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Commit 8df54762 authored by Lee-Ping Wang's avatar Lee-Ping Wang
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Merge branch 'master' of github.com:leeping/openmm

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platforms/cpu/include/CpuKernels.h 0 → 100644
View file @ 8df54762
#ifndef OPENMM_CPUKERNELS_H_
#define OPENMM_CPUKERNELS_H_
/* -------------------------------------------------------------------------- *
* 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) 2013 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. *
* -------------------------------------------------------------------------- */
#include "CpuPlatform.h"
#include "CpuNeighborList.h"
#include "CpuNonbondedForce.h"
#include "openmm/kernels.h"
#include "openmm/System.h"
#include "openmm/internal/ThreadPool.h"
namespace OpenMM {
/**
* This kernel is invoked by NonbondedForce to calculate the forces acting on the system.
*/
class CpuCalcNonbondedForceKernel : public CalcNonbondedForceKernel {
public:
CpuCalcNonbondedForceKernel(std::string name, const Platform& platform) : CalcNonbondedForceKernel(name, platform),
bonded14IndexArray(NULL), bonded14ParamArray(NULL), hasInitializedPme(false) {
}
~CpuCalcNonbondedForceKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the NonbondedForce this kernel will be used for
*/
void initialize(const System& system, const NonbondedForce& force);
/**
* Execute the kernel to calculate the forces and/or energy.
*
* @param context the context in which to execute this kernel
* @param includeForces true if forces should be calculated
* @param includeEnergy true if the energy should be calculated
* @param includeDirect true if direct space interactions should be included
* @param includeReciprocal true if reciprocal space interactions should be included
* @return the potential energy due to the force
*/
double execute(ContextImpl& context, bool includeForces, bool includeEnergy, bool includeDirect, bool includeReciprocal);
/**
* Copy changed parameters over to a context.
*
* @param context the context to copy parameters to
* @param force the NonbondedForce to copy the parameters from
*/
void copyParametersToContext(ContextImpl& context, const NonbondedForce& force);
private:
class PmeIO;
int numParticles, num14;
int **bonded14IndexArray;
double **bonded14ParamArray;
double nonbondedCutoff, switchingDistance, rfDielectric, ewaldAlpha, ewaldSelfEnergy, dispersionCoefficient;
int kmax[3], gridSize[3];
bool useSwitchingFunction, useOptimizedPme, hasInitializedPme;
std::vector<std::set<int> > exclusions;
std::vector<std::pair<float, float> > particleParams;
std::vector<float> posq;
std::vector<float> forces;
std::vector<RealVec> lastPositions;
NonbondedMethod nonbondedMethod;
CpuNeighborList neighborList;
CpuNonbondedForce nonbonded;
ThreadPool threads;
Kernel optimizedPme;
};
} // namespace OpenMM
#endif /*OPENMM_CPUKERNELS_H_*/
platforms/cpu/include/CpuNeighborList.h 0 → 100644
View file @ 8df54762
#ifndef OPENMM_CPU_NEIGHBORLIST_H_
#define OPENMM_CPU_NEIGHBORLIST_H_
/* -------------------------------------------------------------------------- *
* 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) 2013 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. *
* -------------------------------------------------------------------------- */
#include "windowsExportCpu.h"
#include "openmm/internal/ThreadPool.h"
#include <set>
#include <utility>
#include <vector>
namespace OpenMM {
class OPENMM_EXPORT_CPU CpuNeighborList {
public:
class ThreadTask;
class Voxels;
static const int BlockSize;
CpuNeighborList();
void computeNeighborList(int numAtoms, const std::vector<float>& atomLocations, const std::vector<std::set<int> >& exclusions,
const float* periodicBoxSize, bool usePeriodic, float maxDistance, ThreadPool& threads);
int getNumBlocks() const;
const std::vector<int>& getSortedAtoms() const;
const std::vector<int>& getBlockNeighbors(int blockIndex) const;
const std::vector<char>& getBlockExclusions(int blockIndex) const;
/**
* This routine contains the code executed by each thread.
*/
void threadComputeNeighborList(ThreadPool& threads, int threadIndex);
void runThread(int index);
private:
std::vector<int> sortedAtoms;
std::vector<std::vector<int> > blockNeighbors;
std::vector<std::vector<char> > blockExclusions;
// The following variables are used to make information accessible to the individual threads.
float minx, maxx, miny, maxy, minz, maxz;
std::vector<std::pair<int, int> > atomBins;
Voxels* voxels;
const std::vector<std::set<int> >* exclusions;
const float* atomLocations;
const float* periodicBoxSize;
int numAtoms;
bool usePeriodic;
float maxDistance;
};
} // namespace OpenMM
#endif // OPENMM_CPU_NEIGHBORLIST_H_
platforms/reference/include/ReferenceShakeAlgorithm.h → platforms/cpu/include/CpuNonbondedForce.h
View file @ 8df54762
/* Portions copyright (c) 2006-2009 Stanford University and Simbios.
/* Portions copyright (c) 2006-2013 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -22,152 +22,229 @@
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef __ReferenceShakeAlgorithm_H__
#define __ReferenceShakeAlgorithm_H__
#include "ReferenceConstraintAlgorithm.h"
#ifndef OPENMM_CPU_NONBONDED_FORCE_H__
#define OPENMM_CPU_NONBONDED_FORCE_H__
#include "CpuNeighborList.h"
#include "ReferencePairIxn.h"
#include "openmm/internal/ThreadPool.h"
#include "openmm/internal/vectorize.h"
#include <set>
#include <utility>
#include <vector>
// ---------------------------------------------------------------------------------------
class ReferenceShakeAlgorithm : public ReferenceConstraintAlgorithm {
protected:
int _maximumNumberOfIterations;
RealOpenMM _tolerance;
namespace OpenMM {
int _numberOfConstraints;
int** _atomIndices;
RealOpenMM* _distance;
RealOpenMM** _r_ij;
RealOpenMM* _d_ij2;
RealOpenMM* _distanceTolerance;
RealOpenMM* _reducedMasses;
bool _hasInitializedMasses;
public:
/**---------------------------------------------------------------------------------------
ReferenceShakeAlgorithm constructor
@param numberOfConstraints number of constraints
@param atomIndices atom indices for contraints
@param distance distances for constraints
@param tolerance constraint tolerance
--------------------------------------------------------------------------------------- */
ReferenceShakeAlgorithm( int numberOfConstraints, int** atomIndices, RealOpenMM* distance, RealOpenMM tolerance );
class CpuNonbondedForce {
public:
class ComputeDirectTask;
/**---------------------------------------------------------------------------------------
Destructor
Constructor
--------------------------------------------------------------------------------------- */
~ReferenceShakeAlgorithm( );
CpuNonbondedForce();
/**---------------------------------------------------------------------------------------
Get number of constraints
Set the force to use a cutoff.
@return number of constraints
@param distance the cutoff distance
@param neighbors the neighbor list to use
@param solventDielectric the dielectric constant of the bulk solvent
--------------------------------------------------------------------------------------- */
int getNumberOfConstraints( void ) const;
void setUseCutoff(float distance, const CpuNeighborList& neighbors, float solventDielectric);
/**---------------------------------------------------------------------------------------
Get maximum number of iterations
Set the force to use a switching function on the Lennard-Jones interaction.
@return maximum number of iterations
@param distance the switching distance
--------------------------------------------------------------------------------------- */
int getMaximumNumberOfIterations( void ) const;
void setUseSwitchingFunction(float distance);
/**---------------------------------------------------------------------------------------
Set maximum number of iterations
Set the force to use periodic boundary conditions. This requires that a cutoff has
already been set, and the smallest side of the periodic box is at least twice the cutoff
distance.
@param maximumNumberOfIterations new maximum number of iterations
@param boxSize the X, Y, and Z widths of the periodic box
--------------------------------------------------------------------------------------- */
void setMaximumNumberOfIterations( int maximumNumberOfIterations );
void setPeriodic(float* periodicBoxSize);
/**---------------------------------------------------------------------------------------
Get tolerance
Set the force to use Ewald summation.
@return tolerance
@param alpha the Ewald separation parameter
@param kmaxx the largest wave vector in the x direction
@param kmaxy the largest wave vector in the y direction
@param kmaxz the largest wave vector in the z direction
--------------------------------------------------------------------------------------- */
RealOpenMM getTolerance( void ) const;
void setUseEwald(float alpha, int kmaxx, int kmaxy, int kmaxz);
/**---------------------------------------------------------------------------------------
Set tolerance
Set the force to use Particle-Mesh Ewald (PME) summation.
@param tolerance new tolerance
@param alpha the Ewald separation parameter
@param gridSize the dimensions of the mesh
--------------------------------------------------------------------------------------- */
void setTolerance( RealOpenMM tolerance );
void setUsePME(float alpha, int meshSize[3]);
/**---------------------------------------------------------------------------------------
Apply Shake algorithm
Calculate Ewald ixn
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param atomCoordinatesP atom coordinates prime
@param inverseMasses 1/mass
@return SimTKOpenMMCommon::DefaultReturn if converge; else
return SimTKOpenMMCommon::ErrorReturn
@param posq atom coordinates and charges
@param atomCoordinates atom coordinates (in format needed by PME)
@param atomParameters atom parameters (sigma/2, 2*sqrt(epsilon))
@param exclusions atom exclusion indices
exclusions[atomIndex] contains the list of exclusions for that atom
@param forces force array (forces added)
@param totalEnergy total energy
--------------------------------------------------------------------------------------- */
void calculateReciprocalIxn(int numberOfAtoms, float* posq, const std::vector<RealVec>& atomCoordinates,
const std::vector<std::pair<float, float> >& atomParameters, const std::vector<std::set<int> >& exclusions,
std::vector<RealVec>& forces, float* totalEnergy) const;
int apply( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
std::vector<OpenMM::RealVec>& atomCoordinatesP, std::vector<RealOpenMM>& inverseMasses );
/**---------------------------------------------------------------------------------------
Apply constraint algorithm to velocities.
Calculate LJ Coulomb pair ixn
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param velocities atom velocities
@param inverseMasses 1/mass
@return SimTKOpenMMCommon::DefaultReturn if converge; else
return SimTKOpenMMCommon::ErrorReturn
--------------------------------------------------------------------------------------- */
int applyToVelocities(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
std::vector<OpenMM::RealVec>& velocities, std::vector<RealOpenMM>& inverseMasses);
@param posq atom coordinates and charges
@param atomCoordinates atom coordinates (periodic boundary conditions not applied)
@param atomParameters atom parameters (sigma/2, 2*sqrt(epsilon))
@param exclusions atom exclusion indices
exclusions[atomIndex] contains the list of exclusions for that atom
@param forces force array (forces added)
@param totalEnergy total energy
@param threads the thread pool to use
--------------------------------------------------------------------------------------- */
void calculateDirectIxn(int numberOfAtoms, float* posq, const std::vector<RealVec>& atomCoordinates, const std::vector<std::pair<float, float> >& atomParameters,
const std::vector<std::set<int> >& exclusions, float* forces, float* totalEnergy, ThreadPool& threads);
/**
* This routine contains the code executed by each thread.
*/
void threadComputeDirect(ThreadPool& threads, int threadIndex);
private:
bool cutoff;
bool useSwitch;
bool periodic;
bool ewald;
bool pme;
const CpuNeighborList* neighborList;
float periodicBoxSize[3];
float cutoffDistance, switchingDistance;
float krf, crf;
float alphaEwald;
int numRx, numRy, numRz;
int meshDim[3];
std::vector<float> ewaldScaleTable;
float ewaldDX, ewaldDXInv;
std::vector<std::vector<float> > threadForce;
std::vector<double> threadEnergy;
// The following variables are used to make information accessible to the individual threads.
int numberOfAtoms;
float* posq;
RealVec const* atomCoordinates;
std::pair<float, float> const* atomParameters;
std::set<int> const* exclusions;
bool includeEnergy;
static const float TWO_OVER_SQRT_PI;
static const int NUM_TABLE_POINTS;
/**---------------------------------------------------------------------------------------
Report any violated constraints
Calculate LJ Coulomb pair ixn between two atoms
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param message report
@param atom1 the index of the first atom
@param atom2 the index of the second atom
@param forces force array (forces added)
@param totalEnergy total energy
--------------------------------------------------------------------------------------- */
void calculateOneIxn(int atom1, int atom2, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize);
/**---------------------------------------------------------------------------------------
@return number of violated constraints
Calculate all the interactions for one atom block.
@param blockIndex the index of the atom block
@param forces force array (forces added)
@param totalEnergy total energy
--------------------------------------------------------------------------------------- */
void calculateBlockIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize);
/**---------------------------------------------------------------------------------------
Calculate all the interactions for one atom block.
int reportShake( int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::stringstream& message );
@param blockIndex the index of the atom block
@param forces force array (forces added)
@param totalEnergy total energy
--------------------------------------------------------------------------------------- */
void calculateBlockEwaldIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize);
/**
* Compute the displacement and squared distance between two points, optionally using
* periodic boundary conditions.
*/
void getDeltaR(const fvec4& posI, const fvec4& posJ, fvec4& deltaR, float& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const;
/**
* Compute the displacement and squared distance between a collection of points, optionally using
* periodic boundary conditions.
*/
void getDeltaR(const fvec4& posI, const fvec4& x, const fvec4& y, const fvec4& z, fvec4& dx, fvec4& dy, fvec4& dz, fvec4& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const;
/**
* Compute a fast approximation to erfc(x).
*/
static fvec4 erfcApprox(fvec4 x);
/**
* Create a lookup table for the scale factor used with Ewald and PME.
*/
void tabulateEwaldScaleFactor();
/**
* Evaluate the scale factor used with Ewald and PME: erfc(alpha*r) + 2*alpha*r*exp(-alpha*alpha*r*r)/sqrt(PI)
*/
fvec4 ewaldScaleFunction(fvec4 x);
};
} // namespace OpenMM
// ---------------------------------------------------------------------------------------
#endif // __ReferenceShakeAlgorithm_H__
#endif // OPENMM_CPU_NONBONDED_FORCE_H__
platforms/cpu/include/CpuPlatform.h 0 → 100644
View file @ 8df54762
#ifndef OPENMM_CPUPLATFORM_H_
#define OPENMM_CPUPLATFORM_H_
/* -------------------------------------------------------------------------- *
* 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) 2013 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. *
* -------------------------------------------------------------------------- */
#include "ReferencePlatform.h"
#include "windowsExportCpu.h"
namespace OpenMM {
/**
* This Platform subclass uses CPU implementations of the OpenMM kernels.
*/
class OPENMM_EXPORT_CPU CpuPlatform : public ReferencePlatform {
public:
CpuPlatform();
const std::string& getName() const {
static const std::string name = "CPU";
return name;
}
double getSpeed() const;
bool supportsDoublePrecision() const;
static bool isProcessorSupported();
};
} // namespace OpenMM
#endif /*OPENMM_CPUPLATFORM_H_*/
platforms/cpu/include/windowsExportCpu.h 0 → 100644
View file @ 8df54762
#ifndef OPENMM_WINDOWSEXPORTCPU_H_
#define OPENMM_WINDOWSEXPORTCPU_H_
/*
* Shared libraries are messy in Visual Studio. We have to distinguish three
* cases:
* (1) this header is being used to build the OpenMM shared library
* (dllexport)
* (2) this header is being used by a *client* of the OpenMM shared
* library (dllimport)
* (3) we are building the OpenMM static library, or the client is
* being compiled with the expectation of linking with the
* OpenMM static library (nothing special needed)
* In the CMake script for building this library, we define one of the symbols
* OPENMM_CPU_BUILDING_{SHARED|STATIC}_LIBRARY
* Client code normally has no special symbol defined, in which case we'll
* assume it wants to use the shared library. However, if the client defines
* the symbol OPENMM_USE_STATIC_LIBRARIES we'll suppress the dllimport so
* that the client code can be linked with static libraries. Note that
* the client symbol is not library dependent, while the library symbols
* affect only the OpenMM library, meaning that other libraries can
* be clients of this one. However, we are assuming all-static or all-shared.
*/
#ifdef _MSC_VER
// We don't want to hear about how sprintf is "unsafe".
#pragma warning(disable:4996)
// Keep MS VC++ quiet about lack of dll export of private members.
#pragma warning(disable:4251)
#if defined(OPENMM_CPU_BUILDING_SHARED_LIBRARY)
#define OPENMM_EXPORT_CPU __declspec(dllexport)
#elif defined(OPENMM_CPU_BUILDING_STATIC_LIBRARY) || defined(OPENMM_CPU_USE_STATIC_LIBRARIES)
#define OPENMM_EXPORT_CPU
#else
#define OPENMM_EXPORT_CPU __declspec(dllimport) // i.e., a client of a shared library
#endif
#else
#define OPENMM_EXPORT_CPU // Linux, Mac
#endif
#endif // OPENMM_WINDOWSEXPORTCPU_H_
platforms/cpu/sharedTarget/CMakeLists.txt 0 → 100644
View file @ 8df54762
SET_SOURCE_FILES_PROPERTIES(${SOURCE_FILES} PROPERTIES COMPILE_FLAGS "-msse4.1")
ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
SET(MAIN_OPENMM_LIB ${OPENMM_LIBRARY_NAME}_d)
ELSE (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
SET(MAIN_OPENMM_LIB ${OPENMM_LIBRARY_NAME})
ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${MAIN_OPENMM_LIB} ${PTHREADS_LIB})
SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_CPU_BUILDING_SHARED_LIBRARY")
INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_TARGET})
platforms/cpu/src/CpuKernelFactory.cpp 0 → 100644
View file @ 8df54762
/* -------------------------------------------------------------------------- *
* 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) 2013 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. *
* -------------------------------------------------------------------------- */
#include "CpuKernelFactory.h"
#include "CpuKernels.h"
#include "CpuPlatform.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/OpenMMException.h"
using namespace OpenMM;
KernelImpl* CpuKernelFactory::createKernelImpl(std::string name, const Platform& platform, ContextImpl& context) const {
ReferencePlatform::PlatformData& data = *static_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
if (name == CalcNonbondedForceKernel::Name())
return new CpuCalcNonbondedForceKernel(name, platform);
throw OpenMMException((std::string("Tried to create kernel with illegal kernel name '") + name + "'").c_str());
}
platforms/cpu/src/CpuKernels.cpp 0 → 100644
View file @ 8df54762
/* -------------------------------------------------------------------------- *
* 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) 2013 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. *
* -------------------------------------------------------------------------- */
#include "CpuKernels.h"
#include "ReferenceBondForce.h"
#include "ReferenceLJCoulomb14.h"
#include "openmm/Context.h"
#include "openmm/OpenMMException.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/NonbondedForceImpl.h"
#include "RealVec.h"
using namespace OpenMM;
using namespace std;
static vector<RealVec>& extractPositions(ContextImpl& context) {
ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
return *((vector<RealVec>*) data->positions);
}
static vector<RealVec>& extractVelocities(ContextImpl& context) {
ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
return *((vector<RealVec>*) data->velocities);
}
static vector<RealVec>& extractForces(ContextImpl& context) {
ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
return *((vector<RealVec>*) data->forces);
}
static RealVec& extractBoxSize(ContextImpl& context) {
ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
return *(RealVec*) data->periodicBoxSize;
}
class CpuCalcNonbondedForceKernel::PmeIO : public CalcPmeReciprocalForceKernel::IO {
public:
PmeIO(float* posq, float* force, int numParticles) : posq(posq), force(force), numParticles(numParticles) {
}
float* getPosq() {
return posq;
}
void setForce(float* f) {
for (int i = 0; i < numParticles; i++) {
force[4*i] += f[4*i];
force[4*i+1] += f[4*i+1];
force[4*i+2] += f[4*i+2];
}
}
private:
float* posq;
float* force;
int numParticles;
};
CpuCalcNonbondedForceKernel::~CpuCalcNonbondedForceKernel() {
if (bonded14ParamArray != NULL) {
for (int i = 0; i < num14; i++) {
delete[] bonded14IndexArray[i];
delete[] bonded14ParamArray[i];
}
delete bonded14IndexArray;
delete bonded14ParamArray;
}
}
void CpuCalcNonbondedForceKernel::initialize(const System& system, const NonbondedForce& force) {
// Identify which exceptions are 1-4 interactions.
numParticles = force.getNumParticles();
posq.resize(4*numParticles, 0);
forces.resize(4*numParticles, 0);
exclusions.resize(numParticles);
vector<int> nb14s;
for (int i = 0; i < force.getNumExceptions(); i++) {
int particle1, particle2;
double chargeProd, sigma, epsilon;
force.getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon);
exclusions[particle1].insert(particle2);
exclusions[particle2].insert(particle1);
if (chargeProd != 0.0 || epsilon != 0.0)
nb14s.push_back(i);
}
// Record the particle parameters.
num14 = nb14s.size();
bonded14IndexArray = new int*[num14];
for (int i = 0; i < num14; i++)
bonded14IndexArray[i] = new int[2];
bonded14ParamArray = new double*[num14];
for (int i = 0; i < num14; i++)
bonded14ParamArray[i] = new double[3];
particleParams.resize(numParticles);
double sumSquaredCharges = 0.0;
for (int i = 0; i < numParticles; ++i) {
double charge, radius, depth;
force.getParticleParameters(i, charge, radius, depth);
posq[4*i+3] = (float) charge;
particleParams[i] = make_pair((float) (0.5*radius), (float) (2.0*sqrt(depth)));
sumSquaredCharges += charge*charge;
}
// Recorded exception parameters.
for (int i = 0; i < num14; ++i) {
int particle1, particle2;
double charge, radius, depth;
force.getExceptionParameters(nb14s[i], particle1, particle2, charge, radius, depth);
bonded14IndexArray[i][0] = particle1;
bonded14IndexArray[i][1] = particle2;
bonded14ParamArray[i][0] = static_cast<RealOpenMM>(radius);
bonded14ParamArray[i][1] = static_cast<RealOpenMM>(4.0*depth);
bonded14ParamArray[i][2] = static_cast<RealOpenMM>(charge);
}
// Record other parameters.
nonbondedMethod = CalcNonbondedForceKernel::NonbondedMethod(force.getNonbondedMethod());
nonbondedCutoff = force.getCutoffDistance();
if (nonbondedMethod == NoCutoff)
useSwitchingFunction = false;
else {
useSwitchingFunction = force.getUseSwitchingFunction();
switchingDistance = force.getSwitchingDistance();
}
if (nonbondedMethod == Ewald) {
double alpha;
NonbondedForceImpl::calcEwaldParameters(system, force, alpha, kmax[0], kmax[1], kmax[2]);
ewaldAlpha = alpha;
}
else if (nonbondedMethod == PME) {
double alpha;
NonbondedForceImpl::calcPMEParameters(system, force, alpha, gridSize[0], gridSize[1], gridSize[2]);
ewaldAlpha = alpha;
}
if (nonbondedMethod == Ewald || nonbondedMethod == PME)
ewaldSelfEnergy = -ONE_4PI_EPS0*ewaldAlpha*sumSquaredCharges/sqrt(M_PI);
else
ewaldSelfEnergy = 0.0;
rfDielectric = force.getReactionFieldDielectric();
if (force.getUseDispersionCorrection())
dispersionCoefficient = NonbondedForceImpl::calcDispersionCorrection(system, force);
else
dispersionCoefficient = 0.0;
lastPositions.resize(numParticles, Vec3(1e10, 1e10, 1e10));
}
double CpuCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy, bool includeDirect, bool includeReciprocal) {
if (!hasInitializedPme) {
hasInitializedPme = true;
useOptimizedPme = false;
if (nonbondedMethod == PME) {
// If available, use the optimized PME implementation.
try {
optimizedPme = getPlatform().createKernel(CalcPmeReciprocalForceKernel::Name(), context);
optimizedPme.getAs<CalcPmeReciprocalForceKernel>().initialize(gridSize[0], gridSize[1], gridSize[2], numParticles, ewaldAlpha);
useOptimizedPme = true;
}
catch (OpenMMException& ex) {
// The CPU PME plugin isn't available.
