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Commit 45ed59f8 authored by Peter Eastman's avatar Peter Eastman
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Moved obsolete GBSA reference code back to where it was before

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platforms/reference/src/Gbsa/C-source/CommonSimTk.h deleted 100644 → 0
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/* 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 __CommonSimTk_H__
#define __CommonSimTk_H__
// include file containing entries commonly used
// STL includes
#include <vector>
#include <map>
#include <set>
#include <string>
// generic c includes
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <ctype.h>
#include <math.h>
#include <assert.h>
// ---------------------------------------------------------------------------------------
typedef std::vector<int> IntVector;
typedef IntVector::iterator IntVectorI;
typedef IntVector::const_iterator IntVectorCI;
typedef IntVector::reverse_iterator IntVectorRI;
typedef IntVector::const_reverse_iterator IntVectorCRI;
typedef std::map<int, int> IntIntMap;
typedef IntIntMap::iterator IntIntMapI;
typedef IntIntMap::const_iterator IntIntMapCI;
typedef std::set<int> IntSet;
typedef IntSet::iterator IntSetI;
typedef IntSet::const_iterator IntSetCI;
typedef std::multiset<int> IntMultiSet;
typedef IntMultiSet::iterator IntMultiSetI;
typedef IntMultiSet::const_iterator IntMultiSetCI;
typedef std::vector<std::string> StringVector;
typedef StringVector::iterator StringVectorI;
typedef StringVector::const_iterator StringVectorCI;
typedef std::map<std::string, std::string> StringStringMap;
typedef StringStringMap::iterator StringStringMapI;
typedef StringStringMap::const_iterator StringStringMapCI;
// ---------------------------------------------------------------------------------------
// StringComparisonForMap: used to compare strings in STL maps w/ strings as keys
class StringComparisonForMapPtr : public std::binary_function< std::string*, std::string*, bool > {
public:
bool operator()( const std::string* str1, const std::string* str2 ) const {
return strcmp( str1->c_str(), str2->c_str() ) < 0;
}
};
class StringComparisonForMap : public std::binary_function< const std::string&, const std::string&, bool > {
public:
bool operator()( const std::string& str1, const std::string& str2 ) const {
return strcmp( str1.c_str(), str2.c_str() ) < 0;
}
};
// ---------------------------------------------------------------------------------------
// Used to compare integers for sorting, ...
int numericCompareI( const void* point1, const void* point2 );
// ---------------------------------------------------------------------------------------
// string-string map and iterator definitions
typedef std::map<std::string, std::string, StringComparisonForMap> StringMap;
typedef StringMap::iterator StringMapI;
typedef StringMap::const_iterator StringMapCI;
// string set and iterator definitions
typedef std::set<std::string, StringComparisonForMap> StringSet;
typedef StringSet::iterator StringSetI;
typedef StringSet::const_iterator StringSetCI;
// ---------------------------------------------------------------------------------------
#endif // __CommonSimTk_H__
platforms/reference/src/Gbsa/C-source/CpuGbsa.cpp deleted 100644 → 0
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platforms/reference/src/Gbsa/C-source/CpuGbsa.h deleted 100644 → 0
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/* 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 __CpuGbsa_H__
#define __CpuGbsa_H__
#include "GbsaParameters.h"
// ---------------------------------------------------------------------------------------
class CpuGbsa {
private:
// used for direct calls from Gromacs
static CpuGbsa* _cpuGbsa;
// GBSA parameters
GbsaParameters* _gbsaParameters;
// flag to signal whether ACE approximation
// is to be included
bool _includeAceApproximation;
// work arrays and their accessors
float* _gbsaBornForce;
float* _gbsaBornRadiiTemp;
float* getGbsaBornForce( void );
float* getGbsaBornRadiiTemp( void );
// initialize data members (more than
// one constructor, so centralize intialization here)
void initializeDataMembers( void );
// convert units for energy/force
float _forceConversionFactor;
float _energyConversionFactor;
// Ed, 2007-04-27: Store the energy internally
float _gbsaEnergy;
public:
// constructors/destructor
CpuGbsa( int numberOfAtoms, const t_topology* top, FILE* log );
CpuGbsa( GbsaParameters* gbsaParameters );
~CpuGbsa( );
// override of new/delete
static void* operator new( size_t size );
static void operator delete( void *p );
static void* operator new[]( size_t size );
static void operator delete[]( void *p );
// accessor for the energy
float getEnergy( void ) const { return _gbsaEnergy; }
