Skip to content

GitLab

Commit 45ed59f8 authored by Peter Eastman's avatar Peter Eastman
Browse files

Moved obsolete GBSA reference code back to where it was before

parent f3e77e33
Hide whitespace changes
Inline Side-by-side
Showing with 0 additions and 784 deletions
platforms/reference/src/Gbsa/gmxGbsa.h deleted 100644 → 0
View file @ f3e77e33
/* 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
platforms/reference/src/Gbsa/gromacsCpuGrycukInterface.cpp deleted 100644 → 0
View file @ f3e77e33
/* 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 "SimTKOpenMMGromacsUtilities.h"
#include "gromacsCpuGrycukInterface.h"
#include "cpuGrycukInterface.h"
#include "CpuGrycuk.h"
#include "SimTKOpenMMLog.h"
#include "SimTKOpenMMUtilities.h"
#include "SimTKOpenMMRealType.h"
/**---------------------------------------------------------------------------------------
Setup for Grycuk calculations from Gromacs
@param top Gromacs t_topology data struct
@param log log reference (stdlog in md.c)
@param includeAceApproximation if true, then include nonpolar
ACE term in calculations
@param soluteDielectric solute dielectric
@param solventDielectric solvent dielectric
The method creates a CpuGrycuk instance
The created object is a static member of the
class CpuGrycuk; when the force routine, cpuCalculateGrycukForces, is called,
the object is used to compute the forces and energy
The arrays atomicRadii & grycukScaleFactors are allocated off heap
@return 0
--------------------------------------------------------------------------------------- */
extern "C"
int gromacsCpuInitialSetupGrycuk( const t_topology* top, FILE* log, int includeAceApproximation,
float soluteDielectric, float solventDielectric ){
// ---------------------------------------------------------------------------------------
static const char* methodName = "\ngromacsGrycukCpuInitialSetup: ";
static int debug = true;
// ---------------------------------------------------------------------------------------
// set log file, if available
fprintf( log, "%s %.3f %.3f %d", methodName, soluteDielectric, solventDielectric, includeAceApproximation );
fflush( log );
if( soluteDielectric < 1.0 ){
soluteDielectric = 1.0f;
}
if( solventDielectric < 50.0 ){
solventDielectric = 78.3f;
}
if( log ){
SimTKOpenMMLog::setSimTKOpenMMLog( log );
}
// Grycuk scale factors based on atomic mass
int numberOfAtoms = top->atoms.nr;
RealOpenMM* grycukScaleFactors = (RealOpenMM*) malloc( sizeof( RealOpenMM )*numberOfAtoms );
SimTKOpenMMGromacsUtilities::getObcScaleFactors( top, grycukScaleFactors );
// get/set atomic radii (from file)
RealOpenMM* atomicRadii = (RealOpenMM*) malloc( sizeof( RealOpenMM )*numberOfAtoms );
std::string parameterFileName = GrycukParameters::ParameterFileName;
int returnStatus = SimTKOpenMMGromacsUtilities::getMacroModelAtomicRadii( numberOfAtoms,
parameterFileName,
top, atomicRadii );
// abort if problem reading parameter file
if( returnStatus != SimTKOpenMMCommon::DefaultReturn ){
(void) fprintf( (log ? log : stderr), "%s problem getting atomic radii from file=<%s>",
methodName, parameterFileName.c_str() );
(void) fflush( log );
exit(-1);
} else if( log ){
(void) fprintf( log, "%s obtained atomic radii from file=<%s>",
methodName, parameterFileName.c_str() );
(void) fflush( log );
}
int status = cpuSetGrycukParameters( numberOfAtoms, atomicRadii, grycukScaleFactors,
includeAceApproximation, soluteDielectric,
solventDielectric, log );
// set flags so that atomicRadii & scaleFactor arrays are deleted
// if parameter array is deleted
CpuImplicitSolvent* cpuImplicitSolvent = CpuImplicitSolvent::getCpuImplicitSolvent();
CpuGrycuk* cpuGrycuk = static_cast<CpuGrycuk*> (cpuImplicitSolvent);
GrycukParameters* grycukParameters = cpuGrycuk->getGrycukParameters();
grycukParameters->setOwnAtomicRadii( true );
grycukParameters->setOwnScaleFactors( true );
return status;
}
/**---------------------------------------------------------------------------------------
Calculate Grycuk forces and energy
@param atomCoordinates Gromacs atom coordinates ('x' in md.c)
@param partialCharges Gromacs charges ('mdatoms->chargeA' in md.c)
@param forces output forces in kJ/mol.A; the computed forces
are added to the entries in the array
Function calls a static method in CpuGrycuk class to calculate forces/energy
@return 0
--------------------------------------------------------------------------------------- */