}
}
}
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& forceData = extractForces(context);
RealVec boxSize = extractBoxSize(context);
float floatBoxSize[3] = {(float) boxSize[0], (float) boxSize[1], (float) boxSize[2]};
double energy = ewaldSelfEnergy;
bool periodic = (nonbondedMethod == CutoffPeriodic);
bool ewald = (nonbondedMethod == Ewald);
bool pme = (nonbondedMethod == PME);
// Convert the positions to single precision.
if (periodic || ewald || pme)
for (int i = 0; i < numParticles; i++)
for (int j = 0; j < 3; j++) {
RealOpenMM x = posData[i][j];
double base = floor(x/boxSize[j])*boxSize[j];
posq[4*i+j] = (float) (x-base);
}
else
for (int i = 0; i < numParticles; i++) {
posq[4*i] = (float) posData[i][0];
posq[4*i+1] = (float) posData[i][1];
posq[4*i+2] = (float) posData[i][2];
}
for (int i = 0; i < 4*numParticles; i++)
forces[i] = 0.0f;
if (nonbondedMethod != NoCutoff) {
// Determine whether we need to recompute the neighbor list.
double padding = 0.15*nonbondedCutoff;
bool needRecompute = false;
double closeCutoff2 = 0.25*padding*padding;
double farCutoff2 = 0.5*padding*padding;
int maxNumMoved = numParticles/10;
vector<int> moved;
for (int i = 0; i < numParticles; i++) {
RealVec delta = posData[i]-lastPositions[i];
double dist2 = delta.dot(delta);
if (dist2 > closeCutoff2) {
moved.push_back(i);
if (dist2 > farCutoff2 || moved.size() > maxNumMoved) {
needRecompute = true;
break;
}
}
}
if (!needRecompute && moved.size() > 0) {
// Some particles have moved further than half the padding distance. Look for pairs
// that are missing from the neighbor list.
int numMoved = moved.size();
double cutoff2 = nonbondedCutoff*nonbondedCutoff;
double paddedCutoff2 = (nonbondedCutoff+padding)*(nonbondedCutoff+padding);
for (int i = 1; i < numMoved && !needRecompute; i++)
for (int j = 0; j < i; j++) {
RealVec delta = posData[moved[i]]-posData[moved[j]];
if (delta.dot(delta) < cutoff2) {
// These particles should interact. See if they are in the neighbor list.
RealVec oldDelta = lastPositions[moved[i]]-lastPositions[moved[j]];
if (oldDelta.dot(oldDelta) > paddedCutoff2) {
needRecompute = true;
break;
}
}
}
}
if (needRecompute) {
neighborList.computeNeighborList(numParticles, posq, exclusions, floatBoxSize, periodic || ewald || pme, nonbondedCutoff+padding, threads);
lastPositions = posData;
}
nonbonded.setUseCutoff(nonbondedCutoff, neighborList, rfDielectric);
}
if (periodic || ewald || pme) {
double minAllowedSize = 1.999999*nonbondedCutoff;
if (boxSize[0] < minAllowedSize || boxSize[1] < minAllowedSize || boxSize[2] < minAllowedSize)
throw OpenMMException("The periodic box size has decreased to less than twice the nonbonded cutoff.");
nonbonded.setPeriodic(floatBoxSize);
}
if (ewald)
nonbonded.setUseEwald(ewaldAlpha, kmax[0], kmax[1], kmax[2]);
if (pme)
nonbonded.setUsePME(ewaldAlpha, gridSize);
if (useSwitchingFunction)
nonbonded.setUseSwitchingFunction(switchingDistance);
float nonbondedEnergy = 0;
if (includeDirect)
nonbonded.calculateDirectIxn(numParticles, &posq[0], posData, particleParams, exclusions, &forces[0], includeEnergy ? &nonbondedEnergy : NULL, threads);
if (includeReciprocal) {
if (useOptimizedPme) {
PmeIO io(&posq[0], &forces[0], numParticles);
Vec3 periodicBoxSize(boxSize[0], boxSize[1], boxSize[2]);
optimizedPme.getAs<CalcPmeReciprocalForceKernel>().beginComputation(io, periodicBoxSize, includeEnergy);
optimizedPme.getAs<CalcPmeReciprocalForceKernel>().finishComputation(io);
}
else
nonbonded.calculateReciprocalIxn(numParticles, &posq[0], posData, particleParams, exclusions, forceData, includeEnergy ? &nonbondedEnergy : NULL);
}
energy += nonbondedEnergy;
for (int i = 0; i < numParticles; i++) {
forceData[i][0] += forces[4*i];
forceData[i][1] += forces[4*i+1];
forceData[i][2] += forces[4*i+2];
}
if (includeDirect) {
ReferenceBondForce refBondForce;
ReferenceLJCoulomb14 nonbonded14;
refBondForce.calculateForce(num14, bonded14IndexArray, posData, bonded14ParamArray, forceData, includeEnergy ? &energy : NULL, nonbonded14);
if (periodic || ewald || pme)
energy += dispersionCoefficient/(boxSize[0]*boxSize[1]*boxSize[2]);
}
return energy;
}
void CpuCalcNonbondedForceKernel::copyParametersToContext(ContextImpl& context, const NonbondedForce& force) {
if (force.getNumParticles() != numParticles)
throw OpenMMException("updateParametersInContext: The number of particles has changed");
vector<int> nb14s;
for (int i = 0; i < force.getNumExceptions(); i++) {
int particle1, particle2;
double chargeProd, sigma, epsilon;
force.getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon);
if (chargeProd != 0.0 || epsilon != 0.0)
nb14s.push_back(i);
}
if (nb14s.size() != num14)
throw OpenMMException("updateParametersInContext: The number of non-excluded exceptions has changed");
// Record the values.
double sumSquaredCharges = 0.0;
for (int i = 0; i < numParticles; ++i) {
double charge, radius, depth;
force.getParticleParameters(i, charge, radius, depth);
posq[4*i+3] = (float) charge;
particleParams[i] = make_pair((float) (0.5*radius), (float) (2.0*sqrt(depth)));
sumSquaredCharges += charge*charge;
}
if (nonbondedMethod == Ewald || nonbondedMethod == PME)
ewaldSelfEnergy = -ONE_4PI_EPS0*ewaldAlpha*sumSquaredCharges/sqrt(M_PI);
else
ewaldSelfEnergy = 0.0;
for (int i = 0; i < num14; ++i) {
int particle1, particle2;
double charge, radius, depth;
force.getExceptionParameters(nb14s[i], particle1, particle2, charge, radius, depth);
bonded14IndexArray[i][0] = particle1;
bonded14IndexArray[i][1] = particle2;
bonded14ParamArray[i][0] = static_cast<RealOpenMM>(radius);
bonded14ParamArray[i][1] = static_cast<RealOpenMM>(4.0*depth);
bonded14ParamArray[i][2] = static_cast<RealOpenMM>(charge);
}
// Recompute the coefficient for the dispersion correction.
NonbondedForce::NonbondedMethod method = force.getNonbondedMethod();
if (force.getUseDispersionCorrection() && (method == NonbondedForce::CutoffPeriodic || method == NonbondedForce::Ewald || method == NonbondedForce::PME))
dispersionCoefficient = NonbondedForceImpl::calcDispersionCorrection(context.getSystem(), force);
}
platforms/cpu/src/CpuNeighborList.cpp 0 → 100644
View file @ 8df54762
/* -------------------------------------------------------------------------- *
* 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) 2013 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. *
* -------------------------------------------------------------------------- */
#include "CpuNeighborList.h"
#include "openmm/internal/hardware.h"
#include "openmm/internal/vectorize.h"
#include "hilbert.h"
#include <algorithm>
#include <set>
#include <map>
#include <cmath>
#include <smmintrin.h>
using namespace std;
namespace OpenMM {
const int CpuNeighborList::BlockSize = 4;
class VoxelIndex
{
public:
VoxelIndex(int x, int y) : x(x), y(y) {
}
int x;
int y;
};
/**
* This data structure organizes the particles spatially. It divides them into bins along the x and y axes,
* then sorts each bin along the z axis so ranges can be identified quickly with a binary search.
*/
class CpuNeighborList::Voxels {
public:
Voxels(float vsx, float vsy, float minx, float maxx, float miny, float maxy, const float* periodicBoxSize, bool usePeriodic) :
voxelSizeX(vsx), voxelSizeY(vsy), minx(minx), maxx(maxx), miny(miny), maxy(maxy), periodicBoxSize(periodicBoxSize), usePeriodic(usePeriodic) {
if (usePeriodic) {
nx = (int) floorf(periodicBoxSize[0]/voxelSizeX+0.5f);
ny = (int) floorf(periodicBoxSize[1]/voxelSizeY+0.5f);
voxelSizeX = periodicBoxSize[0]/nx;
voxelSizeY = periodicBoxSize[1]/ny;
}
else {
nx = max(1, (int) floorf((maxx-minx)/voxelSizeX+0.5f));
ny = max(1, (int) floorf((maxy-miny)/voxelSizeY+0.5f));
if (maxx > minx)
voxelSizeX = (maxx-minx)/nx;
if (maxy > miny)
voxelSizeY = (maxy-miny)/ny;
}
bins.resize(nx);
for (int i = 0; i < nx; i++) {
bins[i].resize(ny);
for (int j = 0; j < ny; j++)
bins[i][j].resize(0);
}
}
/**
* Insert a particle into the voxel data structure.
*/
void insert(const int& atom, const float* location) {
VoxelIndex voxelIndex = getVoxelIndex(location);
bins[voxelIndex.x][voxelIndex.y].push_back(make_pair(location[2], atom));
}
/**
* Sort the particles in each voxel by z coordinate.
*/
void sortItems() {
for (int i = 0; i < nx; i++)
for (int j = 0; j < ny; j++)
sort(bins[i][j].begin(), bins[i][j].end());
}
/**
* Find the index of the first particle in voxel (x,y) whose z coordinate in >= the specified value.
*/
int findLowerBound(int x, int y, double z) const {
const vector<pair<float, int> >& bin = bins[x][y];
int lower = 0;
int upper = bin.size();
while (lower < upper) {
int middle = (lower+upper)/2;
if (bin[middle].first < z)
lower = middle+1;
else
upper = middle;
}
return lower;
}
/**
* Find the index of the first particle in voxel (x,y) whose z coordinate in greater than the specified value.
*/
int findUpperBound(int x, int y, double z) const {
const vector<pair<float, int> >& bin = bins[x][y];
int lower = 0;
int upper = bin.size();
while (lower < upper) {
int middle = (lower+upper)/2;
if (bin[middle].first > z)
upper = middle;
else
lower = middle+1;
}
return upper;
}
/**
* Get the voxel index containing a particular location.
*/
VoxelIndex getVoxelIndex(const float* location) const {
float xperiodic, yperiodic;
if (!usePeriodic) {
xperiodic = location[0]-minx;
yperiodic = location[1]-miny;
}
else {
xperiodic = location[0]-periodicBoxSize[0]*floorf(location[0]/periodicBoxSize[0]);
yperiodic = location[1]-periodicBoxSize[1]*floorf(location[1]/periodicBoxSize[1]);
}
int x = min(nx-1, int(floorf(xperiodic / voxelSizeX)));
int y = min(ny-1, int(floorf(yperiodic / voxelSizeY)));
return VoxelIndex(x, y);
}
void getNeighbors(vector<int>& neighbors, int blockIndex, fvec4 blockCenter, fvec4 blockWidth, const vector<int>& sortedAtoms, vector<char>& exclusions, float maxDistance, const vector<int> blockAtoms, const float* atomLocations) const {
neighbors.resize(0);
exclusions.resize(0);
fvec4 boxSize(periodicBoxSize[0], periodicBoxSize[1], periodicBoxSize[2], 0);
fvec4 invBoxSize(1/periodicBoxSize[0], 1/periodicBoxSize[1], 1/periodicBoxSize[2], 0);
float maxDistanceSquared = maxDistance * maxDistance;
float refineCutoff = maxDistance-max(max(blockWidth[0], blockWidth[1]), blockWidth[2]);
float refineCutoffSquared = refineCutoff*refineCutoff;
int dIndexX = min(nx/2, int((maxDistance+blockWidth[0])/voxelSizeX)+1); // How may voxels away do we have to look?
int dIndexY = min(ny/2, int((maxDistance+blockWidth[1])/voxelSizeY)+1);
float centerPos[4];
blockCenter.store(centerPos);
VoxelIndex centerVoxelIndex = getVoxelIndex(centerPos);
int startx = centerVoxelIndex.x-dIndexX;
int starty = centerVoxelIndex.y-dIndexY;
int endx = centerVoxelIndex.x+dIndexX;
int endy = centerVoxelIndex.y+dIndexY;
int numRanges;
if (usePeriodic) {
endx = min(endx, centerVoxelIndex.x-dIndexX+nx-1);
endy = min(endy, centerVoxelIndex.y-dIndexY+ny-1);
}
else {
startx = max(startx, 0);
starty = max(starty, 0);
endx = min(endx, nx-1);
endy = min(endy, ny-1);
}
int lastSortedIndex = BlockSize*(blockIndex+1);
VoxelIndex voxelIndex(0, 0);
for (int x = startx; x <= endx; ++x) {
voxelIndex.x = x;
if (usePeriodic)
voxelIndex.x = (x < 0 ? x+nx : (x >= nx ? x-nx : x));
float dx = max(0.0f, voxelSizeX*max(0, abs(centerVoxelIndex.x-x)-1)-blockWidth[0]);
for (int y = starty; y <= endy; ++y) {
voxelIndex.y = y;
if (usePeriodic)
voxelIndex.y = (y < 0 ? y+ny : (y >= ny ? y-ny : y));
float dy = max(0.0f, voxelSizeY*max(0, abs(centerVoxelIndex.y-y)-1)-blockWidth[1]);
// Identify the range of atoms within this bin we need to search. When using periodic boundary
// conditions, there may be two separate ranges.
float dz = maxDistance+blockWidth[2];
dz = sqrtf(max(0.0f, dz*dz-dx*dx-dy*dy));
bool needPeriodic = (voxelIndex.x != x || voxelIndex.y != y || centerPos[2]-dz < 0.0f || centerPos[2]+dz > periodicBoxSize[2]);
int rangeStart[2];
int rangeEnd[2];
rangeStart[0] = findLowerBound(voxelIndex.x, voxelIndex.y, centerPos[2]-dz);
if (needPeriodic) {
numRanges = 2;
rangeEnd[0] = findUpperBound(voxelIndex.x, voxelIndex.y, centerPos[2]+dz);
if (rangeStart[0] > 0) {
rangeStart[1] = 0;
rangeEnd[1] = min(findUpperBound(voxelIndex.x, voxelIndex.y, centerPos[2]+dz-periodicBoxSize[2]), rangeStart[0]);
}
else {
rangeStart[1] = max(findLowerBound(voxelIndex.x, voxelIndex.y, centerPos[2]-dz+periodicBoxSize[2]), rangeEnd[0]);
rangeEnd[1] = bins[voxelIndex.x][voxelIndex.y].size();
}
}
else {
numRanges = 1;
rangeEnd[0] = findUpperBound(voxelIndex.x, voxelIndex.y, centerPos[2]+dz);
}
// Loop over atoms and check to see if they are neighbors of this block.
for (int range = 0; range < numRanges; range++) {
for (int item = rangeStart[range]; item < rangeEnd[range]; item++) {
const int sortedIndex = bins[voxelIndex.x][voxelIndex.y][item].second;
// Avoid duplicate entries.
if (sortedIndex >= lastSortedIndex)
continue;
fvec4 atomPos(atomLocations+4*sortedAtoms[sortedIndex]);
fvec4 delta = atomPos-centerPos;
if (needPeriodic) {
fvec4 base = round(delta*invBoxSize)*boxSize;
delta = delta-base;
}
delta = max(0.0f, abs(delta)-blockWidth);
float dSquared = dot3(delta, delta);
if (dSquared > maxDistanceSquared)
continue;
if (dSquared > refineCutoffSquared) {
// The distance is large enough that there might not be any actual interactions.
// Check individual atom pairs to be sure.
bool any = false;
for (int k = 0; k < (int) blockAtoms.size(); k++) {
fvec4 pos1(&atomLocations[4*blockAtoms[k]]);
delta = atomPos-pos1;
if (needPeriodic) {
fvec4 base = round(delta*invBoxSize)*boxSize;
delta = delta-base;
}
float r2 = dot3(delta, delta);
if (r2 < maxDistanceSquared) {
any = true;
break;
}
}
if (!any)
continue;
}
// Add this atom to the list of neighbors.
neighbors.push_back(sortedAtoms[sortedIndex]);
if (sortedIndex < BlockSize*blockIndex)
exclusions.push_back(0);
else
exclusions.push_back(0xF & (0xF<<(sortedIndex-BlockSize*blockIndex)));
}
}
}
}
}
private:
float voxelSizeX, voxelSizeY;
float minx, maxx, miny, maxy;
int nx, ny;
const float* periodicBoxSize;
const bool usePeriodic;
vector<vector<vector<pair<float, int> > > > bins;
};
class CpuNeighborList::ThreadTask : public ThreadPool::Task {
public:
ThreadTask(CpuNeighborList& owner) : owner(owner) {
}
void execute(ThreadPool& threads, int threadIndex) {
owner.threadComputeNeighborList(threads, threadIndex);
}
CpuNeighborList& owner;
};
CpuNeighborList::CpuNeighborList() {
}
void CpuNeighborList::computeNeighborList(int numAtoms, const vector<float>& atomLocations, const vector<set<int> >& exclusions,
const float* periodicBoxSize, bool usePeriodic, float maxDistance, ThreadPool& threads) {
int numBlocks = (numAtoms+BlockSize-1)/BlockSize;
blockNeighbors.resize(numBlocks);
blockExclusions.resize(numBlocks);
sortedAtoms.resize(numAtoms);
// Record the parameters for the threads.
this->exclusions = &exclusions;
this->atomLocations = &atomLocations[0];
this->periodicBoxSize = periodicBoxSize;
this->numAtoms = numAtoms;
this->usePeriodic = usePeriodic;
this->maxDistance = maxDistance;
// Identify the range of atom positions along each axis.
fvec4 minPos(&atomLocations[0]);
fvec4 maxPos = minPos;
for (int i = 0; i < numAtoms; i++) {
fvec4 pos(&atomLocations[4*i]);
minPos = min(minPos, pos);
maxPos = max(maxPos, pos);
}
minx = minPos[0];
maxx = maxPos[0];
miny = minPos[1];
maxy = maxPos[1];
minz = minPos[2];
maxz = maxPos[2];
// Sort the atoms based on a Hilbert curve.
atomBins.resize(numAtoms);
ThreadTask task(*this);
threads.execute(task);
threads.waitForThreads();
sort(atomBins.begin(), atomBins.end());
// Build the voxel hash.
float edgeSizeX, edgeSizeY;
if (!usePeriodic)
edgeSizeX = edgeSizeY = maxDistance; // TODO - adjust this as needed
else {
edgeSizeX = 0.5f*periodicBoxSize[0]/floorf(periodicBoxSize[0]/maxDistance);
edgeSizeY = 0.5f*periodicBoxSize[1]/floorf(periodicBoxSize[1]/maxDistance);
}
Voxels voxels(edgeSizeX, edgeSizeY, minx, maxx, miny, maxy, periodicBoxSize, usePeriodic);
for (int i = 0; i < numAtoms; i++) {
int atomIndex = atomBins[i].second;
sortedAtoms[i] = atomIndex;
voxels.insert(i, &atomLocations[4*atomIndex]);
}
voxels.sortItems();
this->voxels = &voxels;
// Signal the threads to start running and wait for them to finish.
threads.resumeThreads();
threads.waitForThreads();
// Add padding atoms to fill up the last block.
int numPadding = numBlocks*BlockSize-numAtoms;
if (numPadding > 0) {
char mask = (0xF0 >> numPadding) & 0xF;
for (int i = 0; i < numPadding; i++)
sortedAtoms.push_back(0);
vector<char>& exc = blockExclusions[blockExclusions.size()-1];
for (int i = 0; i < (int) exc.size(); i++)
exc[i] |= mask;
}
}
int CpuNeighborList::getNumBlocks() const {
return sortedAtoms.size()/BlockSize;
}
const std::vector<int>& CpuNeighborList::getSortedAtoms() const {
return sortedAtoms;
}
const std::vector<int>& CpuNeighborList::getBlockNeighbors(int blockIndex) const {
return blockNeighbors[blockIndex];
}
const std::vector<char>& CpuNeighborList::getBlockExclusions(int blockIndex) const {
return blockExclusions[blockIndex];
}
void CpuNeighborList::threadComputeNeighborList(ThreadPool& threads, int threadIndex) {
// Compute the positions of atoms along the Hilbert curve.
float binWidth = max(max(maxx-minx, maxy-miny), maxz-minz)/255.0f;
float invBinWidth = 1.0f/binWidth;
bitmask_t coords[3];
int numThreads = threads.getNumThreads();
for (int i = threadIndex; i < numAtoms; i += numThreads) {
const float* pos = &atomLocations[4*i];
coords[0] = (bitmask_t) ((pos[0]-minx)*invBinWidth);
coords[1] = (bitmask_t) ((pos[1]-miny)*invBinWidth);
coords[2] = (bitmask_t) ((pos[2]-minz)*invBinWidth);
int bin = (int) hilbert_c2i(3, 8, coords);
atomBins[i] = pair<int, int>(bin, i);
}
threads.syncThreads();
// Compute this thread's subset of neighbors.
int numBlocks = blockNeighbors.size();
vector<int> blockAtoms;
for (int i = threadIndex; i < numBlocks; i += numThreads) {
// Find the atoms in this block and compute their bounding box.
int firstIndex = BlockSize*i;
int atomsInBlock = min(BlockSize, numAtoms-firstIndex);
blockAtoms.resize(atomsInBlock);
for (int j = 0; j < atomsInBlock; j++)
blockAtoms[j] = sortedAtoms[firstIndex+j];
fvec4 minPos(&atomLocations[4*sortedAtoms[firstIndex]]);
fvec4 maxPos = minPos;
for (int j = 1; j < atomsInBlock; j++) {
fvec4 pos(&atomLocations[4*sortedAtoms[firstIndex+j]]);
minPos = min(minPos, pos);
maxPos = max(maxPos, pos);
}
voxels->getNeighbors(blockNeighbors[i], i, (maxPos+minPos)*0.5f, (maxPos-minPos)*0.5f, sortedAtoms, blockExclusions[i], maxDistance, blockAtoms, atomLocations);
// Record the exclusions for this block.
for (int j = 0; j < atomsInBlock; j++) {
const set<int>& atomExclusions = (*exclusions)[sortedAtoms[firstIndex+j]];
char mask = 1<<j;
for (int k = 0; k < (int) blockNeighbors[i].size(); k++) {
int atomIndex = blockNeighbors[i][k];
if (atomExclusions.find(atomIndex) != atomExclusions.end())
blockExclusions[i][k] |= mask;
}
}
}
}
} // namespace OpenMM
platforms/cpu/src/CpuNonbondedForce.cpp 0 → 100644
View file @ 8df54762
/* Portions copyright (c) 2006-2013 Stanford University and Simbios.
