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Commit b5858a8e authored by Peter Eastman's avatar Peter Eastman
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Deleted lots of obsolete debugging code from the reference platform

parent c87cee06
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Showing with 2 additions and 1250 deletions
platforms/reference/src/SimTKReference/ReferenceAngleBondIxn.cpp
View file @ b5858a8e
...@@ -149,10 +149,6 @@ int ReferenceAngleBondIxn::calculateBondIxn( int* atomIndices, ...@@ -149,10 +149,6 @@ int ReferenceAngleBondIxn::calculateBondIxn( int* atomIndices,
static const int threeI = 3; static const int threeI = 3;
// debug flag
static const int debug = 0;
static const int LastAtomIndex = 3; static const int LastAtomIndex = 3;
RealOpenMM deltaR[2][ReferenceForce::LastDeltaRIndex]; RealOpenMM deltaR[2][ReferenceForce::LastDeltaRIndex];
...@@ -206,67 +202,5 @@ int ReferenceAngleBondIxn::calculateBondIxn( int* atomIndices, ...@@ -206,67 +202,5 @@ int ReferenceAngleBondIxn::calculateBondIxn( int* atomIndices,
updateEnergy( energy, energiesByBond, LastAtomIndex, atomIndices, energiesByAtom ); updateEnergy( energy, energiesByBond, LastAtomIndex, atomIndices, energiesByAtom );
// debug
if( debug ){
static bool printHeader = false;
std::stringstream message;
message << methodName;
message << std::endl;
if( !printHeader ){
printHeader = true;
message << std::endl;
message << methodName.c_str() << " a0 k [c q p s] r1 r2 angle dt rp p[] dot cosine angle dEdR*r F[]" << std::endl;
}
message << std::endl;
for( int ii = 0; ii < 3; ii++ ){
message << " Atm " << atomIndices[ii] << " [" << atomCoordinates[ii][0] << " " << atomCoordinates[ii][1] << " " << atomCoordinates[ii][2] << "] ";
}
message << std::endl << " Delta:";
for( int ii = 0; ii < 2; ii++ ){
message << " [";
for( int jj = 0; jj < ReferenceForce::LastDeltaRIndex; jj++ ){
message << deltaR[ii][jj] << " ";
}
message << "]";
}
message << std::endl;
message << " a0=" << parameters[0];
message << " k=" << parameters[1];
message << " rab2=" << deltaR[0][ReferenceForce::R2Index];
message << " rcb2=" << deltaR[1][ReferenceForce::R2Index];
message << std::endl << " ";
message << " rp=" << rp;
message << " p[";
SimTKOpenMMUtilities::formatRealStringStream( message, pVector );
message << "] dot=" << dot;
message << " cos=" << cosine;
message << std::endl << " ";
message << " dEdr=" << dEdR;
message << " trmA=" << termA;
message << " trmC=" << termC;
message << " E=" << energy << " F=compute force; f=cumulative force";
message << std::endl << " ";
for( int ii = 0; ii < 3; ii++ ){
message << " F" << (ii+1) << "[";
SimTKOpenMMUtilities::formatRealStringStream( message, deltaCrossP[ii], threeI );
message << "]";
}
message << std::endl << " ";
for( int ii = 0; ii < LastAtomIndex; ii++ ){
message << " f" << (ii+1) << "[";
SimTKOpenMMUtilities::formatRealStringStream( message, forces[atomIndices[ii]], threeI );
message << "]";
}
SimTKOpenMMLog::printMessage( message );
}
return ReferenceForce::DefaultReturn; return ReferenceForce::DefaultReturn;
} }
platforms/reference/src/SimTKReference/ReferenceBondForce.cpp
View file @ b5858a8e
...@@ -99,16 +99,6 @@ int ReferenceBondForce::calculateForce( int numberOfBonds, int** atomIndices, ...@@ -99,16 +99,6 @@ int ReferenceBondForce::calculateForce( int numberOfBonds, int** atomIndices,
for( int ii = 0; ii < numberOfBonds; ii++ ){ for( int ii = 0; ii < numberOfBonds; ii++ ){
// diagnostics
if( 0 ){
std::stringstream message;
message << methodName << " " << ii;
//message << " XAtm" << (unsigned int) atomIndices << " " << (unsigned int) atomIndices[0];
//message << " atm[" << atomIndices[ii][0] << " " << atomIndices[ii][1] << "]";
SimTKOpenMMLog::printMessage( message );
}
// calculate bond ixn // calculate bond ixn
referenceBondIxn.calculateBondIxn( atomIndices[ii], atomCoordinates, parameters[ii], referenceBondIxn.calculateBondIxn( atomIndices[ii], atomCoordinates, parameters[ii],
......
platforms/reference/src/SimTKReference/ReferenceBrownianDynamics.cpp
View file @ b5858a8e
...@@ -107,34 +107,6 @@ RealOpenMM ReferenceBrownianDynamics::getFriction( void ) const { ...@@ -107,34 +107,6 @@ RealOpenMM ReferenceBrownianDynamics::getFriction( void ) const {
return friction; return friction;
} }
/**---------------------------------------------------------------------------------------
Print parameters
@param message message
@return ReferenceDynamics::DefaultReturn
--------------------------------------------------------------------------------------- */
int ReferenceBrownianDynamics::printParameters( std::stringstream& message ) const {
// ---------------------------------------------------------------------------------------
static const char* methodName = "\nReferenceBrownianDynamics::printParameters";
// ---------------------------------------------------------------------------------------
// print parameters
ReferenceDynamics::printParameters( message );
message << " friction=" << getFriction();
message << " T=" << getTemperature();
return ReferenceDynamics::DefaultReturn;
}
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Update -- driver routine for performing Brownian dynamics update of coordinates Update -- driver routine for performing Brownian dynamics update of coordinates
...@@ -161,8 +133,6 @@ int ReferenceBrownianDynamics::update( int numberOfAtoms, RealOpenMM** atomCoord ...@@ -161,8 +133,6 @@ int ReferenceBrownianDynamics::update( int numberOfAtoms, RealOpenMM** atomCoord
static const RealOpenMM zero = 0.0; static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0; static const RealOpenMM one = 1.0;
static int debug = 0;
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
// get work arrays // get work arrays
...@@ -224,138 +194,3 @@ int ReferenceBrownianDynamics::update( int numberOfAtoms, RealOpenMM** atomCoord ...@@ -224,138 +194,3 @@ int ReferenceBrownianDynamics::update( int numberOfAtoms, RealOpenMM** atomCoord
return ReferenceDynamics::DefaultReturn; return ReferenceDynamics::DefaultReturn;
} }
/**---------------------------------------------------------------------------------------
Write state
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param velocities velocities
@param forces forces
@param masses atom masses
@param state 0 if initial state; otherwise nonzero
@param baseFileName base file name
@return ReferenceDynamics::DefaultReturn
--------------------------------------------------------------------------------------- */
