/* Portions copyright (c) 2006 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. */ #ifndef __CpuGBVI_H__ #define __CpuGBVI_H__ #include "GBVIParameters.h" #include "CpuImplicitSolvent.h" // --------------------------------------------------------------------------------------- class CpuGBVI : public CpuImplicitSolvent { private: // GB/VI parameters GBVIParameters* _gbviParameters; // initialize data members (more than // one constructor, so centralize intialization here) void _initializeGBVIDataMembers( void ); public: /**--------------------------------------------------------------------------------------- Constructor @param implicitSolventParameters ImplicitSolventParameters reference @return CpuImplicitSolvent object --------------------------------------------------------------------------------------- */ CpuGBVI( ImplicitSolventParameters* gbviParameters ); /**--------------------------------------------------------------------------------------- Destructor --------------------------------------------------------------------------------------- */ ~CpuGBVI( ); /**--------------------------------------------------------------------------------------- Return GBVIParameters @return GBVIParameters --------------------------------------------------------------------------------------- */ GBVIParameters* getGBVIParameters( void ) const; /**--------------------------------------------------------------------------------------- Set ImplicitSolventParameters @param ImplicitSolventParameters @return SimTKOpenMMCommon::DefaultReturn --------------------------------------------------------------------------------------- */ int setGBVIParameters( GBVIParameters* gbviParameters ); /**--------------------------------------------------------------------------------------- Get Born radii based on Eq. 3 of Labute paper [JCC 29 p. 1693-1698 2008]) @param atomCoordinates atomic coordinates @param bornRadii output array of Born radii @param gbviChain not used @return SimTKOpenMMCommon::DefaultReturn --------------------------------------------------------------------------------------- */ int computeBornRadii( RealOpenMM** atomCoordinates, RealOpenMM* bornRadii, RealOpenMM* gbviChain = NULL ); /**--------------------------------------------------------------------------------------- Get Born energy and forces (not used) @param bornRadii Born radii @param atomCoordinates atomic coordinates @param partialCharges partial charges @param forces forces @return force array --------------------------------------------------------------------------------------- */ int computeBornEnergyForces( RealOpenMM* bornRadii, RealOpenMM** atomCoordinates, const RealOpenMM* partialCharges, RealOpenMM** forces ); int computeBornEnergyForcesPrint( RealOpenMM* bornRadii, RealOpenMM** atomCoordinates, const RealOpenMM* partialCharges, RealOpenMM** forces ); /**--------------------------------------------------------------------------------------- Get state title title (optional) @return state string --------------------------------------------------------------------------------------- */ std::string getStateString( const char* title ) const; /**--------------------------------------------------------------------------------------- Write Born energy and forces (Simbios) @param atomCoordinates atomic coordinates @param partialCharges partial atom charges @param forces force array @param resultsFileName output file name @return SimTKOpenMMCommon::DefaultReturn if file opened; else return SimTKOpenMMCommon::ErrorReturn --------------------------------------------------------------------------------------- */ int writeBornEnergyForces( RealOpenMM** atomCoordinates, const RealOpenMM* partialCharges, RealOpenMM** forces, const std::string& resultsFileName ) const; /**--------------------------------------------------------------------------------------- Write results from first loop @param atomCoordinates atomic coordinates @param RealOpenMM forces forces @param outputFileName output file name @return SimTKOpenMMCommon::DefaultReturn unless file cannot be opened in which case return SimTKOpenMMCommon::ErrorReturn --------------------------------------------------------------------------------------- */ static int writeForceLoop1( int numberOfAtoms, RealOpenMM** forces, const RealOpenMM* bornForce, const std::string& outputFileName ); /**--------------------------------------------------------------------------------------- Write results @param numberOfAtoms number of atoms @param chunkSizes vector of chunk sizes for realRealOpenMMVector @param realRealOpenMMVector vector of RealOpenMM** @param realVector vector of RealOpenMM* @param outputFileName output file name @return SimTKOpenMMCommon::DefaultReturn unless file cannot be opened in which case return SimTKOpenMMCommon::ErrorReturn --------------------------------------------------------------------------------------- */ static int writeForceLoop( int numberOfAtoms, const IntVector& chunkSizes, const RealOpenMMPtrPtrVector& realRealOpenMMVector, const