// accessor for static member _cpuGbsa
static int setCpuGbsa( CpuGbsa* cpuGbsa ){ _cpuGbsa = cpuGbsa; return 0; };
static CpuGbsa* getCpuGbsa( void ){ return _cpuGbsa; };
static int deleteCpuGbsa( void );
// accessors for Gbsa parameters
GbsaParameters* getGbsaParameters( void ) const { return _gbsaParameters; };
int setGbsaParameters( GbsaParameters* gbsaParameters ){ _gbsaParameters = gbsaParameters; return 0; };
// accessors ACE approximation
bool includeAceApproximation( void ) const { return _includeAceApproximation; };
int setIncludeAceApproximation( bool includeAceApproximation ){ _includeAceApproximation = includeAceApproximation; return 0; };
// energy/force conversion factors
float getForceConversionFactor( void ) const { return _forceConversionFactor; };
float getEnergyConversionFactor( void ) const { return _energyConversionFactor; };
int setForceConversionFactor( float forceConversionFactor ){ _forceConversionFactor = forceConversionFactor; return 0; };
int setEnergyConversionFactor( float energyConversionFactor ){ _energyConversionFactor = energyConversionFactor; return 0; };
/**---------------------------------------------------------------------------------------
Get Born energy and forces based on J. Phys. Chem. A V101 No 16, p. 3005 (Simbios)
@param atomCoordinates atomic coordinates
@param partialCharges partial charges
@param forces forces (output); if not set on input, then memory is allocated
@param log if set, then print error messages to log file
@return force array
--------------------------------------------------------------------------------------- */
static float** computeGbsaForces( const rvec *atomCoordinates, const float* partialCharges,
float** forces, FILE* log );
/**---------------------------------------------------------------------------------------
Get Born radii based on J. Phys. Chem. A V101 No 16, p. 3005 (Simbios)
@param atomCoordinates atomic coordinates
@param bornRadii output array of Born radii
@return array of Born radii
--------------------------------------------------------------------------------------- */
int computeBornRadii( const rvec *atomCoordinates, float* bornRadii );
/**---------------------------------------------------------------------------------------
Get exclusions for specific atom (Simbios)
@param numberOfAtoms number of atoms
@param gbsaBondsArray array of bonds
@param atomI atom index of atom for which exclusions are to be set
@param exclusionWorkArray exclusionWorkArray[j] = 1, if atom j is to be excluded
value may be null on input in which space is allocated
@param previousIndex previousIndex -- if < 0, then iniitialize all entries to 0
@param log if set, then print error messages to log file
@return 0
--------------------------------------------------------------------------------------- */
int getExclusionsForAtom( int numberOfAtoms, gbsaBonds** gbsaBondsArray,
int atomI, int* exclusionWorkArray, int previousIndex,
FILE* log ) const;
/**---------------------------------------------------------------------------------------
Set exclusions for specific atom (Simbios)
@param gbsaBonds gbsa bond
@param setValue set value
@param exclusionWorkArray exclusionWorkArray[j] = 1, if atom j is to be excluded
value may be null on input in which space is allocated
@param log if set, then print error messages to log file
@return array of Born radii
--------------------------------------------------------------------------------------- */
int setExclusionValue( gbsaBonds* gbsaBonds, int setValue, int* exclusionWorkArray, FILE* log ) const;
/**---------------------------------------------------------------------------------------
Get Born energy and forces based on J. Phys. Chem. A V101 No 16, p. 3005 (Simbios)
@param bornRadii Born radii
@param atomCoordinates atomic coordinates
@param partialCharges partial charges
@param forces forces
@return force array
--------------------------------------------------------------------------------------- */
float** computeBornEnergyForces( float* bornRadii, const rvec *atomCoordinates,
const float* partialCharges, float** forces );
/**---------------------------------------------------------------------------------------
Get Born energy and forces based on J. Phys. Chem. A V101 No 16, p. 3005 (Simbios)
@param top GMX t_topology struct
@param bornRadii Born radii
@param atomCoordinates atomic coordinates
@param partialCharges atom partial charges
@param energy energy
@param debugOn enable debug
@param debugAtomI debug flag for atomI (outer loop atom)
@param debugAtomJ debug flag for atomJ (inner loop atom)
@param debugReport flag signalling what quantities are to be saved for comparisons
@param saveLoopForces flag signalling whether intermediate results for each loop
are to be retained
@param printOn print flag
@param unsetDebugValue ?