extern "C" int gromacsCpuCalculateGrycukForces( const rvec* atomCoordinates,
const RealOpenMM* partialChargesIn,
rvec* forces ){
// ---------------------------------------------------------------------------------------
static const char* methodName = "\ngromacsCpuCalculateGrycukForces: ";
static RealOpenMM* partialCharges = NULL;
static RealOpenMM** coordinates = NULL;
static RealOpenMM** localForces = NULL;
static const int updateBornRadii = 0;
// ---------------------------------------------------------------------------------------
CpuImplicitSolvent* cpuImplicitSolvent = CpuImplicitSolvent::getCpuImplicitSolvent();
if( cpuImplicitSolvent == NULL ){
(void) fprintf( stderr, "%s implicit solvent not initialized -- aborting" );
(void) fflush( stderr );
exit(-1);
}
int numberOfAtoms = cpuImplicitSolvent->getNumberOfAtoms();
// first time through, allocate memory for coordinates, ..
// Note: memory never freed!
if( coordinates == NULL ){
coordinates = SimTKOpenMMUtilities::allocateTwoDRealOpenMMArray( numberOfAtoms, 3, NULL, true, (RealOpenMM) 0.0 );
localForces = SimTKOpenMMUtilities::allocateTwoDRealOpenMMArray( numberOfAtoms, 3, NULL, true, (RealOpenMM) 0.0 );
// required if Gromacs float != RealOpenMM (i.e., RealOpenMM = double)
partialCharges = new RealOpenMM[numberOfAtoms];
for( int ii = 0; ii < numberOfAtoms; ii++ ){
partialCharges[ii] = (RealOpenMM) partialChargesIn[ii];
}
}
// convert coordinates from nm -> Angstrom
RealOpenMM distanceScaleFactor = (RealOpenMM) 10.0;
for( int ii = 0; ii < numberOfAtoms; ii++ ){
coordinates[ii][0] = (RealOpenMM) (distanceScaleFactor*atomCoordinates[ii][0]);
coordinates[ii][1] = (RealOpenMM) (distanceScaleFactor*atomCoordinates[ii][1]);
coordinates[ii][2] = (RealOpenMM) (distanceScaleFactor*atomCoordinates[ii][2]);
}
CpuImplicitSolvent::computeImplicitSolventForces( coordinates, partialCharges,
localForces, updateBornRadii );
float forceScaleFactor = 0.4184f;
for( int ii = 0; ii < numberOfAtoms; ii++ ){
forces[ii][0] += (float) forceScaleFactor*localForces[ii][0];
forces[ii][1] += (float) forceScaleFactor*localForces[ii][1];
forces[ii][2] += (float) forceScaleFactor*localForces[ii][2];
}
//RealOpenMM energy = cpuImplicitSolvent->getEnergy();
//printf( "\ngromacsCpuCalculateGrycukForces E=%.5e", energy );
return 0;
}
platforms/reference/src/Gbsa/gromacsCpuGrycukInterface.h deleted 100644 → 0
View file @ f3e77e33
/* 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 __GromacsCpuGrycukInterface_H__
#define __GromacsCpuGrycukInterface_H__
#ifdef __cplusplus
#define externC extern "C"
#else
#define externC extern
#endif
/**---------------------------------------------------------------------------------------
Setup for Grycuk calculations
@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 soluteDielectric solute dielectric
@param solventDielectric solvent dielectric
Method creates a CpuGrycuk instance w/ Grycuk parameters set
The created object is a static member of the
class CpuGrycuk that is referenced to calculate the implicit solvation
forces and energy
@return 0
--------------------------------------------------------------------------------------- */
externC
int gromacsCpuInitialSetupGrycuk( const t_topology* top, FILE* log, int includeAceApproximation,
float soluteDielectric, float solventDielectric );
/**---------------------------------------------------------------------------------------
Calculate Grycuk forces and energy
@param atomCoordinates Gromacs atom coordinates ('x' in md.c)
@param partialCharges Gromacs charges ('mdatoms->chargeA' in md.c)
@param forces output forces in kJ/mol.A; the computed forces
are added to the entries in the array
Function calls a static method in CpuGrycuk class to calculate forces/energy
@return 0
--------------------------------------------------------------------------------------- */
externC
int gromacsCpuCalculateGrycukForces( const rvec* atomCoordinates, const float* partialChargesIn,
rvec* forces );
#endif
platforms/reference/src/Gbsa/gromacsCpuObcInterface.cpp deleted 100644 → 0
View file @ f3e77e33
/* 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 "SimTKOpenMMGromacsUtilities.h"
#include "gromacsCpuObcInterface.h"
#include "cpuObcInterface.h"
#include "CpuObc.h"
#include "SimTKOpenMMLog.h"
#include "SimTKOpenMMUtilities.h"
#include "SimTKOpenMMRealType.h"
/**---------------------------------------------------------------------------------------