* Contributors: Pande Group
*
* 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.
*/
#include <string.h>
#include <complex>
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMUtilities.h"
#include "CpuNonbondedForce.h"
#include "ReferenceForce.h"
#include "ReferencePME.h"
#include "openmm/internal/SplineFitter.h"
#include "openmm/internal/vectorize.h"
// In case we're using some primitive version of Visual Studio this will
// make sure that erf() and erfc() are defined.
#include "openmm/internal/MSVC_erfc.h"
using namespace std;
using namespace OpenMM;
const float CpuNonbondedForce::TWO_OVER_SQRT_PI = (float) (2/sqrt(PI_M));
const int CpuNonbondedForce::NUM_TABLE_POINTS = 1025;
class CpuNonbondedForce::ComputeDirectTask : public ThreadPool::Task {
public:
ComputeDirectTask(CpuNonbondedForce& owner) : owner(owner) {
}
void execute(ThreadPool& threads, int threadIndex) {
owner.threadComputeDirect(threads, threadIndex);
}
CpuNonbondedForce& owner;
};
/**---------------------------------------------------------------------------------------
CpuNonbondedForce constructor
--------------------------------------------------------------------------------------- */
CpuNonbondedForce::CpuNonbondedForce() : cutoff(false), useSwitch(false), periodic(false), ewald(false), pme(false) {
}
/**---------------------------------------------------------------------------------------
Set the force to use a cutoff.
@param distance the cutoff distance
@param neighbors the neighbor list to use
@param solventDielectric the dielectric constant of the bulk solvent
--------------------------------------------------------------------------------------- */
void CpuNonbondedForce::setUseCutoff(float distance, const CpuNeighborList& neighbors, float solventDielectric) {
cutoff = true;
cutoffDistance = distance;
neighborList = &neighbors;
krf = pow(cutoffDistance, -3.0f)*(solventDielectric-1.0)/(2.0*solventDielectric+1.0);
crf = (1.0/cutoffDistance)*(3.0*solventDielectric)/(2.0*solventDielectric+1.0);
}
/**---------------------------------------------------------------------------------------
Set the force to use a switching function on the Lennard-Jones interaction.
@param distance the switching distance
--------------------------------------------------------------------------------------- */
void CpuNonbondedForce::setUseSwitchingFunction(float distance) {
useSwitch = true;
switchingDistance = distance;
}
/**---------------------------------------------------------------------------------------
Set the force to use periodic boundary conditions. This requires that a cutoff has
also been set, and the smallest side of the periodic box is at least twice the cutoff
distance.
@param boxSize the X, Y, and Z widths of the periodic box
--------------------------------------------------------------------------------------- */
void CpuNonbondedForce::setPeriodic(float* periodicBoxSize) {
assert(cutoff);
assert(periodicBoxSize[0] >= 2*cutoffDistance);
assert(periodicBoxSize[1] >= 2*cutoffDistance);
assert(periodicBoxSize[2] >= 2*cutoffDistance);
periodic = true;
this->periodicBoxSize[0] = periodicBoxSize[0];
this->periodicBoxSize[1] = periodicBoxSize[1];
this->periodicBoxSize[2] = periodicBoxSize[2];
}
/**---------------------------------------------------------------------------------------
Set the force to use Ewald summation.
@param alpha the Ewald separation parameter
@param kmaxx the largest wave vector in the x direction
@param kmaxy the largest wave vector in the y direction
@param kmaxz the largest wave vector in the z direction
--------------------------------------------------------------------------------------- */
void CpuNonbondedForce::setUseEwald(float alpha, int kmaxx, int kmaxy, int kmaxz) {
alphaEwald = alpha;
numRx = kmaxx;
numRy = kmaxy;
numRz = kmaxz;
ewald = true;
tabulateEwaldScaleFactor();
}
/**---------------------------------------------------------------------------------------
Set the force to use Particle-Mesh Ewald (PME) summation.
@param alpha the Ewald separation parameter
@param gridSize the dimensions of the mesh
--------------------------------------------------------------------------------------- */
void CpuNonbondedForce::setUsePME(float alpha, int meshSize[3]) {
alphaEwald = alpha;
meshDim[0] = meshSize[0];
meshDim[1] = meshSize[1];
meshDim[2] = meshSize[2];
pme = true;
tabulateEwaldScaleFactor();
}
void CpuNonbondedForce::tabulateEwaldScaleFactor() {
ewaldDX = cutoffDistance/(NUM_TABLE_POINTS-2);
ewaldDXInv = 1.0f/ewaldDX;
vector<double> x(NUM_TABLE_POINTS+1);
vector<double> y(NUM_TABLE_POINTS+1);
vector<double> deriv;
for (int i = 0; i < NUM_TABLE_POINTS+1; i++) {
double r = i*cutoffDistance/(NUM_TABLE_POINTS-2);
double alphaR = alphaEwald*r;
x[i] = r;
y[i] = erfc(alphaR) + TWO_OVER_SQRT_PI*alphaR*exp(-alphaR*alphaR);
}
SplineFitter::createNaturalSpline(x, y, deriv);
ewaldScaleTable.resize(4*NUM_TABLE_POINTS);
for (int i = 0; i < NUM_TABLE_POINTS; i++) {
ewaldScaleTable[4*i] = (float) y[i];
ewaldScaleTable[4*i+1] = (float) y[i+1];
ewaldScaleTable[4*i+2] = (float) (deriv[i]*ewaldDX*ewaldDX/6);
ewaldScaleTable[4*i+3] = (float) (deriv[i+1]*ewaldDX*ewaldDX/6);
}
}
void CpuNonbondedForce::calculateReciprocalIxn(int numberOfAtoms, float* posq, const vector<RealVec>& atomCoordinates,
const vector<pair<float, float> >& atomParameters, const vector<set<int> >& exclusions,
vector<RealVec>& forces, float* totalEnergy) const {
typedef std::complex<float> d_complex;
static const float epsilon = 1.0;
int kmax = (ewald ? std::max(numRx, std::max(numRy,numRz)) : 0);
float factorEwald = -1 / (4*alphaEwald*alphaEwald);
float TWO_PI = 2.0 * PI_M;
float recipCoeff = (float)(ONE_4PI_EPS0*4*PI_M/(periodicBoxSize[0] * periodicBoxSize[1] * periodicBoxSize[2]) /epsilon);
if (pme) {
pme_t pmedata;
RealOpenMM virial[3][3];
pme_init(&pmedata, alphaEwald, numberOfAtoms, meshDim, 5, 1);
vector<RealOpenMM> charges(numberOfAtoms);
for (int i = 0; i < numberOfAtoms; i++)
charges[i] = posq[4*i+3];
RealOpenMM boxSize[3] = {periodicBoxSize[0], periodicBoxSize[1], periodicBoxSize[2]};
RealOpenMM recipEnergy = 0.0;
pme_exec(pmedata, atomCoordinates, forces, charges, boxSize, &recipEnergy, virial);
if (totalEnergy)
*totalEnergy += recipEnergy;
pme_destroy(pmedata);
}
// Ewald method
else if (ewald) {
// setup reciprocal box
float recipBoxSize[3] = { TWO_PI / periodicBoxSize[0], TWO_PI / periodicBoxSize[1], TWO_PI / periodicBoxSize[2]};
// setup K-vectors
#define EIR(x, y, z) eir[(x)*numberOfAtoms*3+(y)*3+z]
vector<d_complex> eir(kmax*numberOfAtoms*3);
vector<d_complex> tab_xy(numberOfAtoms);
vector<d_complex> tab_qxyz(numberOfAtoms);
for (int i = 0; (i < numberOfAtoms); i++) {
float* pos = posq+4*i;
for (int m = 0; (m < 3); m++)
EIR(0, i, m) = d_complex(1,0);
for (int m=0; (m<3); m++)
EIR(1, i, m) = d_complex(cos(pos[m]*recipBoxSize[m]),
sin(pos[m]*recipBoxSize[m]));
for (int j=2; (j<kmax); j++)
for (int m=0; (m<3); m++)
EIR(j, i, m) = EIR(j-1, i, m) * EIR(1, i, m);
}
// calculate reciprocal space energy and forces
int lowry = 0;
int lowrz = 1;
for (int rx = 0; rx < numRx; rx++) {
float kx = rx * recipBoxSize[0];
for (int ry = lowry; ry < numRy; ry++) {
float ky = ry * recipBoxSize[1];
if (ry >= 0) {
for (int n = 0; n < numberOfAtoms; n++)
tab_xy[n] = EIR(rx, n, 0) * EIR(ry, n, 1);
}
else {
for (int n = 0; n < numberOfAtoms; n++)
tab_xy[n]= EIR(rx, n, 0) * conj (EIR(-ry, n, 1));
}
for (int rz = lowrz; rz < numRz; rz++) {
if (rz >= 0) {
for (int n = 0; n < numberOfAtoms; n++)
tab_qxyz[n] = posq[4*n+3] * (tab_xy[n] * EIR(rz, n, 2));
}
else {
for (int n = 0; n < numberOfAtoms; n++)
tab_qxyz[n] = posq[4*n+3] * (tab_xy[n] * conj(EIR(-rz, n, 2)));
}
float cs = 0.0f;
float ss = 0.0f;
for (int n = 0; n < numberOfAtoms; n++) {
cs += tab_qxyz[n].real();
ss += tab_qxyz[n].imag();
}
float kz = rz * recipBoxSize[2];
float k2 = kx * kx + ky * ky + kz * kz;
float ak = exp(k2*factorEwald) / k2;
for (int n = 0; n < numberOfAtoms; n++) {
float force = ak * (cs * tab_qxyz[n].imag() - ss * tab_qxyz[n].real());
forces[n][0] += 2 * recipCoeff * force * kx;
forces[n][1] += 2 * recipCoeff * force * ky;
forces[n][2] += 2 * recipCoeff * force * kz;
}
if (totalEnergy)
*totalEnergy += recipCoeff * ak * (cs * cs + ss * ss);
lowrz = 1 - numRz;
}
lowry = 1 - numRy;
}
}
}
}
void CpuNonbondedForce::calculateDirectIxn(int numberOfAtoms, float* posq, const vector<RealVec>& atomCoordinates, const vector<pair<float, float> >& atomParameters,
const vector<set<int> >& exclusions, float* forces, float* totalEnergy, ThreadPool& threads) {
// Record the parameters for the threads.
this->numberOfAtoms = numberOfAtoms;
this->posq = posq;
this->atomCoordinates = &atomCoordinates[0];
this->atomParameters = &atomParameters[0];
this->exclusions = &exclusions[0];
includeEnergy = (totalEnergy != NULL);
threadEnergy.resize(threads.getNumThreads());
threadForce.resize(threads.getNumThreads());
// Signal the threads to start running and wait for them to finish.
ComputeDirectTask task(*this);
threads.execute(task);
threads.waitForThreads();
// Combine the results from all the threads.
double directEnergy = 0;
int numThreads = threads.getNumThreads();
for (int i = 0; i < numThreads; i++)
directEnergy += threadEnergy[i];
for (int i = 0; i < numberOfAtoms; i++) {
fvec4 f(forces+4*i);
for (int j = 0; j < numThreads; j++)
f += fvec4(&threadForce[j][4*i]);
f.store(forces+4*i);
}
if (totalEnergy != NULL)
*totalEnergy += (float) directEnergy;
}
void CpuNonbondedForce::threadComputeDirect(ThreadPool& threads, int threadIndex) {
// Compute this thread's subset of interactions.
int numThreads = threads.getNumThreads();
threadEnergy[threadIndex] = 0;
double* energyPtr = (includeEnergy ? &threadEnergy[threadIndex] : NULL);
threadForce[threadIndex].resize(4*numberOfAtoms, 0.0f);
float* forces = &threadForce[threadIndex][0];
for (int i = 0; i < 4*numberOfAtoms; i++)
forces[i] = 0.0f;
fvec4 boxSize(periodicBoxSize[0], periodicBoxSize[1], periodicBoxSize[2], 0);
fvec4 invBoxSize((1/periodicBoxSize[0]), (1/periodicBoxSize[1]), (1/periodicBoxSize[2]), 0);
if (ewald || pme) {
// Compute the interactions from the neighbor list.
for (int i = threadIndex; i < neighborList->getNumBlocks(); i += numThreads)
calculateBlockEwaldIxn(i, forces, energyPtr, boxSize, invBoxSize);
// Now subtract off the exclusions, since they were implicitly included in the reciprocal space sum.
fvec4 boxSize(periodicBoxSize[0], periodicBoxSize[1], periodicBoxSize[2], 0);
fvec4 invBoxSize((1/periodicBoxSize[0]), (1/periodicBoxSize[1]), (1/periodicBoxSize[2]), 0);
for (int i = threadIndex; i < numberOfAtoms; i += numThreads) {
fvec4 posI((float) atomCoordinates[i][0], (float) atomCoordinates[i][1], (float) atomCoordinates[i][2], 0.0f);
for (set<int>::const_iterator iter = exclusions[i].begin(); iter != exclusions[i].end(); ++iter) {
if (*iter > i) {
int j = *iter;
fvec4 deltaR;
fvec4 posJ((float) atomCoordinates[j][0], (float) atomCoordinates[j][1], (float) atomCoordinates[j][2], 0.0f);
float r2;
getDeltaR(posJ, posI, deltaR, r2, false, boxSize, invBoxSize);
float r = sqrtf(r2);
float inverseR = 1/r;
float chargeProd = ONE_4PI_EPS0*posq[4*i+3]*posq[4*j+3];
float alphaR = alphaEwald*r;
float erfcAlphaR = erfcApprox(alphaR)[0];
float dEdR = (float) (chargeProd * inverseR * inverseR * inverseR);
dEdR = (float) (dEdR * (1.0f-erfcAlphaR-TWO_OVER_SQRT_PI*alphaR*exp(-alphaR*alphaR)));
fvec4 result = deltaR*dEdR;
(fvec4(forces+4*i)-result).store(forces+4*i);
(fvec4(forces+4*j)+result).store(forces+4*j);
if (includeEnergy)
threadEnergy[threadIndex] -= chargeProd*inverseR*(1.0f-erfcAlphaR);
}
}
}
}
else if (cutoff) {
// Compute the interactions from the neighbor list.
for (int i = threadIndex; i < neighborList->getNumBlocks(); i += numThreads)
calculateBlockIxn(i, forces, energyPtr, boxSize, invBoxSize);
}
else {
// Loop over all atom pairs
for (int i = threadIndex; i < numberOfAtoms; i += numThreads){
for (int j = i+1; j < numberOfAtoms; j++)
if (exclusions[j].find(i) == exclusions[j].end())
calculateOneIxn(i, j, forces, energyPtr, boxSize, invBoxSize);
}
}
}
void CpuNonbondedForce::calculateOneIxn(int ii, int jj, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) {
// get deltaR, R2, and R between 2 atoms
fvec4 deltaR;
fvec4 posI(posq+4*ii);
fvec4 posJ(posq+4*jj);
float r2;
getDeltaR(posJ, posI, deltaR, r2, periodic, boxSize, invBoxSize);
if (cutoff && r2 >= cutoffDistance*cutoffDistance)
return;
float r = sqrtf(r2);
float inverseR = 1/r;
float switchValue = 1, switchDeriv = 0;
if (useSwitch && r > switchingDistance) {
float t = (r-switchingDistance)/(cutoffDistance-switchingDistance);
switchValue = 1+t*t*t*(-10+t*(15-t*6));
switchDeriv = t*t*(-30+t*(60-t*30))/(cutoffDistance-switchingDistance);
}
float sig = atomParameters[ii].first + atomParameters[jj].first;
float sig2 = inverseR*sig;
sig2 *= sig2;
float sig6 = sig2*sig2*sig2;
float eps = atomParameters[ii].second*atomParameters[jj].second;
float dEdR = switchValue*eps*(12.0f*sig6 - 6.0f)*sig6;
float chargeProd = ONE_4PI_EPS0*posq[4*ii+3]*posq[4*jj+3];
if (cutoff)
dEdR += (float) (chargeProd*(inverseR-2.0f*krf*r2));
else
dEdR += (float) (chargeProd*inverseR);
dEdR *= inverseR*inverseR;
float energy = eps*(sig6-1.0f)*sig6;
if (useSwitch) {
dEdR -= energy*switchDeriv*inverseR;
energy *= switchValue;
}
// accumulate energies
if (totalEnergy) {
if (cutoff)
energy += (float) (chargeProd*(inverseR+krf*r2-crf));
else
energy += (float) (chargeProd*inverseR);
*totalEnergy += energy;
}
// accumulate forces
fvec4 result = deltaR*dEdR;
(fvec4(forces+4*ii)+result).store(forces+4*ii);
(fvec4(forces+4*jj)-result).store(forces+4*jj);
}
void CpuNonbondedForce::calculateBlockIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) {
// Load the positions and parameters of the atoms in the block.
int blockAtom[4];
fvec4 blockAtomPosq[4];
fvec4 blockAtomForce[4];
for (int i = 0; i < 4; i++) {
blockAtom[i] = neighborList->getSortedAtoms()[4*blockIndex+i];
blockAtomPosq[i] = fvec4(posq+4*blockAtom[i]);
blockAtomForce[i] = fvec4(0.0f);
}
fvec4 blockAtomX = fvec4(blockAtomPosq[0][0], blockAtomPosq[1][0], blockAtomPosq[2][0], blockAtomPosq[3][0]);
fvec4 blockAtomY = fvec4(blockAtomPosq[0][1], blockAtomPosq[1][1], blockAtomPosq[2][1], blockAtomPosq[3][1]);
fvec4 blockAtomZ = fvec4(blockAtomPosq[0][2], blockAtomPosq[1][2], blockAtomPosq[2][2], blockAtomPosq[3][2]);
fvec4 blockAtomCharge = fvec4(ONE_4PI_EPS0)*fvec4(blockAtomPosq[0][3], blockAtomPosq[1][3], blockAtomPosq[2][3], blockAtomPosq[3][3]);
fvec4 blockAtomSigma(atomParameters[blockAtom[0]].first, atomParameters[blockAtom[1]].first, atomParameters[blockAtom[2]].first, atomParameters[blockAtom[3]].first);
fvec4 blockAtomEpsilon(atomParameters[blockAtom[0]].second, atomParameters[blockAtom[1]].second, atomParameters[blockAtom[2]].second, atomParameters[blockAtom[3]].second);
bool needPeriodic = false;
if (periodic) {
for (int i = 0; i < 4 && !needPeriodic; i++)
for (int j = 0; j < 3; j++)
if (blockAtomPosq[i][j]-cutoffDistance < 0.0 || blockAtomPosq[i][j]+cutoffDistance > boxSize[j]) {
needPeriodic = true;
break;
}
}
// Loop over neighbors for this block.
const vector<int>& neighbors = neighborList->getBlockNeighbors(blockIndex);
const vector<char>& exclusions = neighborList->getBlockExclusions(blockIndex);
bool include[4];
for (int i = 0; i < (int) neighbors.size(); i++) {
// Load the next neighbor.
int atom = neighbors[i];
fvec4 atomPosq(posq+4*atom);
// Compute the distances to the block atoms.
bool any = false;
fvec4 dx, dy, dz, r2;
getDeltaR(atomPosq, blockAtomX, blockAtomY, blockAtomZ, dx, dy, dz, r2, needPeriodic, boxSize, invBoxSize);
for (int j = 0; j < 4; j++) {
include[j] = (((exclusions[i]>>j)&1) == 0 && (!cutoff || r2[j] < cutoffDistance*cutoffDistance));
any |= include[j];
}
if (!any)
continue; // No interactions to compute.
