#ifndef OPENMM_BROOK_COMMON_H_ #define OPENMM_BROOK_COMMON_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 #include "BrookFloatStreamInternal.h" #include "BrookIntStreamInternal.h" #include "BrookPlatform.h" namespace OpenMM { /** * This kernel is invoked by StandardMMForceField to calculate the forces acting on the system. */ class BrookCommon { public: // return values static const int DefaultReturnValue = 0; static const int ErrorReturnValue = -1; // --------------------------------------------------------------------------------------- // Stream names // bonded stream names static const std::string BondedAtomIndicesStream; static const std::string BondedParametersStream; static const std::string UnrolledForceStream; static const std::string BondedChargeStream; static const std::string BondedInverseMapStreams; // nonbonded stream names static const std::string NonBondedExclusionStream; static const std::string OuterVdwStream; static const std::string InnerSigmaStream; static const std::string InnerEpsilonStream; static const std::string NonBondedChargeStream; static const std::string PartialForceStream; // OBC Gbsa streams static const std::string ObcAtomicRadiiStream; static const std::string ObcScaledAtomicRadiiStream; static const std::string ObcAtomicRadiiWithDielectricOffsetStream; static const std::string ObcBornRadiiStream; static const std::string ObcBornRadii2Stream; static const std::string ObcIntermediateForceStream; static const std::string ObcChainStream; // Stochastic Dynamics streams static const std::string SDPC1Stream; static const std::string SDPC2Stream; static const std::string SD2XStream; static const std::string SD1VStream; static const std::string VPrimeStream; static const std::string XPrimeStream; static const std::string InverseMassStream; // Shake streams static const std::string ShakeAtomIndicesStream; static const std::string ShakeAtomParameterStream; static const std::string ShakeXCons0Stream; static const std::string ShakeXCons1Stream; static const std::string ShakeXCons2Stream; static const std::string ShakeXCons3Stream; static const std::string ShakeInverseMapStream; // Random number generator streams static const std::string ShuffleStream; // --------------------------------------------------------------------------------------- /** * Constructor * */ BrookCommon( ); /** * Destructor * */ ~BrookCommon(); /** * Return number of atoms * * @return number of atoms * */ int getNumberOfAtoms( void ) const; /** * Get atom ceiling parameter * * @return atom ceiling parameter * */ int getAtomSizeCeiling( void ) const; /** * Get atom stream width * * @param platform platform reference * * @return atom stream width */ int getAtomStreamWidth( const Platform& platform ); /** * Get atom stream width * * @return atom stream width */ int getAtomStreamWidth( void ) const; /** * Get atom stream height * * @param platform platform reference * * @return atom stream height */ int getAtomStreamHeight( const Platform& platform ); /** * Get atom stream height * * @return atom stream height */ int getAtomStreamHeight( void ) const; /** * Get atom stream size * * @param platform platform reference * * @return atom stream size */ int getAtomStreamSize( const Platform& platform ); /** * Get atom stream size * * @return atom stream size */ int getAtomStreamSize( void ) const; /** * Set log file reference * * @param log file reference * * @return DefaultReturnValue * */ int setLog( FILE* log ); /* * Get contents of object * * @param level of dump * * @return string containing contents * * */ std::string getContents( int level ) const; /** * Get log file reference * * @return log file reference * */ FILE* getLog( void ) const; /** * Get verbose flag * * @return verbosity flag * */ int getVerbosity( void ) const; /** * Set verbosity flag * * @param verbosity flag * */ int setVerbosity( int verbosity ); /* * Given number of stream elements and width, returns the appropriate * height of the stream * * @param streamSize stream size * @param width stream width * * @return stream height * */ static int getStreamHeight( int streamSize, int streamWidth ); /* * Given number of stream elements, get stream width & height * * @param streamSize stream size * @param streamWidth output stream width * @param streamHeight output stream height * * @return stream height * */ static void getStreamDimensions( int streamSize, int *streamWidth, int *streamHeight ); protected: // number of atoms int _numberOfAtoms; // atom stream dimensions int _atomStreamWidth; int _atomStreamHeight; int _atomStreamSize; // atom size mod int _atomSizeModified; // log file reference FILE* _log; // verbosity int _verbosity; /** * Set number of atoms * * @param numberOfAtoms number of atoms * */ int setNumberOfAtoms( int numberOfAtoms ); /** * Get atom stream dimensions * * @param platform platform * */ void _getAtomStreamDimensions( const Platform& platform ); /* * Get line * * @param tab tab * @param description description * @param value value * * @return string containing contents * * */ std::string _getLine( const std::string& tab, const std::string& description, const std::string& value ) const; }; } // namespace OpenMM #endif /* OPENMM_BROOK_COMMON_H_ */