#ifndef BrookBonded_H_ #define BrookBonded_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 "BrookFloatStreamImpl.h" #include "BrookIntStreamImpl.h" #include "BrookPlatform.h" #include "BrookCommon.h" #include "OpenMMContext.h" namespace OpenMM { /** * This kernel is invoked by StandardMMForceField to calculate the forces acting on the system. */ class BrookBonded : public BrookCommon { public: static const int DefaultReturnValue = 0; static const int ErrorReturnValue = -1; BrookBonded( ); ~BrookBonded(); /** * Initialize the kernel, setting up the values of all the force field parameters. * * @param bondIndices the two atoms connected by each bond term * @param bondParameters the force parameters (length, k) for each bond term * @param angleIndices the three atoms connected by each angle term * @param angleParameters the force parameters (angle, k) for each angle term * @param periodicTorsionIndices the four atoms connected by each periodic torsion term * @param periodicTorsionParameters the force parameters (k, phase, periodicity) for each periodic torsion term * @param rbTorsionIndices the four atoms connected by each Ryckaert-Bellemans torsion term * @param rbTorsionParameters the coefficients (in order of increasing powers) for each Ryckaert-Bellemans torsion term * @param bonded14Indices each element contains the indices of two atoms 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 atom * @param lj14Scale the factor by which van der Waals interactions should be reduced for bonded 1-4 pairs * @param coulomb14Scale the factor by which Coulomb interactions should be reduced for bonded 1-4 pairs * @param log log reference * * @return nonzero value if error * */ int setup( int numberOfAtoms, const std::vector >& bondIndices, const std::vector >& bondParameters, const std::vector >& angleIndices, const std::vector >& angleParameters, const std::vector >& periodicTorsionIndices, const std::vector >& periodicTorsionParameters, const std::vector >& rbTorsionIndices, const std::vector >& rbTorsionParameters, const std::vector >& bonded14Indices, const std::vector >& nonbondedParameters, double lj14Scale, double coulomb14Scale, const BrookPlatform& platform ); /** * 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 Brook stream handle * * @return */ BrookFloatStreamImpl* getBrookAtomIndices( void ) const; /** * Get LJ 14 scale factor * * @return LJ 14 scaling (fudge) factor * */ BrookOpenMMFloat getLJ_14Scale( void ) const; /** * Get Coulomb factor * * @return Coulomb factor * */ BrookOpenMMFloat getCoulombFactor( void ) const; /** * Get bonded atom indices stream * * @return atom indices stream * */ BrookFloatStreamImpl* getAtomIndicesStream( void ) const; /** * Get array of bonded parameter streams * * @return array of bonded parameter streams * */ BrookFloatStreamImpl** getBondedParameterStreams( void ); /** * Get array of force streams * * @return array * */ BrookFloatStreamImpl** getBondedForceStreams( void ); /** * Get array of inverse map streams * * @param index array index * * @return array inverse map streams * */ BrookFloatStreamImpl** 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 getContents( int level ) const; private: static const int NumberOfParameterStreams = 5; static const int NumberOfForceStreams = 4; static const int MaxNumberOfInverseMaps = 9; enum { StreamI, StreamJ, StreamK, StreamL, StreamMax }; // inverse map stream width int _invMapStreamWidth; // actual max number of inverse maps int _maxNumberOfInverseMaps; // scale factors for 1-4 ixn BrookOpenMMFloat _ljScale; BrookOpenMMFloat _coulombFactor; // streams BrookFloatStreamImpl* _atomIndicesStream; BrookFloatStreamImpl* _bondedParameters[NumberOfParameterStreams]; BrookFloatStreamImpl* _bondedForceStreams[NumberOfForceStreams]; BrookFloatStreamImpl* _chargeStream; BrookFloatStreamImpl* _inverseStreamMaps[NumberOfForceStreams][MaxNumberOfInverseMaps]; int _maxInverseMapStreamCount[NumberOfForceStreams]; int _inverseMapStreamCount[NumberOfForceStreams]; // helper methods in setup of parameters void flipQuartet( int ibonded, int *atoms ); int matchTorsion( int i, int j, int k, int l, int nbondeds, int *atoms ); int matchAngle( int i, int j, int k, int nbondeds, int *atoms, int *flag ); int matchBond( int i, int j, int nbondeds, int *atoms, int *flag ); int matchPair( int i, int j, int nbondeds, int *atoms ); /** * Setup Ryckaert-Bellemans parameters/atom indices * * @param nbondeds number of bonded entries * @param atoms array of atom indices * @param params arrays of bond parameters * @param rbTorsionIndices the four atoms 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 addRBDihedrals( int *nbondeds, int *atoms, BrookOpenMMFloat* params[], const std::vector >& rbTorsionIndices, const std::vector >& rbTorsionParameters ); /** * Setup periodic torsion parameters/atom indices * * @param nbondeds number of bonded entries * @param atoms array of atom indices * @param params arrays of bond parameters * @param periodicTorsionIndices the four atoms 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 addPDihedrals( int *nbondeds, int *atoms, BrookOpenMMFloat* params[], const std::vector >& periodicTorsionIndices, const std::vector >& periodicTorsionParameters ); /** * Setup angle bond parameters/atom indices * * @param nbondeds number of bonded entries * @param atoms array of atom indices * @param params arrays of bond parameters * @param angleIndices the angle bond atom indices * @param angleParameters the angle parameters (angle in radians, force constant) * * @return nonzero value if error * */ int addAngles( int *nbondeds, int *atoms, BrookOpenMMFloat* params[], const std::vector >& angleIndices, const std::vector >& angleParameters ); /** * Setup harmonic bond parameters/atom indices * * @param nbondeds number of bonded entries * @param atoms array of atom indices * @param params arrays of bond parameters * @param bondIndices two harmonic bond atom indices * @param bondParameters the force parameters (distance, k) * * @return nonzero value if error * */ int addBonds( int *nbondeds, int *atoms, BrookOpenMMFloat* params[], const std::vector >& bondIndices, const std::vector >& bondParameters ); /** * Setup LJ/Coulomb 1-4 parameters/atom indices * * @param nbondeds number of bonded entries * @param atoms array of atom indices * @param params arrays of bond parameters * @param charges array of charges * @param bonded14Indices each element contains the indices of two atoms 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 atom * @param lj14Scale the factor by which van der Waals interactions should be reduced for bonded 1-4 pairs * * @return nonzero value if error * */ int addPairs( int *nbondeds, int *atoms, BrookOpenMMFloat* params[], BrookOpenMMFloat* charges, const std::vector >& bonded14Indices, const std::vector >& nonbondedParameters, double lj14Scale, double coulombScale ); /** * Create and load inverse maps for bonded ixns * * @param nbondeds number of bonded entries * @param natoms number of atoms * @param atoms arrays of atom indices (atoms[numberOfBonds][4]) * @param platform BrookPlatform reference * @param log log file reference (optional) * * @return nonzero value if error * */ int loadInvMaps( int nbondeds, int natoms, int *atoms, const BrookPlatform& platform ); /** * Get inverse amp stream width * * @return stream width * */ int getInvMapStreamWidth( void ) const; /** * 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; }; } // namespace OpenMM #endif /*OPENMM_BROOKKERNELS_H_*/