RealOpenMMPtrVector& realVector, const std::string& outputFileName ); /**--------------------------------------------------------------------------------------- Get volume Eq. 4 of Labute paper [JCC 29 p. 1693-1698 2008]) @param r distance between atoms i & j @param R atomic radius @param S scaled atomic radius @return volume --------------------------------------------------------------------------------------- */ static RealOpenMM getVolume( RealOpenMM r, RealOpenMM R, RealOpenMM S ); /**--------------------------------------------------------------------------------------- Get L (analytical solution for volume integrals) @param r distance between atoms i & j @param R atomic radius @param S scaled atomic radius @return L value (Eq. 4 of Labute paper [JCC 29 p. 1693-1698 2008]) --------------------------------------------------------------------------------------- */ static RealOpenMM getL( RealOpenMM r, RealOpenMM x, RealOpenMM S ); /**--------------------------------------------------------------------------------------- Get partial derivative of L wrt r @param r distance between atoms i & j @param R atomic radius @param S scaled atomic radius @return partial derivative based on Eq. 4 of Labute paper [JCC 29 p. 1693-1698 2008]) --------------------------------------------------------------------------------------- */ static RealOpenMM dL_dr( RealOpenMM r, RealOpenMM x, RealOpenMM S ); /**--------------------------------------------------------------------------------------- Get partial derivative of L wrt x @param r distance between atoms i & j @param R atomic radius @param S scaled atomic radius @return partial derivative based on Eq. 4 of Labute paper [JCC 29 p. 1693-1698 2008]) --------------------------------------------------------------------------------------- */ static RealOpenMM dL_dx( RealOpenMM r, RealOpenMM x, RealOpenMM S ); /**--------------------------------------------------------------------------------------- Sgb function @param t r*r*G_i*G_j @return Sgb (p. 1694 of Labute paper [JCC 29 p. 1693-1698 2008]) --------------------------------------------------------------------------------------- */ static RealOpenMM Sgb( RealOpenMM t ); /**--------------------------------------------------------------------------------------- Get GB/VI energy @param bornRadii Born radii @param atomCoordinates atomic coordinates @param partialCharges partial charges @return energy --------------------------------------------------------------------------------------- */ RealOpenMM computeBornEnergy( const RealOpenMM* bornRadii, RealOpenMM** atomCoordinates, const RealOpenMM* partialCharges ); /**--------------------------------------------------------------------------------------- Get GB/VI forces @param bornRadii Born radii @param atomCoordinates atomic coordinates @param partialCharges partial charges @param forces output forces @return SimTKOpenMMCommon::DefaultReturn; --------------------------------------------------------------------------------------- */ int computeBornForces( const RealOpenMM* bornRadii, RealOpenMM** atomCoordinates, const RealOpenMM* partialCharges, RealOpenMM** inputForces ); /**--------------------------------------------------------------------------------------- Get volume Eq. 4 of Labute paper [JCC 29 p. 1693-1698 2008]) @param r distance between atoms i & j @param R atomic radius @param S scaled atomic radius @return volume --------------------------------------------------------------------------------------- */ static double getVolumeD( double r, double R, double S ); /**--------------------------------------------------------------------------------------- Get L (analytical solution for volume integrals) @param r distance between atoms i & j @param R atomic radius @param S scaled atomic radius @return L value (Eq. 4 of Labute paper [JCC 29 p. 1693-1698 2008]) --------------------------------------------------------------------------------------- */ static double getLD( double r, double x, double S ); /**--------------------------------------------------------------------------------------- Get partial derivative of L wrt r @param r distance between atoms i & j @param R atomic radius @param S scaled atomic radius @return partial derivative based on Eq. 4 of Labute paper [JCC 29 p. 1693-1698 2008]) --------------------------------------------------------------------------------------- */ static double dL_drD( double r, double x, double S ); /**--------------------------------------------------------------------------------------- Get partial derivative of L wrt x @param r distance between atoms i & j @param R atomic radius @param S scaled atomic radius @return partial derivative based on Eq. 4 of Labute paper [JCC 29 p. 1693-1698 2008]) --------------------------------------------------------------------------------------- */ static double dL_dxD( double r, double x, double S ); }; // --------------------------------------------------------------------------------------- #endif // __CpuGBVI_H__