Setup for Obc calculations from Gromacs
@param top Gromacs t_topology data struct
@param log log reference (stdlog in md.c)
@param includeAceApproximation if true, then include nonpolar
ACE term in calculations
@param soluteDielectric solute dielectric
@param solventDielectric solvent dielectric
The method creates a CpuObc instance
The created object is a static member of the
class CpuObc; when the force routine, cpuCalculateObcForces, is called,
the object is used to compute the forces and energy
The arrays atomicRadii & obcScaleFactors are allocated off heap
@return 0
--------------------------------------------------------------------------------------- */
extern "C"
int gromacsCpuInitialSetupObc( const t_topology* top, FILE* log, int includeAceApproximation,
float soluteDielectric, float solventDielectric ){
// ---------------------------------------------------------------------------------------
static const char* methodName = "\ngromacsObcCpuInitialSetup: ";
static int debug = true;
// ---------------------------------------------------------------------------------------
// set log file, if available
fprintf( log, "%s %.3f %.3f %d", methodName, soluteDielectric, solventDielectric, includeAceApproximation );
fflush( log );
if( soluteDielectric < 1.0 ){
soluteDielectric = 1.0f;
}
if( solventDielectric < 50.0 ){
solventDielectric = 78.3f;
}
if( log ){
SimTKOpenMMLog::setSimTKOpenMMLog( log );
}
// OBC scale factors based on atomic mass
int numberOfAtoms = top->atoms.nr;
RealOpenMM* obcScaleFactors = (RealOpenMM*) malloc( sizeof( RealOpenMM )*numberOfAtoms );
SimTKOpenMMGromacsUtilities::getObcScaleFactors( top, obcScaleFactors );
// get/set atomic radii (from file)
RealOpenMM* atomicRadii = (RealOpenMM*) malloc( sizeof( RealOpenMM )*numberOfAtoms );
std::string parameterFileName = ObcParameters::ParameterFileName;
int returnStatus = SimTKOpenMMGromacsUtilities::getMacroModelAtomicRadii( numberOfAtoms,
parameterFileName,
top, atomicRadii );
// abort if problem reading parameter file
if( returnStatus != SimTKOpenMMCommon::DefaultReturn ){
(void) fprintf( (log ? log : stderr), "%s problem getting atomic radii from file=<%s>",
methodName, parameterFileName.c_str() );
(void) fflush( log );
exit(-1);
} else if( log ){
(void) fprintf( log, "%s obtained atomic radii from file=<%s>",
methodName, parameterFileName.c_str() );
(void) fflush( log );
}
int status = cpuSetObcParameters( numberOfAtoms, atomicRadii, obcScaleFactors,
includeAceApproximation, soluteDielectric,
solventDielectric, log );
// set flags so that atomicRadii & scaleFactor arrays are deleted
// if parameter array is deleted
CpuImplicitSolvent* cpuImplicitSolvent = CpuImplicitSolvent::getCpuImplicitSolvent();
CpuObc* cpuObc = static_cast<CpuObc*> (cpuImplicitSolvent);
ObcParameters* obcParameters = cpuObc->getObcParameters();
obcParameters->setOwnAtomicRadii( true );
obcParameters->setOwnScaleFactors( true );
return status;
}
/**---------------------------------------------------------------------------------------
Calculate Obc forces and energy
@param atomCoordinates Gromacs atom coordinates ('x' in md.c)
@param partialCharges Gromacs charges ('mdatoms->chargeA' in md.c)
@param forces output forces in kJ/mol.A; the computed forces
are added to the entries in the array
Function calls a static method in CpuObc class to calculate forces/energy
@return 0
--------------------------------------------------------------------------------------- */
extern "C" int gromacsCpuCalculateObcForces( const rvec* atomCoordinates,
const RealOpenMM* partialChargesIn,
rvec* forces ){
// ---------------------------------------------------------------------------------------
static const char* methodName = "\ngromacsCpuCalculateObcForces: ";
static RealOpenMM* partialCharges = NULL;
static RealOpenMM** coordinates = NULL;
static RealOpenMM** localForces = NULL;
static const int updateBornRadii = 0;
static int debug = 0;
// ---------------------------------------------------------------------------------------
CpuImplicitSolvent* cpuImplicitSolvent = CpuImplicitSolvent::getCpuImplicitSolvent();
if( cpuImplicitSolvent == NULL ){
(void) fprintf( stderr, "%s implicit solvent not initialized -- aborting" );
(void) fflush( stderr );
exit(-1);
}
int numberOfAtoms = cpuImplicitSolvent->getNumberOfAtoms();
// first time through, allocate memory for coordinates, ..
