#ifndef OPENMM_BROOK_BONDED_H_ #define OPENMM_BROOK_BONDED_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) 2008 Stanford University and the Authors. * * Authors: Peter Eastman, Mark Friedrichs * * Contributors: * * * * Permission is hereby granted, free of charge, to any person obtaining a * * copy of this software and associated documentation files (the "Software"), * * to deal in the Software without restriction, including without limitation * * the rights to use, copy, modify, merge, publish, distribute, sublicense, * * and/or sell copies of the Software, and to permit persons to whom the * * Software is furnished to do so, subject to the following conditions: * * * * The above copyright notice and this permission notice shall be included in * * all copies or substantial portions of the Software. * * * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR * * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, * * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL * * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, * * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR * * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE * * USE OR OTHER DEALINGS IN THE SOFTWARE. * * -------------------------------------------------------------------------- */ #include #include "BrookStreamImpl.h" #include "BrookCommon.h" #include "OpenMMContext.h" #include "BrookBondParameters.h" namespace OpenMM { /** * Calculate Brook bonded forces */ class BrookBonded : public BrookCommon { public: /** * * BrookBonded constructor * */ BrookBonded( ); /** * * BrookBonded desstructor * */ ~BrookBonded( ); /** * Initialize the kernel, setting up the values of all the force field parameters. * * @param numberOfParticles numberOfParticles * @param harmonicBondBrookBondParameters force parameters (length, k) for each bond term * @param harmonicAngleBrookBondParameters force parameters (angle, k) for each angle term * @param periodicTorsionBrookBondParameters force parameters (k, phase, periodicity) for each periodic torsion term * @param rbTorsionBrookBondParameters coefficients (in order of increasing powers) for each Ryckaert-Bellemans torsion term * @param nonBonded14ForceParameters nonbonded 14 force parameters (charge, sigma, epsilon) for each particle * @param particleStreamWidth stream width * @param particleStreamSize stream size * * @return nonzero value if error * */ int setup( int numberOfParticles, BrookBondParameters* harmonicBondBrookBondParameters, BrookBondParameters* harmonicAngleBrookBondParameters, BrookBondParameters* periodicTorsionBrookBondParameters, BrookBondParameters* rbTorsionBrookBondParameters, BrookBondParameters* nonBonded14ForceParameters, int particleStreamWidth, int particleStreamSize ); /** * Get inverse map stream width * * @return stream width * */ int getInverseMapStreamWidth( void ) const; /** * Return number of parameter streams * * @return number of parameter streams * */ int getNumberOfParameterStreams( void ) const; /** * Return number of force streams * * @return number of force streams * */ int getNumberOfForceStreams( void ) const; /** * Return stream count for specifed index (i, j, k, l) * * @return stream count for specifed index * * @throw throws OpenMMException if index out of range */ int getInverseMapStreamCount( int index ) const; /** * Return max stream count * * @return max stream count */ int getMaxInverseMapStreamCount( void ) const; /** * Return max stream count for specified index * * @param index index of force stream * * @return max stream count * */ int getMaxInverseMapStreamCount( int index ) const; /** * Return Brook stream handle * * @return */ BrookFloatStreamInternal* getBrookParticleIndices( void ) const; /** * Get Coulomb factor * * @return Coulomb factor * */ BrookOpenMMFloat getCoulombFactor( void ) const; /** * Get bonded particle indices stream * * @return particle indices stream * */ BrookFloatStreamInternal* getParticleIndicesStream( void ) const; /** * Get bonded charge stream * * @return charge stream * */ BrookFloatStreamInternal* getChargeStream( void ) const; /** * Get array of bonded parameter streams * * @return array of bonded parameter streams * */ BrookFloatStreamInternal** getBondedParameterStreams( void ); /** * Get array of force streams * * @return array * */ BrookFloatStreamInternal** getBondedForceStreams( void ); /** * Get array of inverse map streams * * @param index array index * * @return array inverse map streams * */ BrookFloatStreamInternal** getInverseStreamMapsStreams( int index ); /** * Return true if force[index] stream is set * * @param index into force stream * @return true if index is valid && force[index] stream is set; else false * */ int isForceStreamSet( int index ) const; /** * Return true if paramsterSet[index] stream is set * * @param index into parameter stream * * @return true if index is valid && paramsterSet[index] stream is set; else false * */ int isParameterStreamSet( int index ) const; /** * Return string showing if all inverse map streams are set * * @param index into inverse map stream array * * @return informative string * */ std::string checkInverseMapStream( int index ) const; /* * Get contents of object * * * @param level level of dump * * @return string containing contents * * */ std::string getContentsString( int level = 0 ) const; /** * Compute forces * */ void computeForces( BrookStreamImpl& positionStream, BrookStreamImpl& forceStream ); /** * Return SetupCompleted flag * * @return SetupCompleted flag */ int isSetupCompleted( void ) const; /** * Set SetupCompleted flag * * @param SetupCompleted flag * * @return SetupCompleted flag */ int setupCompleted( int isSetupCompleted ); private: static const int NumberOfParameterStreams = 5; static const int NumberOfForceStreams = 4; static const int MaxNumberOfInverseMaps = 9; enum { StreamI, StreamJ, StreamK, StreamL, StreamMax }; int _setupCompleted; // inverse map stream width int _inverseMapStreamWidth; // actual max number of inverse maps int _maxNumberOfInverseMaps; // scale factors for 1-4 ixn BrookOpenMMFloat _coulombFactor; // streams BrookFloatStreamInternal* _particleIndicesStream; BrookFloatStreamInternal* _bondedParameters[NumberOfParameterStreams]; BrookFloatStreamInternal* _bondedForceStreams[NumberOfForceStreams]; BrookFloatStreamInternal* _chargeStream; BrookFloatStreamInternal* _inverseStreamMaps[NumberOfForceStreams][MaxNumberOfInverseMaps]; int _maxInverseMapStreamCount[NumberOfForceStreams]; int _inverseMapStreamCount[NumberOfForceStreams]; // helper methods in setup of parameters void _flipQuartet( int ibonded, int *particles ); int _matchTorsion( int i, int j, int k, int l, int nbondeds, int *particles ); int _matchAngle( int i, int j, int k, int nbondeds, int *particles, int *flag ); int _matchBond( int i, int j, int nbondeds, int *particles, int *flag ); int _matchPair( int i, int j, int nbondeds, int *particles ); /** * Setup Ryckaert-Bellemans parameters/particle indices * * @param nbondeds number of bonded entries * @param particles array of particle indices * @param params arrays of bond parameters * @param rbTorsionIndices the four particles connected by each Ryckaert-Bellemans torsion term * @param rbTorsionParameters the coefficients (in order of increasing powers) for each Ryckaert-Bellemans torsion term * * @return nonzero value if error * */ int _addRBTorsions( int *nbondeds, int *particles, BrookOpenMMFloat* params[], const std::vector >& rbTorsionIndices, const std::vector >& rbTorsionParameters ); /** * Setup periodic torsion parameters/particle indices * * @param nbondeds number of bonded entries * @param particles array of particle indices * @param params arrays of bond parameters * @param periodicTorsionIndices the four particles connected by each periodic torsion term * @param periodicTorsionParameters the force parameters (k, phase, periodicity) for each periodic torsion term * * @return nonzero value if error * */ int _addPTorsions( int *nbondeds, int *particles, BrookOpenMMFloat* params[], const std::vector >& periodicTorsionIndices, const std::vector >& periodicTorsionParameters ); /** * Setup angle bond parameters/particle indices * * @param nbondeds number of bonded entries * @param particles array of particle indices * @param params arrays of bond parameters * @param angleIndices the angle bond particle indices * @param angleParameters the angle parameters (angle in radians, force constant) * * @return nonzero value if error * */ int _addAngles( int *nbondeds, int *particles, BrookOpenMMFloat* params[], const std::vector >& angleIndices, const std::vector >& angleParameters ); /** * Setup harmonic bond parameters/particle indices * * @param nbondeds number of bonded entries * @param particles array of particle indices * @param params arrays of bond parameters * @param bondIndices two harmonic bond particle indices * @param bondParameters the force parameters (distance, k) * * @return nonzero value if error * */ int _addBonds( int *nbondeds, int *particles, BrookOpenMMFloat* params[], const std::vector >& bondIndices, const std::vector >& bondParameters ); /** * Setup LJ/Coulomb 1-4 parameters/particle indices * * @param nbondeds number of bonded entries * @param particles array of particle indices * @param params arrays of bond parameters * @param charges array of charges * @param bonded14Indices each element contains the indices of two particles whose nonbonded interactions should be reduced since * they form a bonded 1-4 pair * @param nonbondedParameters the nonbonded force parameters (charge, sigma, epsilon) for each particle * * @return nonzero value if error * */ int _addPairs( int *nbondeds, int *particles, BrookOpenMMFloat* params[], BrookOpenMMFloat* charges, const std::vector >& bonded14Indices, const std::vector >& nonbondedParameters ); /** * Create and load inverse maps for bonded ixns * * @param nbondeds number of bonded entries * @param nparticles number of particles * @param particles arrays of particle indices (particles[numberOfBonds][4]) * @param platform BrookPlatform reference * @param log log file reference (optional) * * @return nonzero value if error * */ //int loadInvMaps( int nbondeds, int nparticles, int *particles, const BrookPlatform& platform ); int _loadInvMaps( int nbondeds, int nparticles, int *particles, int particleStreamWidth, int particleStreamSize ); /** * Validate inverse map count * * @param index index to check (1-4) * @param count count for index * * @return -1 if count invalid * * @tthrow OpenMMException exeception if count invalid * */ int _validateInverseMapStreamCount( int index, int count ) const; /* * Helper functions for building inverse maps for * torsions, impropers and angles. * * For each particle, calculates the positions at which it's * forces are to be picked up from and stores the position * in the appropriate index. * * Input: number of torsions, the particle indices, and a flag indicating * whether we're doing i(0), j(1), k(2) or l(3) * Output: an array of counts per particle * arrays of inversemaps * nimaps - the number of invmaps actually used. * * @param posflag 0-niparticles-1 * @param niparticles 3 for angles, 4 for torsions, impropers * @param nints number of interactions * @param nparticles number of particles * @param *particles gromacs interaction list * @param nmaps maximum number of inverse maps * @param counts[] output counts of how many places each particle occurs * @param *invmaps[] output array of nmaps inverse maps * @param *nimaps, output max number of inverse maps actually used * * @return DefaultReturnValue, unless error in which case exits w/ OpenMM exception * **/ int _gpuCalcInvMap( int posflag, int niparticles, int nints, int nparticles, int *particles, int nmaps, int counts[], float4 *invmaps[], int *nimaps ); void _gpuPrintInvMaps( int nmaps, int nparticles, int counts[], float4 *invmap[], FILE* logFile ); /* * We are still plagued by kernel call overheads. This is for a big fat * merged inverse gather kernel: * Since we have 32 bit floats, we have 23 bits of mantissa or the largest * integer we can represent is 2^23. So it should be quite safe to add * 100000 * n to the index where n is the stream in which we should do the * lookup. This assumes that nints < 100000, preferably nints << 100000 * which should always be true * **/ int _gpuCalcInvMap_merged( int nints, int nparticles, int *particles, int nmaps, int counts[], float4 *invmaps[], int *nimaps ); /* * Repacks the invmap streams for more efficient access in the * merged inverse gather kernel * * buf should be nimaps * nparticles large. * **/ int _gpuRepackInvMap_merged( int nparticles, int nmaps, int *counts, float4 *invmaps[], float4 *buf ); }; } // namespace OpenMM #endif /* OPENMM_BROOK_BONDED_H_ */