int ReferenceBrownianDynamics::writeState( int numberOfAtoms, RealOpenMM** atomCoordinates,
RealOpenMM** velocities,
RealOpenMM** forces, RealOpenMM* masses,
int state, const std::string& baseFileName ) const {
// ---------------------------------------------------------------------------------------
static const char* methodName = "\nReferenceBrownianDynamics::writeState";
static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0;
static const int threeI = 3;
// ---------------------------------------------------------------------------------------
std::stringstream stateFileName;
stateFileName << baseFileName;
stateFileName << "_Step" << getTimeStep();
// stateFileName << "_State" << state;
stateFileName << ".txt";
// ---------------------------------------------------------------------------------------
// open file -- return if unsuccessful
FILE* stateFile = NULL;
#ifdef _MSC_VER
fopen_s( &stateFile, stateFileName.str().c_str(), "w" );
#else
stateFile = fopen( stateFileName.str().c_str(), "w" );
#endif
// ---------------------------------------------------------------------------------------
// diagnostics
if( stateFile != NULL ){
std::stringstream message;
message << methodName;
message << " Opened file=<" << stateFileName.str() << ">.\n";
SimTKOpenMMLog::printMessage( message );
} else {
std::stringstream message;
message << methodName;
message << " could not open file=<" << stateFileName.str() << "> -- abort output.\n";
SimTKOpenMMLog::printMessage( message );
return ReferenceDynamics::ErrorReturn;
}
// ---------------------------------------------------------------------------------------
StringVector scalarNameI;
IntVector scalarI;
StringVector scalarNameR;
RealOpenMMVector scalarR;
StringVector scalarNameR1;
RealOpenMMPtrVector scalarR1;
StringVector scalarNameR2;
RealOpenMMPtrPtrVector scalarR2;
scalarI.push_back( getNumberOfAtoms() );
scalarNameI.push_back( "Atoms" );
scalarI.push_back( getTimeStep() );
scalarNameI.push_back( "Timestep" );
if( state == 0 || state == -1 ){
scalarR.push_back( getDeltaT() );
scalarNameR.push_back( "delta_t" );
scalarR.push_back( getTemperature() );
scalarNameR.push_back( "T" );
scalarR.push_back( getFriction() );
scalarNameR.push_back( "Friction" );
scalarR1.push_back( masses );
scalarNameR1.push_back( "mass" );
scalarR2.push_back( atomCoordinates );
scalarNameR2.push_back( "coord" );
scalarR2.push_back( velocities );
scalarNameR2.push_back( "velocities" );
scalarR2.push_back( forces );
scalarNameR2.push_back( "forces" );
if( state == -1 ){
RealOpenMM** xPrime = get2DArrayAtIndex( xPrime2D );
scalarR2.push_back( xPrime );
scalarNameR2.push_back( "xPrime" );
}
} else {
scalarR2.push_back( atomCoordinates );
scalarNameR2.push_back( "coord" );
scalarR2.push_back( velocities );
scalarNameR2.push_back( "velocities" );
}
writeStateToFile( stateFile, scalarNameI, scalarI, scalarNameR, scalarR, getNumberOfAtoms(), scalarNameR1, scalarR1, threeI, scalarNameR2, scalarR2 );
(void) fclose( stateFile );
return ReferenceDynamics::DefaultReturn;
}
platforms/reference/src/SimTKReference/ReferenceBrownianDynamics.h
View file @ b5858a8e
...@@ -71,18 +71,6 @@ class ReferenceBrownianDynamics : public ReferenceDynamics { ...@@ -71,18 +71,6 @@ class ReferenceBrownianDynamics : public ReferenceDynamics {
RealOpenMM getFriction( void ) const; RealOpenMM getFriction( void ) const;
/**---------------------------------------------------------------------------------------
Print parameters
@param message message
@return ReferenceDynamics::DefaultReturn
--------------------------------------------------------------------------------------- */
int printParameters( std::stringstream& message ) const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Update Update
...@@ -100,26 +88,6 @@ class ReferenceBrownianDynamics : public ReferenceDynamics { ...@@ -100,26 +88,6 @@ class ReferenceBrownianDynamics : public ReferenceDynamics {
int update( int numberOfAtoms, RealOpenMM** atomCoordinates, int update( int numberOfAtoms, RealOpenMM** atomCoordinates,
RealOpenMM** velocities, RealOpenMM** forces, RealOpenMM* masses ); RealOpenMM** velocities, RealOpenMM** forces, RealOpenMM* masses );
/**---------------------------------------------------------------------------------------
Write state
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param velocities velocities
@param forces forces
@param masses atom masses
@param state 0 if initial state; otherwise nonzero
@param baseFileName base file name
@return ReferenceDynamics::DefaultReturn
--------------------------------------------------------------------------------------- */
int writeState( int numberOfAtoms, RealOpenMM** atomCoordinates,
RealOpenMM** velocities, RealOpenMM** forces, RealOpenMM* masses,
int state, const std::string& baseFileName ) const;
}; };
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
......
platforms/reference/src/SimTKReference/ReferenceCCMAAlgorithm.cpp
View file @ b5858a8e
...@@ -363,8 +363,6 @@ int ReferenceCCMAAlgorithm::apply( int numberOfAtoms, RealOpenMM** atomCoordinat ...@@ -363,8 +363,6 @@ int ReferenceCCMAAlgorithm::apply( int numberOfAtoms, RealOpenMM** atomCoordinat
static const RealOpenMM epsilon6 = (RealOpenMM) 1.0e-06; static const RealOpenMM epsilon6 = (RealOpenMM) 1.0e-06;
static int debug = 0;
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
// temp arrays // temp arrays
...@@ -465,26 +463,6 @@ int ReferenceCCMAAlgorithm::apply( int numberOfAtoms, RealOpenMM** atomCoordinat ...@@ -465,26 +463,6 @@ int ReferenceCCMAAlgorithm::apply( int numberOfAtoms, RealOpenMM** atomCoordinat
} }
} }
// diagnostics
if( debug || numberConverged < _numberOfConstraints ){
std::stringstream message;
message << methodName;
message << " iterations=" << iterations << " no. converged=" << numberConverged << " out of " << _numberOfConstraints;
if( numberConverged == _numberOfConstraints ){
message << " SUCCESS";
} else {
message << " FAILED";
}
message << "\n";
int errors = reportCCMA( numberOfAtoms, atomCoordinatesP, message );
if( !errors ){
message << "*** no errors recorded in explicit check ***";
}
message << "\n";
SimTKOpenMMLog::printMessage( message );
}
return (numberConverged == _numberOfConstraints ? ReferenceDynamics::DefaultReturn : ReferenceDynamics::ErrorReturn); return (numberConverged == _numberOfConstraints ? ReferenceDynamics::DefaultReturn : ReferenceDynamics::ErrorReturn);
} }
......