// Compute the interactions.
fvec4 r = sqrt(r2);
fvec4 inverseR = fvec4(1.0f)/r;
fvec4 switchValue(1.0f), switchDeriv(0.0f);
if (useSwitch) {
fvec4 t = (r>switchingDistance) & ((r-switchingDistance)/(cutoffDistance-switchingDistance));
switchValue = 1+t*t*t*(-10.0f+t*(15.0f-t*6.0f));
switchDeriv = t*t*(-30.0f+t*(60.0f-t*30.0f))/(cutoffDistance-switchingDistance);
}
fvec4 sig = blockAtomSigma+atomParameters[atom].first;
fvec4 sig2 = inverseR*sig;
sig2 *= sig2;
fvec4 sig6 = sig2*sig2*sig2;
fvec4 eps = blockAtomEpsilon*atomParameters[atom].second;
fvec4 dEdR = switchValue*eps*(12.0f*sig6 - 6.0f)*sig6;
fvec4 chargeProd = blockAtomCharge*posq[4*atom+3];
if (cutoff)
dEdR += chargeProd*(inverseR-2.0f*krf*r2);
else
dEdR += chargeProd*inverseR;
dEdR *= inverseR*inverseR;
fvec4 energy = eps*(sig6-1.0f)*sig6;
if (useSwitch) {
dEdR -= energy*switchDeriv*inverseR;
energy *= switchValue;
}
// Accumulate energies.
if (totalEnergy) {
if (cutoff)
energy += chargeProd*(inverseR+krf*r2-crf);
else
energy += chargeProd*inverseR;
for (int j = 0; j < 4; j++)
if (include[j])
*totalEnergy += energy[j];
}
// Accumulate forces.
fvec4 result[4] = {dx*dEdR, dy*dEdR, dz*dEdR, 0.0f};
transpose(result[0], result[1], result[2], result[3]);
fvec4 atomForce(forces+4*atom);
for (int j = 0; j < 4; j++) {
if (include[j]) {
blockAtomForce[j] += result[j];
atomForce -= result[j];
}
}
atomForce.store(forces+4*atom);
}
// Record the forces on the block atoms.
for (int j = 0; j < 4; j++)
(fvec4(forces+4*blockAtom[j])+blockAtomForce[j]).store(forces+4*blockAtom[j]);
}
void CpuNonbondedForce::calculateBlockEwaldIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) {
// Load the positions and parameters of the atoms in the block.
int blockAtom[4];
fvec4 blockAtomPosq[4];
fvec4 blockAtomForce[4];
for (int i = 0; i < 4; i++) {
blockAtom[i] = neighborList->getSortedAtoms()[4*blockIndex+i];
blockAtomPosq[i] = fvec4(posq+4*blockAtom[i]);
blockAtomForce[i] = fvec4(0.0f);
}
fvec4 blockAtomX = fvec4(blockAtomPosq[0][0], blockAtomPosq[1][0], blockAtomPosq[2][0], blockAtomPosq[3][0]);
fvec4 blockAtomY = fvec4(blockAtomPosq[0][1], blockAtomPosq[1][1], blockAtomPosq[2][1], blockAtomPosq[3][1]);
fvec4 blockAtomZ = fvec4(blockAtomPosq[0][2], blockAtomPosq[1][2], blockAtomPosq[2][2], blockAtomPosq[3][2]);
fvec4 blockAtomCharge = fvec4(ONE_4PI_EPS0)*fvec4(blockAtomPosq[0][3], blockAtomPosq[1][3], blockAtomPosq[2][3], blockAtomPosq[3][3]);
fvec4 blockAtomSigma(atomParameters[blockAtom[0]].first, atomParameters[blockAtom[1]].first, atomParameters[blockAtom[2]].first, atomParameters[blockAtom[3]].first);
fvec4 blockAtomEpsilon(atomParameters[blockAtom[0]].second, atomParameters[blockAtom[1]].second, atomParameters[blockAtom[2]].second, atomParameters[blockAtom[3]].second);
bool needPeriodic = false;
for (int i = 0; i < 4 && !needPeriodic; i++)
for (int j = 0; j < 3; j++)
if (blockAtomPosq[i][j]-cutoffDistance < 0.0 || blockAtomPosq[i][j]+cutoffDistance > boxSize[j]) {
needPeriodic = true;
break;
}
// Loop over neighbors for this block.
const vector<int>& neighbors = neighborList->getBlockNeighbors(blockIndex);
const vector<char>& exclusions = neighborList->getBlockExclusions(blockIndex);
bool include[4];
for (int i = 0; i < (int) neighbors.size(); i++) {
// Load the next neighbor.
int atom = neighbors[i];
fvec4 atomPosq(posq+4*atom);
// Compute the distances to the block atoms.
bool any = false;
fvec4 dx, dy, dz, r2;
getDeltaR(atomPosq, blockAtomX, blockAtomY, blockAtomZ, dx, dy, dz, r2, needPeriodic, boxSize, invBoxSize);
for (int j = 0; j < 4; j++) {
include[j] = (((exclusions[i]>>j)&1) == 0 && r2[j] < cutoffDistance*cutoffDistance);
any |= include[j];
}
if (!any)
continue; // No interactions to compute.
// Compute the interactions.
fvec4 r = sqrt(r2);
fvec4 inverseR = fvec4(1.0f)/r;
fvec4 switchValue(1.0f), switchDeriv(0.0f);
if (useSwitch) {
fvec4 t = (r>switchingDistance) & ((r-switchingDistance)/(cutoffDistance-switchingDistance));
switchValue = 1+t*t*t*(-10.0f+t*(15.0f-t*6.0f));
switchDeriv = t*t*(-30.0f+t*(60.0f-t*30.0f))/(cutoffDistance-switchingDistance);
}
fvec4 chargeProd = blockAtomCharge*posq[4*atom+3];
fvec4 dEdR = chargeProd*inverseR*ewaldScaleFunction(r);
fvec4 sig = blockAtomSigma+atomParameters[atom].first;
fvec4 sig2 = inverseR*sig;
sig2 *= sig2;
fvec4 sig6 = sig2*sig2*sig2;
fvec4 eps = blockAtomEpsilon*atomParameters[atom].second;
dEdR += switchValue*eps*(12.0f*sig6 - 6.0f)*sig6;
dEdR *= inverseR*inverseR;
fvec4 energy = eps*(sig6-1.0f)*sig6;
if (useSwitch) {
dEdR -= energy*switchDeriv*inverseR;
energy *= switchValue;
}
// Accumulate energies.
if (totalEnergy) {
energy += chargeProd*inverseR*erfcApprox(alphaEwald*r);
for (int j = 0; j < 4; j++)
if (include[j])
*totalEnergy += energy[j];
}
// Accumulate forces.
fvec4 result[4] = {dx*dEdR, dy*dEdR, dz*dEdR, 0.0f};
transpose(result[0], result[1], result[2], result[3]);
fvec4 atomForce(forces+4*atom);
for (int j = 0; j < 4; j++) {
if (include[j]) {
blockAtomForce[j] += result[j];
atomForce -= result[j];
}
}
atomForce.store(forces+4*atom);
}
// Record the forces on the block atoms.
for (int j = 0; j < 4; j++)
(fvec4(forces+4*blockAtom[j])+blockAtomForce[j]).store(forces+4*blockAtom[j]);
}
void CpuNonbondedForce::getDeltaR(const fvec4& posI, const fvec4& posJ, fvec4& deltaR, float& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const {
deltaR = posJ-posI;
if (periodic) {
fvec4 base = round(deltaR*invBoxSize)*boxSize;
deltaR = deltaR-base;
}
r2 = dot3(deltaR, deltaR);
}
void CpuNonbondedForce::getDeltaR(const fvec4& posI, const fvec4& x, const fvec4& y, const fvec4& z, fvec4& dx, fvec4& dy, fvec4& dz, fvec4& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const {
dx = x-posI[0];
dy = y-posI[1];
dz = z-posI[2];
if (periodic) {
dx -= round(dx*invBoxSize[0])*boxSize[0];
dy -= round(dy*invBoxSize[1])*boxSize[1];
dz -= round(dz*invBoxSize[2])*boxSize[2];
}
r2 = dx*dx + dy*dy + dz*dz;
}
fvec4 CpuNonbondedForce::erfcApprox(fvec4 x) {
// This approximation for erfc is from Abramowitz and Stegun (1964) p. 299. They cite the following as
// the original source: C. Hastings, Jr., Approximations for Digital Computers (1955). It has a maximum
// error of 3e-7.
fvec4 t = 1.0f+(0.0705230784f+(0.0422820123f+(0.0092705272f+(0.0001520143f+(0.0002765672f+0.0000430638f*x)*x)*x)*x)*x)*x;
t *= t;
t *= t;
t *= t;
return 1.0f/(t*t);
}
fvec4 CpuNonbondedForce::ewaldScaleFunction(fvec4 x) {
// Compute the tabulated Ewald scale factor: erfc(alpha*r) + 2*alpha*r*exp(-alpha*alpha*r*r)/sqrt(PI)
float y[4];
fvec4 x1 = x*ewaldDXInv;
ivec4 index = floor(x1);
fvec4 coeff[4];
coeff[1] = x1-index;
coeff[0] = 1.0f-coeff[1];
coeff[2] = coeff[0]*coeff[0]*coeff[0]-coeff[0];
coeff[3] = coeff[1]*coeff[1]*coeff[1]-coeff[1];
transpose(coeff[0], coeff[1], coeff[2], coeff[3]);
for (int i = 0; i < 4; i++) {
if (index[i] < NUM_TABLE_POINTS)
y[i] = dot4(coeff[i], fvec4(&ewaldScaleTable[4*index[i]]));
}
return fvec4(y);
}
platforms/cpu/src/CpuPlatform.cpp 0 → 100644
View file @ 8df54762
/* -------------------------------------------------------------------------- *
* 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) 2013 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. *
* -------------------------------------------------------------------------- */
#include "CpuPlatform.h"
#include "CpuKernelFactory.h"
#include "CpuKernels.h"
#include "openmm/internal/hardware.h"
using namespace OpenMM;
extern "C" OPENMM_EXPORT_CPU void registerPlatforms() {
// Only register this platform if the CPU supports SSE 4.1.
if (CpuPlatform::isProcessorSupported())
Platform::registerPlatform(new CpuPlatform());
}
CpuPlatform::CpuPlatform() {
CpuKernelFactory* factory = new CpuKernelFactory();
registerKernelFactory(CalcNonbondedForceKernel::Name(), factory);
}
double CpuPlatform::getSpeed() const {
return 10;
}
bool CpuPlatform::supportsDoublePrecision() const {
return false;
}
bool CpuPlatform::isProcessorSupported() {
// Make sure the CPU supports SSE 4.1.
int cpuInfo[4];
cpuid(cpuInfo, 0);
if (cpuInfo[0] >= 1) {
cpuid(cpuInfo, 1);
return ((cpuInfo[2] & ((int) 1 << 19)) != 0);
}
return false;
}
platforms/cpu/tests/CMakeLists.txt 0 → 100644
View file @ 8df54762
#
# Testing
#
ENABLE_TESTING()
SET( INCLUDE_SERIALIZATION FALSE )
#SET( INCLUDE_SERIALIZATION TRUE )
IF( INCLUDE_SERIALIZATION )
INCLUDE_DIRECTORIES(${OPENMM_DIR}/serialization/include)
SET( SHARED_OPENMM_SERIALIZATION "OpenMMSerialization" )
ENDIF( INCLUDE_SERIALIZATION )
# Automatically create tests using files named "Test*.cpp"
FILE(GLOB TEST_PROGS "*Test*.cpp")
FOREACH(TEST_PROG ${TEST_PROGS})
GET_FILENAME_COMPONENT(TEST_ROOT ${TEST_PROG} NAME_WE)
# Link with shared library
ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET})
ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} single)
ENDFOREACH(TEST_PROG ${TEST_PROGS})
platforms/cpu/tests/TestCpuEwald.cpp 0 → 100644
View file @ 8df54762
/* -------------------------------------------------------------------------- *
* 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) 2008-2013 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 CPU implementation of NonbondedForce.
*/
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "CpuPlatform.h"
#include "ReferencePlatform.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/LangevinIntegrator.h"
#include "openmm/VerletIntegrator.h"
#include "openmm/internal/ContextImpl.h"
#include "SimTKOpenMMRealType.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
CpuPlatform platform;
const double TOL = 1e-5;
void testEwaldPME(bool includeExceptions) {
// Use amorphous NaCl system for the tests
const int numParticles = 894;
const double cutoff = 1.2;
const double boxSize = 3.00646;
double tol = 1e-5;
ReferencePlatform reference;
System system;
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->setNonbondedMethod(NonbondedForce::Ewald);
nonbonded->setCutoffDistance(cutoff);
nonbonded->setEwaldErrorTolerance(tol);
for (int i = 0; i < numParticles/2; i++)
system.addParticle(22.99);
for (int i = 0; i < numParticles/2; i++)
system.addParticle(35.45);
for (int i = 0; i < numParticles/2; i++)
nonbonded->addParticle(1.0, 1.0,0.0);
for (int i = 0; i < numParticles/2; i++)
nonbonded->addParticle(-1.0, 1.0,0.0);
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
system.addForce(nonbonded);
vector<Vec3> positions(numParticles);
#include "nacl_amorph.dat"
if (includeExceptions) {
// Add some exclusions.
for (int i = 0; i < numParticles-1; i++) {
Vec3 delta = positions[i]-positions[i+1];
if (sqrt(delta.dot(delta)) < 0.5*cutoff)
nonbonded->addException(i, i+1, i%2 == 0 ? 0.0 : 0.5, 1.0, 0.0);
}
}
// (1) Check whether the Reference and CPU platforms agree when using Ewald Method
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context cpuContext(system, integrator1, platform);
Context referenceContext(system, integrator2, reference);
cpuContext.setPositions(positions);
referenceContext.setPositions(positions);
State cpuState = cpuContext.getState(State::Forces | State::Energy);
State referenceState = referenceContext.getState(State::Forces | State::Energy);
tol = 1e-2;
for (int i = 0; i < numParticles; i++) {
ASSERT_EQUAL_VEC(referenceState.getForces()[i], cpuState.getForces()[i], tol);
}
tol = 1e-5;
ASSERT_EQUAL_TOL(referenceState.getPotentialEnergy(), cpuState.getPotentialEnergy(), tol);
// (2) Check whether Ewald method in CPU is self-consistent
double norm = 0.0;
for (int i = 0; i < numParticles; ++i) {
Vec3 f = cpuState.getForces()[i];
norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
}
norm = std::sqrt(norm);
const double delta = 5e-3;
double step = delta/norm;
for (int i = 0; i < numParticles; ++i) {
Vec3 p = positions[i];
Vec3 f = cpuState.getForces()[i];
positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
}
VerletIntegrator integrator3(0.01);
Context cpuContext2(system, integrator3, platform);
cpuContext2.setPositions(positions);
tol = 1e-2;
State cpuState2 = cpuContext2.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (cpuState2.getPotentialEnergy()-cpuState.getPotentialEnergy())/delta, tol)
// (3) Check whether the Reference and CPU platforms agree when using PME
nonbonded->setNonbondedMethod(NonbondedForce::PME);
cpuContext.reinitialize();
referenceContext.reinitialize();
cpuContext.setPositions(positions);
referenceContext.setPositions(positions);
cpuState = cpuContext.getState(State::Forces | State::Energy);
referenceState = referenceContext.getState(State::Forces | State::Energy);
tol = 1e-2;
for (int i = 0; i < numParticles; i++) {
ASSERT_EQUAL_VEC(referenceState.getForces()[i], cpuState.getForces()[i], tol);
}
tol = 1e-5;
ASSERT_EQUAL_TOL(referenceState.getPotentialEnergy(), cpuState.getPotentialEnergy(), tol);
// (4) Check whether PME method in CPU is self-consistent
norm = 0.0;
for (int i = 0; i < numParticles; ++i) {
Vec3 f = cpuState.getForces()[i];
norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
}
norm = std::sqrt(norm);
step = delta/norm;
for (int i = 0; i < numParticles; ++i) {
Vec3 p = positions[i];
Vec3 f = cpuState.getForces()[i];
positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
}
VerletIntegrator integrator4(0.01);
Context cpuContext3(system, integrator4, platform);
cpuContext3.setPositions(positions);
tol = 1e-2;
State cpuState3 = cpuContext3.getState(State::Energy);
ASSERT_EQUAL_TOL(norm, (cpuState3.getPotentialEnergy()-cpuState.getPotentialEnergy())/delta, tol)
}
void testEwald2Ions() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->addParticle(1.0, 1, 0);
nonbonded->addParticle(-1.0, 1, 0);
nonbonded->setNonbondedMethod(NonbondedForce::Ewald);
const double cutoff = 2.0;
nonbonded->setCutoffDistance(cutoff);
nonbonded->setEwaldErrorTolerance(TOL);
system.setDefaultPeriodicBoxVectors(Vec3(6, 0, 0), Vec3(0, 6, 0), Vec3(0, 0, 6));
system.addForce(nonbonded);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(3.048000,2.764000,3.156000);
positions[1] = Vec3(2.809000,2.888000,2.571000);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(-123.711, 64.1877, -302.716), forces[0], 10*TOL);
ASSERT_EQUAL_VEC(Vec3( 123.711, -64.1877, 302.716), forces[1], 10*TOL);
ASSERT_EQUAL_TOL(-217.276, state.getPotentialEnergy(), 0.01/*10*TOL*/);
}
void testErrorTolerance(NonbondedForce::NonbondedMethod method) {
// Create a cloud of random point charges.
const int numParticles = 51;
const double boxWidth = 5.0;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(boxWidth, 0, 0), Vec3(0, boxWidth, 0), Vec3(0, 0, boxWidth));
NonbondedForce* force = new NonbondedForce();
system.addForce(force);
vector<Vec3> positions(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.0);
force->addParticle(-1.0+i*2.0/(numParticles-1), 1.0, 0.0);
positions[i] = Vec3(boxWidth*genrand_real2(sfmt), boxWidth*genrand_real2(sfmt), boxWidth*genrand_real2(sfmt));
}
force->setNonbondedMethod(method);
// For various values of the cutoff and error tolerance, see if the actual error is reasonable.
for (double cutoff = 1.0; cutoff < boxWidth/2; cutoff *= 1.2) {
force->setCutoffDistance(cutoff);
vector<Vec3> refForces;
double norm = 0.0;
for (double tol = 5e-5; tol < 1e-3; tol *= 2.0) {
force->setEwaldErrorTolerance(tol);
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
context.setPositions(positions);
State state = context.getState(State::Forces);
if (refForces.size() == 0) {
refForces = state.getForces();
for (int i = 0; i < numParticles; i++)
norm += refForces[i].dot(refForces[i]);
norm = sqrt(norm);
}
else {
double diff = 0.0;
for (int i = 0; i < numParticles; i++) {
Vec3 delta = refForces[i]-state.getForces()[i];
diff += delta.dot(delta);
}
diff = sqrt(diff)/norm;
ASSERT(diff < 2*tol);
}
}
}
}
int main(int argc, char* argv[]) {
try {
if (!CpuPlatform::isProcessorSupported()) {
cout << "CPU is not supported. Exiting." << endl;
return 0;
}
testEwaldPME(false);
testEwaldPME(true);
// testEwald2Ions();
testErrorTolerance(NonbondedForce::Ewald);
testErrorTolerance(NonbondedForce::PME);
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
platforms/cpu/tests/TestCpuNeighborList.cpp 0 → 100644
View file @ 8df54762
/* -------------------------------------------------------------------------- *
* 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) 2013 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 all the CPU implementation of neighbor list construction.
*/
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/internal/ThreadPool.h"
#include "CpuNeighborList.h"
#include "CpuPlatform.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <set>
#include <utility>
#include <vector>
using namespace OpenMM;
using namespace std;
void testNeighborList(bool periodic) {
const int numParticles = 500;
const float cutoff = 2.0f;
const float boxSize[3] = {20.0f, 15.0f, 22.0f};
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<float> positions(4*numParticles);
for (int i = 0; i < 4*numParticles; i++)
if (i%4 < 3)
positions[i] = boxSize[i%4]*genrand_real2(sfmt);
vector<set<int> > exclusions(numParticles);
for (int i = 0; i < numParticles; i++) {
int num = min(i+1, 10);
for (int j = 0; j < num; j++) {
exclusions[i].insert(i-j);
exclusions[i-j].insert(i);
}
}
ThreadPool threads;
CpuNeighborList neighborList;
neighborList.computeNeighborList(numParticles, positions, exclusions, boxSize, periodic, cutoff, threads);
// Convert the neighbor list to a set for faster lookup.
set<pair<int, int> > neighbors;
for (int i = 0; i < (int) neighborList.getSortedAtoms().size(); i++) {
int blockIndex = i/CpuNeighborList::BlockSize;
int indexInBlock = i-blockIndex*CpuNeighborList::BlockSize;
char mask = 1<<indexInBlock;
for (int j = 0; j < (int) neighborList.getBlockExclusions(blockIndex).size(); j++) {
if ((neighborList.getBlockExclusions(blockIndex)[j] & mask) == 0) {
int atom1 = neighborList.getSortedAtoms()[i];
int atom2 = neighborList.getBlockNeighbors(blockIndex)[j];
pair<int, int> entry = make_pair(min(atom1, atom2), max(atom1, atom2));
ASSERT(neighbors.find(entry) == neighbors.end() && neighbors.find(make_pair(entry.second, entry.first)) == neighbors.end()); // No duplicates
neighbors.insert(entry);
}
}
}
// Check each particle pair and figure out whether they should be in the neighbor list.
for (int i = 0; i < numParticles; i++)
for (int j = 0; j <= i; j++) {
bool shouldInclude = (exclusions[i].find(j) == exclusions[i].end());
float dx = positions[4*i]-positions[4*j];
float dy = positions[4*i+1]-positions[4*j+1];
float dz = positions[4*i+2]-positions[4*j+2];
if (periodic) {
dx -= floor(dx/boxSize[0]+0.5f)*boxSize[0];
dy -= floor(dy/boxSize[1]+0.5f)*boxSize[1];
dz -= floor(dz/boxSize[2]+0.5f)*boxSize[2];
}
if (dx*dx + dy*dy + dz*dz > cutoff*cutoff)
shouldInclude = false;
bool isIncluded = (neighbors.find(make_pair(i, j)) != neighbors.end() || neighbors.find(make_pair(j, i)) != neighbors.end());
if (shouldInclude)
ASSERT(isIncluded);
}
}
int main() {
try {
if (!CpuPlatform::isProcessorSupported()) {
cout << "CPU is not supported. Exiting." << endl;
return 0;
}
testNeighborList(false);
testNeighborList(true);
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
platforms/cpu/tests/TestCpuNonbondedForce.cpp 0 → 100644
View file @ 8df54762
/* -------------------------------------------------------------------------- *
* 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) 2008-2013 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 all the different force terms in the CUDA implementation of NonbondedForce.