@param numberOfDebugStreams
number of debug streams
@param debugStreams array of debug streams
@param forces force array (may be null)
@param log if set, then print error messages to log file
@return 0 always; fixed value for G_pol in array 'gPolFixed'
--------------------------------------------------------------------------------------- */
float** computeBornEnergyForcesDebug( const t_topology* top,
float* bornRadii, const rvec *atomCoordinates,
const float* partialCharges, float* energy,
bool debugOn, int debugAtomI, int debugAtomJ,
int debugReport, bool* saveLoopForces,
bool printOn, float unsetDebugValue, int numberOfDebugStreams,
float** debugStreams, float** forces, FILE* log );
/**---------------------------------------------------------------------------------------
Write Born energy and forces (Simbios)
@param top GMX t_topology struct
@param atomCoordinates atomic coordinates
@param partialCharges partial atom charges
@param forces force array
@param gbsaResultsFileName output file name
@param log if set, then print error messages to log file
@return 0 always
--------------------------------------------------------------------------------------- */
int writeBornEnergyForces( const t_topology* top, const rvec *atomCoordinates,
const float* partialCharges, float** forces,
const char* gbsaResultsFileName, FILE* log ) const;
/**---------------------------------------------------------------------------------------
Print state to log file (Simbios)
title title (optional)
log print state to log file
@return 0 always;
--------------------------------------------------------------------------------------- */
int logState( const char* title, FILE* log ) const;
/**---------------------------------------------------------------------------------------
Write Tinker xyz file (Simbios)
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param header header
@param xyzFileName output file name
@param gbsaBondsArray bond array -- used to print 1-2 bonds
@param top GMX t_topology struct
@param log if set, then print error messages to log file
@return 0 unless error detected
Currently no attempt is made to get the atom name/type to accurately
reflect the Tinker names/types. Rather method is used to output atoms
in Gromacs order and then reorder those in a corresponding xyz file
w/ the correct atom names/types so that they match the Gromacs order
This makes it easier to compare results between Gromacs and Tinker
--------------------------------------------------------------------------------------- */
static int writeXyzFile( int numberOfAtoms, const rvec* atomCoordinates,
const char* header, const char* xyzFileName,
gbsaBonds** gbsaBondsArray, const t_topology* top, FILE* log );
};
// ---------------------------------------------------------------------------------------
#endif // __CpuGbsa_H__
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platforms/reference/src/Gbsa/C-source/RealTypeSimTk.h deleted 100644 → 0
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/* 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 __RealSimTk_H_
#define __RealSimTk_H__
#ifndef RealType
#define RealType 2
#endif
#if RealType == 1
#define Real float
#define SQRT sqrtf
#define POW powf
#define SIN sinf
#define COS cosf
#define TAN tanf
// LOG is used in Vishal's gpu code; modifying LOG -> LN
#define LN logf
#define EXP expf
#define FABS fabsf
#define ACOS acosf
#define ASIN asinf
#define ATAN atanf
#else
#define Real double
#define SQRT sqrt
#define POW pow
#define SIN sin
#define COS cos
#define TAN tan
// LOG is used in Vishal's gpu code; modifying LOG -> LN
#define LN log
#define EXP exp
#define FABS fabs
#define ACOS acos
#define ASIN asin
#define ATAN atan
#endif
#define DOT3(u,v) ((u[0])*(v[0]) + (u[1])*(v[1]) + (u[2])*(v[2]))
#define MATRIXDOT3(u,v) u[0]*v[0] + u[1]*v[1] + u[2]*v[2] + \
u[3]*v[3] + u[4]*v[4] + u[5]*v[5] + \
u[6]*v[6] + u[7]*v[7] + u[8]*v[8]
#define PI 3.141592653589f
#define TWO_SIX 1.122462048309372981f
#define RADIAN 57.29577951308f
#define LOG_TEN 2.302585092994045684f
#define SQRT_TWO 1.41421356237309504f
#define RADIAN_INVERSE 0.01745329252f
#endif // __RealSimTk_H__
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/* 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.
