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Commit 6718e0cc authored by Mark Friedrichs's avatar Mark Friedrichs
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Code cleanup

parent 1079a319
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Showing with 654 additions and 1154 deletions
plugins/freeEnergy/platforms/reference/src/gbsa/CpuGBVISoftcore.cpp
View file @ 6718e0cc
......@@ -23,15 +23,13 @@
*/
#include <string.h>
#include <math.h>
#include <sstream>
#include <vector>
#include "../SimTKUtilities/SimTKOpenMMCommon.h"
#include "../SimTKUtilities/SimTKOpenMMLog.h"
#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
#include "CpuGBVISoftcore.h"
#include "../SimTKReference/ReferenceForce.h"
#include <math.h>
#include "CpuGBVISoftcore.h"
using std::vector;
using OpenMM::RealVec;
......
plugins/freeEnergy/platforms/reference/src/gbsa/CpuObcSoftcore.h
View file @ 6718e0cc
......@@ -30,7 +30,7 @@
// ---------------------------------------------------------------------------------------
class CpuObcSoftcore : public CpuImplicitSolvent {
class CpuObcSoftcore {
private:
......@@ -40,13 +40,12 @@ class CpuObcSoftcore : public CpuImplicitSolvent {
// arrays containing OBC chain derivative
std::vector<RealOpenMM> _obcChain;
std::vector<RealOpenMM> _obcChainTemp;
RealOpenMMVector _obcChain;
// initialize data members (more than
// one constructor, so centralize intialization here)
// flag to signal whether ACE approximation
// is to be included
void _initializeObcDataMembers( void );
int _includeAceApproximation;
public:
......@@ -60,7 +59,7 @@ class CpuObcSoftcore : public CpuImplicitSolvent {
--------------------------------------------------------------------------------------- */
CpuObcSoftcore( ImplicitSolventParameters* obcSoftcoreParameters );
CpuObcSoftcore( ObcSoftcoreParameters* obcSoftcoreParameters );
/**---------------------------------------------------------------------------------------
......@@ -92,26 +91,45 @@ class CpuObcSoftcore : public CpuImplicitSolvent {
/**---------------------------------------------------------------------------------------
Return OBC chain derivative: size = _implicitSolventParameters->getNumberOfAtoms()
On first call, memory for array is allocated if not set
Return flag signalling whether AceApproximation for nonpolar term is to be included
@return array
@return flag
--------------------------------------------------------------------------------------- */
std::vector<RealOpenMM>& getObcChain( void );
const std::vector<RealOpenMM>& getObcChainConst( void ) const;
int includeAceApproximation( void ) const;
/**---------------------------------------------------------------------------------------
Set flag indicating whether AceApproximation is to be included
@param includeAceApproximation new includeAceApproximation value
--------------------------------------------------------------------------------------- */
void setIncludeAceApproximation( int includeAceApproximation );
/**---------------------------------------------------------------------------------------
Return OBC chain temp work array of size=_implicitSolventParameters->getNumberOfAtoms()
Get energy
@return energy
--------------------------------------------------------------------------------------- */
RealOpenMM getEnergy( void ) const;
/**---------------------------------------------------------------------------------------
Return OBC chain derivative: size = _implicitSolventParameters->getNumberOfAtoms()
On first call, memory for array is allocated if not set
@return array
--------------------------------------------------------------------------------------- */
std::vector<RealOpenMM>& getObcChainTemp( void );
RealOpenMMVector& getObcChain( void );
/**---------------------------------------------------------------------------------------
......@@ -124,7 +142,7 @@ class CpuObcSoftcore : public CpuImplicitSolvent {
--------------------------------------------------------------------------------------- */
void computeBornRadii( std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<RealOpenMM>& bornRadii );
void computeBornRadii( std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMMVector& bornRadii );
/**---------------------------------------------------------------------------------------
......@@ -139,22 +157,23 @@ class CpuObcSoftcore : public CpuImplicitSolvent {
--------------------------------------------------------------------------------------- */
void computeAceNonPolarForce( const ObcSoftcoreParameters* obcSoftcoreParameters,
const std::vector<RealOpenMM>& bornRadii, RealOpenMM* energy,
std::vector<RealOpenMM>& forces ) const;
const RealOpenMMVector& bornRadii, RealOpenMM* energy,
RealOpenMMVector& forces ) const;
/**---------------------------------------------------------------------------------------
Get Born energy and forces based on OBC
@param bornRadii Born radii
@param atomCoordinates atomic coordinates
@param partialCharges partial charges
@param forces forces
@return energy
--------------------------------------------------------------------------------------- */
void computeBornEnergyForces( std::vector<RealOpenMM>& bornRadii, std::vector<OpenMM::RealVec>& atomCoordinates,
const RealOpenMM* partialCharges, std::vector<OpenMM::RealVec>& forces );
RealOpenMM computeBornEnergyForces( std::vector<OpenMM::RealVec>& atomCoordinates,
const RealOpenMMVector& partialCharges, std::vector<OpenMM::RealVec>& forces );
};
// ---------------------------------------------------------------------------------------
......