*/
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "CpuPlatform.h"
#include "ReferencePlatform.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
#include "openmm/LangevinIntegrator.h"
#include "openmm/VerletIntegrator.h"
#include "openmm/internal/ContextImpl.h"
#include "SimTKOpenMMRealType.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
using namespace std;
CpuPlatform platform;
const double TOL = 1e-5;
void testCoulomb() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
NonbondedForce* forceField = new NonbondedForce();
forceField->addParticle(0.5, 1, 0);
forceField->addParticle(-1.5, 1, 0);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(2, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double force = ONE_4PI_EPS0*(-0.75)/4.0;
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], TOL);
ASSERT_EQUAL_TOL(ONE_4PI_EPS0*(-0.75)/2.0, state.getPotentialEnergy(), TOL);
}
void testLJ() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
NonbondedForce* forceField = new NonbondedForce();
forceField->addParticle(0, 1.2, 1);
forceField->addParticle(0, 1.4, 2);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(2, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double x = 1.3/2.0;
double eps = SQRT_TWO;
double force = 4.0*eps*(12*std::pow(x, 12.0)-6*std::pow(x, 6.0))/2.0;
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], TOL);
ASSERT_EQUAL_TOL(4.0*eps*(std::pow(x, 12.0)-std::pow(x, 6.0)), state.getPotentialEnergy(), TOL);
}
void testExclusionsAnd14() {
System system;
NonbondedForce* nonbonded = new NonbondedForce();
for (int i = 0; i < 5; ++i) {
system.addParticle(1.0);
nonbonded->addParticle(0, 1.5, 0);
}
vector<pair<int, int> > bonds;
bonds.push_back(pair<int, int>(0, 1));
bonds.push_back(pair<int, int>(1, 2));
bonds.push_back(pair<int, int>(2, 3));
bonds.push_back(pair<int, int>(3, 4));
nonbonded->createExceptionsFromBonds(bonds, 0.0, 0.0);
int first14, second14;
for (int i = 0; i < nonbonded->getNumExceptions(); i++) {
int particle1, particle2;
double chargeProd, sigma, epsilon;
nonbonded->getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon);
if ((particle1 == 0 && particle2 == 3) || (particle1 == 3 && particle2 == 0))
first14 = i;
if ((particle1 == 1 && particle2 == 4) || (particle1 == 4 && particle2 == 1))
second14 = i;
}
system.addForce(nonbonded);
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
for (int i = 1; i < 5; ++i) {
// Test LJ forces
vector<Vec3> positions(5);
const double r = 1.0;
for (int j = 0; j < 5; ++j) {
nonbonded->setParticleParameters(j, 0, 1.5, 0);
positions[j] = Vec3(0, j, 0);
}
nonbonded->setParticleParameters(0, 0, 1.5, 1);
nonbonded->setParticleParameters(i, 0, 1.5, 1);
nonbonded->setExceptionParameters(first14, 0, 3, 0, 1.5, i == 3 ? 0.5 : 0.0);
nonbonded->setExceptionParameters(second14, 1, 4, 0, 1.5, 0.0);
positions[i] = Vec3(r, 0, 0);
context.reinitialize();
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double x = 1.5/r;
double eps = 1.0;
double force = 4.0*eps*(12*std::pow(x, 12.0)-6*std::pow(x, 6.0))/r;
double energy = 4.0*eps*(std::pow(x, 12.0)-std::pow(x, 6.0));
if (i == 3) {
force *= 0.5;
energy *= 0.5;
}
if (i < 3) {
force = 0;
energy = 0;
}
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[i], TOL);
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), TOL);
// Test Coulomb forces
nonbonded->setParticleParameters(0, 2, 1.5, 0);
nonbonded->setParticleParameters(i, 2, 1.5, 0);
nonbonded->setExceptionParameters(first14, 0, 3, i == 3 ? 4/1.2 : 0, 1.5, 0);
nonbonded->setExceptionParameters(second14, 1, 4, 0, 1.5, 0);
context.reinitialize();
context.setPositions(positions);
state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces2 = state.getForces();
force = ONE_4PI_EPS0*4/(r*r);
energy = ONE_4PI_EPS0*4/r;
if (i == 3) {
force /= 1.2;
energy /= 1.2;
}
if (i < 3) {
force = 0;
energy = 0;
}
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces2[0], TOL);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces2[i], TOL);
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), TOL);
}
}
void testCutoff() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
NonbondedForce* forceField = new NonbondedForce();
forceField->addParticle(1.0, 1, 0);
forceField->addParticle(1.0, 1, 0);
forceField->addParticle(1.0, 1, 0);
forceField->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
const double cutoff = 2.9;
forceField->setCutoffDistance(cutoff);
const double eps = 50.0;
forceField->setReactionFieldDielectric(eps);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(3);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(0, 2, 0);
positions[2] = Vec3(0, 3, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
const double krf = (1.0/(cutoff*cutoff*cutoff))*(eps-1.0)/(2.0*eps+1.0);
const double crf = (1.0/cutoff)*(3.0*eps)/(2.0*eps+1.0);
const double force1 = ONE_4PI_EPS0*(1.0)*(0.25-2.0*krf*2.0);
const double force2 = ONE_4PI_EPS0*(1.0)*(1.0-2.0*krf*1.0);
ASSERT_EQUAL_VEC(Vec3(0, -force1, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, force1-force2, 0), forces[1], TOL);
ASSERT_EQUAL_VEC(Vec3(0, force2, 0), forces[2], TOL);
const double energy1 = ONE_4PI_EPS0*(1.0)*(0.5+krf*4.0-crf);
const double energy2 = ONE_4PI_EPS0*(1.0)*(1.0+krf*1.0-crf);
ASSERT_EQUAL_TOL(energy1+energy2, state.getPotentialEnergy(), TOL);
}
void testCutoff14() {
System system;
VerletIntegrator integrator(0.01);
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
for (int i = 0; i < 5; ++i) {
system.addParticle(1.0);
nonbonded->addParticle(0, 1.5, 0);
}
const double cutoff = 3.5;
nonbonded->setCutoffDistance(cutoff);
const double eps = 30.0;
nonbonded->setReactionFieldDielectric(eps);
vector<pair<int, int> > bonds;
bonds.push_back(pair<int, int>(0, 1));
bonds.push_back(pair<int, int>(1, 2));
bonds.push_back(pair<int, int>(2, 3));
bonds.push_back(pair<int, int>(3, 4));
nonbonded->createExceptionsFromBonds(bonds, 0.0, 0.0);
int first14, second14;
for (int i = 0; i < nonbonded->getNumExceptions(); i++) {
int particle1, particle2;
double chargeProd, sigma, epsilon;
nonbonded->getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon);
if ((particle1 == 0 && particle2 == 3) || (particle1 == 3 && particle2 == 0))
first14 = i;
if ((particle1 == 1 && particle2 == 4) || (particle1 == 4 && particle2 == 1))
second14 = i;
}
system.addForce(nonbonded);
Context context(system, integrator, platform);
vector<Vec3> positions(5);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(1, 0, 0);
positions[2] = Vec3(2, 0, 0);
positions[3] = Vec3(3, 0, 0);
positions[4] = Vec3(4, 0, 0);
for (int i = 1; i < 5; ++i) {
// Test LJ forces
nonbonded->setParticleParameters(0, 0, 1.5, 1);
for (int j = 1; j < 5; ++j)
nonbonded->setParticleParameters(j, 0, 1.5, 0);
nonbonded->setParticleParameters(i, 0, 1.5, 1);
nonbonded->setExceptionParameters(first14, 0, 3, 0, 1.5, i == 3 ? 0.5 : 0.0);
nonbonded->setExceptionParameters(second14, 1, 4, 0, 1.5, 0.0);
context.reinitialize();
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double r = positions[i][0];
double x = 1.5/r;
double e = 1.0;
double force = 4.0*e*(12*std::pow(x, 12.0)-6*std::pow(x, 6.0))/r;
double energy = 4.0*e*(std::pow(x, 12.0)-std::pow(x, 6.0));
if (i == 3) {
force *= 0.5;
energy *= 0.5;
}
if (i < 3 || r > cutoff) {
force = 0;
energy = 0;
}
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[i], TOL);
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), TOL);
// Test Coulomb forces
const double q = 0.7;
nonbonded->setParticleParameters(0, q, 1.5, 0);
nonbonded->setParticleParameters(i, q, 1.5, 0);
nonbonded->setExceptionParameters(first14, 0, 3, i == 3 ? q*q/1.2 : 0, 1.5, 0);
nonbonded->setExceptionParameters(second14, 1, 4, 0, 1.5, 0);
context.reinitialize();
context.setPositions(positions);
state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces2 = state.getForces();
force = ONE_4PI_EPS0*q*q/(r*r);
energy = ONE_4PI_EPS0*q*q/r;
if (i == 3) {
force /= 1.2;
energy /= 1.2;
}
if (i < 3 || r > cutoff) {
force = 0;
energy = 0;
}
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces2[0], TOL);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces2[i], TOL);
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), TOL);
}
}
void testPeriodic() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->addParticle(1.0, 1, 0);
nonbonded->addParticle(1.0, 1, 0);
nonbonded->addParticle(1.0, 1, 0);
nonbonded->addException(0, 1, 0.0, 1.0, 0.0);
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
const double cutoff = 2.0;
nonbonded->setCutoffDistance(cutoff);
system.setDefaultPeriodicBoxVectors(Vec3(4, 0, 0), Vec3(0, 4, 0), Vec3(0, 0, 4));
system.addForce(nonbonded);
Context context(system, integrator, platform);
vector<Vec3> positions(3);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(2, 0, 0);
positions[2] = Vec3(3, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
const double eps = 78.3;
const double krf = (1.0/(cutoff*cutoff*cutoff))*(eps-1.0)/(2.0*eps+1.0);
const double crf = (1.0/cutoff)*(3.0*eps)/(2.0*eps+1.0);
const double force = ONE_4PI_EPS0*(1.0)*(1.0-2.0*krf*1.0);
ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[1], TOL);
ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[2], TOL);
ASSERT_EQUAL_TOL(2*ONE_4PI_EPS0*(1.0)*(1.0+krf*1.0-crf), state.getPotentialEnergy(), TOL);
}
void testLargeSystem() {
const int numMolecules = 600;
const int numParticles = numMolecules*2;
const double cutoff = 2.0;
const double boxSize = 20.0;
const double tol = 2e-3;
ReferencePlatform reference;
System system;
for (int i = 0; i < numParticles; i++)
system.addParticle(1.0);
NonbondedForce* nonbonded = new NonbondedForce();
HarmonicBondForce* bonds = new HarmonicBondForce();
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numMolecules; i++) {
if (i < numMolecules/2) {
nonbonded->addParticle(-1.0, 0.2, 0.1);
nonbonded->addParticle(1.0, 0.1, 0.1);
}
else {
nonbonded->addParticle(-1.0, 0.2, 0.2);
nonbonded->addParticle(1.0, 0.1, 0.2);
}
positions[2*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
velocities[2*i] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
velocities[2*i+1] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
bonds->addBond(2*i, 2*i+1, 1.0, 0.1);
nonbonded->addException(2*i, 2*i+1, 0.0, 0.15, 0.0);
}
// Try with cutoffs but not periodic boundary conditions, and make sure the cl and Reference
// platforms agree.
nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
nonbonded->setCutoffDistance(cutoff);
system.addForce(nonbonded);
system.addForce(bonds);
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context cpuContext(system, integrator1, platform);
Context referenceContext(system, integrator2, reference);
cpuContext.setPositions(positions);
cpuContext.setVelocities(velocities);
referenceContext.setPositions(positions);
referenceContext.setVelocities(velocities);
State cpuState = cpuContext.getState(State::Positions | State::Velocities | State::Forces | State::Energy);
State referenceState = referenceContext.getState(State::Positions | State::Velocities | State::Forces | State::Energy);
for (int i = 0; i < numParticles; i++) {
ASSERT_EQUAL_VEC(cpuState.getPositions()[i], referenceState.getPositions()[i], tol);
ASSERT_EQUAL_VEC(cpuState.getVelocities()[i], referenceState.getVelocities()[i], tol);
ASSERT_EQUAL_VEC(cpuState.getForces()[i], referenceState.getForces()[i], tol);
}
ASSERT_EQUAL_TOL(cpuState.getPotentialEnergy(), referenceState.getPotentialEnergy(), tol);
// Now do the same thing with periodic boundary conditions.
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
cpuContext.reinitialize();
referenceContext.reinitialize();
cpuContext.setPositions(positions);
cpuContext.setVelocities(velocities);
referenceContext.setPositions(positions);
referenceContext.setVelocities(velocities);
cpuState = cpuContext.getState(State::Positions | State::Velocities | State::Forces | State::Energy);
referenceState = referenceContext.getState(State::Positions | State::Velocities | State::Forces | State::Energy);
for (int i = 0; i < numParticles; i++) {
double dx = cpuState.getPositions()[i][0]-referenceState.getPositions()[i][0];
double dy = cpuState.getPositions()[i][1]-referenceState.getPositions()[i][1];
double dz = cpuState.getPositions()[i][2]-referenceState.getPositions()[i][2];
ASSERT_EQUAL_TOL(fmod(cpuState.getPositions()[i][0]-referenceState.getPositions()[i][0], boxSize), 0, tol);
ASSERT_EQUAL_TOL(fmod(cpuState.getPositions()[i][1]-referenceState.getPositions()[i][1], boxSize), 0, tol);
ASSERT_EQUAL_TOL(fmod(cpuState.getPositions()[i][2]-referenceState.getPositions()[i][2], boxSize), 0, tol);
ASSERT_EQUAL_VEC(cpuState.getVelocities()[i], referenceState.getVelocities()[i], tol);
ASSERT_EQUAL_VEC(cpuState.getForces()[i], referenceState.getForces()[i], tol);
}
ASSERT_EQUAL_TOL(cpuState.getPotentialEnergy(), referenceState.getPotentialEnergy(), tol);
}
void testDispersionCorrection() {
// Create a box full of identical particles.
int gridSize = 5;
int numParticles = gridSize*gridSize*gridSize;
double boxSize = gridSize*0.7;
double cutoff = boxSize/3;
System system;
VerletIntegrator integrator(0.01);
NonbondedForce* nonbonded = new NonbondedForce();
vector<Vec3> positions(numParticles);
int index = 0;
for (int i = 0; i < gridSize; i++)
for (int j = 0; j < gridSize; j++)
for (int k = 0; k < gridSize; k++) {
system.addParticle(1.0);
nonbonded->addParticle(0, 1.1, 0.5);
positions[index] = Vec3(i*boxSize/gridSize, j*boxSize/gridSize, k*boxSize/gridSize);
index++;
}
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
nonbonded->setCutoffDistance(cutoff);
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
system.addForce(nonbonded);
// See if the correction has the correct value.
Context context(system, integrator, platform);
context.setPositions(positions);
double energy1 = context.getState(State::Energy).getPotentialEnergy();
nonbonded->setUseDispersionCorrection(false);
context.reinitialize();
context.setPositions(positions);
double energy2 = context.getState(State::Energy).getPotentialEnergy();
double term1 = (0.5*pow(1.1, 12)/pow(cutoff, 9))/9;
double term2 = (0.5*pow(1.1, 6)/pow(cutoff, 3))/3;
double expected = 8*M_PI*numParticles*numParticles*(term1-term2)/(boxSize*boxSize*boxSize);
ASSERT_EQUAL_TOL(expected, energy1-energy2, 1e-4);
// Now modify half the particles to be different, and see if it is still correct.
int numType2 = 0;
for (int i = 0; i < numParticles; i += 2) {
nonbonded->setParticleParameters(i, 0, 1, 1);
numType2++;
}
int numType1 = numParticles-numType2;
nonbonded->updateParametersInContext(context);
energy2 = context.getState(State::Energy).getPotentialEnergy();
nonbonded->setUseDispersionCorrection(true);
context.reinitialize();
context.setPositions(positions);
energy1 = context.getState(State::Energy).getPotentialEnergy();
term1 = ((numType1*(numType1+1))/2)*(0.5*pow(1.1, 12)/pow(cutoff, 9))/9;
term2 = ((numType1*(numType1+1))/2)*(0.5*pow(1.1, 6)/pow(cutoff, 3))/3;
term1 += ((numType2*(numType2+1))/2)*(1*pow(1.0, 12)/pow(cutoff, 9))/9;
term2 += ((numType2*(numType2+1))/2)*(1*pow(1.0, 6)/pow(cutoff, 3))/3;
double combinedSigma = 0.5*(1+1.1);
double combinedEpsilon = sqrt(1*0.5);
term1 += (numType1*numType2)*(combinedEpsilon*pow(combinedSigma, 12)/pow(cutoff, 9))/9;
term2 += (numType1*numType2)*(combinedEpsilon*pow(combinedSigma, 6)/pow(cutoff, 3))/3;
term1 /= (numParticles*(numParticles+1))/2;
term2 /= (numParticles*(numParticles+1))/2;
expected = 8*M_PI*numParticles*numParticles*(term1-term2)/(boxSize*boxSize*boxSize);
ASSERT_EQUAL_TOL(expected, energy1-energy2, 1e-4);
}
void testChangingParameters() {
const int numMolecules = 600;
const int numParticles = numMolecules*2;
const double cutoff = 2.0;
const double boxSize = 20.0;
const double tol = 2e-3;
ReferencePlatform reference;
System system;
for (int i = 0; i < numParticles; i++)
system.addParticle(1.0);
NonbondedForce* nonbonded = new NonbondedForce();
vector<Vec3> positions(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numMolecules; i++) {
if (i < numMolecules/2) {
nonbonded->addParticle(-1.0, 0.2, 0.1);
nonbonded->addParticle(1.0, 0.1, 0.1);
}
else {
nonbonded->addParticle(-1.0, 0.2, 0.2);
nonbonded->addParticle(1.0, 0.1, 0.2);
}
positions[2*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
system.addConstraint(2*i, 2*i+1, 1.0);
nonbonded->addException(2*i, 2*i+1, 0.0, 0.15, 0.0);
}
nonbonded->setNonbondedMethod(NonbondedForce::PME);
nonbonded->setCutoffDistance(cutoff);
system.addForce(nonbonded);
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
// See if Reference and CPU give the same forces and energies.