*/
#include "CpuGbsa.h"
// 'gmxGbsa.h' has declarations for cpuSetGbsaParameters() and
// and cpuCalculateGbsaForces()
#include "gmxGbsa.h"
/**---------------------------------------------------------------------------------------
Example calling sequence:
float** forces = NULL;
float energy;
cpuSetGbsaParameters( mdatoms->nr, top, stdlog );
// if 'forces' array is initially null, then memory will
// be allocated by cpuCalculateGbsaForces()
// format for 'forces' array:
// forces[3][numberAtoms]
forces = cpuCalculateGbsaForces( x, mdatoms->chargeA, &energy,
forces, stdlog );
--------------------------------------------------------------------------------------- */
/**---------------------------------------------------------------------------------------
Setup for Gbsa calculations
@param numberOfAtoms number of atoms
@param top Gromacs t_topology (as in md.c)
@param log log reference (stdlog in md.c)
@param includeAceApproximation if true, then include nonpolar
ACE term in calculataions
@param innerDielectric nonsolvent dielectric
@param solventDielectric solvent dielectric
function creates a CpuGbsa instance; the created object is a static member of the
class CpuGbsa; when the force routine (a static method) is called, the object is
used to compute the forces and energy
@return 0
--------------------------------------------------------------------------------------- */
extern "C" int
cpuSetGbsaParameters( int numberOfAtoms, const t_topology* top, FILE* log,
bool includeAceApproximation,
float innerDielectric, float solventDielectric ){
// ---------------------------------------------------------------------------------------
static bool printGbsaParameters = false;
static const char* methodName = "\ncpuSetGbsaParameters: ";
// static bool debug = true;
static bool debug = false;
// ---------------------------------------------------------------------------------------
// toggle whether logging enabled
FILE* cpuGbsaLog = debug ? log : NULL;
CpuGbsa* cpuGbsa = new CpuGbsa( numberOfAtoms, top, cpuGbsaLog );
// include/not include ACE approximation (nonpolar solvation)
cpuGbsa->setIncludeAceApproximation( includeAceApproximation );
// cpuGbsa->setIncludeAceApproximation( false );
// cpuGbsa->setIncludeAceApproximation( true );
// default values are 1.0/1.0 -> gives values in 10.0*kcal/A (force) and 100*kcal/A (energy)
// if values are 0.41868/0.41868 -> gives values in Gromacs units kJ/nm
if( !debug ){
cpuGbsa->setForceConversionFactor( 0.41868f );
cpuGbsa->setEnergyConversionFactor( 0.41868f );
}
// dielectrics
cpuGbsa->getGbsaParameters()->setSolventDielectric( solventDielectric );
cpuGbsa->getGbsaParameters()->setInnerDielectric( innerDielectric );
// set static member for subsequent calls to calculate forces/energy
CpuGbsa::setCpuGbsa( cpuGbsa );
// ---------------------------------------------------------------------------------------
if( log != NULL ){
cpuGbsa->logState( methodName, log );
(void) fprintf( log, "%s done", methodName );
(void) fflush( log );
}
// ---------------------------------------------------------------------------------------
return 0;
}
/**---------------------------------------------------------------------------------------
Calculate Gbsa forces and energy \n
@param atomCoordinates Gromacs atom coordinates ('x' in md.c)
@param partialCharges Gromacs charges ('mdatoms->chargeA' in md.c)
@param energy output energy
@param forces output forces (format currently forces[3][numberOfAtoms])
if 'forces' reference is NULL upon input, then \n
memory is allocated for array; responsibilty of callee \n
to free \n
delete forces[0]; \n
delete forces; \n
Note memory is allocated as single block of size \n