platforms/reference/src/SimTKReference/ReferenceConstraint.cpp
View file @ b5858a8e
...@@ -217,32 +217,3 @@ int ReferenceShakeConstraint::getLightAtomIndex( void ){ ...@@ -217,32 +217,3 @@ int ReferenceShakeConstraint::getLightAtomIndex( void ){
return _atomIndices[1]; return _atomIndices[1];
} }
/**---------------------------------------------------------------------------------------
Print state
@param message message
@return ReferenceDynamics::DefaultReturn
--------------------------------------------------------------------------------------- */
int ReferenceShakeConstraint::printState( std::stringstream& message ){
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceShakeConstraint::printState";
// ---------------------------------------------------------------------------------------
// print state
message << " atoms[" << _atomIndices[0] << " " << _atomIndices[1] << "]";
message << " d=" << _constraintDistance;
message << " massI[" << _inverseMasses[0] << " " << _inverseMasses[1] << "]";
return ReferenceDynamics::DefaultReturn;
}
platforms/reference/src/SimTKReference/ReferenceConstraint.h
View file @ b5858a8e
...@@ -135,19 +135,6 @@ class ReferenceShakeConstraint : public ReferenceConstraint { ...@@ -135,19 +135,6 @@ class ReferenceShakeConstraint : public ReferenceConstraint {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
int getLightAtomIndex( void ); int getLightAtomIndex( void );
/**---------------------------------------------------------------------------------------
Print state
@param message message
@return ReferenceDynamics::DefaultReturn
--------------------------------------------------------------------------------------- */
int printState( std::stringstream& message );
}; };
typedef std::vector<ReferenceShakeConstraint*> ShakeVector; typedef std::vector<ReferenceShakeConstraint*> ShakeVector;
......
platforms/reference/src/SimTKReference/ReferenceDynamics.cpp
View file @ b5858a8e
...@@ -474,8 +474,6 @@ int ReferenceDynamics::update( int numberOfAtoms, RealOpenMM** atomCoordinates, ...@@ -474,8 +474,6 @@ int ReferenceDynamics::update( int numberOfAtoms, RealOpenMM** atomCoordinates,
static const RealOpenMM zero = 0.0; static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0; static const RealOpenMM one = 1.0;
static int debug = 0;
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
return ReferenceDynamics::DefaultReturn; return ReferenceDynamics::DefaultReturn;
...@@ -500,8 +498,6 @@ int ReferenceDynamics::removeTotalLinearMomentum( int numberOfAtoms, RealOpenMM* ...@@ -500,8 +498,6 @@ int ReferenceDynamics::removeTotalLinearMomentum( int numberOfAtoms, RealOpenMM*
static const char* methodName = "\nReferenceDynamics::removeTotalLinearMomentum"; static const char* methodName = "\nReferenceDynamics::removeTotalLinearMomentum";
static const int debug = 1;
static const RealOpenMM zero = 0.0; static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0; static const RealOpenMM one = 1.0;
...@@ -514,341 +510,21 @@ int ReferenceDynamics::removeTotalLinearMomentum( int numberOfAtoms, RealOpenMM* ...@@ -514,341 +510,21 @@ int ReferenceDynamics::removeTotalLinearMomentum( int numberOfAtoms, RealOpenMM*
linearMomentum[0] += masses[ii]*velocities[ii][0]; linearMomentum[0] += masses[ii]*velocities[ii][0];
linearMomentum[1] += masses[ii]*velocities[ii][1]; linearMomentum[1] += masses[ii]*velocities[ii][1];
linearMomentum[2] += masses[ii]*velocities[ii][2]; linearMomentum[2] += masses[ii]*velocities[ii][2];
/*
if( debug ){
std::stringstream message;
message << ii << " TotalM=" << totalMass << " m=" << masses[ii] << " linearMomentum [";
SimTKOpenMMUtilities::formatRealStringStream( message, linearMomentum, 3, one );
message << "] [";
SimTKOpenMMUtilities::formatRealStringStream( message, velocities[ii], 3, one );
message << "]\n";
SimTKOpenMMLog::printMessage( message );
}
*/
} }
if( totalMass > zero ){ if( totalMass > zero ){
RealOpenMM totalMassI = one/totalMass; RealOpenMM totalMassI = one/totalMass;
/*
if( debug ){
std::stringstream message;
message << " Pre scale linearMomentum [";
SimTKOpenMMUtilities::formatRealStringStream( message, linearMomentum, 3, one );
message << "]\n";
SimTKOpenMMLog::printMessage( message );
}
*/
linearMomentum[0] *= totalMassI; linearMomentum[0] *= totalMassI;
linearMomentum[1] *= totalMassI; linearMomentum[1] *= totalMassI;
linearMomentum[2] *= totalMassI; linearMomentum[2] *= totalMassI;
/*
if( debug ){
std::stringstream message;
message << " Pre sub linearMomentum [";
SimTKOpenMMUtilities::formatRealStringStream( message, linearMomentum, 3, one );
message << "]\n";
SimTKOpenMMLog::printMessage( message );
}
*/
for( int ii = 0; ii < numberOfAtoms; ii++ ){ for( int ii = 0; ii < numberOfAtoms; ii++ ){
velocities[ii][0] -= linearMomentum[0]; velocities[ii][0] -= linearMomentum[0];
velocities[ii][1] -= linearMomentum[1]; velocities[ii][1] -= linearMomentum[1];
velocities[ii][2] -= linearMomentum[2]; velocities[ii][2] -= linearMomentum[2];
} }
// debug
if( debug ){
RealOpenMM tempV[3];
std::stringstream message;
int maxPrint = 5;
message << methodName;
message << " TotalM=" << totalMass << " linearMomentum: [";
SimTKOpenMMUtilities::formatRealStringStream( message, linearMomentum, 3, one );
message << "]\nSample v:\n";
for( int ii = 0; ii < maxPrint; ii++ ){
tempV[0] = velocities[ii][0] + linearMomentum[0];
tempV[1] = velocities[ii][1] + linearMomentum[1];
tempV[2] = velocities[ii][2] + linearMomentum[2];
message << "OldV[ ";
SimTKOpenMMUtilities::formatRealStringStream( message, tempV, 3, one );
message << "] NewV[ ";
SimTKOpenMMUtilities::formatRealStringStream( message, velocities[ii], 3, one );
message << "]" << std::endl;
}
SimTKOpenMMLog::printMessage( message );
}
}
return ReferenceDynamics::DefaultReturn;
}
/**---------------------------------------------------------------------------------------
Print parameters
@param message message
@return ReferenceDynamics::DefaultReturn
--------------------------------------------------------------------------------------- */
int ReferenceDynamics::printParameters( std::stringstream& message ) const {
// ---------------------------------------------------------------------------------------
static const char* methodName = "\nReferenceDynamics::printParameters";
// ---------------------------------------------------------------------------------------
message << "atoms=" << getNumberOfAtoms() << " ";
message << "delta_t=" << getDeltaT() << " ";
message << "temperature=" << getTemperature() << " ";
message << "step=" << getTimeStep() << " ";
message << "seed=" << SimTKOpenMMUtilities::getRandomNumberSeed() << " ";
message << std::endl;
return ReferenceDynamics::DefaultReturn;
}
/**---------------------------------------------------------------------------------------
Write state
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param velocities velocities
@param forces forces
@param masses atom masses
@param state 0 if initial state; otherwise nonzero
@param baseFileName base file name
@return ReferenceDynamics::DefaultReturn
--------------------------------------------------------------------------------------- */
int ReferenceDynamics::writeState( int numberOfAtoms, RealOpenMM** atomCoordinates,