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context cpuContext(system, integrator1, platform);
Context referenceContext(system, integrator2, reference);
cpuContext.setPositions(positions);
referenceContext.setPositions(positions);
State cpuState = cpuContext.getState(State::Forces | State::Energy);
State referenceState = referenceContext.getState(State::Forces | State::Energy);
for (int i = 0; i < numParticles; i++)
ASSERT_EQUAL_VEC(cpuState.getForces()[i], referenceState.getForces()[i], tol);
ASSERT_EQUAL_TOL(cpuState.getPotentialEnergy(), referenceState.getPotentialEnergy(), tol);
// Now modify parameters and see if they still agree.
for (int i = 0; i < numParticles; i += 5) {
double charge, sigma, epsilon;
nonbonded->getParticleParameters(i, charge, sigma, epsilon);
nonbonded->setParticleParameters(i, 1.5*charge, 1.1*sigma, 1.7*epsilon);
}
nonbonded->updateParametersInContext(cpuContext);
nonbonded->updateParametersInContext(referenceContext);
cpuState = cpuContext.getState(State::Forces | State::Energy);
referenceState = referenceContext.getState(State::Forces | State::Energy);
for (int i = 0; i < numParticles; i++)
ASSERT_EQUAL_VEC(cpuState.getForces()[i], referenceState.getForces()[i], tol);
ASSERT_EQUAL_TOL(cpuState.getPotentialEnergy(), referenceState.getPotentialEnergy(), tol);
}
void testSwitchingFunction(NonbondedForce::NonbondedMethod method) {
System system;
system.setDefaultPeriodicBoxVectors(Vec3(6, 0, 0), Vec3(0, 6, 0), Vec3(0, 0, 6));
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->addParticle(0, 1.2, 1);
nonbonded->addParticle(0, 1.4, 2);
nonbonded->setNonbondedMethod(method);
nonbonded->setCutoffDistance(2.0);
nonbonded->setUseSwitchingFunction(true);
nonbonded->setSwitchingDistance(1.5);
nonbonded->setUseDispersionCorrection(false);
system.addForce(nonbonded);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
double eps = SQRT_TWO;
// Compute the interaction at various distances.
for (double r = 1.0; r < 2.5; r += 0.1) {
positions[1] = Vec3(r, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
// See if the energy is correct.
double x = 1.3/r;
double expectedEnergy = 4.0*eps*(std::pow(x, 12.0)-std::pow(x, 6.0));
double switchValue;
if (r <= 1.5)
switchValue = 1;
else if (r >= 2.0)
switchValue = 0;
else {
double t = (r-1.5)/0.5;
switchValue = 1+t*t*t*(-10+t*(15-t*6));
}
ASSERT_EQUAL_TOL(switchValue*expectedEnergy, state.getPotentialEnergy(), TOL);
// See if the force is the gradient of the energy.
double delta = 1e-3;
positions[1] = Vec3(r-delta, 0, 0);
context.setPositions(positions);
double e1 = context.getState(State::Energy).getPotentialEnergy();
positions[1] = Vec3(r+delta, 0, 0);
context.setPositions(positions);
double e2 = context.getState(State::Energy).getPotentialEnergy();
ASSERT_EQUAL_TOL((e2-e1)/(2*delta), state.getForces()[0][0], 1e-3);
}
}
int main(int argc, char* argv[]) {
try {
if (!CpuPlatform::isProcessorSupported()) {
cout << "CPU is not supported. Exiting." << endl;
return 0;
}
testCoulomb();
testLJ();
testExclusionsAnd14();
testCutoff();
testCutoff14();
testPeriodic();
testLargeSystem();
testDispersionCorrection();
testChangingParameters();
testSwitchingFunction(NonbondedForce::CutoffNonPeriodic);
testSwitchingFunction(NonbondedForce::PME);
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
return 1;
}
cout << "Done" << endl;
return 0;
}
platforms/cpu/tests/nacl_amorph.dat 0 → 100644
View file @ 8df54762
positions[0] = Vec3(1.066000,1.628000,0.835000);
positions[1] = Vec3(1.072000,0.428000,0.190000);
positions[2] = Vec3(0.524000,1.442000,1.160000);
positions[3] = Vec3(2.383000,1.524000,1.119000);
positions[4] = Vec3(0.390000,1.441000,0.575000);
positions[5] = Vec3(0.618000,0.399000,0.819000);
positions[6] = Vec3(1.003000,1.257000,1.543000);
positions[7] = Vec3(2.933000,1.569000,0.642000);
positions[8] = Vec3(0.849000,0.739000,0.089000);
positions[9] = Vec3(0.060000,0.794000,0.766000);
positions[10] = Vec3(1.652000,1.405000,1.010000);
positions[11] = Vec3(2.843000,1.533000,1.781000);
positions[12] = Vec3(0.952000,1.309000,0.996000);
positions[13] = Vec3(1.847000,1.402000,0.313000);
positions[14] = Vec3(2.674000,0.083000,1.691000);
positions[15] = Vec3(1.763000,2.104000,0.728000);
positions[16] = Vec3(0.914000,0.574000,0.982000);
positions[17] = Vec3(0.514000,0.078000,0.891000);
positions[18] = Vec3(0.538000,0.766000,1.110000);
positions[19] = Vec3(0.808000,0.676000,0.570000);
positions[20] = Vec3(0.178000,0.014000,0.628000);
positions[21] = Vec3(1.329000,1.333000,0.339000);
positions[22] = Vec3(1.029000,1.678000,0.503000);
positions[23] = Vec3(1.423000,1.767000,1.104000);
positions[24] = Vec3(1.966000,1.051000,0.282000);
positions[25] = Vec3(1.596000,1.971000,0.194000);
positions[26] = Vec3(1.025000,1.043000,2.809000);
positions[27] = Vec3(1.628000,2.614000,0.088000);
positions[28] = Vec3(0.440000,0.606000,0.141000);
positions[29] = Vec3(1.050000,2.821000,2.517000);
positions[30] = Vec3(0.644000,1.604000,0.770000);
positions[31] = Vec3(0.637000,0.917000,0.392000);
positions[32] = Vec3(0.611000,2.768000,0.013000);
positions[33] = Vec3(1.892000,0.660000,0.473000);
positions[34] = Vec3(1.052000,2.081000,0.982000);
positions[35] = Vec3(1.508000,2.300000,0.439000);
positions[36] = Vec3(2.617000,0.328000,1.099000);
positions[37] = Vec3(0.910000,0.040000,0.259000);
positions[38] = Vec3(1.195000,1.494000,1.202000);
positions[39] = Vec3(2.657000,0.997000,0.564000);
positions[40] = Vec3(1.465000,1.580000,0.648000);
positions[41] = Vec3(0.154000,2.538000,1.331000);
positions[42] = Vec3(0.849000,1.476000,1.365000);
positions[43] = Vec3(0.898000,0.987000,1.178000);
positions[44] = Vec3(0.958000,0.656000,1.358000);
positions[45] = Vec3(1.067000,0.934000,0.211000);
positions[46] = Vec3(1.030000,0.319000,1.281000);
positions[47] = Vec3(2.709000,0.807000,0.240000);
positions[48] = Vec3(0.837000,1.362000,0.588000);
positions[49] = Vec3(2.080000,0.791000,2.947000);
positions[50] = Vec3(0.200000,0.266000,1.474000);
positions[51] = Vec3(0.848000,0.379000,1.625000);
positions[52] = Vec3(0.637000,1.071000,0.821000);
positions[53] = Vec3(1.324000,0.757000,2.951000);
positions[54] = Vec3(2.666000,0.935000,1.373000);
positions[55] = Vec3(1.584000,1.025000,1.703000);
positions[56] = Vec3(1.699000,0.636000,0.038000);
positions[57] = Vec3(1.099000,1.644000,1.879000);
positions[58] = Vec3(2.897000,1.302000,1.522000);
positions[59] = Vec3(1.753000,0.949000,2.885000);
positions[60] = Vec3(2.502000,1.321000,0.752000);
positions[61] = Vec3(0.545000,0.193000,1.959000);
positions[62] = Vec3(1.098000,2.646000,1.706000);
positions[63] = Vec3(0.001000,1.205000,0.670000);
positions[64] = Vec3(2.997000,0.061000,1.040000);
positions[65] = Vec3(0.662000,0.828000,1.535000);
positions[66] = Vec3(1.252000,1.246000,0.780000);
positions[67] = Vec3(1.173000,0.472000,0.810000);
positions[68] = Vec3(0.124000,0.622000,2.992000);
positions[69] = Vec3(1.036000,0.883000,0.848000);
positions[70] = Vec3(1.423000,2.146000,1.340000);
positions[71] = Vec3(2.391000,1.136000,1.165000);
positions[72] = Vec3(1.189000,2.961000,0.425000);
positions[73] = Vec3(1.584000,2.500000,0.782000);
positions[74] = Vec3(0.565000,1.122000,1.240000);
positions[75] = Vec3(1.733000,1.716000,1.763000);
positions[76] = Vec3(1.548000,1.522000,0.041000);
positions[77] = Vec3(1.485000,0.561000,0.369000);
positions[78] = Vec3(0.350000,1.661000,0.928000);
positions[79] = Vec3(1.653000,1.223000,0.578000);
positions[80] = Vec3(0.648000,1.349000,0.253000);
positions[81] = Vec3(0.340000,1.820000,0.483000);
positions[82] = Vec3(2.926000,0.119000,1.421000);
positions[83] = Vec3(1.512000,1.084000,0.156000);
positions[84] = Vec3(1.600000,2.115000,1.792000);
positions[85] = Vec3(1.089000,0.934000,1.584000);
positions[86] = Vec3(1.276000,1.104000,1.230000);
positions[87] = Vec3(0.485000,0.305000,0.428000);
positions[88] = Vec3(1.317000,1.261000,1.795000);
positions[89] = Vec3(0.039000,1.413000,1.085000);
positions[90] = Vec3(0.453000,0.701000,0.605000);
positions[91] = Vec3(1.283000,1.937000,0.752000);
positions[92] = Vec3(0.212000,1.416000,1.447000);
positions[93] = Vec3(0.203000,0.358000,0.723000);
positions[94] = Vec3(0.556000,0.445000,1.364000);
positions[95] = Vec3(1.436000,0.861000,0.911000);
positions[96] = Vec3(0.358000,0.966000,0.176000);
positions[97] = Vec3(1.478000,2.715000,0.427000);
positions[98] = Vec3(1.581000,0.575000,0.809000);
positions[99] = Vec3(1.007000,2.153000,2.887000);
positions[100] = Vec3(2.343000,0.663000,2.513000);
positions[101] = Vec3(2.105000,0.649000,1.635000);
positions[102] = Vec3(0.875000,0.743000,2.459000);
positions[103] = Vec3(0.229000,1.315000,1.879000);
positions[104] = Vec3(0.285000,0.935000,1.700000);
positions[105] = Vec3(2.269000,1.284000,2.234000);
positions[106] = Vec3(1.406000,1.149000,2.767000);
positions[107] = Vec3(1.076000,0.220000,1.849000);
positions[108] = Vec3(2.001000,1.532000,2.881000);
positions[109] = Vec3(2.893000,0.485000,1.860000);
positions[110] = Vec3(1.621000,1.786000,2.624000);
positions[111] = Vec3(0.500000,0.616000,1.818000);
positions[112] = Vec3(0.938000,2.978000,2.104000);
positions[113] = Vec3(0.550000,2.081000,0.454000);
positions[114] = Vec3(1.121000,0.685000,2.196000);
positions[115] = Vec3(1.088000,1.385000,2.184000);
positions[116] = Vec3(1.122000,2.705000,2.080000);
positions[117] = Vec3(0.918000,1.767000,2.861000);
positions[118] = Vec3(2.748000,0.232000,2.126000);
positions[119] = Vec3(1.238000,2.766000,0.109000);
positions[120] = Vec3(1.380000,0.785000,1.961000);
positions[121] = Vec3(1.236000,1.757000,0.150000);
positions[122] = Vec3(1.339000,2.187000,2.592000);
positions[123] = Vec3(1.414000,0.342000,2.714000);
positions[124] = Vec3(1.310000,0.770000,2.589000);
positions[125] = Vec3(1.686000,0.765000,2.321000);
positions[126] = Vec3(1.659000,1.367000,2.780000);
positions[127] = Vec3(0.141000,0.095000,1.903000);
positions[128] = Vec3(2.084000,1.002000,2.520000);
positions[129] = Vec3(2.819000,1.286000,2.626000);
positions[130] = Vec3(1.257000,1.044000,2.401000);
positions[131] = Vec3(1.064000,0.546000,2.839000);
positions[132] = Vec3(0.078000,1.246000,0.010000);
positions[133] = Vec3(1.506000,0.420000,2.223000);
positions[134] = Vec3(1.778000,0.699000,1.920000);
positions[135] = Vec3(1.315000,1.721000,2.733000);
positions[136] = Vec3(0.114000,0.281000,0.279000);
positions[137] = Vec3(1.082000,1.421000,2.596000);
positions[138] = Vec3(3.001000,0.592000,2.276000);
positions[139] = Vec3(1.384000,2.227000,2.992000);
positions[140] = Vec3(1.353000,0.044000,1.985000);
positions[141] = Vec3(1.367000,1.832000,2.383000);
positions[142] = Vec3(0.853000,1.119000,2.230000);
positions[143] = Vec3(1.675000,1.482000,2.295000);
positions[144] = Vec3(1.334000,1.890000,1.904000);
positions[145] = Vec3(1.630000,0.140000,2.939000);
positions[146] = Vec3(0.195000,1.290000,2.300000);
positions[147] = Vec3(2.178000,1.173000,3.001000);
positions[148] = Vec3(0.637000,0.655000,2.126000);
positions[149] = Vec3(0.993000,1.796000,2.529000);
positions[150] = Vec3(0.910000,0.701000,1.845000);
positions[151] = Vec3(0.191000,2.128000,0.355000);
positions[152] = Vec3(0.692000,1.163000,2.578000);
positions[153] = Vec3(1.154000,1.052000,1.974000);
positions[154] = Vec3(1.682000,0.335000,2.509000);
positions[155] = Vec3(0.569000,1.032000,1.895000);
positions[156] = Vec3(1.800000,2.796000,1.295000);
positions[157] = Vec3(2.517000,2.347000,2.878000);
positions[158] = Vec3(0.639000,2.470000,1.678000);
positions[159] = Vec3(0.634000,2.006000,1.829000);
positions[160] = Vec3(0.892000,0.215000,0.566000);
positions[161] = Vec3(1.800000,2.143000,1.491000);
positions[162] = Vec3(1.898000,0.226000,2.765000);
positions[163] = Vec3(0.791000,1.738000,0.260000);
positions[164] = Vec3(0.437000,1.740000,2.048000);
positions[165] = Vec3(1.687000,2.438000,1.166000);
positions[166] = Vec3(1.337000,2.304000,1.643000);
positions[167] = Vec3(1.270000,2.397000,1.033000);
positions[168] = Vec3(0.702000,2.429000,0.591000);
positions[169] = Vec3(0.842000,1.976000,0.724000);
positions[170] = Vec3(1.965000,0.095000,1.206000);
positions[171] = Vec3(0.355000,2.710000,0.618000);
positions[172] = Vec3(0.745000,1.434000,2.781000);
positions[173] = Vec3(0.707000,2.171000,1.502000);
positions[174] = Vec3(1.294000,2.696000,0.847000);
positions[175] = Vec3(1.143000,2.075000,0.276000);
positions[176] = Vec3(1.111000,2.474000,0.312000);
positions[177] = Vec3(1.144000,2.316000,0.633000);
positions[178] = Vec3(1.335000,0.292000,0.515000);
positions[179] = Vec3(1.926000,2.813000,2.703000);
positions[180] = Vec3(0.559000,2.314000,2.904000);
positions[181] = Vec3(1.308000,1.605000,1.534000);
positions[182] = Vec3(0.773000,2.913000,1.217000);
positions[183] = Vec3(1.612000,0.082000,1.027000);
positions[184] = Vec3(1.510000,0.287000,1.787000);
positions[185] = Vec3(0.716000,1.424000,1.843000);
positions[186] = Vec3(1.267000,0.685000,1.160000);
positions[187] = Vec3(0.306000,1.653000,1.717000);
positions[188] = Vec3(0.349000,0.020000,1.275000);
positions[189] = Vec3(0.166000,1.979000,0.804000);
positions[190] = Vec3(1.523000,2.992000,0.711000);
positions[191] = Vec3(1.998000,2.146000,0.088000);
positions[192] = Vec3(0.047000,2.513000,0.642000);
positions[193] = Vec3(0.501000,1.793000,1.438000);
positions[194] = Vec3(1.099000,2.010000,1.626000);
positions[195] = Vec3(2.580000,2.854000,1.328000);
positions[196] = Vec3(1.080000,2.779000,1.190000);
positions[197] = Vec3(0.901000,2.561000,0.948000);
positions[198] = Vec3(0.920000,2.990000,0.844000);
positions[199] = Vec3(0.819000,2.924000,1.711000);
positions[200] = Vec3(0.434000,1.516000,0.063000);
positions[201] = Vec3(1.470000,0.058000,0.231000);
positions[202] = Vec3(0.530000,3.005000,1.550000);
positions[203] = Vec3(0.447000,2.330000,1.277000);
positions[204] = Vec3(1.632000,2.683000,1.593000);
positions[205] = Vec3(0.885000,1.835000,2.072000);
positions[206] = Vec3(0.868000,2.601000,1.425000);
positions[207] = Vec3(0.720000,2.242000,0.907000);
positions[208] = Vec3(1.194000,0.144000,1.065000);
positions[209] = Vec3(0.448000,2.485000,0.959000);
positions[210] = Vec3(1.377000,2.694000,1.352000);
positions[211] = Vec3(1.305000,2.928000,2.713000);
positions[212] = Vec3(1.784000,2.456000,1.981000);
positions[213] = Vec3(0.354000,2.136000,1.563000);
positions[214] = Vec3(0.489000,2.000000,1.108000);
positions[215] = Vec3(1.884000,2.221000,0.461000);
positions[216] = Vec3(1.860000,2.540000,0.306000);
positions[217] = Vec3(1.753000,2.335000,2.768000);
positions[218] = Vec3(1.536000,2.441000,2.344000);
positions[219] = Vec3(0.531000,0.025000,2.235000);
positions[220] = Vec3(0.809000,0.011000,2.834000);
positions[221] = Vec3(0.289000,2.614000,2.879000);
positions[222] = Vec3(0.613000,1.891000,2.337000);
positions[223] = Vec3(0.507000,0.037000,2.694000);
positions[224] = Vec3(0.882000,2.185000,2.583000);
positions[225] = Vec3(0.503000,2.051000,2.615000);
positions[226] = Vec3(1.907000,1.956000,2.831000);
positions[227] = Vec3(2.833000,2.769000,1.644000);
positions[228] = Vec3(1.141000,0.113000,2.945000);
positions[229] = Vec3(0.600000,1.338000,2.200000);
positions[230] = Vec3(0.904000,2.360000,1.952000);
positions[231] = Vec3(0.738000,1.568000,2.437000);
positions[232] = Vec3(1.136000,2.535000,2.805000);
positions[233] = Vec3(1.430000,2.767000,2.321000);
positions[234] = Vec3(1.078000,2.470000,2.385000);
positions[235] = Vec3(0.296000,2.376000,2.560000);
positions[236] = Vec3(0.719000,0.300000,0.075000);
positions[237] = Vec3(0.518000,1.911000,0.080000);
positions[238] = Vec3(0.381000,1.570000,2.450000);
positions[239] = Vec3(0.716000,2.581000,2.697000);
positions[240] = Vec3(1.473000,2.617000,1.936000);
positions[241] = Vec3(0.421000,2.449000,0.229000);
positions[242] = Vec3(0.425000,2.817000,1.910000);
positions[243] = Vec3(1.312000,2.294000,2.057000);
positions[244] = Vec3(1.239000,0.007000,1.539000);
positions[245] = Vec3(0.822000,0.379000,2.086000);
positions[246] = Vec3(0.560000,2.562000,2.227000);
positions[247] = Vec3(0.863000,2.417000,0.050000);
positions[248] = Vec3(1.263000,0.151000,2.332000);
positions[249] = Vec3(0.237000,0.208000,2.336000);
positions[250] = Vec3(0.437000,2.370000,1.910000);
positions[251] = Vec3(1.119000,2.058000,2.207000);
positions[252] = Vec3(1.960000,1.749000,0.118000);
positions[253] = Vec3(2.415000,0.870000,2.757000);
positions[254] = Vec3(1.781000,0.342000,0.366000);
positions[255] = Vec3(2.172000,1.279000,1.421000);
positions[256] = Vec3(1.986000,0.715000,1.301000);
positions[257] = Vec3(1.657000,1.804000,0.810000);
positions[258] = Vec3(2.405000,1.202000,0.416000);
positions[259] = Vec3(1.932000,1.457000,0.786000);
positions[260] = Vec3(1.901000,1.271000,1.207000);
positions[261] = Vec3(1.864000,0.301000,0.810000);
positions[262] = Vec3(1.658000,0.673000,1.558000);
positions[263] = Vec3(2.637000,2.247000,0.396000);
positions[264] = Vec3(1.353000,0.369000,1.438000);
positions[265] = Vec3(0.530000,2.688000,1.346000);
positions[266] = Vec3(0.237000,0.485000,1.047000);
positions[267] = Vec3(2.806000,0.601000,0.822000);
positions[268] = Vec3(1.617000,2.018000,2.136000);
positions[269] = Vec3(2.000000,2.898000,0.022000);
positions[270] = Vec3(2.049000,1.883000,1.001000);
positions[271] = Vec3(2.477000,0.355000,1.786000);
positions[272] = Vec3(1.646000,0.983000,1.266000);
positions[273] = Vec3(1.683000,2.097000,1.114000);
positions[274] = Vec3(2.161000,0.921000,1.065000);
positions[275] = Vec3(2.099000,0.463000,1.942000);
positions[276] = Vec3(2.561000,1.638000,0.572000);
positions[277] = Vec3(2.205000,0.395000,1.005000);
positions[278] = Vec3(2.836000,0.203000,0.698000);
positions[279] = Vec3(2.662000,0.909000,0.966000);
positions[280] = Vec3(0.334000,0.350000,2.767000);
positions[281] = Vec3(2.241000,2.934000,1.248000);
positions[282] = Vec3(2.599000,2.953000,0.921000);
positions[283] = Vec3(2.219000,0.262000,0.058000);
positions[284] = Vec3(0.274000,0.656000,1.456000);
positions[285] = Vec3(1.814000,1.008000,0.882000);
positions[286] = Vec3(2.793000,1.395000,0.316000);
positions[287] = Vec3(0.773000,1.753000,1.639000);
positions[288] = Vec3(2.321000,0.994000,1.591000);
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positions[290] = Vec3(0.178000,1.342000,0.327000);
positions[291] = Vec3(1.623000,1.756000,1.426000);
