Skip to content

GitLab

Commit 1db349e5 authored by Peter Eastman's avatar Peter Eastman
Browse files

Major cleanup of the AMOEBA API

parent a919f305
Expand all Hide whitespace changes
Inline Side-by-side
Showing with 68 additions and 953 deletions
plugins/amoeba/platforms/cuda2/tests/TestCudaAmoebaGeneralizedKirkwoodForce.cpp
View file @ 1db349e5
......@@ -36,7 +36,6 @@
#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"
......@@ -53,9 +52,11 @@
using namespace OpenMM;
const double TOL = 1e-4;
 
extern "C" void registerAmoebaCudaKernelFactories();
// setup for 2 ammonia molecules
 
static void setupAndGetForcesEnergyMultipoleAmmonia( AmoebaMultipoleForce::AmoebaPolarizationType polarizationType,
static void setupAndGetForcesEnergyMultipoleAmmonia( AmoebaMultipoleForce::PolarizationType polarizationType,
int includeCavityTerm, std::vector<Vec3>& forces, double& energy, FILE* log ){
 
// beginning of Multipole setup
......@@ -316,7 +317,7 @@ static void setupAndGetForcesEnergyMultipoleAmmonia( AmoebaMultipoleForce::Amoeb
 
// setup for villin
 
static void setupAndGetForcesEnergyMultipoleVillin( AmoebaMultipoleForce::AmoebaPolarizationType polarizationType,
static void setupAndGetForcesEnergyMultipoleVillin( AmoebaMultipoleForce::PolarizationType polarizationType,
int includeCavityTerm, std::vector<Vec3>& forces, double& energy, FILE* log ){
 