RealOpenMM** velocities,
RealOpenMM** forces, RealOpenMM* masses,
int state, const std::string& baseFileName ) const {
// ---------------------------------------------------------------------------------------
static const char* methodName = "\nReferenceStochasticDynamics::writeState";
static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0;
static const int threeI = 3;
// ---------------------------------------------------------------------------------------
std::stringstream stateFileName;
stateFileName << baseFileName;
stateFileName << "_Step" << getTimeStep();
// stateFileName << "_State" << state;
stateFileName << ".txt";
// ---------------------------------------------------------------------------------------
// open file -- return if unsuccessful
FILE* stateFile = NULL;
#ifdef _MSC_VER
fopen_s( &stateFile, stateFileName.str().c_str(), "w" );
#else
stateFile = fopen( stateFileName.str().c_str(), "w" );
#endif
// ---------------------------------------------------------------------------------------
// diagnostics
if( stateFile != NULL ){
std::stringstream message;
message << methodName;
message << " Opened file=<" << stateFileName.str() << ">.\n";
SimTKOpenMMLog::printMessage( message );
} else {
std::stringstream message;
message << methodName;
message << " could not open file=<" << stateFileName.str() << "> -- abort output.\n";
SimTKOpenMMLog::printMessage( message );
return ReferenceDynamics::ErrorReturn;
}
// ---------------------------------------------------------------------------------------
StringVector scalarNameI;
IntVector scalarI;
StringVector scalarNameR;
RealOpenMMVector scalarR;
StringVector scalarNameR1;
RealOpenMMPtrVector scalarR1;
StringVector scalarNameR2;
RealOpenMMPtrPtrVector scalarR2;
scalarI.push_back( getNumberOfAtoms() );
scalarNameI.push_back( "Atoms" );
scalarI.push_back( getTimeStep() );
scalarNameI.push_back( "Timestep" );
scalarR.push_back( getDeltaT() );
scalarNameR.push_back( "delta_t" );
scalarR.push_back( static_cast<RealOpenMM>(SimTKOpenMMUtilities::getRandomNumberSeed()) );
scalarNameR.push_back( "seed" );
scalarR.push_back( getTemperature() );
scalarNameR.push_back( "T" );
if( masses ){
scalarR1.push_back( masses );
scalarNameR1.push_back( "mass" );
}
if( atomCoordinates ){
scalarR2.push_back( atomCoordinates );
scalarNameR2.push_back( "coord" );
}
if( velocities ){
scalarR2.push_back( velocities );
scalarNameR2.push_back( "velocities" );
}
if( forces ){
scalarR2.push_back( forces );
scalarNameR2.push_back( "forces" );
}
writeStateToFile( stateFile, scalarNameI, scalarI, scalarNameR, scalarR, getNumberOfAtoms(), scalarNameR1, scalarR1, threeI, scalarNameR2, scalarR2 );
(void) fclose( stateFile );
return ReferenceDynamics::DefaultReturn;
}
/**---------------------------------------------------------------------------------------
Write state
@param stateFile file to write to
@param scalarNameI vector of scalar names for ints
@param scalarI vector of scalar ints
@param scalarNameR vector of scalar names for real
@param scalarR vector of scalar reals
@param dimension1 size of first dimension for 1D & 2D real arrays
@param scalarNameR1 vector of names for 1D real arrays
@param scalarR1 vector of 1D real arrays
@param dimension2 size of second dimension for 2D real arrays
@param scalarNameR2 vector of names for 2D real arrays
@param scalarR2 vector of 2D real arrays
@return ReferenceDynamics::DefaultReturn
--------------------------------------------------------------------------------------- */
int ReferenceDynamics::writeStateToFile( FILE* stateFile,
StringVector& scalarNameI, IntVector& scalarI,
StringVector& scalarNameR, RealOpenMMVector& scalarR,
int dimension1, StringVector& scalarNameR1,
RealOpenMMPtrVector& scalarR1,
int dimension2, StringVector& scalarNameR2,
RealOpenMMPtrPtrVector& scalarR2 ) const {
// ---------------------------------------------------------------------------------------
static const char* methodName = "\nReferenceDynamics::writeState";
// ---------------------------------------------------------------------------------------
// validate vector sizes
std::stringstream message;
message << methodName << std::endl;
int errors = 0;
if( scalarNameI.size() != scalarI.size() ){
message << " int name size=" << scalarNameI.size() << " != " << " int vector size=" << scalarI.size() << std::endl;
errors++;
}
if( scalarNameR.size() != scalarR.size() ){
message << " real name size=" << scalarNameR.size() << " != " << " real vector size=" << scalarR.size() << std::endl;
errors++;
}
if( scalarNameR1.size() != scalarR1.size() ){
message << " real* name size=" << scalarNameR1.size() << " != " << " real* vector size=" << scalarR1.size() << std::endl;
errors++;
}
if( scalarNameR2.size() != scalarR2.size() ){
message << " real** name size=" << scalarNameR2.size() << " != " << " real** vector size=" << scalarR2.size() << std::endl;
errors++;
}
if( errors ){
SimTKOpenMMLog::printError( message );
return ReferenceDynamics::ErrorReturn;
} }
// ---------------------------------------------------------------------------------------
// array header
(void) fprintf( stateFile, "# " );
for( unsigned int ii = 0; ii < scalarNameR1.size(); ii++ ){
(void) fprintf( stateFile, " %s", scalarNameR1[ii].c_str() );
}
for( unsigned int ii = 0; ii < scalarNameR2.size(); ii++ ){
(void) fprintf( stateFile, " %s", scalarNameR2[ii].c_str() );
}
(void) fprintf( stateFile, "\n" );
// int scalars
for( unsigned int ii = 0; ii < scalarI.size(); ii++ ){
(void) fprintf( stateFile, "%6d # %s\n", scalarI[ii], scalarNameI[ii].c_str() );
}
// real scalars
for( unsigned int ii = 0; ii < scalarR.size(); ii++ ){
(void) fprintf( stateFile, "%14.6e # %s\n", scalarR[ii], scalarNameR[ii].c_str() );
}
// arrays
int maxPerLine = 3;
for( unsigned int ii = 0; ii < (unsigned int) dimension1; ii++ ){
(void) fprintf( stateFile, "%5d ", ii );
for( RealOpenMMPtrVectorI jj = scalarR1.begin(); jj != scalarR1.end(); jj++ ){
(void) fprintf( stateFile, "%14.6e ", (*jj)[ii] );
}
int r2Count = 0;
for( RealOpenMMPtrPtrVectorI jj = scalarR2.begin(); jj != scalarR2.end(); jj++ ){
RealOpenMM** array = *jj;
for( int kk = 0; kk < dimension2; kk++ ){
(void) fprintf( stateFile, "%14.6e ", array[ii][kk] );
}
(void) fprintf( stateFile, " " );
r2Count++;
if( r2Count == maxPerLine && ( (r2Count % (int) (scalarR2.size()-1)) > 2) ){
(void) fprintf( stateFile, "\n " );
r2Count = 0;
}
}
(void) fprintf( stateFile, "\n" );
}
return ReferenceDynamics::DefaultReturn; return ReferenceDynamics::DefaultReturn;
} }
platforms/reference/src/SimTKReference/ReferenceDynamics.h
View file @ b5858a8e
...@@ -237,18 +237,6 @@ class OPENMM_EXPORT ReferenceDynamics { ...@@ -237,18 +237,6 @@ class OPENMM_EXPORT ReferenceDynamics {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
int removeTotalLinearMomentum( int numberOfAtoms, RealOpenMM* masses, RealOpenMM** velocities ) const; int removeTotalLinearMomentum( int numberOfAtoms, RealOpenMM* masses, RealOpenMM** velocities ) const;
/**---------------------------------------------------------------------------------------
Print parameters
@param message message
@return ReferenceDynamics::DefaultReturn
--------------------------------------------------------------------------------------- */