positions[292] = Vec3(2.252000,0.109000,0.375000);
positions[293] = Vec3(3.003000,1.895000,1.895000);
positions[294] = Vec3(0.407000,0.831000,2.756000);
positions[295] = Vec3(2.193000,0.956000,0.632000);
positions[296] = Vec3(2.405000,0.641000,1.107000);
positions[297] = Vec3(2.361000,0.958000,0.162000);
positions[298] = Vec3(2.173000,1.544000,0.528000);
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positions[300] = Vec3(2.342000,0.538000,0.253000);
positions[301] = Vec3(1.910000,0.701000,0.954000);
positions[302] = Vec3(2.910000,0.288000,2.938000);
positions[303] = Vec3(0.257000,1.189000,0.958000);
positions[304] = Vec3(0.134000,1.775000,1.243000);
positions[305] = Vec3(2.476000,1.583000,1.956000);
positions[306] = Vec3(1.838000,1.791000,2.354000);
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positions[308] = Vec3(2.413000,2.869000,0.166000);
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positions[311] = Vec3(0.082000,2.857000,0.020000);
positions[312] = Vec3(2.408000,1.499000,0.062000);
positions[313] = Vec3(2.349000,0.267000,1.415000);
positions[314] = Vec3(2.327000,1.717000,2.350000);
positions[315] = Vec3(2.928000,0.810000,1.582000);
positions[316] = Vec3(2.150000,0.336000,0.576000);
positions[317] = Vec3(2.664000,1.085000,2.962000);
positions[318] = Vec3(2.851000,0.670000,1.174000);
positions[319] = Vec3(1.954000,1.013000,1.975000);
positions[320] = Vec3(2.474000,1.542000,1.545000);
positions[321] = Vec3(2.826000,0.455000,1.490000);
positions[322] = Vec3(2.140000,2.826000,0.558000);
positions[323] = Vec3(2.151000,1.684000,1.780000);
positions[324] = Vec3(0.174000,0.673000,0.397000);
positions[325] = Vec3(0.066000,1.708000,0.160000);
positions[326] = Vec3(2.158000,0.303000,2.582000);
positions[327] = Vec3(2.602000,1.611000,2.632000);
positions[328] = Vec3(2.566000,1.138000,2.465000);
positions[329] = Vec3(2.026000,1.443000,2.477000);
positions[330] = Vec3(2.365000,0.309000,2.255000);
positions[331] = Vec3(1.636000,1.107000,2.058000);
positions[332] = Vec3(2.522000,2.584000,2.399000);
positions[333] = Vec3(2.537000,2.900000,2.158000);
positions[334] = Vec3(2.660000,0.537000,2.577000);
positions[335] = Vec3(2.679000,1.158000,1.724000);
positions[336] = Vec3(0.220000,1.894000,2.498000);
positions[337] = Vec3(2.266000,1.248000,1.837000);
positions[338] = Vec3(0.055000,1.656000,2.128000);
positions[339] = Vec3(2.899000,1.902000,2.823000);
positions[340] = Vec3(0.085000,2.994000,2.720000);
positions[341] = Vec3(0.013000,0.889000,2.468000);
positions[342] = Vec3(1.804000,0.372000,1.636000);
positions[343] = Vec3(0.201000,1.616000,2.824000);
positions[344] = Vec3(0.369000,1.273000,2.699000);
positions[345] = Vec3(2.996000,0.355000,2.596000);
positions[346] = Vec3(2.867000,1.314000,2.107000);
positions[347] = Vec3(2.611000,0.563000,2.140000);
positions[348] = Vec3(2.676000,2.954000,2.955000);
positions[349] = Vec3(0.256000,0.848000,2.062000);
positions[350] = Vec3(2.530000,0.028000,2.528000);
positions[351] = Vec3(0.537000,1.273000,1.596000);
positions[352] = Vec3(0.004000,1.004000,0.401000);
positions[353] = Vec3(1.676000,1.060000,2.463000);
positions[354] = Vec3(2.622000,1.473000,2.257000);
positions[355] = Vec3(2.917000,2.991000,2.316000);
positions[356] = Vec3(0.672000,1.123000,2.984000);
positions[357] = Vec3(2.229000,1.806000,2.673000);
positions[358] = Vec3(0.463000,0.951000,2.383000);
positions[359] = Vec3(2.126000,0.049000,2.037000);
positions[360] = Vec3(2.868000,0.876000,2.015000);
positions[361] = Vec3(2.720000,2.582000,0.079000);
positions[362] = Vec3(1.966000,0.693000,2.624000);
positions[363] = Vec3(1.971000,0.398000,2.318000);
positions[364] = Vec3(0.337000,0.630000,2.458000);
positions[365] = Vec3(2.562000,1.044000,2.040000);
positions[366] = Vec3(2.817000,1.485000,2.963000);
positions[367] = Vec3(2.514000,0.621000,2.992000);
positions[368] = Vec3(3.000000,1.551000,2.496000);
positions[369] = Vec3(0.698000,2.167000,2.180000);
positions[370] = Vec3(2.693000,0.849000,2.389000);
positions[371] = Vec3(2.092000,2.565000,2.986000);
positions[372] = Vec3(2.010000,3.001000,0.819000);
positions[373] = Vec3(2.392000,2.622000,1.636000);
positions[374] = Vec3(2.086000,2.325000,1.340000);
positions[375] = Vec3(2.578000,2.971000,0.502000);
positions[376] = Vec3(1.871000,2.789000,2.225000);
positions[377] = Vec3(2.230000,2.985000,1.594000);
positions[378] = Vec3(2.860000,2.788000,0.729000);
positions[379] = Vec3(2.051000,1.928000,1.472000);
positions[380] = Vec3(2.307000,2.219000,1.067000);
positions[381] = Vec3(2.369000,2.572000,1.289000);
positions[382] = Vec3(2.206000,1.924000,0.693000);
positions[383] = Vec3(1.984000,2.058000,2.005000);
positions[384] = Vec3(2.287000,1.854000,0.317000);
positions[385] = Vec3(2.525000,0.345000,0.686000);
positions[386] = Vec3(2.933000,1.920000,1.053000);
positions[387] = Vec3(0.324000,2.324000,0.601000);
positions[388] = Vec3(2.042000,1.576000,1.277000);
positions[389] = Vec3(0.031000,2.376000,0.949000);
positions[390] = Vec3(2.519000,2.250000,1.465000);
positions[391] = Vec3(0.221000,2.722000,1.652000);
positions[392] = Vec3(2.409000,2.361000,2.051000);
positions[393] = Vec3(2.472000,1.917000,1.673000);
positions[394] = Vec3(0.999000,2.715000,0.562000);
positions[395] = Vec3(1.669000,0.017000,1.508000);
positions[396] = Vec3(1.924000,1.777000,0.542000);
positions[397] = Vec3(2.635000,2.634000,1.905000);
positions[398] = Vec3(2.042000,2.628000,1.025000);
positions[399] = Vec3(2.694000,1.974000,2.009000);
positions[400] = Vec3(2.988000,2.221000,1.333000);
positions[401] = Vec3(1.772000,0.196000,1.978000);
positions[402] = Vec3(2.893000,2.961000,0.283000);
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positions[404] = Vec3(2.797000,2.521000,1.412000);
positions[405] = Vec3(0.013000,2.497000,0.246000);
positions[406] = Vec3(1.875000,2.861000,1.801000);
positions[407] = Vec3(2.800000,2.617000,1.049000);
positions[408] = Vec3(2.824000,1.858000,1.487000);
positions[409] = Vec3(2.434000,1.868000,1.275000);
positions[410] = Vec3(2.814000,0.526000,0.384000);
positions[411] = Vec3(2.844000,2.545000,2.246000);
positions[412] = Vec3(1.896000,2.587000,0.719000);
positions[413] = Vec3(0.350000,0.055000,0.076000);
positions[414] = Vec3(2.686000,1.784000,0.222000);
positions[415] = Vec3(2.724000,1.604000,0.989000);
positions[416] = Vec3(0.807000,1.761000,1.122000);
positions[417] = Vec3(2.120000,2.382000,2.226000);
positions[418] = Vec3(2.058000,1.587000,2.067000);
positions[419] = Vec3(2.904000,2.571000,2.686000);
positions[420] = Vec3(2.228000,2.910000,2.410000);
positions[421] = Vec3(2.797000,2.142000,0.114000);
positions[422] = Vec3(2.905000,1.875000,0.480000);
positions[423] = Vec3(1.881000,2.565000,2.469000);
positions[424] = Vec3(2.404000,1.929000,2.999000);
positions[425] = Vec3(2.389000,2.814000,2.782000);
positions[426] = Vec3(2.520000,0.301000,2.815000);
positions[427] = Vec3(2.726000,1.907000,2.339000);
positions[428] = Vec3(2.880000,2.273000,2.500000);
positions[429] = Vec3(2.574000,2.045000,2.716000);
positions[430] = Vec3(2.988000,2.288000,2.001000);
positions[431] = Vec3(0.011000,2.341000,2.904000);
positions[432] = Vec3(0.215000,2.265000,2.257000);
positions[433] = Vec3(2.268000,2.311000,0.234000);
positions[434] = Vec3(2.462000,2.621000,0.550000);
positions[435] = Vec3(1.530000,2.540000,2.728000);
positions[436] = Vec3(2.162000,2.306000,2.687000);
positions[437] = Vec3(2.748000,2.301000,1.734000);
positions[438] = Vec3(2.334000,1.976000,2.041000);
positions[439] = Vec3(1.981000,2.076000,2.443000);
positions[440] = Vec3(2.301000,1.367000,2.665000);
positions[441] = Vec3(2.399000,2.164000,2.403000);
positions[442] = Vec3(0.244000,2.713000,2.257000);
positions[443] = Vec3(0.683000,0.488000,2.781000);
positions[444] = Vec3(2.194000,2.711000,1.993000);
positions[445] = Vec3(2.947000,2.848000,2.001000);
positions[446] = Vec3(0.223000,1.981000,2.913000);
positions[447] = Vec3(0.010000,1.226000,0.917000);
positions[448] = Vec3(1.911000,0.426000,0.582000);
positions[449] = Vec3(2.204000,0.015000,0.136000);
positions[450] = Vec3(0.927000,0.138000,1.645000);
positions[451] = Vec3(0.155000,0.885000,1.479000);
positions[452] = Vec3(1.550000,1.933000,1.261000);
positions[453] = Vec3(1.304000,0.407000,0.287000);
positions[454] = Vec3(0.270000,1.384000,2.910000);
positions[455] = Vec3(0.516000,1.817000,1.695000);
positions[456] = Vec3(1.458000,2.879000,1.523000);
positions[457] = Vec3(1.702000,1.670000,0.593000);
positions[458] = Vec3(1.974000,1.380000,0.534000);
positions[459] = Vec3(2.835000,1.185000,0.479000);
positions[460] = Vec3(0.548000,2.979000,1.126000);
positions[461] = Vec3(1.202000,2.174000,1.466000);
positions[462] = Vec3(1.237000,1.701000,0.653000);
positions[463] = Vec3(2.939000,0.761000,0.349000);
positions[464] = Vec3(1.667000,2.119000,0.377000);
positions[465] = Vec3(1.196000,0.552000,1.372000);
positions[466] = Vec3(1.416000,0.901000,1.178000);
positions[467] = Vec3(0.519000,1.577000,2.227000);
positions[468] = Vec3(1.214000,1.281000,1.063000);
positions[469] = Vec3(0.822000,0.433000,1.375000);
positions[470] = Vec3(0.095000,2.760000,0.604000);
positions[471] = Vec3(1.325000,2.144000,1.848000);
positions[472] = Vec3(0.681000,0.896000,1.285000);
positions[473] = Vec3(0.406000,2.936000,0.717000);
positions[474] = Vec3(0.565000,1.852000,0.349000);
positions[475] = Vec3(0.597000,1.651000,1.020000);
positions[476] = Vec3(1.236000,0.170000,1.335000);
positions[477] = Vec3(0.586000,0.441000,1.980000);
positions[478] = Vec3(1.443000,1.208000,1.575000);
positions[479] = Vec3(0.247000,0.243000,0.502000);
positions[480] = Vec3(1.386000,1.564000,0.236000);
positions[481] = Vec3(0.871000,1.063000,0.930000);
positions[482] = Vec3(0.136000,0.992000,0.621000);
positions[483] = Vec3(0.889000,0.986000,0.010000);
positions[484] = Vec3(1.107000,2.731000,1.452000);
positions[485] = Vec3(0.942000,2.471000,0.517000);
positions[486] = Vec3(0.989000,0.652000,0.747000);
positions[487] = Vec3(0.899000,1.235000,2.707000);
positions[488] = Vec3(1.105000,0.684000,0.068000);
positions[489] = Vec3(1.660000,1.235000,2.276000);
positions[490] = Vec3(1.593000,1.883000,1.915000);
positions[491] = Vec3(1.528000,1.613000,0.920000);
positions[492] = Vec3(0.459000,1.046000,1.011000);
positions[493] = Vec3(0.213000,0.612000,0.644000);
positions[494] = Vec3(0.078000,1.392000,1.676000);
positions[495] = Vec3(0.605000,0.491000,0.574000);
positions[496] = Vec3(0.990000,1.586000,1.076000);
positions[497] = Vec3(0.297000,1.434000,1.028000);
positions[498] = Vec3(1.101000,1.471000,1.443000);
positions[499] = Vec3(0.072000,0.139000,1.653000);
positions[500] = Vec3(0.633000,0.884000,0.645000);
positions[501] = Vec3(0.352000,2.841000,1.463000);
positions[502] = Vec3(0.418000,0.774000,0.350000);
positions[503] = Vec3(2.641000,0.198000,0.869000);
positions[504] = Vec3(0.608000,1.341000,0.695000);
positions[505] = Vec3(1.778000,1.151000,1.830000);
positions[506] = Vec3(1.669000,0.342000,2.768000);
positions[507] = Vec3(1.256000,0.994000,0.798000);
positions[508] = Vec3(1.068000,0.375000,1.036000);
positions[509] = Vec3(0.910000,0.758000,1.589000);
positions[510] = Vec3(0.243000,2.452000,0.805000);
positions[511] = Vec3(1.018000,0.764000,1.122000);
positions[512] = Vec3(2.464000,1.089000,1.404000);
positions[513] = Vec3(0.670000,0.564000,0.034000);
positions[514] = Vec3(0.030000,1.296000,1.310000);
positions[515] = Vec3(1.210000,1.785000,1.691000);
positions[516] = Vec3(0.022000,0.620000,0.974000);
positions[517] = Vec3(1.499000,1.277000,2.986000);
positions[518] = Vec3(1.227000,1.896000,1.006000);
positions[519] = Vec3(0.528000,1.022000,1.635000);
positions[520] = Vec3(1.887000,2.670000,0.089000);
positions[521] = Vec3(1.661000,0.825000,0.793000);
positions[522] = Vec3(0.831000,1.494000,0.374000);
positions[523] = Vec3(1.356000,0.613000,0.930000);
positions[524] = Vec3(0.667000,0.600000,0.968000);
positions[525] = Vec3(1.154000,1.702000,2.925000);
positions[526] = Vec3(1.420000,1.581000,1.289000);
positions[527] = Vec3(1.383000,0.041000,0.932000);
positions[528] = Vec3(1.727000,0.140000,1.725000);
positions[529] = Vec3(0.711000,1.215000,2.004000);
positions[530] = Vec3(1.061000,1.067000,1.366000);
positions[531] = Vec3(0.377000,0.597000,1.224000);
positions[532] = Vec3(0.274000,0.719000,1.842000);
positions[533] = Vec3(0.840000,1.658000,1.874000);
positions[534] = Vec3(0.877000,0.290000,0.311000);
positions[535] = Vec3(2.130000,1.153000,1.196000);
positions[536] = Vec3(1.028000,1.379000,0.747000);
positions[537] = Vec3(1.107000,2.450000,2.079000);
positions[538] = Vec3(1.419000,1.333000,0.585000);
positions[539] = Vec3(0.430000,1.305000,1.369000);
positions[540] = Vec3(0.775000,1.363000,1.596000);
positions[541] = Vec3(1.522000,2.009000,0.736000);
positions[542] = Vec3(0.857000,1.722000,0.696000);
positions[543] = Vec3(0.722000,2.831000,1.478000);
positions[544] = Vec3(0.411000,1.673000,0.681000);
positions[545] = Vec3(1.511000,0.456000,0.597000);
positions[546] = Vec3(2.684000,0.820000,2.996000);
positions[547] = Vec3(1.593000,1.713000,2.369000);
positions[548] = Vec3(1.113000,0.803000,1.958000);
positions[549] = Vec3(1.267000,1.095000,0.254000);
positions[550] = Vec3(2.120000,0.540000,2.477000);
positions[551] = Vec3(0.566000,1.409000,2.588000);
positions[552] = Vec3(0.261000,0.872000,2.546000);
positions[553] = Vec3(1.878000,1.446000,2.680000);
positions[554] = Vec3(0.878000,1.606000,2.658000);
positions[555] = Vec3(1.564000,0.749000,1.786000);
positions[556] = Vec3(1.412000,1.942000,2.625000);
positions[557] = Vec3(1.660000,1.114000,2.710000);
positions[558] = Vec3(1.118000,0.813000,2.424000);
positions[559] = Vec3(1.482000,0.893000,2.434000);
positions[560] = Vec3(1.093000,1.129000,1.740000);
positions[561] = Vec3(2.163000,0.849000,2.709000);
positions[562] = Vec3(1.201000,1.429000,1.957000);
positions[563] = Vec3(0.235000,2.258000,2.002000);
positions[564] = Vec3(0.413000,1.444000,0.314000);
positions[565] = Vec3(0.164000,0.450000,2.408000);
positions[566] = Vec3(1.551000,0.851000,0.033000);
positions[567] = Vec3(0.659000,0.228000,2.807000);
positions[568] = Vec3(0.741000,0.131000,2.124000);
positions[569] = Vec3(0.455000,0.567000,2.682000);
positions[570] = Vec3(0.729000,0.971000,2.408000);
positions[571] = Vec3(1.487000,2.820000,0.162000);
positions[572] = Vec3(1.855000,0.700000,2.858000);
positions[573] = Vec3(0.305000,1.074000,1.926000);
positions[574] = Vec3(1.300000,0.153000,1.747000);
positions[575] = Vec3(1.272000,1.249000,2.568000);
positions[576] = Vec3(0.431000,0.743000,2.238000);
positions[577] = Vec3(0.493000,0.240000,0.184000);
positions[578] = Vec3(1.734000,0.506000,2.317000);
positions[579] = Vec3(0.874000,0.631000,2.692000);
positions[580] = Vec3(0.473000,2.790000,2.161000);
positions[581] = Vec3(1.310000,0.571000,2.759000);
positions[582] = Vec3(0.677000,0.798000,1.916000);
positions[583] = Vec3(0.944000,0.442000,1.858000);
positions[584] = Vec3(3.006000,2.098000,2.976000);
positions[585] = Vec3(0.864000,0.592000,2.231000);
positions[586] = Vec3(1.366000,0.611000,2.147000);
positions[587] = Vec3(2.871000,1.217000,2.880000);
positions[588] = Vec3(1.674000,2.664000,2.336000);
positions[589] = Vec3(1.757000,0.879000,2.101000);
positions[590] = Vec3(1.293000,2.939000,2.457000);
positions[591] = Vec3(1.108000,1.131000,2.206000);
positions[592] = Vec3(1.207000,1.658000,2.498000);
positions[593] = Vec3(0.850000,1.373000,2.312000);
positions[594] = Vec3(1.413000,1.060000,1.939000);
positions[595] = Vec3(1.138000,0.140000,2.102000);
positions[596] = Vec3(0.752000,1.307000,1.190000);
positions[597] = Vec3(1.254000,0.942000,2.790000);
positions[598] = Vec3(1.544000,1.614000,2.800000);
positions[599] = Vec3(2.128000,0.302000,2.833000);
positions[600] = Vec3(0.300000,1.744000,0.027000);
positions[601] = Vec3(1.878000,2.986000,2.060000);
positions[602] = Vec3(1.528000,0.233000,2.045000);
positions[603] = Vec3(1.146000,1.817000,2.067000);
positions[604] = Vec3(1.037000,2.746000,0.813000);
positions[605] = Vec3(0.524000,0.610000,1.566000);
positions[606] = Vec3(0.945000,2.964000,0.503000);
positions[607] = Vec3(1.788000,2.565000,0.965000);
positions[608] = Vec3(0.471000,2.510000,0.491000);
positions[609] = Vec3(0.512000,2.043000,1.371000);
positions[610] = Vec3(2.316000,2.423000,1.494000);
positions[611] = Vec3(1.575000,2.394000,2.953000);
positions[612] = Vec3(2.845000,2.869000,0.985000);
positions[613] = Vec3(1.016000,2.335000,1.003000);
positions[614] = Vec3(0.998000,2.830000,1.879000);
positions[615] = Vec3(0.624000,2.508000,0.075000);
positions[616] = Vec3(1.362000,2.808000,2.069000);
positions[617] = Vec3(1.747000,0.068000,0.810000);
positions[618] = Vec3(1.768000,2.355000,0.661000);
positions[619] = Vec3(1.535000,2.410000,2.085000);
positions[620] = Vec3(0.844000,2.004000,1.646000);
positions[621] = Vec3(1.124000,0.280000,0.649000);
positions[622] = Vec3(0.689000,2.170000,0.648000);
positions[623] = Vec3(0.849000,2.666000,1.175000);
positions[624] = Vec3(2.975000,1.963000,1.308000);
positions[625] = Vec3(1.074000,2.082000,0.714000);
positions[626] = Vec3(1.284000,2.651000,1.110000);
positions[627] = Vec3(1.669000,0.205000,0.180000);
positions[628] = Vec3(1.716000,0.047000,1.253000);
positions[629] = Vec3(0.501000,2.241000,1.043000);
positions[630] = Vec3(1.038000,1.833000,0.305000);
positions[631] = Vec3(0.646000,2.431000,1.424000);
positions[632] = Vec3(1.383000,2.059000,2.230000);
positions[633] = Vec3(0.370000,2.566000,1.192000);
positions[634] = Vec3(1.355000,2.006000,0.120000);
positions[635] = Vec3(2.113000,0.075000,0.589000);
positions[636] = Vec3(1.850000,0.448000,1.890000);
positions[637] = Vec3(1.215000,2.704000,0.405000);
positions[638] = Vec3(0.575000,2.997000,1.798000);
positions[639] = Vec3(0.967000,2.586000,2.603000);
positions[640] = Vec3(0.276000,1.669000,1.430000);
positions[641] = Vec3(1.483000,2.284000,1.128000);
positions[642] = Vec3(0.983000,3.003000,1.099000);
positions[643] = Vec3(0.539000,2.222000,1.720000);
positions[644] = Vec3(0.648000,2.826000,2.751000);
positions[645] = Vec3(0.803000,1.994000,0.993000);
positions[646] = Vec3(0.451000,0.216000,1.438000);
positions[647] = Vec3(1.604000,2.512000,0.334000);
positions[648] = Vec3(1.980000,2.022000,0.588000);
positions[649] = Vec3(1.843000,2.834000,1.544000);