// Note: memory never freed!
if( coordinates == NULL ){
coordinates = SimTKOpenMMUtilities::allocateTwoDRealOpenMMArray( numberOfAtoms, 3, NULL, true, (RealOpenMM) 0.0 );
localForces = SimTKOpenMMUtilities::allocateTwoDRealOpenMMArray( numberOfAtoms, 3, NULL, true, (RealOpenMM) 0.0 );
// required if Gromacs float != RealOpenMM (i.e., RealOpenMM = double)
partialCharges = new RealOpenMM[numberOfAtoms];
for( int ii = 0; ii < numberOfAtoms; ii++ ){
partialCharges[ii] = (RealOpenMM) partialChargesIn[ii];
}
}
// convert coordinates from nm -> Angstrom
RealOpenMM distanceScaleFactor = (RealOpenMM) 10.0;
//RealOpenMM distanceScaleFactor = (RealOpenMM) 1.0;
for( int ii = 0; ii < numberOfAtoms; ii++ ){
coordinates[ii][0] = (RealOpenMM) (distanceScaleFactor*atomCoordinates[ii][0]);
coordinates[ii][1] = (RealOpenMM) (distanceScaleFactor*atomCoordinates[ii][1]);
coordinates[ii][2] = (RealOpenMM) (distanceScaleFactor*atomCoordinates[ii][2]);
}
CpuImplicitSolvent::computeImplicitSolventForces( coordinates, partialCharges,
localForces, updateBornRadii );
float forceScaleFactor = 41.84f;
for( int ii = 0; ii < numberOfAtoms; ii++ ){
forces[ii][0] += (float) forceScaleFactor*localForces[ii][0];
forces[ii][1] += (float) forceScaleFactor*localForces[ii][1];
forces[ii][2] += (float) forceScaleFactor*localForces[ii][2];
}
if( debug ){
int maxPrint = 10;
std::stringstream message;
message << methodName;
message << "\nSample OBC forces:\n";
for( int ii = 0; ii < numberOfAtoms && ii < maxPrint; ii++ ){
message << " " << ii << " Obc[" << forceScaleFactor*localForces[ii][0] << " " << forceScaleFactor*localForces[ii][1] << " " << forceScaleFactor*localForces[ii][2];
message << "] F[" << forces[ii][0] << " " << forces[ii][1] << " " << forces[ii][2] << "]" << std::endl;
}
SimTKOpenMMLog::printMessage( message );
debug = 0;
}
//RealOpenMM energy = cpuImplicitSolvent->getEnergy();
//printf( "\ngromacsCpuCalculateObcForces E=%.5e", energy );
return 0;
}
/**---------------------------------------------------------------------------------------
Write Tinker Xyz file
@param atomCoordinates Gromacs atom coordinates ('x' in md.c)
@param top Gromacs t_topology (as in md.c)
@param inputHeader xyz file header
@param inputXyzFileName xyz file name
@param log log file reference (may be NULL)
@return 0
--------------------------------------------------------------------------------------- */
extern "C" int cpuWriteXyzFile( const rvec *atomCoordinates, const t_topology* top,
const char* inputHeader, const char* inputXyzFileName, FILE* log ){
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\ncpuWriteXyzFile: ";
// ---------------------------------------------------------------------------------------
// set logging, if log != NULL
if( log ){
SimTKOpenMMLog::setSimTKOpenMMLog( log );
}
// set header & file name
std::string header;
if( inputHeader ){
header = std::string( inputHeader );
} else {
header = "Test";
}
std::string xyzFileName;
if( inputXyzFileName ){
xyzFileName = std::string( inputXyzFileName );
} else {
xyzFileName = "Test";
}
// write file
SimTKOpenMMGromacsUtilities::writeTinkerXyzFile( top->atoms.nr, atomCoordinates,
header, xyzFileName, top );
return 0;
}
/**---------------------------------------------------------------------------------------
Read Xyz file
@param numberOfAtoms number of atoms
@param atomCoordinates Gromacs atom coordinates ('x' in md.c)
@param top Gromacs t_topology (as in md.c)
@param inputXyzFileName xyz file name
@param log log file reference (may be NULL)
@return 0
--------------------------------------------------------------------------------------- */
extern "C" int cpuReadXyzFile( int numberOfAtoms, rvec *atomCoordinates, const t_topology* top,