int printParameters( std::stringstream& message ) const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -288,52 +276,6 @@ class OPENMM_EXPORT ReferenceDynamics { ...@@ -288,52 +276,6 @@ class OPENMM_EXPORT ReferenceDynamics {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
int setReferenceConstraintAlgorithm( ReferenceConstraintAlgorithm* referenceConstraint ); int setReferenceConstraintAlgorithm( ReferenceConstraintAlgorithm* referenceConstraint );
/**---------------------------------------------------------------------------------------
Write state
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param velocities velocities
@param forces forces
@param masses atom masses
@param state 0 if initial state; otherwise nonzero
@param baseFileName base file name
@return ReferenceDynamics::DefaultReturn
--------------------------------------------------------------------------------------- */
int writeState( int numberOfAtoms, RealOpenMM** atomCoordinates,
RealOpenMM** velocities, RealOpenMM** forces, RealOpenMM* masses,
int state, const std::string& baseFileName ) const;
/**---------------------------------------------------------------------------------------
Write state
@param stateFile file to write to
@param scalarNameI vector of scalar names for ints
@param scalarI vector of scalar ints
@param scalarNameR vector of scalar names for real
@param scalarR vector of scalar reals
@param dimension1 size of first dimension for 1D & 2D real arrays
@param scalarNameR1 vector of names for 1D real arrays
@param scalarR1 vector of 1D real arrays
@param dimension2 size of second dimension for 2D real arrays
@param scalarNameR2 vector of names for 2D real arrays
@param scalarR2 vector of 2D real arrays
@return ReferenceDynamics::DefaultReturn
--------------------------------------------------------------------------------------- */
int writeStateToFile( FILE* stateFile, StringVector& scalarNameI, IntVector& scalarI,
StringVector& scalarNameR, RealOpenMMVector& scalarR,
int dimension1, StringVector& scalarNameR1, RealOpenMMPtrVector& scalarR1,
int dimension2, StringVector& scalarNameR2, RealOpenMMPtrPtrVector& scalarR2 ) const;
}; };
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
......
platforms/reference/src/SimTKReference/ReferenceForce.cpp
View file @ b5858a8e
...@@ -171,109 +171,3 @@ int ReferenceForce::getDeltaROnly( const RealOpenMM* atomCoordinatesI, ...@@ -171,109 +171,3 @@ int ReferenceForce::getDeltaROnly( const RealOpenMM* atomCoordinatesI,
return ReferenceForce::DefaultReturn; return ReferenceForce::DefaultReturn;
} }
/**---------------------------------------------------------------------------------------
Write coordinates, energies and forces (Simbios)
@param numberOfAtoms number of atoms
@param atomsPerBond atoms/bond
@param atomCoordinates atomic coordinates
@param forces forces
@param energies energies (optional)
@param resultsFileName output file name
@param lengthConversion length conversion (optional defaults to 1)
@param energyConversion energy conversion (optional defaults to 1)
@param forceConversion force conversion (optional defaults to 1)
@return ReferenceForce::DefaultReturn unless
file cannot be opened
in which case return ReferenceForce::ErrorReturn
--------------------------------------------------------------------------------------- */
int ReferenceForce::writeForces( int numberOfAtoms, int atomsPerBond,
RealOpenMM** atomCoordinates, RealOpenMM** forces,
RealOpenMM* energies, const std::string& resultsFileName,
RealOpenMM lengthConversion = 1.0,
RealOpenMM forceConversion = 1.0,
RealOpenMM energyConversion = 1.0 ){
// ---------------------------------------------------------------------------------------
static const char* methodName = "\nReferenceForce::writeBornEnergyForces";
static const RealOpenMM zero = 0.0;
// ---------------------------------------------------------------------------------------
// open file -- return if unsuccessful
FILE* resultsFile = NULL;
#ifdef _MSC_VER
fopen_s( &resultsFile, resultsFileName.c_str(), "w" );
#else
resultsFile = fopen( resultsFileName.c_str(), "w" );
#endif
// ---------------------------------------------------------------------------------------
// diagnostics
std::stringstream message;
message << methodName;
if( resultsFile != NULL ){
std::stringstream message;
message << methodName;
message << " Opened file=<" << resultsFileName << ">.";
SimTKOpenMMLog::printMessage( message );
} else {
std::stringstream message;
message << methodName;
message << " could not open file=<" << resultsFileName << "> -- abort output.";
SimTKOpenMMLog::printMessage( message );
return ReferenceForce::ErrorReturn;
}
// total energy and normalize by number of atoms/bond
RealOpenMM totalEnergy = zero;
if( energies ){
for( int ii = 1; ii < numberOfAtoms; ii++ ){
totalEnergy += energies[ii];
}
if( atomsPerBond > 0 ){
totalEnergy /= (RealOpenMM) atomsPerBond;
}
}
// header
(void) fprintf( resultsFile, "# %d atoms E=%.7e format: coords(3) forces(3) energies\n",
numberOfAtoms, totalEnergy );
// output
if( forces != NULL && atomCoordinates != NULL ){
for( int ii = 0; ii < numberOfAtoms; ii++ ){
(void) fprintf( resultsFile, "%5d %15.7e %15.7e %15.7e %15.7e %15.7e %15.7e", ii,
lengthConversion*atomCoordinates[ii][0],
lengthConversion*atomCoordinates[ii][1],
lengthConversion*atomCoordinates[ii][2],
forceConversion*forces[ii][0],
forceConversion*forces[ii][1],
forceConversion*forces[ii][2]
);
if( energies != NULL ){
(void) fprintf( resultsFile, " %15.7e", energyConversion*energies[ii] );
}
(void) fprintf( resultsFile, "\n" );
}
}
(void) fclose( resultsFile );
return ReferenceForce::DefaultReturn;
}
platforms/reference/src/SimTKReference/ReferenceForce.h
View file @ b5858a8e
...@@ -118,33 +118,6 @@ class OPENMM_EXPORT ReferenceForce { ...@@ -118,33 +118,6 @@ class OPENMM_EXPORT ReferenceForce {
static int getDeltaROnly( const RealOpenMM* atomCoordinatesI, const RealOpenMM* atomCoordinatesJ, static int getDeltaROnly( const RealOpenMM* atomCoordinatesI, const RealOpenMM* atomCoordinatesJ,
RealOpenMM* deltaR ); RealOpenMM* deltaR );
/**---------------------------------------------------------------------------------------
Write coordinates, energies and forces (Simbios)
@param numberOfAtoms number of atoms
@param atomsPerBond atoms/bond (used to normalize total energy)
@param atomCoordinates atomic coordinates
@param forces forces
@param energies energies (optional)
@param resultsFileName output file name
@param lengthConversion length conversion (optional defaults to 1)
@param forceConversion force conversion (optional defaults to 1)
@param energyConversion energy conversion (optional defaults to 1)
@return ReferenceForce::DefaultReturn unless
file cannot be opened
in which case return ReferenceForce::ErrorReturn
--------------------------------------------------------------------------------------- */
static int writeForces( int numberOfAtoms, int atomsPerBond, RealOpenMM** atomCoordinates,
RealOpenMM** forces, RealOpenMM* energies,
const std::string& resultsFileName,
RealOpenMM lengthConversion, RealOpenMM forceConversion,
RealOpenMM energyConversion );
}; };
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
......