positions[650] = Vec3(1.835000,3.005000,2.858000);
positions[651] = Vec3(0.679000,2.499000,0.838000);
positions[652] = Vec3(0.012000,2.637000,1.524000);
positions[653] = Vec3(0.314000,2.065000,0.602000);
positions[654] = Vec3(1.157000,0.004000,0.173000);
positions[655] = Vec3(0.736000,1.705000,1.382000);
positions[656] = Vec3(1.511000,2.736000,0.690000);
positions[657] = Vec3(1.330000,2.541000,1.735000);
positions[658] = Vec3(0.744000,0.170000,0.785000);
positions[659] = Vec3(2.593000,2.794000,0.703000);
positions[660] = Vec3(0.275000,1.872000,1.043000);
positions[661] = Vec3(1.624000,2.608000,1.341000);
positions[662] = Vec3(1.382000,0.122000,2.855000);
positions[663] = Vec3(1.326000,2.434000,0.783000);
positions[664] = Vec3(0.117000,0.116000,1.254000);
positions[665] = Vec3(1.045000,2.970000,2.748000);
positions[666] = Vec3(1.341000,2.692000,2.799000);
positions[667] = Vec3(1.797000,2.586000,2.709000);
positions[668] = Vec3(0.890000,2.484000,1.716000);
positions[669] = Vec3(2.373000,2.558000,1.889000);
positions[670] = Vec3(1.566000,2.323000,2.574000);
positions[671] = Vec3(1.257000,2.280000,0.399000);
positions[672] = Vec3(0.679000,2.130000,2.434000);
positions[673] = Vec3(2.016000,2.334000,2.462000);
positions[674] = Vec3(1.077000,2.213000,2.416000);
positions[675] = Vec3(0.581000,1.950000,2.081000);
positions[676] = Vec3(0.805000,2.315000,2.810000);
positions[677] = Vec3(0.844000,1.787000,2.322000);
positions[678] = Vec3(0.980000,2.205000,0.129000);
positions[679] = Vec3(2.468000,0.603000,2.740000);
positions[680] = Vec3(2.366000,2.403000,2.299000);
positions[681] = Vec3(0.337000,2.487000,2.329000);
positions[682] = Vec3(2.007000,2.793000,2.452000);
positions[683] = Vec3(1.072000,2.571000,0.063000);
positions[684] = Vec3(1.217000,2.283000,2.806000);
positions[685] = Vec3(0.459000,2.477000,2.728000);
positions[686] = Vec3(0.958000,1.975000,2.710000);
positions[687] = Vec3(0.914000,2.111000,2.052000);
positions[688] = Vec3(0.768000,2.958000,0.075000);
positions[689] = Vec3(0.474000,1.805000,2.533000);
positions[690] = Vec3(1.313000,2.552000,2.395000);
positions[691] = Vec3(1.853000,2.014000,2.229000);
positions[692] = Vec3(2.405000,2.230000,2.658000);
positions[693] = Vec3(0.727000,1.781000,0.016000);
positions[694] = Vec3(0.974000,2.791000,2.271000);
positions[695] = Vec3(0.438000,0.096000,2.457000);
positions[696] = Vec3(0.652000,2.392000,2.064000);
positions[697] = Vec3(1.972000,2.209000,2.834000);
positions[698] = Vec3(0.333000,0.141000,2.088000);
positions[699] = Vec3(1.813000,1.952000,0.063000);
positions[700] = Vec3(0.166000,2.838000,1.877000);
positions[701] = Vec3(1.772000,0.487000,0.951000);
positions[702] = Vec3(1.924000,1.404000,1.434000);
positions[703] = Vec3(2.734000,0.348000,1.712000);
positions[704] = Vec3(2.874000,0.729000,1.811000);
positions[705] = Vec3(1.841000,0.877000,1.137000);
positions[706] = Vec3(2.327000,1.491000,1.768000);
positions[707] = Vec3(1.916000,1.483000,1.057000);
positions[708] = Vec3(2.783000,0.850000,0.745000);
positions[709] = Vec3(1.829000,1.526000,0.085000);
positions[710] = Vec3(2.426000,1.082000,0.652000);
positions[711] = Vec3(1.645000,1.241000,1.217000);
positions[712] = Vec3(2.286000,0.725000,0.084000);
positions[713] = Vec3(2.755000,0.691000,1.421000);
positions[714] = Vec3(2.651000,0.591000,1.023000);
positions[715] = Vec3(2.040000,0.863000,0.442000);
positions[716] = Vec3(0.035000,0.109000,2.497000);
positions[717] = Vec3(0.127000,1.410000,0.572000);
positions[718] = Vec3(2.174000,0.357000,0.307000);
positions[719] = Vec3(2.705000,1.508000,0.758000);
positions[720] = Vec3(2.223000,1.407000,2.913000);
positions[721] = Vec3(2.528000,1.722000,1.088000);
positions[722] = Vec3(2.860000,0.345000,0.198000);
positions[723] = Vec3(2.580000,1.789000,1.479000);
positions[724] = Vec3(2.779000,0.295000,1.295000);
positions[725] = Vec3(0.097000,0.434000,2.826000);
positions[726] = Vec3(2.952000,1.654000,1.091000);
positions[727] = Vec3(0.119000,1.878000,0.343000);
positions[728] = Vec3(1.718000,1.173000,0.327000);
positions[729] = Vec3(2.833000,0.016000,0.527000);
positions[730] = Vec3(2.085000,1.779000,2.888000);
positions[731] = Vec3(2.754000,2.952000,1.485000);
positions[732] = Vec3(2.826000,0.935000,1.162000);
positions[733] = Vec3(1.564000,1.585000,1.615000);
positions[734] = Vec3(2.132000,0.645000,1.093000);
positions[735] = Vec3(2.294000,1.490000,1.350000);
positions[736] = Vec3(0.081000,0.490000,1.479000);
positions[737] = Vec3(2.118000,1.165000,1.642000);
positions[738] = Vec3(2.141000,0.121000,1.390000);
positions[739] = Vec3(2.385000,0.389000,1.196000);
positions[740] = Vec3(0.049000,0.166000,0.817000);
positions[741] = Vec3(1.993000,0.806000,1.814000);
positions[742] = Vec3(0.006000,1.450000,0.171000);
positions[743] = Vec3(2.297000,0.428000,0.764000);
positions[744] = Vec3(2.851000,0.469000,2.114000);
positions[745] = Vec3(1.814000,1.957000,0.945000);
positions[746] = Vec3(0.386000,0.327000,0.902000);
positions[747] = Vec3(2.452000,1.070000,1.807000);
positions[748] = Vec3(2.309000,1.537000,2.159000);
positions[749] = Vec3(2.712000,1.497000,2.007000);
positions[750] = Vec3(1.727000,0.924000,1.503000);
positions[751] = Vec3(0.861000,0.801000,0.344000);
positions[752] = Vec3(1.740000,1.245000,0.819000);
positions[753] = Vec3(0.117000,0.042000,0.197000);
positions[754] = Vec3(2.557000,0.996000,0.317000);
positions[755] = Vec3(2.228000,1.588000,2.548000);
positions[756] = Vec3(2.849000,1.557000,2.708000);
positions[757] = Vec3(0.152000,1.107000,0.219000);
positions[758] = Vec3(2.460000,1.318000,1.002000);
positions[759] = Vec3(2.405000,1.436000,0.528000);
positions[760] = Vec3(2.135000,1.179000,2.046000);
positions[761] = Vec3(1.726000,0.588000,0.286000);
positions[762] = Vec3(2.831000,1.053000,1.538000);
positions[763] = Vec3(1.932000,1.556000,1.833000);
positions[764] = Vec3(2.423000,0.900000,1.064000);
positions[765] = Vec3(3.001000,1.807000,0.709000);
positions[766] = Vec3(0.578000,1.095000,0.223000);
positions[767] = Vec3(2.215000,1.160000,0.252000);
positions[768] = Vec3(2.050000,0.921000,0.835000);
positions[769] = Vec3(2.080000,1.682000,0.738000);
positions[770] = Vec3(2.851000,1.753000,0.027000);
positions[771] = Vec3(0.203000,0.509000,0.202000);
positions[772] = Vec3(1.967000,1.018000,0.018000);
positions[773] = Vec3(1.869000,0.878000,2.472000);
positions[774] = Vec3(1.917000,0.228000,2.507000);
positions[775] = Vec3(0.316000,0.795000,2.991000);
positions[776] = Vec3(2.175000,1.229000,2.472000);
positions[777] = Vec3(2.405000,1.062000,2.931000);
positions[778] = Vec3(2.501000,0.511000,2.369000);
positions[779] = Vec3(2.641000,0.819000,2.141000);
positions[780] = Vec3(0.649000,1.384000,3.006000);
positions[781] = Vec3(1.012000,0.329000,2.963000);
positions[782] = Vec3(2.755000,0.350000,2.718000);
positions[783] = Vec3(2.315000,0.153000,2.454000);
positions[784] = Vec3(2.583000,1.696000,2.389000);
positions[785] = Vec3(0.439000,2.593000,1.776000);
positions[786] = Vec3(2.630000,1.390000,0.116000);
positions[787] = Vec3(2.854000,0.669000,2.478000);
positions[788] = Vec3(2.551000,1.342000,2.621000);
positions[789] = Vec3(2.533000,2.734000,2.987000);
positions[790] = Vec3(2.772000,2.446000,2.875000);
positions[791] = Vec3(2.817000,1.051000,2.498000);
positions[792] = Vec3(2.688000,1.404000,1.621000);
positions[793] = Vec3(0.083000,2.737000,2.775000);
positions[794] = Vec3(2.514000,0.322000,2.041000);
positions[795] = Vec3(2.470000,0.900000,2.504000);
positions[796] = Vec3(2.790000,0.444000,0.624000);
positions[797] = Vec3(0.040000,0.840000,2.202000);
positions[798] = Vec3(0.530000,1.067000,2.764000);
positions[799] = Vec3(0.191000,1.385000,2.541000);
positions[800] = Vec3(2.465000,0.363000,0.051000);
positions[801] = Vec3(1.850000,1.902000,2.592000);
positions[802] = Vec3(1.432000,0.306000,2.449000);
positions[803] = Vec3(2.259000,0.489000,1.753000);
positions[804] = Vec3(2.803000,1.118000,1.956000);
positions[805] = Vec3(2.426000,0.147000,1.636000);
positions[806] = Vec3(2.880000,1.846000,2.133000);
positions[807] = Vec3(2.862000,2.110000,1.867000);
positions[808] = Vec3(0.424000,1.184000,2.299000);
positions[809] = Vec3(2.518000,1.218000,2.228000);
positions[810] = Vec3(2.153000,0.834000,1.468000);
positions[811] = Vec3(0.105000,1.397000,2.088000);
positions[812] = Vec3(2.579000,0.601000,0.316000);
positions[813] = Vec3(2.594000,2.106000,2.968000);
positions[814] = Vec3(0.448000,1.435000,1.783000);
positions[815] = Vec3(2.125000,0.299000,2.132000);
positions[816] = Vec3(2.849000,1.402000,2.356000);
positions[817] = Vec3(2.956000,0.091000,2.078000);
positions[818] = Vec3(0.156000,1.696000,2.357000);
positions[819] = Vec3(1.566000,2.211000,1.557000);
positions[820] = Vec3(2.047000,0.194000,0.985000);
positions[821] = Vec3(1.947000,2.680000,0.488000);
positions[822] = Vec3(2.343000,2.796000,1.447000);
positions[823] = Vec3(2.006000,2.332000,0.265000);
positions[824] = Vec3(2.396000,1.834000,0.546000);
positions[825] = Vec3(2.538000,2.059000,2.207000);
positions[826] = Vec3(0.110000,2.360000,0.447000);
positions[827] = Vec3(2.198000,2.448000,1.136000);
positions[828] = Vec3(2.420000,2.121000,1.271000);
positions[829] = Vec3(0.422000,2.192000,0.260000);
positions[830] = Vec3(2.145000,2.767000,2.839000);
positions[831] = Vec3(2.434000,2.398000,0.421000);
positions[832] = Vec3(2.489000,2.175000,1.718000);
positions[833] = Vec3(2.870000,2.527000,0.814000);
positions[834] = Vec3(2.741000,2.016000,0.337000);
positions[835] = Vec3(1.997000,2.574000,2.107000);
positions[836] = Vec3(0.002000,2.128000,0.932000);
positions[837] = Vec3(2.787000,2.375000,0.234000);
positions[838] = Vec3(2.235000,1.852000,1.620000);
positions[839] = Vec3(2.782000,1.642000,0.422000);
positions[840] = Vec3(2.915000,1.760000,1.699000);
positions[841] = Vec3(2.047000,2.178000,1.549000);
positions[842] = Vec3(1.808000,1.878000,1.556000);
positions[843] = Vec3(2.224000,2.043000,0.913000);
positions[844] = Vec3(2.619000,2.611000,1.237000);
positions[845] = Vec3(2.916000,2.726000,0.168000);
positions[846] = Vec3(2.021000,2.833000,1.176000);
positions[847] = Vec3(2.967000,2.308000,2.258000);
positions[848] = Vec3(2.778000,2.270000,1.477000);
positions[849] = Vec3(2.121000,1.834000,2.002000);
positions[850] = Vec3(2.097000,2.752000,0.808000);
positions[851] = Vec3(1.897000,0.566000,1.501000);
positions[852] = Vec3(0.359000,2.802000,0.036000);
positions[853] = Vec3(2.966000,2.454000,1.186000);
positions[854] = Vec3(2.461000,2.964000,1.132000);
positions[855] = Vec3(2.093000,1.821000,1.243000);
positions[856] = Vec3(1.706000,2.659000,1.841000);
positions[857] = Vec3(2.074000,1.709000,0.342000);
positions[858] = Vec3(2.137000,2.894000,1.813000);
positions[859] = Vec3(0.223000,2.293000,1.417000);
positions[860] = Vec3(2.637000,0.007000,0.197000);
positions[861] = Vec3(1.416000,0.050000,0.483000);
positions[862] = Vec3(1.845000,2.250000,1.251000);
positions[863] = Vec3(2.906000,0.034000,2.896000);
positions[864] = Vec3(2.481000,0.204000,0.474000);
positions[865] = Vec3(2.234000,2.051000,0.158000);
positions[866] = Vec3(0.185000,2.453000,0.055000);
positions[867] = Vec3(2.509000,0.048000,2.786000);
positions[868] = Vec3(2.202000,2.206000,2.027000);
positions[869] = Vec3(0.061000,2.367000,2.656000);
positions[870] = Vec3(3.003000,2.755000,2.241000);
positions[871] = Vec3(0.297000,2.131000,2.463000);
positions[872] = Vec3(1.553000,0.429000,1.573000);
positions[873] = Vec3(2.506000,1.832000,1.911000);
positions[874] = Vec3(2.472000,1.814000,2.759000);
positions[875] = Vec3(1.922000,1.563000,2.278000);
positions[876] = Vec3(2.623000,2.666000,2.169000);
positions[877] = Vec3(0.120000,1.834000,2.723000);
positions[878] = Vec3(0.294000,0.103000,2.826000);
positions[879] = Vec3(2.364000,2.821000,0.417000);
positions[880] = Vec3(2.446000,1.734000,0.153000);
positions[881] = Vec3(2.777000,2.037000,2.565000);
positions[882] = Vec3(2.837000,2.477000,1.924000);
positions[883] = Vec3(2.221000,1.961000,2.443000);
positions[884] = Vec3(2.284000,2.895000,2.157000);
positions[885] = Vec3(2.728000,2.880000,1.861000);
positions[886] = Vec3(0.454000,2.080000,2.868000);
positions[887] = Vec3(2.430000,2.790000,2.524000);
positions[888] = Vec3(1.808000,2.213000,1.899000);
positions[889] = Vec3(2.666000,0.053000,2.309000);
positions[890] = Vec3(2.290000,2.408000,2.995000);
positions[891] = Vec3(2.646000,2.592000,1.625000);
positions[892] = Vec3(2.750000,2.508000,2.489000);
positions[893] = Vec3(0.211000,1.753000,1.939000);
platforms/cuda/src/CudaIntegrationUtilities.cpp
View file @ 8df54762
......@@ -123,15 +123,21 @@ CudaIntegrationUtilities::CudaIntegrationUtilities(CudaContext& context, const S
// Record the set of constraints and how many constraints each atom is involved in.
int numConstraints = system.getNumConstraints();
vector<int> atom1(numConstraints);
vector<int> atom2(numConstraints);
vector<double> distance(numConstraints);
vector<int> atom1;
vector<int> atom2;
vector<double> distance;
vector<int> constraintCount(context.getNumAtoms(), 0);
for (int i = 0; i < numConstraints; i++) {
system.getConstraintParameters(i, atom1[i], atom2[i], distance[i]);
constraintCount[atom1[i]]++;
constraintCount[atom2[i]]++;
for (int i = 0; i < system.getNumConstraints(); i++) {
int p1, p2;
double d;
system.getConstraintParameters(i, p1, p2, d);
if (system.getParticleMass(p1) != 0 || system.getParticleMass(p2) != 0) {
atom1.push_back(p1);
atom2.push_back(p2);
distance.push_back(d);
constraintCount[p1]++;
constraintCount[p2]++;
}
}
// Identify clusters of three atoms that can be treated with SETTLE. First, for every
......
platforms/cuda/src/CudaKernels.cpp
View file @ 8df54762
......@@ -5752,7 +5752,7 @@ void CudaRemoveCMMotionKernel::initialize(const System& system, const CMMotionRe
for (int i = 0; i < numAtoms; i++)
totalMass += system.getParticleMass(i);
map<string, string> defines;
defines["INVERSE_TOTAL_MASS"] = cu.doubleToString(1.0/totalMass);
defines["INVERSE_TOTAL_MASS"] = cu.doubleToString(totalMass == 0 ? 0.0 : 1.0/totalMass);
CUmodule module = cu.createModule(CudaKernelSources::removeCM, defines);
kernel1 = cu.getKernel(module, "calcCenterOfMassMomentum");
kernel2 = cu.getKernel(module, "removeCenterOfMassMomentum");
......
platforms/cuda/src/kernels/gbsaObc1.cu
View file @ 8df54762
......@@ -468,11 +468,16 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo
real expTerm = EXP(-D_ij);
real denominator2 = r2 + alpha2_ij*expTerm;
real denominator = SQRT(denominator2);
real tempEnergy = (PREFACTOR*posq1.w*posq2.w)*RECIP(denominator);
real scaledChargeProduct = PREFACTOR*posq1.w*posq2.w;
real tempEnergy = scaledChargeProduct*RECIP(denominator);
real Gpol = tempEnergy*RECIP(denominator2);
real dGpol_dalpha2_ij = -0.5f*Gpol*expTerm*(1.0f+D_ij);
real dEdR = Gpol*(1.0f - 0.25f*expTerm);
force.w += dGpol_dalpha2_ij*bornRadius2;
#ifdef USE_CUTOFF
if (atom1 != y*TILE_SIZE+j)
tempEnergy -= scaledChargeProduct/CUTOFF;
#endif
energy += 0.5f*tempEnergy;
delta *= dEdR;
force.x -= delta.x;
......@@ -520,11 +525,15 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo
real expTerm = EXP(-D_ij);
real denominator2 = r2 + alpha2_ij*expTerm;
real denominator = SQRT(denominator2);
real tempEnergy = (PREFACTOR*posq1.w*posq2.w)*RECIP(denominator);
real scaledChargeProduct = PREFACTOR*posq1.w*posq2.w;
real tempEnergy = scaledChargeProduct*RECIP(denominator);
real Gpol = tempEnergy*RECIP(denominator2);
real dGpol_dalpha2_ij = -0.5f*Gpol*expTerm*(1.0f+D_ij);
real dEdR = Gpol*(1.0f - 0.25f*expTerm);
force.w += dGpol_dalpha2_ij*bornRadius2;
#ifdef USE_CUTOFF
tempEnergy -= scaledChargeProduct/CUTOFF;
#endif
energy += tempEnergy;
delta *= dEdR;
force.x -= delta.x;
......@@ -670,11 +679,15 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo
real expTerm = EXP(-D_ij);
real denominator2 = r2 + alpha2_ij*expTerm;
real denominator = SQRT(denominator2);
real tempEnergy = (PREFACTOR*posq1.w*posq2.w)*RECIP(denominator);
real scaledChargeProduct = PREFACTOR*posq1.w*posq2.w;
real tempEnergy = scaledChargeProduct*RECIP(denominator);
real Gpol = tempEnergy*RECIP(denominator2);
real dGpol_dalpha2_ij = -0.5f*Gpol*expTerm*(1.0f+D_ij);
real dEdR = Gpol*(1.0f - 0.25f*expTerm);
force.w += dGpol_dalpha2_ij*bornRadius2;
#ifdef USE_CUTOFF
tempEnergy -= scaledChargeProduct/CUTOFF;
#endif
energy += tempEnergy;
delta *= dEdR;
force.x -= delta.x;
......@@ -717,11 +730,15 @@ extern "C" __global__ void computeGBSAForce1(unsigned long long* __restrict__ fo
real expTerm = EXP(-D_ij);
real denominator2 = r2 + alpha2_ij*expTerm;
real denominator = SQRT(denominator2);
real tempEnergy = (PREFACTOR*posq1.w*posq2.w)*RECIP(denominator);
real scaledChargeProduct = PREFACTOR*posq1.w*posq2.w;
real tempEnergy = scaledChargeProduct*RECIP(denominator);
real Gpol = tempEnergy*RECIP(denominator2);
real dGpol_dalpha2_ij = -0.5f*Gpol*expTerm*(1.0f+D_ij);
real dEdR = Gpol*(1.0f - 0.25f*expTerm);
force.w += dGpol_dalpha2_ij*bornRadius2;
#ifdef USE_CUTOFF
tempEnergy -= scaledChargeProduct/CUTOFF;
#endif
energy += tempEnergy;
delta *= dEdR;
force.x -= delta.x;
......
platforms/cuda/tests/TestCudaBrownianIntegrator.cpp
View file @ 8df54762
......@@ -172,6 +172,37 @@ void testConstraints() {
}
}
void testConstrainedMasslessParticles() {
System system;
system.addParticle(0.0);
system.addParticle(1.0);
system.addConstraint(0, 1, 1.5);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
BrownianIntegrator integrator(300.0, 2.0, 0.01);
bool failed = false;
try {
// This should throw an exception.
Context context(system, integrator, platform);
}
catch (exception& ex) {
failed = true;
}
ASSERT(failed);
// Now make both particles massless, which should work.
system.setParticleMass(1, 0.0);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setVelocitiesToTemperature(300.0);
integrator.step(1);
State state = context.getState(State::Velocities);
ASSERT_EQUAL(0.0, state.getVelocities()[0][0]);
}
void testRandomSeed() {
const int numParticles = 8;
const double temp = 100.0;
......@@ -237,6 +268,7 @@ int main(int argc, char* argv[]) {
testSingleBond();
testTemperature();
testConstraints();
testConstrainedMasslessParticles();
testRandomSeed();
}
catch(const exception& e) {
......
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