3*numberOfAtoms*sizeof( float ), so only free \n
'forces[0]' \n
@param log log reference (stdlog in md.c)
Function calls a static method in CpuGbsa class to calculate forces/energy
Logging can be toggled by setting cpuGbsaLog to input 'log' or NULL
@return force array; energy is returned in *energy
--------------------------------------------------------------------------------------- */
extern "C" float**
cpuCalculateGbsaForces( const rvec *atomCoordinates, const float* partialCharges,
float** forces, FILE* log ){
// ---------------------------------------------------------------------------------------
static const char* methodName = "\ncpuCalculateGbsaForces: ";
// ---------------------------------------------------------------------------------------
// FILE* cpuGbsaLog = NULL;
FILE* cpuGbsaLog = log;
// (void) fprintf( log, "%s start", methodName );
// (void) fflush( log );
forces = CpuGbsa::computeGbsaForces( atomCoordinates, partialCharges, forces, cpuGbsaLog );
// *energy = CpuGbsa::getCpuGbsa()->getEnergy();
// (void) fprintf( log, "%s done E=%.4f", methodName, *energy );
// (void) fflush( log );
return forces;
}
/**---------------------------------------------------------------------------------------
Retrieve the calculated Gbsa energy from the static class member
@return the calculated Gbsa energy from the static class member
--------------------------------------------------------------------------------------- */
extern "C" float cpuGetEnergy( void ){
return CpuGbsa::getCpuGbsa()->getEnergy();
}
/**---------------------------------------------------------------------------------------
Delete the Gbsa associated object(s)
@return 0 if static CpuGbsa object was set; else return -1
--------------------------------------------------------------------------------------- */
extern "C" int cpuDeleteGbsaParameters( void ){
return CpuGbsa::deleteCpuGbsa();
}
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/* 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 __GmxGbsa_H__
#define __GmxGbsa_H__
// Include gromacs types
#include "typedefs.h"
#ifdef __cplusplus
#define externC extern "C"
#else
#define externC extern
#endif
/* Set parameters for GBSA on CPU (Simbios) */
externC int
cpuSetGbsaParameters( int numberOfAtoms, const t_topology* top, FILE* log,
bool includeAceApproximation,
float innerDielectric, float solventDielectric );
/* Calculate GBSA forces on CPU (Simbios) (test/example) */
externC float**
cpuCalculateGbsaForces( const rvec *atomCoordinates, const float* partialCharges,
float** forces, FILE* log );
/* Get GBSA energy */
externC float cpuGetEnergy( void );
/* Delete Gbsa memory */
externC int cpuDeleteGbsaParameters( void );
#endif
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Microsoft Visual Studio Solution File, Format Version 9.00
# Visual Studio 2005
Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "Gbsa", "Gbsa-old-2005.vcproj", "{519D78EF-DC26-47E3-B240-994A447774E5}"
EndProject
Global
GlobalSection(SolutionConfigurationPlatforms) = preSolution
Debug|Win32 = Debug|Win32
Release|Win32 = Release|Win32
EndGlobalSection
GlobalSection(ProjectConfigurationPlatforms) = postSolution
{519D78EF-DC26-47E3-B240-994A447774E5}.Debug|Win32.ActiveCfg = Debug|Win32
{519D78EF-DC26-47E3-B240-994A447774E5}.Debug|Win32.Build.0 = Debug|Win32
{519D78EF-DC26-47E3-B240-994A447774E5}.Release|Win32.ActiveCfg = Release|Win32
{519D78EF-DC26-47E3-B240-994A447774E5}.Release|Win32.Build.0 = Release|Win32
EndGlobalSection
GlobalSection(SolutionProperties) = preSolution
HideSolutionNode = FALSE
EndGlobalSection
EndGlobal
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