = 1.0;
(void) fprintf( log, "\n%s: expected energy=%14.7e %14.7e no conversion\n", testName.c_str(), conversion*expectedEnergy, conversion*energy );
if( conversion != 1.0 )conversion = -1.0;
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,
conversion*expectedForces[ii][0], conversion*expectedForces[ii][1], conversion*expectedForces[ii][2],
conversion*forces[ii][0], conversion*forces[ii][1], conversion*forces[ii][2] );
}
(void) fflush( log );
}
#endif
for( unsigned int ii = 0; ii < forces.size(); ii++ )
std::cout << forces[ii]<<" "<<expectedForces[ii]<< std::endl;
std::cout << energy<<" "<<expectedEnergy<< std::endl;
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
ASSERT_EQUAL_VEC_MOD( expectedForces[ii], forces[ii], tolerance, testName );
}
ASSERT_EQUAL_TOL_MOD( expectedEnergy, energy, tolerance, testName );
}
// test GK direct polarization for system comprised of two ammonia molecules
static void testGeneralizedKirkwoodAmmoniaDirectPolarization( FILE* log ) {
std::string testName = "testGeneralizedKirkwoodAmmoniaDirectPolarization";
int numberOfParticles = 8;
std::vector<Vec3> forces;
double energy;
setupAndGetForcesEnergyMultipoleAmmonia( AmoebaMultipoleForce::Direct, 0, forces, energy, log );
std::vector<Vec3> expectedForces(numberOfParticles);
double expectedEnergy = -7.6636680e+01;
expectedForces[0] = Vec3( -6.9252994e+02, -8.9085133e+00, 9.6489739e+01 );
expectedForces[1] = Vec3( 1.5593797e+02, -6.0331931e+01, 1.5104507e+01 );
expectedForces[2] = Vec3( 1.5870088e+02, 6.1702809e+01, 6.7708985e+00 );
expectedForces[3] = Vec3( 1.4089885e+02, 7.5870617e+00, -1.1362294e+02 );
expectedForces[4] = Vec3( -1.8916205e+02, 2.1465549e-01, -4.3433152e+02 );
expectedForces[5] = Vec3( 1.0208290e+01, 6.2676753e+01, 1.4987953e+02 );
expectedForces[6] = Vec3( 4.0621859e+02, 1.8962203e-01, 1.3021956e+02 );
expectedForces[7] = Vec3( 9.7274235e+00, -6.3130458e+01, 1.4949024e+02 );
double tolerance = 1.0e-04;
compareForcesEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance, log );
}
// test GK mutual polarization for system comprised of two ammonia molecules
static void testGeneralizedKirkwoodAmmoniaMutualPolarization( FILE* log ) {
std::string testName = "testGeneralizedKirkwoodAmmoniaMutualPolarization";
int numberOfParticles = 8;
std::vector<Vec3> forces;
double energy;
setupAndGetForcesEnergyMultipoleAmmonia( AmoebaMultipoleForce::Mutual, 0, forces, energy, log );
std::vector<Vec3> expectedForces(numberOfParticles);
double expectedEnergy = -7.8018875e+01;
expectedForces[0] = Vec3( -7.6820301e+02, -1.0102760e+01, 1.0094389e+02 );
expectedForces[1] = Vec3( 1.7037307e+02, -7.5621857e+01, 2.3320365e+01 );
expectedForces[2] = Vec3( 1.7353828e+02, 7.7199741e+01, 1.3965379e+01 );
expectedForces[3] = Vec3( 1.5045244e+02, 8.5784569e+00, -1.3377619e+02 );
expectedForces[4] = Vec3( -2.1811615e+02, -1.6818022e-01, -4.6103163e+02 );
expectedForces[5] = Vec3( 6.2091942e+00, 7.6748687e+01, 1.5883463e+02 );
expectedForces[6] = Vec3( 4.8035662e+02, 4.9704902e-01, 1.3948083e+02 );
expectedForces[7] = Vec3( 5.3895456e+00, -7.7131137e+01, 1.5826273e+02 );
double tolerance = 1.0e-04;
compareForcesEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance, log );
}
// test GK mutual polarization for system comprised of two ammonia molecules
static void testGeneralizedKirkwoodAmmoniaMutualPolarizationWithCavityTerm( FILE* log ) {
std::string testName = "testGeneralizedKirkwoodAmmoniaMutualPolarizationWithCavityTerm";
int numberOfParticles = 8;
std::vector<Vec3> forces;
double energy;
setupAndGetForcesEnergyMultipoleAmmonia( AmoebaMultipoleForce::Mutual, 1, forces, energy, log );
std::vector<Vec3> expectedForces(numberOfParticles);
double expectedEnergy = -6.0434582e+01;
expectedForces[0] = Vec3( -7.8323218e+02, -1.0097644e+01, 1.0256890e+02 );
expectedForces[1] = Vec3( 1.7078480e+02, -7.1896701e+01, 2.0840172e+01 );
expectedForces[2] = Vec3( 1.7394089e+02, 7.3488594e+01, 1.1484648e+01 );
expectedForces[3] = Vec3( 1.5169364e+02, 8.5611299e+00, -1.2968050e+02 );
expectedForces[4] = Vec3( -2.1669693e+02, -1.5926823e-01, -4.6636274e+02 );
expectedForces[5] = Vec3( 8.7397444e+00, 7.3330990e+01, 1.6016898e+02 );
expectedForces[6] = Vec3( 4.8684950e+02, 4.8937161e-01, 1.4137061e+02 );
expectedForces[7] = Vec3( 7.9205382e+00, -7.3716473e+01, 1.5960993e+02 );
double tolerance = 1.0e-04;
compareForcesEnergy( testName, expectedEnergy, energy, expectedForces, forces, tolerance, log );
}
int main( int numberOfArguments, char* argv[] ) {
try {
std::cout << "TestCudaAmoebaMultipoleForce running test..." << std::endl;
registerAmoebaCudaKernelFactories();
FILE* log = NULL;
// test direct and mutual polarization cases and
// mutual polarization w/ the cavity term
testGeneralizedKirkwoodAmmoniaDirectPolarization( log );
testGeneralizedKirkwoodAmmoniaMutualPolarization( log );
testGeneralizedKirkwoodAmmoniaMutualPolarizationWithCavityTerm( 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 << "Done" << std::endl;
return 0;
}
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