// beginning of Multipole setup
......
plugins/amoeba/platforms/cuda2/tests/TestCudaAmoebaHarmonicAngleForce.cpp
View file @ 1db349e5
......@@ -34,7 +34,6 @@
*/
#include "openmm/internal/AssertionUtilities.h"
#include "AmoebaTinkerParameterFile.h"
#include "openmm/Context.h"
#include "OpenMMAmoeba.h"
#include "openmm/System.h"
......@@ -44,6 +43,8 @@
using namespace OpenMM;
extern "C" void registerAmoebaCudaKernelFactories();
const double TOL = 1e-5;
#define PI_M 3.141592653589
#define RADIAN 57.29577951308
......
plugins/amoeba/platforms/cuda2/tests/TestCudaAmoebaHarmonicBondForce.cpp
View file @ 1db349e5
......@@ -35,7 +35,6 @@
#include "openmm/internal/AssertionUtilities.h"
#include "CudaPlatform.h"
#include "AmoebaTinkerParameterFile.h"
#include "openmm/Context.h"
#include "OpenMMAmoeba.h"
#include "openmm/System.h"
......@@ -45,6 +44,8 @@
using namespace OpenMM;
extern "C" void registerAmoebaCudaKernelFactories();
const double TOL = 1e-5;
static void computeAmoebaHarmonicBondForce(int bondIndex, std::vector<Vec3>& positions, AmoebaHarmonicBondForce& amoebaHarmonicBondForce,
std::vector<Vec3>& forces, double* energy ) {
......
plugins/amoeba/platforms/cuda2/tests/TestCudaAmoebaHarmonicInPlaneAngleForce.cpp
View file @ 1db349e5
......@@ -34,7 +34,6 @@
*/
#include "openmm/internal/AssertionUtilities.h"
#include "AmoebaTinkerParameterFile.h"
#include "openmm/Context.h"
#include "OpenMMAmoeba.h"
#include "openmm/System.h"
......@@ -44,6 +43,8 @@
using namespace OpenMM;
extern "C" void registerAmoebaCudaKernelFactories();
const double TOL = 1e-5;
#define PI_M 3.141592653589
#define RADIAN 57.29577951308
......
plugins/amoeba/platforms/cuda2/tests/TestCudaAmoebaMultipoleForce.cpp
View file @ 1db349e5
......@@ -36,7 +36,6 @@
#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"
......@@ -53,10 +52,12 @@
using namespace OpenMM;
const double TOL = 1e-4;
extern "C" void registerAmoebaCudaKernelFactories();
// setup for 2 ammonia molecules
static void setupAndGetForcesEnergyMultipoleAmmonia( AmoebaMultipoleForce::AmoebaNonbondedMethod nonbondedMethod,
AmoebaMultipoleForce::AmoebaPolarizationType polarizationType,
static void setupAndGetForcesEnergyMultipoleAmmonia( AmoebaMultipoleForce::NonbondedMethod nonbondedMethod,
AmoebaMultipoleForce::PolarizationType polarizationType,
double cutoff, int inputPmeGridDimension, std::vector<Vec3>& forces, double& energy, FILE* log ){
// beginning of Multipole setup
......@@ -498,8 +499,8 @@ static void testMultipoleAmmoniaMutualPolarization( FILE* log ) {
// setup for box of 4 water molecules -- used to test PME
static void setupAndGetForcesEnergyMultipoleWater( AmoebaMultipoleForce::AmoebaNonbondedMethod nonbondedMethod,
AmoebaMultipoleForce::AmoebaPolarizationType polarizationType,
static void setupAndGetForcesEnergyMultipoleWater( AmoebaMultipoleForce::NonbondedMethod nonbondedMethod,
AmoebaMultipoleForce::PolarizationType polarizationType,
double cutoff, int inputPmeGridDimension, std::vector<Vec3>& forces,
double& energy, FILE* log ){
......@@ -938,8 +939,8 @@ static void testQuadrupoleValidation( FILE* log ){
// this method does too much; I tried passing the context ptr back to
// the tests methods, but the tests would seg fault w/ a bad_alloc error
static void setupAndGetForcesEnergyMultipoleIonsAndWater( AmoebaMultipoleForce::AmoebaNonbondedMethod nonbondedMethod,
AmoebaMultipoleForce::AmoebaPolarizationType polarizationType,
static void setupAndGetForcesEnergyMultipoleIonsAndWater( AmoebaMultipoleForce::NonbondedMethod nonbondedMethod,
AmoebaMultipoleForce::PolarizationType polarizationType,
double cutoff, int inputPmeGridDimension, std::string testName,
std::vector<Vec3>& forces, double& energy, FILE* log ){
......@@ -1204,8 +1205,8 @@ static void testMultipoleIonsAndWaterPMEMutualPolarization( FILE* log ) {
// setup for box of 216 water molecules -- used to test PME
static void setupAndGetForcesEnergyMultipoleLargeWater( AmoebaMultipoleForce::AmoebaNonbondedMethod nonbondedMethod,
AmoebaMultipoleForce::AmoebaPolarizationType polarizationType,
static void setupAndGetForcesEnergyMultipoleLargeWater( AmoebaMultipoleForce::NonbondedMethod nonbondedMethod,
AmoebaMultipoleForce::PolarizationType polarizationType,
double cutoff, int inputPmeGridDimension, std::string& testName,
std::vector<Vec3>& forces, double& energy,
std::vector< double >& outputMultipoleMoments,
......@@ -1993,8 +1994,7 @@ static void setupAndGetForcesEnergyMultipoleLargeWater( AmoebaMultipoleForce::Am
context.setPositions(positions);
if( testName == "testSystemMultipoleMoments" ){
Vec3 origin( 0.0, 0.0, 0.0 );
amoebaMultipoleForce->getSystemMultipoleMoments( origin, context, outputMultipoleMoments );
amoebaMultipoleForce->getSystemMultipoleMoments(context, outputMultipoleMoments );