platforms/reference/src/SimTKReference/ReferenceLJCoulomb14.cpp
View file @ b5858a8e
...@@ -110,10 +110,6 @@ int ReferenceLJCoulomb14::calculateBondIxn( int* atomIndices, RealOpenMM** atomC ...@@ -110,10 +110,6 @@ int ReferenceLJCoulomb14::calculateBondIxn( int* atomIndices, RealOpenMM** atomC
static const int numberOfParameters = 3; static const int numberOfParameters = 3;
// debug flag
static const int debug = 0;
static const int LastAtomIndex = 2; static const int LastAtomIndex = 2;
RealOpenMM deltaR[2][ReferenceForce::LastDeltaRIndex]; RealOpenMM deltaR[2][ReferenceForce::LastDeltaRIndex];
...@@ -151,58 +147,5 @@ int ReferenceLJCoulomb14::calculateBondIxn( int* atomIndices, RealOpenMM** atomC ...@@ -151,58 +147,5 @@ int ReferenceLJCoulomb14::calculateBondIxn( int* atomIndices, RealOpenMM** atomC
updateEnergy( energy, energiesByBond, LastAtomIndex, atomIndices, energiesByAtom ); updateEnergy( energy, energiesByBond, LastAtomIndex, atomIndices, energiesByAtom );
// debug
if( debug ){
static bool printHeader = false;
std::stringstream message;
message << methodName;
message << std::endl;
if( !printHeader ){
printHeader = true;
message << std::endl;
message << methodName.c_str() << " a0 k [c q p s] r1 r2 angle dt rp p[] dot cosine angle dEdR*r F[]" << std::endl;
}
message << std::endl;
for( int ii = 0; ii < LastAtomIndex; ii++ ){
message << " Atm " << atomIndices[ii] << " [" << atomCoordinates[atomIndices[ii]][0] << " " << atomCoordinates[atomIndices[ii]][1] << "] ";
}
message << std::endl << " Delta:";
for( int ii = 0; ii < (LastAtomIndex - 1); ii++ ){
message << " [";
for( int jj = 0; jj < ReferenceForce::LastDeltaRIndex; jj++ ){
message << deltaR[ii][jj] << " ";
}
message << "]";
}
message << std::endl;
message << " p1=" << parameters[0];
message << " p2=" << parameters[1];
message << " p3=" << parameters[2];
message << std::endl << " ";
message << " dEdR=" << dEdR;
message << " E=" << energy << " force factors: ";
message << "F=compute force; f=cumulative force";
message << std::endl << " ";
for( int ii = 0; ii < LastAtomIndex; ii++ ){
message << " F" << (ii+1) << "[";
SimTKOpenMMUtilities::formatRealStringStream( message, deltaR[0], threeI, dEdR );
message << "]";
}
message << std::endl << " ";
for( int ii = 0; ii < LastAtomIndex; ii++ ){
message << " f" << (ii+1) << "[";
SimTKOpenMMUtilities::formatRealStringStream( message, forces[atomIndices[ii]], threeI );
message << "]";
}
SimTKOpenMMLog::printMessage( message );
}
return ReferenceForce::DefaultReturn; return ReferenceForce::DefaultReturn;
} }
platforms/reference/src/SimTKReference/ReferenceLJCoulombIxn.cpp
View file @ b5858a8e
...@@ -555,10 +555,6 @@ int ReferenceLJCoulombIxn::calculateOneIxn( int ii, int jj, RealOpenMM** atomCoo ...@@ -555,10 +555,6 @@ int ReferenceLJCoulombIxn::calculateOneIxn( int ii, int jj, RealOpenMM** atomCoo
static const int threeI = 3; static const int threeI = 3;
// debug flag
static const int debug = -1;
static const int LastAtomIndex = 2; static const int LastAtomIndex = 2;
RealOpenMM deltaR[2][ReferenceForce::LastDeltaRIndex]; RealOpenMM deltaR[2][ReferenceForce::LastDeltaRIndex];
...@@ -611,58 +607,6 @@ int ReferenceLJCoulombIxn::calculateOneIxn( int ii, int jj, RealOpenMM** atomCoo ...@@ -611,58 +607,6 @@ int ReferenceLJCoulombIxn::calculateOneIxn( int ii, int jj, RealOpenMM** atomCoo
} }
} }
// debug
if( debug == ii ){
static bool printHeader = false;
std::stringstream message;
message << methodName;
message << std::endl;
int pairArray[2] = { ii, jj };
if( !printHeader ){
printHeader = true;
message << std::endl;
message << methodName.c_str() << " a0 k [c q p s] r1 r2 angle dt rp p[] dot cosine angle dEdR*r F[]" << std::endl;
}
message << std::endl;
for( int kk = 0; kk < 2; kk++ ){
message << " Atm " << pairArray[kk] << " [" << atomCoordinates[pairArray[kk]][0] << " " << atomCoordinates[pairArray[kk]][1] << " " << atomCoordinates[pairArray[kk]][2] << "] ";
}
message << std::endl << " Delta:";
for( int kk = 0; kk < (LastAtomIndex - 1); kk++ ){
message << " [";
for( int jj = 0; jj < ReferenceForce::LastDeltaRIndex; jj++ ){
message << deltaR[kk][jj] << " ";
}
message << "]";
}
message << std::endl;
for( int kk = 0; kk < 2; kk++ ){
message << " p" << pairArray[kk] << " [";
message << atomParameters[pairArray[kk]][0] << " " << atomParameters[pairArray[kk]][1] << " " << atomParameters[pairArray[kk]][2];
message << "]";
}
message << std::endl;
message << " dEdR=" << dEdR;
message << " E=" << energy << " force factors: ";
message << "F=compute force; f=cumulative force";
message << std::endl << " ";
message << " f" << ii << "[";
SimTKOpenMMUtilities::formatRealStringStream( message, deltaR[0], threeI, dEdR );
message << "]";
for( int kk = 0; kk < 2; kk++ ){
message << " F" << pairArray[kk] << " [";
SimTKOpenMMUtilities::formatRealStringStream( message, forces[pairArray[kk]], threeI );
message << "]";
}
SimTKOpenMMLog::printMessage( message );
}
return ReferenceForce::DefaultReturn; return ReferenceForce::DefaultReturn;
} }
platforms/reference/src/SimTKReference/ReferenceProperDihedralBond.cpp
View file @ b5858a8e
...@@ -105,10 +105,6 @@ int ReferenceProperDihedralBond::calculateBondIxn( int* atomIndices, ...@@ -105,10 +105,6 @@ int ReferenceProperDihedralBond::calculateBondIxn( int* atomIndices,
static const int threeI = 3; static const int threeI = 3;
// debug flag
static const int debug = 0;
static const int LastAtomIndex = 4; static const int LastAtomIndex = 4;
RealOpenMM deltaR[3][ReferenceForce::LastDeltaRIndex]; RealOpenMM deltaR[3][ReferenceForce::LastDeltaRIndex];
...@@ -191,82 +187,5 @@ int ReferenceProperDihedralBond::calculateBondIxn( int* atomIndices, ...@@ -191,82 +187,5 @@ int ReferenceProperDihedralBond::calculateBondIxn( int* atomIndices,
updateEnergy( energy, energiesByBond, LastAtomIndex, atomIndices, energiesByAtom ); updateEnergy( energy, energiesByBond, LastAtomIndex, atomIndices, energiesByAtom );
// debug
if( debug ){
static bool printHeader = false;
std::stringstream message;
message << methodName;
message << std::endl;
if( !printHeader ){
printHeader = true;
message << std::endl;
message << methodName.c_str() << " a0 k [c q p s] r1 r2 angle dt rp p[] dot cosine angle dEdR*r F[]" << std::endl;
}
message << std::endl;
for( int ii = 0; ii < 4; ii++ ){
message << " Atm " << atomIndices[ii] << " [" << atomCoordinates[atomIndices[ii]][0] << " " << atomCoordinates[atomIndices[ii]][1] << " " << atomCoordinates[atomIndices[ii]][2] << "] ";
}
message << std::endl << " Delta:";
for( int ii = 0; ii < (LastAtomIndex - 1); ii++ ){
message << " [";
for( int jj = 0; jj < ReferenceForce::LastDeltaRIndex; jj++ ){
message << deltaR[ii][jj] << " ";
}
message << "]";
}
message << std::endl;
message << std::endl << " Cross:";
for( int ii = 0; ii < 2; ii++ ){
message << " [";
for( int jj = 0; jj < 3; jj++ ){
message << crossProduct[ii][jj] << " ";
}
message << "]";
}
message << std::endl;
message << " k=" << parameters[0];
message << " a=" << parameters[1];
message << " m=" << parameters[2];
message << " ang=" << dihedralAngle;
message << " dotD=" << dotDihedral;
message << " sign=" << signOfAngle;
message << std::endl << " ";
message << " deltaAngle=" << deltaAngle;
message << " dEdAngle=" << dEdAngle;
message << " E=" << energy << " force factors: [";
for( int ii = 0; ii < 4; ii++ ){
message << forceFactors[ii] << " ";
}
message << "] F=compute force; f=cumulative force";
message << std::endl << " ";
for( int ii = 0; ii < LastAtomIndex; ii++ ){
message << " F" << (ii+1) << "[";
SimTKOpenMMUtilities::formatRealStringStream( message, internalF[ii], threeI );
message << "]";
}
message << std::endl << " ";
for( int ii = 0; ii < LastAtomIndex; ii++ ){
message << " f" << (ii+1) << "[";
SimTKOpenMMUtilities::formatRealStringStream( message, forces[atomIndices[ii]], threeI );
message << "]";
}
SimTKOpenMMLog::printMessage( message );
}
if( debug ){
std::stringstream message;
message << methodName << " DONE";
message << std::endl;
SimTKOpenMMLog::printMessage( message );
}
return ReferenceForce::DefaultReturn; return ReferenceForce::DefaultReturn;
} }
platforms/reference/src/SimTKReference/ReferenceRbDihedralBond.cpp
View file @ b5858a8e
...@@ -107,10 +107,6 @@ int ReferenceRbDihedralBond::calculateBondIxn( int* atomIndices, ...@@ -107,10 +107,6 @@ int ReferenceRbDihedralBond::calculateBondIxn( int* atomIndices,
static const int numberOfParameters = 6; static const int numberOfParameters = 6;
// debug flag
static int debug = 0;
static const int LastAtomIndex = 4; static const int LastAtomIndex = 4;
RealOpenMM deltaR[3][ReferenceForce::LastDeltaRIndex]; RealOpenMM deltaR[3][ReferenceForce::LastDeltaRIndex];
...@@ -206,85 +202,5 @@ int ReferenceRbDihedralBond::calculateBondIxn( int* atomIndices, ...@@ -206,85 +202,5 @@ int ReferenceRbDihedralBond::calculateBondIxn( int* atomIndices,
updateEnergy( energy, energiesByBond, LastAtomIndex, atomIndices, energiesByAtom ); updateEnergy( energy, energiesByBond, LastAtomIndex, atomIndices, energiesByAtom );
// debug
if( debug ){
static bool printHeader = false;
std::stringstream message;
message << methodName;
message << std::endl;
if( !printHeader ){
printHeader = true;
message << std::endl;
message << methodName.c_str() << " a0 k [c q p s] r1 r2 angle dt rp p[] dot cosine angle dEdR*r F[]" << std::endl;
}
message << std::endl;
for( int ii = 0; ii < 4; ii++ ){
message << " Atm " << atomIndices[ii] << " [" << atomCoordinates[atomIndices[ii]][0] << " ";
message << atomCoordinates[atomIndices[ii]][1] << " " << atomCoordinates[atomIndices[ii]][2] << "] ";
}
message << std::endl << " Delta:";
for( int ii = 0; ii < (LastAtomIndex - 1); ii++ ){
message << " [";
for( int jj = 0; jj < ReferenceForce::LastDeltaRIndex; jj++ ){
message << deltaR[ii][jj] << " ";
}
message << "]";
}
message << std::endl;
message << std::endl << " Cross:";
for( int ii = 0; ii < 2; ii++ ){
message << " [";
for( int jj = 0; jj < 3; jj++ ){
message << crossProduct[ii][jj] << " ";
}
message << "]";
}
message << std::endl;
message << std::endl << numberOfParameters << " Parameters: [";
for( int ii = 0; ii < numberOfParameters; ii++ ){
message << parameters[ii] << " ";
}
message << " ]" << std::endl;
message << " ang=" << dihederalAngle;
message << " dotD=" << cosPhi;
message << " sign=" << signOfAngle;
message << std::endl << " ";
message << " dEdAngle=" << dEdAngle;
message << " E=" << energy << " force factors: [";
for( int ii = 0; ii < 4; ii++ ){
message << forceFactors[ii] << " ";
}
message << "] F=compute force; f=cumulative force";
message << std::endl << " ";
for( int ii = 0; ii < LastAtomIndex; ii++ ){
message << " F" << (ii+1) << "[";
SimTKOpenMMUtilities::formatRealStringStream( message, internalF[ii], threeI );
message << "]";
}
message << std::endl << " ";
for( int ii = 0; ii < LastAtomIndex; ii++ ){
message << " f" << (ii+1) << "[";
SimTKOpenMMUtilities::formatRealStringStream( message, forces[atomIndices[ii]], threeI );
message << "]";
}
SimTKOpenMMLog::printMessage( message );
}
if( debug ){
std::stringstream message;
message << methodName << " DONE";
message << std::endl;
SimTKOpenMMLog::printMessage( message );
}
return ReferenceForce::DefaultReturn; return ReferenceForce::DefaultReturn;
} }
platforms/reference/src/SimTKReference/ReferenceShakeAlgorithm.cpp
View file @ b5858a8e
...@@ -235,8 +235,6 @@ int ReferenceShakeAlgorithm::apply( int numberOfAtoms, RealOpenMM** atomCoordina ...@@ -235,8 +235,6 @@ int ReferenceShakeAlgorithm::apply( int numberOfAtoms, RealOpenMM** atomCoordina
static const RealOpenMM epsilon6 = (RealOpenMM) 1.0e-06; static const RealOpenMM epsilon6 = (RealOpenMM) 1.0e-06;
static int debug = 0;
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
int numberOfConstraints = getNumberOfConstraints(); int numberOfConstraints = getNumberOfConstraints();
...@@ -313,22 +311,6 @@ int ReferenceShakeAlgorithm::apply( int numberOfAtoms, RealOpenMM** atomCoordina ...@@ -313,22 +311,6 @@ int ReferenceShakeAlgorithm::apply( int numberOfAtoms, RealOpenMM** atomCoordina
atomCoordinatesP[atomJ][jj] -= inverseMasses[atomJ]*dr; atomCoordinatesP[atomJ][jj] -= inverseMasses[atomJ]*dr;
} }
} }
/*
if( ii < -3 ){
std::stringstream message;
message << iterations << " C0 it=" << ii << " [" << atomI << " " << atomJ << "]";
message << " rp2=" << rp2 << " tol=" << d_ij2[ii];
message << " diff=" << diff << " acor=" << acor;
message << " m2=" << reducedMasses[ii];
message << " rm[" << inverseMasses[atomI] << " " << inverseMasses[atomJ];
message << " [" << atomCoordinatesP[atomI][0] << " " << atomCoordinatesP[atomI][1] << " " << atomCoordinatesP[atomI][2] << "] ";
message << " [" << atomCoordinatesP[atomJ][0] << " " << atomCoordinatesP[atomJ][1] << " " << atomCoordinatesP[atomJ][2] << "] ";
message << " rrpr=" << rrpr << " rijx=" << r_ij[ii][0];
message << " \n";
SimTKOpenMMLog::printMessage( message );
} */
} else { } else {
numberConverged++; numberConverged++;
} }
...@@ -337,26 +319,6 @@ if( ii < -3 ){ ...@@ -337,26 +319,6 @@ if( ii < -3 ){
done = true; done = true;
} }
} }
// diagnostics
if( debug || !done ){
std::stringstream message;
message << methodName;
message << " iterations=" << iterations << " no. converged=" << numberConverged << " out of " << _numberOfConstraints;
if( done ){
message << " SUCCESS";
} else {
message << " FAILED";
}
message << "\n";
int errors = reportShake( numberOfAtoms, atomCoordinatesP, message );
if( !errors ){
message << "*** no errors recorded in explicit check ***";
}
message << "\n";
SimTKOpenMMLog::printMessage( message );
}
return (done ? ReferenceDynamics::DefaultReturn : ReferenceDynamics::ErrorReturn); return (done ? ReferenceDynamics::DefaultReturn : ReferenceDynamics::ErrorReturn);
......
platforms/reference/src/SimTKReference/ReferenceShakeAlgorithm.h
View file @ b5858a8e
...@@ -119,18 +119,6 @@ class ReferenceShakeAlgorithm : public ReferenceConstraintAlgorithm { ...@@ -119,18 +119,6 @@ class ReferenceShakeAlgorithm : public ReferenceConstraintAlgorithm {
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void setTolerance( RealOpenMM tolerance ); void setTolerance( RealOpenMM tolerance );
/**---------------------------------------------------------------------------------------
Print parameters
@param message message
@return ReferenceShakeAlgorithm::DefaultReturn
--------------------------------------------------------------------------------------- */
int printParameters( std::stringstream& message ) const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
......
platforms/reference/src/SimTKReference/ReferenceStochasticDynamics.cpp
View file @ b5858a8e
...@@ -57,7 +57,7 @@ ReferenceStochasticDynamics::ReferenceStochasticDynamics( int numberOfAtoms, ...@@ -57,7 +57,7 @@ ReferenceStochasticDynamics::ReferenceStochasticDynamics( int numberOfAtoms,
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
// insure tau is not zero -- if it is print warning message // ensure tau is not zero -- if it is print warning message
if( _tau == zero ){ if( _tau == zero ){
...@@ -110,34 +110,6 @@ RealOpenMM ReferenceStochasticDynamics::getTau( void ) const { ...@@ -110,34 +110,6 @@ RealOpenMM ReferenceStochasticDynamics::getTau( void ) const {
return _tau; return _tau;
} }
/**---------------------------------------------------------------------------------------
Print parameters
@param message message
@return ReferenceDynamics::DefaultReturn
--------------------------------------------------------------------------------------- */
int ReferenceStochasticDynamics::printParameters( std::stringstream& message ) const {
// ---------------------------------------------------------------------------------------
//static const char* methodName = "\nReferenceStochasticDynamics::printParameters";
// ---------------------------------------------------------------------------------------
// print parameters
ReferenceDynamics::printParameters( message );
message << " tau=" << getTau();
message << " T=" << getTemperature();
return ReferenceDynamics::DefaultReturn;
}
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
First SD update; based on code in update.c do_update_sd() Gromacs 3.1.4 First SD update; based on code in update.c do_update_sd() Gromacs 3.1.4
......
platforms/reference/src/SimTKReference/ReferenceStochasticDynamics.h
View file @ b5858a8e
...@@ -71,18 +71,6 @@ class ReferenceStochasticDynamics : public ReferenceDynamics { ...@@ -71,18 +71,6 @@ class ReferenceStochasticDynamics : public ReferenceDynamics {
RealOpenMM getTau( void ) const; RealOpenMM getTau( void ) const;
/**---------------------------------------------------------------------------------------
Print parameters
@param message message
@return ReferenceDynamics::DefaultReturn
--------------------------------------------------------------------------------------- */
int printParameters( std::stringstream& message ) const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Update Update
......
platforms/reference/src/SimTKReference/ReferenceVariableStochasticDynamics.cpp
View file @ b5858a8e
...@@ -58,7 +58,7 @@ ReferenceVariableStochasticDynamics::ReferenceVariableStochasticDynamics( int nu ...@@ -58,7 +58,7 @@ ReferenceVariableStochasticDynamics::ReferenceVariableStochasticDynamics( int nu
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
// insure tau is not zero -- if it is print warning message // ensure tau is not zero -- if it is print warning message
if( _tau == zero ){ if( _tau == zero ){
...@@ -133,34 +133,6 @@ RealOpenMM ReferenceVariableStochasticDynamics::getTau( void ) const { ...@@ -133,34 +133,6 @@ RealOpenMM ReferenceVariableStochasticDynamics::getTau( void ) const {
return _tau; return _tau;
} }
/**---------------------------------------------------------------------------------------
Print parameters
@param message message
@return ReferenceDynamics::DefaultReturn
--------------------------------------------------------------------------------------- */
int ReferenceVariableStochasticDynamics::printParameters( std::stringstream& message ) const {
// ---------------------------------------------------------------------------------------
//static const char* methodName = "\nReferenceVariableStochasticDynamics::printParameters";
// ---------------------------------------------------------------------------------------
// print parameters
ReferenceDynamics::printParameters( message );
message << " tau=" << getTau();
message << " T=" << getTemperature();
return ReferenceDynamics::DefaultReturn;
}
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
First SD update; based on code in update.c do_update_sd() Gromacs 3.1.4 First SD update; based on code in update.c do_update_sd() Gromacs 3.1.4
......
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