plugins/freeEnergy/platforms/reference/src/gbsa/ObcSoftcoreParameters.h
View file @ 6718e0cc
/* Portions copyright (c) 2006-2009 Stanford University and Simbios.
* Contributors: Pande Group
*
......@@ -26,11 +25,10 @@
#define __ObcSoftcoreParameters_H__
#include "../SimTKUtilities/SimTKOpenMMCommon.h"
#include "gbsa/ImplicitSolventParameters.h"
// ---------------------------------------------------------------------------------------
class ObcSoftcoreParameters : public ImplicitSolventParameters {
class ObcSoftcoreParameters {
public:
......@@ -38,37 +36,42 @@ class ObcSoftcoreParameters : public ImplicitSolventParameters {
enum ObcType { ObcTypeI, ObcTypeII };
static const std::string ParameterFileName;
private:
int _numberOfAtoms;
// OBC constants & parameters
RealOpenMM _dielectricOffset;
RealOpenMM _alphaObc;
RealOpenMM _betaObc;
RealOpenMM _gammaObc;
RealOpenMM _probeRadius;
RealOpenMM _pi4Asolv;
ObcType _obcType;
RealOpenMM _nonPolarPreFactor;
RealOpenMM _solventDielectric;
RealOpenMM _soluteDielectric;
RealOpenMM _electricConstant;
// scaling factors for nonpolar term
int _ownNonPolarScaleFactors;
RealOpenMM* _nonPolarScaleFactors;
RealOpenMMVector _atomicRadii;
RealOpenMMVector _nonPolarScaleFactors;
// scaled radius factors (S_kk in HCT paper)
int _ownScaledRadiusFactors;
RealOpenMM* _scaledRadiusFactors;
RealOpenMMVector _scaledRadiusFactors;
// cutoff and periodic boundary conditions
bool cutoff;
bool periodic;
RealOpenMM periodicBoxSize[3];
RealOpenMM cutoffDistance;
bool _cutoff;
bool _periodic;
RealOpenMM _periodicBoxSize[3];
RealOpenMM _cutoffDistance;
public:
......@@ -92,153 +95,194 @@ class ObcSoftcoreParameters : public ImplicitSolventParameters {
/**---------------------------------------------------------------------------------------
Get OBC type
Get number of atoms
@return OBC type
@return number of atoms
--------------------------------------------------------------------------------------- */
ObcSoftcoreParameters::ObcType getObcType( void ) const;
int getNumberOfAtoms( void ) const;
/**---------------------------------------------------------------------------------------
Set OBC type specific parameters
Get electric constant
@param obcType OBC type (ObcTypeI or ObcTypeII -- Eq. 7 or 8)
@return electric constant
--------------------------------------------------------------------------------------- */
void setObcTypeParameters( ObcSoftcoreParameters::ObcType obcType );
RealOpenMM getElectricConstant( void ) const;
/**---------------------------------------------------------------------------------------
Get alpha OBC (Eqs. 6 & 7) in Proteins paper
Get probe radius (Simbios)
@return alphaObc
@return probeRadius
--------------------------------------------------------------------------------------- */
RealOpenMM getAlphaObc( void ) const;
RealOpenMM getProbeRadius( void ) const;
/**---------------------------------------------------------------------------------------
Get beta OBC (Eqs. 6 & 7) in Proteins paper
Set probe radius (Simbios)
@return betaObc
@param probeRadius probe radius
--------------------------------------------------------------------------------------- */
RealOpenMM getBetaObc( void ) const;
void setProbeRadius( RealOpenMM probeRadius );
/**---------------------------------------------------------------------------------------
Get gamma OBC (Eqs. 6 & 7) in Proteins paper
Get pi4Asolv: used in ACE approximation for nonpolar term
((RealOpenMM) M_PI)*4.0f*0.0049f*1000.0f; (Simbios)
@return gammaObc
@return pi4Asolv
--------------------------------------------------------------------------------------- */
RealOpenMM getGammaObc( void ) const;
RealOpenMM getPi4Asolv( void ) const;
/**---------------------------------------------------------------------------------------
Get solvent dielectric (Simbios)
Get solvent dielectric
@return dielectricOffset dielectric offset
@return solvent dielectric
--------------------------------------------------------------------------------------- */
RealOpenMM getDielectricOffset( void ) const;
RealOpenMM getSolventDielectric( void ) const;
/**---------------------------------------------------------------------------------------
Return OBC scale factors
Set solvent dielectric
@return array
@param solventDielectric solvent dielectric
--------------------------------------------------------------------------------------- */
const RealOpenMM* getScaledRadiusFactors( void ) const;
void setSolventDielectric( RealOpenMM solventDielectric );
/**---------------------------------------------------------------------------------------
Return OBC scale factors
Get solute dielectric
@return array
@return soluteDielectric
--------------------------------------------------------------------------------------- */
void setScaledRadiusFactors( RealOpenMM* scaledRadiusFactors );
#if RealOpenMMType == 0
void setScaledRadiusFactors( float* scaledRadiusFactors );
#endif
void setScaledRadiusFactors( const RealOpenMMVector& scaledRadiusFactors );
RealOpenMM getSoluteDielectric( void ) const;
/**---------------------------------------------------------------------------------------
Set flag indicating whether scale factors arra should be deleted
Set solute dielectric
@param ownScaledRadiusFactors flag indicating whether scale factors
array should be deleted
@param soluteDielectric solute dielectric
--------------------------------------------------------------------------------------- */
void setOwnScaleFactors( int ownScaledRadiusFactors );
void setSoluteDielectric( RealOpenMM soluteDielectric );
/**---------------------------------------------------------------------------------------
Get AtomicRadii array w/ dielectric offset applied
Get OBC type
@return array of atom volumes
@return OBC type
--------------------------------------------------------------------------------------- */
RealOpenMM* getAtomicRadii( void ) const;
ObcSoftcoreParameters::ObcType getObcType( void ) const;
/**---------------------------------------------------------------------------------------
Set AtomicRadii array
Set OBC type specific parameters
@param atomicRadii array of atomic radii
@param obcType OBC type (ObcTypeI or ObcTypeII -- Eq. 7 or 8)
--------------------------------------------------------------------------------------- */
void setAtomicRadii( RealOpenMM* atomicRadii );
void setObcTypeParameters( ObcSoftcoreParameters::ObcType obcType );
/**---------------------------------------------------------------------------------------
Set AtomicRadii array
Get alpha OBC (Eqs. 6 & 7) in Proteins paper
@param atomicRadii vector of atomic radii
@return alphaObc
--------------------------------------------------------------------------------------- */
void setAtomicRadii( const RealOpenMMVector& atomicRadii );
RealOpenMM getAlphaObc( void ) const;
/**---------------------------------------------------------------------------------------
Map Gmx atom name to Tinker atom number (Simbios)
Get beta OBC (Eqs. 6 & 7) in Proteins paper
@param atomName atom name (CA, HA, ...); upper and lower case should both work
@param log if set, then print error messages to log file
@return betaObc
return Tinker atom number if atom name is valid; else return -1
--------------------------------------------------------------------------------------- */
RealOpenMM getBetaObc( void ) const;
/**---------------------------------------------------------------------------------------
Get gamma OBC (Eqs. 6 & 7) in Proteins paper
@return gammaObc
--------------------------------------------------------------------------------------- */
int mapGmxAtomNameToTinkerAtomNumber( const char* atomName, FILE* log ) const;
RealOpenMM getGammaObc( void ) const;
/**---------------------------------------------------------------------------------------
Get solvent dielectric (Simbios)
@return dielectricOffset dielectric offset
--------------------------------------------------------------------------------------- */
RealOpenMM getDielectricOffset( void ) const;
/**---------------------------------------------------------------------------------------
Return OBC scale factors
@return array
--------------------------------------------------------------------------------------- */
const RealOpenMMVector& getScaledRadiusFactors( void ) const;
/**---------------------------------------------------------------------------------------
Set OBC scale factors
@param input vector of radius factors
--------------------------------------------------------------------------------------- */
void setScaledRadiusFactors( const RealOpenMMVector& scaledRadiusFactors );
/**---------------------------------------------------------------------------------------
Get string w/ state
Get AtomicRadii array w/ dielectric offset applied
@param title title (optional)
@return array of atom volumes
@return string
--------------------------------------------------------------------------------------- */
const RealOpenMMVector& getAtomicRadii( void ) const;
/**---------------------------------------------------------------------------------------
Set AtomicRadii array
@param atomicRadii vector of atomic radii
--------------------------------------------------------------------------------------- */
std::string getStateString( const char* title ) const;
void setAtomicRadii( const RealOpenMMVector& atomicRadii );
/**---------------------------------------------------------------------------------------
......@@ -256,7 +300,7 @@ class ObcSoftcoreParameters : public ImplicitSolventParameters {
--------------------------------------------------------------------------------------- */
bool getUseCutoff();
bool getUseCutoff( void );
/**---------------------------------------------------------------------------------------
......@@ -264,7 +308,7 @@ class ObcSoftcoreParameters : public ImplicitSolventParameters {
--------------------------------------------------------------------------------------- */
RealOpenMM getCutoffDistance();
RealOpenMM getCutoffDistance( void );
/**---------------------------------------------------------------------------------------
......@@ -284,7 +328,7 @@ class ObcSoftcoreParameters : public ImplicitSolventParameters {
--------------------------------------------------------------------------------------- */
bool getPeriodic();
bool getPeriodic( void );
/**---------------------------------------------------------------------------------------
......@@ -292,29 +336,17 @@ class ObcSoftcoreParameters : public ImplicitSolventParameters {
--------------------------------------------------------------------------------------- */
const RealOpenMM* getPeriodicBox();
/**---------------------------------------------------------------------------------------
Set flag indicating whether scale factors array should be deleted
@param ownNonPolarScaleFactors flag indicating whether scale factors
array should be deleted
--------------------------------------------------------------------------------------- */
void setOwnNonPolarScaleFactors( int ownNonPolarScaleFactors );
const RealOpenMM* getPeriodicBox( void );
/**---------------------------------------------------------------------------------------
Return non-polar scale factors
If not previously set, allocate space
@return array
--------------------------------------------------------------------------------------- */
const RealOpenMM* getNonPolarScaleFactors( void ) const;
const RealOpenMMVector& getNonPolarScaleFactors( void ) const;
/**---------------------------------------------------------------------------------------
......@@ -338,19 +370,6 @@ class ObcSoftcoreParameters : public ImplicitSolventParameters {
};
/**---------------------------------------------------------------------------------------
Qsort/heapsort integer comparison (Simbios)
@parma a first value to compare
@param b second value to compare
@return -1, 0, 1
--------------------------------------------------------------------------------------- */
int integerComparison( const void *a, const void *b);
// ---------------------------------------------------------------------------------------
#endif // __ObcSoftcoreParameters_H__
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