const char* inputXyzFileName, FILE* log ){
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\ncpuReadXyzFile: ";
// ---------------------------------------------------------------------------------------
// set logging, if log != NULL
if( log ){
SimTKOpenMMLog::setSimTKOpenMMLog( log );
}
// set file name
const char* xyzFileName;
if( inputXyzFileName ){
xyzFileName = inputXyzFileName;
} else {
xyzFileName = "Test";
}
// read file
SimTKOpenMMGromacsUtilities::readXyzFile( top->atoms.nr, atomCoordinates, top, xyzFileName );
return 0;
}
platforms/reference/src/Gbsa/gromacsCpuObcInterface.h deleted 100644 → 0
View file @ f3e77e33
/* 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 __GromacsCpuObcInterface_H__
#define __GromacsCpuObcInterface_H__
#ifdef __cplusplus
#define externC extern "C"
#else
#define externC extern
#endif
/**---------------------------------------------------------------------------------------
Setup for Obc calculations
@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 soluteDielectric solute dielectric
@param solventDielectric solvent dielectric
Method creates a CpuObc instance w/ OBC parameters set
The created object is a static member of the
class CpuObc that is referenced to calculate the implicit solvation
forces and energy
@return 0
--------------------------------------------------------------------------------------- */
externC
int gromacsCpuInitialSetupObc( const t_topology* top, FILE* log, int includeAceApproximation,
float soluteDielectric, float solventDielectric );
/**---------------------------------------------------------------------------------------
Calculate Obc forces and energy
@param atomCoordinates Gromacs atom coordinates ('x' in md.c)
@param partialCharges Gromacs charges ('mdatoms->chargeA' in md.c)
@param forces output forces in kJ/mol.A; the computed forces
are added to the entries in the array
Function calls a static method in CpuObc class to calculate forces/energy
@return 0
--------------------------------------------------------------------------------------- */
externC
int gromacsCpuCalculateObcForces( const rvec* atomCoordinates, const float* partialChargesIn,
rvec* forces );
/**---------------------------------------------------------------------------------------
Read Xyz file
@param numberOfAtoms number of atoms
@param atomCoordinates Gromacs atom coordinates ('x' in md.c)
@param top Gromacs t_topology (as in md.c)
@param inputXyzFileName xyz file name
@param log log file reference (may be NULL)
@return 0
--------------------------------------------------------------------------------------- */
externC int cpuReadXyzFile( int numberOfAtoms, rvec *atomCoordinates, const t_topology* top,
const char* inputXyzFileName, FILE* log );
/**---------------------------------------------------------------------------------------
Write Tinker Xyz file \n
@param atomCoordinates Gromacs atom coordinates ('x' in md.c)
@param top Gromacs t_topology (as in md.c)
@param inputHeader xyz file header
@param inputXyzFileName xyz file name
@param log log file reference (may be NULL)
@return 0
--------------------------------------------------------------------------------------- */
externC
int cpuWriteXyzFile( const rvec *atomCoordinates, const t_topology* top,
const char* inputHeader, const char* inputXyzFileName, FILE* log );
/**---------------------------------------------------------------------------------------
Retrieve the calculated implicit solvation energy from the static class member
@return the calculated energy from the static class member
--------------------------------------------------------------------------------------- */
externC float cpuGetObcEnergy( void );
#endif
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment