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Commit bf93e42f authored by Mark Friedrichs's avatar Mark Friedrichs
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Converted units from kcal/A to Joule/nm

parent 099b8e55
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Showing with 65 additions and 73 deletions
platforms/reference/src/gbsa/CpuImplicitSolvent.cpp
View file @ bf93e42f
......@@ -699,8 +699,7 @@ int CpuImplicitSolvent::computeImplicitSolventForces( RealOpenMM** atomCoordinat
// compute forces
computeBornEnergyForces( getBornRadii(), atomCoordinates,
partialCharges, forces );
computeBornEnergyForces( getBornRadii(), atomCoordinates, partialCharges, forces );
// diagnostics
......
platforms/reference/src/gbsa/CpuObc.cpp
View file @ bf93e42f
......@@ -225,7 +225,7 @@ int CpuObc::computeBornRadii( RealOpenMM** atomCoordinates, RealOpenMM* bornRadi
static const RealOpenMM half = (RealOpenMM) 0.5;
static const RealOpenMM fourth = (RealOpenMM) 0.25;
// static const char* methodName = "\nCpuObc::computeBornRadii";
static const char* methodName = "\nCpuObc::computeBornRadii";
// ---------------------------------------------------------------------------------------
......@@ -320,8 +320,7 @@ if( logFile && atomI == 0 ){
if( logFile && atomI >= 0 ){
(void) fprintf( logFile, "\nRRQ %d sum=%12.6e tanhS=%12.6e radI=%.5f %.5f born=%12.6e obc=%12.6e",
atomI, sum, tanhSum, radiusI, offsetRadiusI, bornRadii[atomI], obcChain[atomI] );
}
*/
} */
}
......@@ -381,7 +380,6 @@ int CpuObc::computeBornEnergyForces( RealOpenMM* bornRadii, RealOpenMM** atomCoo
// constants
const RealOpenMM preFactor = obcParameters->getPreFactor();
const RealOpenMM electricConstant = obcParameters->getElectricConstant();
const RealOpenMM dielectricOffset = obcParameters->getDielectricOffset();
// ---------------------------------------------------------------------------------------
......@@ -594,7 +592,15 @@ int CpuObc::computeBornEnergyForces( RealOpenMM* bornRadii, RealOpenMM** atomCoo
obcChainTemp[atomI] = (one - tanhSum*tanhSum)*obcChainTemp[atomI]/radiusI;
}
setEnergy( obcEnergy );
// cal to Joule conversion
RealOpenMM conversion = 0.4184;
for( int atomI = 0; atomI < numberOfAtoms; atomI++ ){
forces[atomI][0] *= conversion;
forces[atomI][1] *= conversion;
forces[atomI][2] *= conversion;
}
setEnergy( obcEnergy*conversion );
// copy new Born radii and obcChain values into permanent array
......@@ -882,9 +888,9 @@ int CpuObc::computeBornEnergyForcesPrint( RealOpenMM* bornRadii, RealOpenMM** at
#pragma warning(disable:4996)
#endif
//FILE* logFile = NULL;
FILE* logFile = NULL;
//FILE* logFile = SimTKOpenMMLog::getSimTKOpenMMLogFile( );
FILE* logFile = fopen( "bF", "w" );
//FILE* logFile = fopen( "bF", "w" );
#if defined(_MSC_VER)
#pragma warning(pop)
......@@ -895,7 +901,6 @@ FILE* logFile = fopen( "bF", "w" );
// constants
const RealOpenMM preFactor = obcParameters->getPreFactor();
const RealOpenMM electricConstant = obcParameters->getElectricConstant();
const RealOpenMM dielectricOffset = obcParameters->getDielectricOffset();
// ---------------------------------------------------------------------------------------
......@@ -919,6 +924,14 @@ FILE* logFile = fopen( "bF", "w" );
if( includeAceApproximation() ){
computeAceNonPolarForce( obcParameters, bornRadii, &obcEnergy, bornForces );
if( logFile ){
(void) fprintf( logFile, "\nACE E=%.5e\n", obcEnergy );
for( int atomI = 0; atomI < numberOfAtoms; atomI++ ){
(void) fprintf( logFile, " %d bR=%.6e bF=%.6e\n", atomI, bornRadii[atomI], bornForces[atomI] );
}
}
}
// ---------------------------------------------------------------------------------------
......@@ -989,7 +1002,9 @@ FILE* logFile = fopen( "bF", "w" );
obcEnergy += Gpol;
bornForces[atomI] += dGpol_dalpha2_ij*bornRadii[atomJ];
if( logFile && (atomI == -1 || atomJ == -1) ){
/*
if( logFile ){
//if( logFile && (atomI == -1 || atomJ == -1) ){
// (void) fprintf( logFile, "\nWWX %d %d F[%.6e %.6e %.6e] bF=[%.6e %.6e] Gpl[%.6e %.6e %.6e] rb[%6.4f %7.4f] rs[%6.4f %7.4f] ",
// atomI, atomJ,
// forces[atomI][0], forces[atomI][1], forces[atomI][2],
......@@ -1004,16 +1019,17 @@ if( logFile && (atomI == -1 || atomJ == -1) ){
bornRadii[atomI], bornRadii[atomJ],
dGpol_dalpha2_ij*bornRadii[atomJ], dGpol_dalpha2_ij*bornRadii[atomI] );
}
*/
}
}
if( logFile ){
(void) fprintf( logFile, "\nWXX bF & F E=%.8e", obcEnergy );
(void) fprintf( logFile, "\nWXX bF & F E=%.8e preFactor=%.5f", obcEnergy, preFactor );
for( int atomI = 0; atomI < numberOfAtoms; atomI++ ){
(void) fprintf( logFile, "\nWXX %d %.6e q=%.3f F[%.6e %.6e %.6e] ",
atomI, partialCharges[atomI], bornForces[atomI], forces[atomI][0], forces[atomI][1], forces[atomI][2] );
(void) fprintf( logFile, "\nWXX %d q=%.4f bR=%.5e bF=%.3f F[%.6e %.6e %.6e] ",
atomI, partialCharges[atomI], bornRadii[atomI], bornForces[atomI], forces[atomI][0], forces[atomI][1], forces[atomI][2] );
}
}
......@@ -1187,7 +1203,13 @@ if( logFile && atomI >= 0 ){
}
setEnergy( obcEnergy );
RealOpenMM conversion = 0.4184;
for( int atomI = 0; atomI < numberOfAtoms; atomI++ ){
forces[atomI][0] *= conversion;
forces[atomI][1] *= conversion;
forces[atomI][2] *= conversion;
}
setEnergy( obcEnergy*conversion );
if( 0 ){
......
platforms/reference/src/gbsa/ImplicitSolventParameters.cpp
View file @ bf93e42f
......@@ -478,14 +478,12 @@ int ImplicitSolventParameters::setAtomicRadii( RealOpenMM* atomicRadii ){
Set AtomicRadii array
@param atomicRadii array of atomic radii
@param units units flag: SimTKOpenMMCommon::KcalAngUnits or
SimTKOpenMMCommon::MdUnits
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
int ImplicitSolventParameters::setAtomicRadii( const RealOpenMMVector& atomicRadii, int units ){
int ImplicitSolventParameters::setAtomicRadii( const RealOpenMMVector& atomicRadii ){
// ---------------------------------------------------------------------------------------
......@@ -511,18 +509,9 @@ int ImplicitSolventParameters::setAtomicRadii( const RealOpenMMVector& atomicRad
numberOfAtoms = numberOfAtoms < (int) atomicRadii.size() ? numberOfAtoms : (int) atomicRadii.size();
}
// force kcal/A units
if( units == SimTKOpenMMCommon::MdUnits ){
RealOpenMM ten = (RealOpenMM) 10.0;
for( int ii = 0; ii < numberOfAtoms; ii++ ){
_atomicRadii[ii] = ten*atomicRadii[ii];
}
} else {
for( int ii = 0; ii < numberOfAtoms; ii++ ){
_atomicRadii[ii] = atomicRadii[ii];
}
}
return SimTKOpenMMCommon::DefaultReturn;
}
......@@ -532,14 +521,12 @@ int ImplicitSolventParameters::setAtomicRadii( const RealOpenMMVector& atomicRad
Set AtomicRadii array
@param atomicRadii array of atomic radii
@param units units flag: SimTKOpenMMCommon::KcalAngUnits or
SimTKOpenMMCommon::MdUnits
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
int ImplicitSolventParameters::setAtomicRadii( RealOpenMM* atomicRadii, int units ){
/*
int ImplicitSolventParameters::setAtomicRadii( RealOpenMM* atomicRadii ){
// ---------------------------------------------------------------------------------------
......@@ -559,19 +546,12 @@ int ImplicitSolventParameters::setAtomicRadii( RealOpenMM* atomicRadii, int unit
// force kcal/A units
if( units == SimTKOpenMMCommon::MdUnits ){
RealOpenMM ten = (RealOpenMM) 10.0;
for( int ii = 0; ii < numberOfAtoms; ii++ ){
_atomicRadii[ii] = ten*atomicRadii[ii];
}
} else {
for( int ii = 0; ii < numberOfAtoms; ii++ ){
_atomicRadii[ii] = atomicRadii[ii];
}
}
return SimTKOpenMMCommon::DefaultReturn;
}
} */
/**---------------------------------------------------------------------------------------
......@@ -656,13 +636,16 @@ void ImplicitSolventParameters::_initializeImplicitSolventConstants( void ){
_soluteDielectric = (RealOpenMM) 1.0;
_solventDielectric = (RealOpenMM) 78.3;
_kcalA_To_kJNm = (RealOpenMM) 0.4184;
_probeRadius = (RealOpenMM) 1.4;
_probeRadius = (RealOpenMM) 0.14;
_electricConstant = (RealOpenMM) -166.02691;
// _pi4Asolv = (RealOpenMM) PI_M*4.0*0.0049*1000.0;
//_pi4Asolv = (RealOpenMM) PI_M*4.0*0.0049*1000.0;
//_pi4Asolv = (RealOpenMM) PI_M*19.6;
// _pi4Asolv = (RealOpenMM) PI_M*4.0*0.0054;
_pi4Asolv = (RealOpenMM) (PI_M*0.0216);
//_pi4Asolv = (RealOpenMM) PI_M*4.0*0.0054;
_pi4Asolv = (RealOpenMM) (PI_M*0.0216*1000.0);
//_pi4Asolv = (RealOpenMM) -400.71504079;
//_pi4Asolv = (RealOpenMM) 0.0;
_resetPreFactor();
}
......@@ -771,7 +754,7 @@ int ImplicitSolventParameters::isNotReady( void ) const {
&stdDev, &minValue, &minIndex,
&maxValue, &maxIndex );
if( average < 1.0 || average > 10.0 || minValue < 0.5 ){
if( average < 0.1 || average > 1.0 || minValue < 0.05 ){
errors++;
message << "\n atomic radii appear not to be set correctly -- radii should be in Angstroms";
message << "\n average radius=" << average << " min radius=" << minValue << " at atom index=" << minIndex;
......@@ -822,6 +805,7 @@ int ImplicitSolventParameters::isNotReady( void ) const {
warning++;
message << "\n Warning: probe radius=" << getProbeRadius() << " is large.";
}
/*
if( getPi4Asolv() <= 0.0 ){
errors++;
......@@ -832,6 +816,7 @@ int ImplicitSolventParameters::isNotReady( void ) const {
warning++;
message << "\n Warning: Pi4Asolv=" << getPi4Asolv() << " is large.";
}
*/
if( errors || warning ){
message << std::endl;
......
platforms/reference/src/gbsa/ImplicitSolventParameters.h
View file @ bf93e42f
......@@ -310,29 +310,24 @@ class ImplicitSolventParameters {
Set AtomicRadii array
@param atomicRadii vector of atomic radii
@param units units flag SimTKOpenMMCommon::MdUnits or
SimTKOpenMMCommon::KcalAngUnits
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
virtual int setAtomicRadii( const RealOpenMMVector& atomicRadii,
int units = SimTKOpenMMCommon::MdUnits );
virtual int setAtomicRadii( const RealOpenMMVector& atomicRadii );
/**---------------------------------------------------------------------------------------
Set AtomicRadii array
@param atomicRadii array of atomic radii
@param units units flag: SimTKOpenMMCommon::KcalAngUnits or
SimTKOpenMMCommon::MdUnits
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
virtual int setAtomicRadii( RealOpenMM* atomicRadii, int units );
//virtual int setAtomicRadii( RealOpenMM* atomicRadii );
/**---------------------------------------------------------------------------------------
......@@ -354,7 +349,6 @@ class ImplicitSolventParameters {
Print state to log file (Simbios)
@param title title (optional)
@param log print state to log file
@return SimTKOpenMMCommon::DefaultReturn
......
platforms/reference/src/gbsa/ObcParameters.cpp
View file @ bf93e42f
......@@ -110,7 +110,7 @@ ObcParameters::ObcParameters( int numberOfAtoms, ObcParameters::ObcType obcType
// ---------------------------------------------------------------------------------------
_obcType = obcType;
_dielectricOffset = 0.09f;
_dielectricOffset = 0.009f;
_ownScaledRadiusFactors = 0;
_scaledRadiusFactors = NULL;
......@@ -315,14 +315,12 @@ RealOpenMM* ObcParameters::getAtomicRadii( void ) const {
Set AtomicRadii array
@param atomicRadii array of atomic radii
@param units units flag: SimTKOpenMMCommon::KcalAngUnits or
SimTKOpenMMCommon::MdUnits
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
int ObcParameters::setAtomicRadii( RealOpenMM* atomicRadii, int units ){
int ObcParameters::setAtomicRadii( RealOpenMM* atomicRadii ){
// ---------------------------------------------------------------------------------------
......@@ -330,7 +328,7 @@ int ObcParameters::setAtomicRadii( RealOpenMM* atomicRadii, int units ){
// ---------------------------------------------------------------------------------------
return ImplicitSolventParameters::setAtomicRadii( atomicRadii, units );
return ImplicitSolventParameters::setAtomicRadii( atomicRadii );
}
/**---------------------------------------------------------------------------------------
......@@ -338,14 +336,12 @@ int ObcParameters::setAtomicRadii( RealOpenMM* atomicRadii, int units ){
Set AtomicRadii array
@param atomicRadii vector of atomic radii
@param units units flag: SimTKOpenMMCommon::KcalAngUnits or
SimTKOpenMMCommon::MdUnits
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
int ObcParameters::setAtomicRadii( const RealOpenMMVector& atomicRadii, int units ){
int ObcParameters::setAtomicRadii( const RealOpenMMVector& atomicRadii ){
// ---------------------------------------------------------------------------------------
......@@ -353,7 +349,7 @@ int ObcParameters::setAtomicRadii( const RealOpenMMVector& atomicRadii, int unit
// ---------------------------------------------------------------------------------------
return ImplicitSolventParameters::setAtomicRadii( atomicRadii, units );
return ImplicitSolventParameters::setAtomicRadii( atomicRadii );
}
/**---------------------------------------------------------------------------------------
......@@ -646,7 +642,7 @@ int ObcParameters::isNotReady( void ) const {
if( average < 0.3 || average > 2.0 || minValue < 0.1 ){
errors++;
message << "\n scale factors for atomic radii appear not to be set correctly -- radii should be in Angstroms";
message << "\n scale factors for atomic radii appear not to be set correctly -- radii should be in nm";
message << "\n average radius=" << average << " min radius=" << minValue << " at atom index=" << minIndex;
}
......
platforms/reference/src/gbsa/ObcParameters.h
View file @ bf93e42f
......@@ -232,28 +232,24 @@ class ObcParameters : public ImplicitSolventParameters {
Set AtomicRadii array
@param atomicRadii array of atomic radii
@param units units flag: SimTKOpenMMCommon::KcalAngUnits or
SimTKOpenMMCommon::MdUnits
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
int setAtomicRadii( RealOpenMM* atomicRadii, int units = SimTKOpenMMCommon::MdUnits );
int setAtomicRadii( RealOpenMM* atomicRadii );
/**---------------------------------------------------------------------------------------
Set AtomicRadii array
@param atomicRadii vector of atomic radii
@param units units flag: SimTKOpenMMCommon::KcalAngUnits or
SimTKOpenMMCommon::MdUnits
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
int setAtomicRadii( const RealOpenMMVector& atomicRadii, int units = SimTKOpenMMCommon::MdUnits );
int setAtomicRadii( const RealOpenMMVector& atomicRadii );
/**---------------------------------------------------------------------------------------
......
platforms/reference/src/gbsa/cpuObcInterface.cpp
View file @ bf93e42f
......@@ -86,7 +86,7 @@ cpuSetObcParameters( int numberOfAtoms, RealOpenMM* atomicRadii, RealOpenMM* obc
ObcParameters* obcParameters = new ObcParameters( numberOfAtoms, ObcParameters::ObcTypeII );
obcParameters->setScaledRadiusFactors( obcScaleFactors );
obcParameters->setAtomicRadii( atomicRadii, SimTKOpenMMCommon::KcalAngUnits );
obcParameters->setAtomicRadii( atomicRadii );
// dielectric constants
......
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