} else if( testName == "testMultipoleGridPotential" ){
amoebaMultipoleForce->getElectrostaticPotential( inputGrid, context, outputGridPotential );
} else {
......
plugins/amoeba/platforms/cuda2/tests/TestCudaAmoebaOutOfPlaneBendForce.cpp
View file @ 1db349e5
......@@ -34,7 +34,6 @@
*/
#include "openmm/internal/AssertionUtilities.h"
#include "AmoebaTinkerParameterFile.h"
#include "openmm/Context.h"
#include "OpenMMAmoeba.h"
#include "openmm/System.h"
......@@ -44,6 +43,8 @@
using namespace OpenMM;
extern "C" void registerAmoebaCudaKernelFactories();
const double TOL = 1e-3;
#define PI_M 3.141592653589
#define RADIAN 57.29577951308
......
plugins/amoeba/platforms/cuda2/tests/TestCudaAmoebaPiTorsionForce.cpp
View file @ 1db349e5
......@@ -34,7 +34,6 @@
*/
#include "openmm/internal/AssertionUtilities.h"
#include "AmoebaTinkerParameterFile.h"
#include "openmm/Context.h"
#include "OpenMMAmoeba.h"
#include "openmm/System.h"
......@@ -44,6 +43,8 @@
using namespace OpenMM;
extern "C" void registerAmoebaCudaKernelFactories();
const double TOL = 1e-5;
#define PI_M 3.141592653589
#define RADIAN 57.29577951308
......
plugins/amoeba/platforms/cuda2/tests/TestCudaAmoebaStretchBendForce.cpp
View file @ 1db349e5
......@@ -34,7 +34,6 @@
*/
#include "openmm/internal/AssertionUtilities.h"
#include "AmoebaTinkerParameterFile.h"
#include "openmm/Context.h"
#include "OpenMMAmoeba.h"
#include "openmm/System.h"
......@@ -44,9 +43,12 @@
using namespace OpenMM;
extern "C" void registerAmoebaCudaKernelFactories();
const double TOL = 1e-5;
#define PI_M 3.141592653589
#define RADIAN 57.29577951308
const double DegreesToRadians = PI_M/180.0;
/* ---------------------------------------------------------------------------------------
......
plugins/amoeba/platforms/cuda2/tests/TestCudaAmoebaTorsionTorsionForce.cpp
View file @ 1db349e5
......@@ -37,13 +37,15 @@
#include "openmm/Context.h"
#include "OpenMMAmoeba.h"
#include "openmm/System.h"
#include "AmoebaTinkerParameterFile.h"
#include "openmm/AmoebaTorsionTorsionForce.h"
#include "openmm/LangevinIntegrator.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
extern "C" void registerAmoebaCudaKernelFactories();
const double TOL = 1e-4;
TorsionTorsionGrid& getTorsionGrid( int gridIndex ) {
......
plugins/amoeba/platforms/cuda2/tests/TestCudaWcaDispersionForce.cpp
View file @ 1db349e5
......@@ -36,7 +36,6 @@
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "OpenMMAmoeba.h"
#include "AmoebaTinkerParameterFile.h"
#include "openmm/System.h"
#include "openmm/AmoebaWcaDispersionForce.h"
#include "openmm/LangevinIntegrator.h"
......@@ -53,6 +52,8 @@
using namespace OpenMM;
const double TOL = 1e-4;
extern "C" void registerAmoebaCudaKernelFactories();
void setupAndGetForcesEnergyWcaDispersionAmmonia( std::vector<Vec3>& forces, double& energy, FILE* log ){
// beginning of WcaDispersion setup
......
plugins/amoeba/platforms/reference/src/AmoebaReferenceKernelFactory.cpp
View file @ 1db349e5
......@@ -53,10 +53,8 @@ extern "C" void initAmoebaReferenceKernels() {
AmoebaReferenceKernelFactory* factory = new AmoebaReferenceKernelFactory();
platform.registerKernelFactory(CalcAmoebaHarmonicBondForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaUreyBradleyForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaHarmonicAngleForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaHarmonicInPlaneAngleForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaTorsionForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaPiTorsionForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaStretchBendForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaOutOfPlaneBendForceKernel::Name(), factory);
......@@ -79,18 +77,12 @@ KernelImpl* AmoebaReferenceKernelFactory::createKernelImpl(std::string name, con
if (name == CalcAmoebaHarmonicBondForceKernel::Name())
return new ReferenceCalcAmoebaHarmonicBondForceKernel(name, platform, context.getSystem());
if (name == CalcAmoebaUreyBradleyForceKernel::Name())
return new ReferenceCalcAmoebaUreyBradleyForceKernel(name, platform, context.getSystem());
if (name == CalcAmoebaHarmonicAngleForceKernel::Name())
return new ReferenceCalcAmoebaHarmonicAngleForceKernel(name, platform, context.getSystem());
if (name == CalcAmoebaHarmonicInPlaneAngleForceKernel::Name())
return new ReferenceCalcAmoebaHarmonicInPlaneAngleForceKernel(name, platform, context.getSystem());
if (name == CalcAmoebaTorsionForceKernel::Name())
return new ReferenceCalcAmoebaTorsionForceKernel(name, platform, context.getSystem());
if (name == CalcAmoebaPiTorsionForceKernel::Name())
return new ReferenceCalcAmoebaPiTorsionForceKernel(name, platform, context.getSystem());
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment