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Commit 7a51ccf6 authored by Mark Friedrichs's avatar Mark Friedrichs
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Mods

parent 56755055
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platforms/brook/src/BrookBonded.cpp
View file @ 7a51ccf6
...@@ -42,6 +42,9 @@ ...@@ -42,6 +42,9 @@
using namespace OpenMM; using namespace OpenMM;
using namespace std; using namespace std;
// 'defines' used to format paramater and atom index arrays
// carry over from original code
#define ATOMS(X,Y) (particles[ 5*(X) + (Y) + 1 ]) #define ATOMS(X,Y) (particles[ 5*(X) + (Y) + 1 ])
#define PARAMS(X,Y,Z) (params[(Y)][4*(X) + Z]) #define PARAMS(X,Y,Z) (params[(Y)][4*(X) + Z])
...@@ -62,7 +65,7 @@ BrookBonded::BrookBonded( ){ ...@@ -62,7 +65,7 @@ BrookBonded::BrookBonded( ){
_setupCompleted = 0; _setupCompleted = 0;
_numberOfParticles = 0; _numberOfParticles = 0;
_coulombFactor = (BrookOpenMMFloat) 138.935485; _coulombFactor = static_cast<BrookOpenMMFloat>( 138.935485 );
_particleIndicesStream = NULL; _particleIndicesStream = NULL;
_chargeStream = NULL; _chargeStream = NULL;
...@@ -476,6 +479,8 @@ void BrookBonded::_flipQuartet( int ibonded, int *particles ){ ...@@ -476,6 +479,8 @@ void BrookBonded::_flipQuartet( int ibonded, int *particles ){
//For now, simply flip the indices //For now, simply flip the indices
//we're just studying the packing //we're just studying the packing
// see 'defines' at top of file
tmp = ATOMS( ibonded, 0 ); tmp = ATOMS( ibonded, 0 );
ATOMS( ibonded, 0 ) = ATOMS( ibonded, 3 ); ATOMS( ibonded, 0 ) = ATOMS( ibonded, 3 );
ATOMS( ibonded, 3 ) = ATOMS( ibonded, 0 ); ATOMS( ibonded, 3 ) = ATOMS( ibonded, 0 );
...@@ -496,7 +501,9 @@ int BrookBonded::_matchTorsion( int i, int j, int k, int l, int nbondeds, int *p ...@@ -496,7 +501,9 @@ int BrookBonded::_matchTorsion( int i, int j, int k, int l, int nbondeds, int *p
int tmp; int tmp;
if( j > k ){ if( j > k ){
//swap into order //swap into order
tmp = i; tmp = i;
i = l; i = l;
l = tmp; l = tmp;
...@@ -580,7 +587,8 @@ int BrookBonded::_matchAngle( int i, int j, int k, int nbondeds, ...@@ -580,7 +587,8 @@ int BrookBonded::_matchAngle( int i, int j, int k, int nbondeds,
return ErrorReturnValue; return ErrorReturnValue;
} }
/*flag = 0 means match i-j, 1 means j-k and 2 means k-l /*
* flag = 0 means match i-j, 1 means j-k and 2 means k-l
* Again, like above, if we have uninitialized slots, we take em * Again, like above, if we have uninitialized slots, we take em
* *
* */ * */
...@@ -631,6 +639,7 @@ int BrookBonded::_matchBond( int i, int j, int nbondeds, int *particles, int *fl ...@@ -631,6 +639,7 @@ int BrookBonded::_matchBond( int i, int j, int nbondeds, int *particles, int *fl
} }
//Try third spot //Try third spot
if( ATOMS(n, 3) == -1 ){ if( ATOMS(n, 3) == -1 ){
if( i == ATOMS(n, 2) ){ if( i == ATOMS(n, 2) ){
ATOMS(n, 3) = j; ATOMS(n, 3) = j;
...@@ -678,6 +687,7 @@ int BrookBonded::_matchPair( int i, int j, int nbondeds, int *particles ){ ...@@ -678,6 +687,7 @@ int BrookBonded::_matchPair( int i, int j, int nbondeds, int *particles ){
} }
//If the l-particle is available //If the l-particle is available
if( ATOMS(n, 3) == -1 ){ if( ATOMS(n, 3) == -1 ){
if( ATOMS(n, 0) == i ){ if( ATOMS(n, 0) == i ){
ATOMS(n, 3) = j; ATOMS(n, 3) = j;
...@@ -690,6 +700,7 @@ int BrookBonded::_matchPair( int i, int j, int nbondeds, int *particles ){ ...@@ -690,6 +700,7 @@ int BrookBonded::_matchPair( int i, int j, int nbondeds, int *particles ){
} }
//Both are unavailable, both much match //Both are unavailable, both much match
if( ( i == ATOMS(n, 0) && j == ATOMS(n, 3) ) if( ( i == ATOMS(n, 0) && j == ATOMS(n, 3) )
|| ( i == ATOMS(n, 3) && j == ATOMS(n, 0) ) ){ || ( i == ATOMS(n, 3) && j == ATOMS(n, 0) ) ){
return n; return n;
...@@ -718,11 +729,11 @@ int BrookBonded::_addRBTorsions( int *nbondeds, int *particles, float *params[], ...@@ -718,11 +729,11 @@ int BrookBonded::_addRBTorsions( int *nbondeds, int *particles, float *params[],
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
static const std::string methodName = "BrookBonded::_addRBTorsions"; static const std::string methodName = "BrookBonded::_addRBTorsions";
static const int debug = 0; static const int printOn = 0;
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
if( debug && getLog() ){ if( printOn && getLog() ){
(void) fprintf( getLog(), "%s number of bonds=%d\n", methodName.c_str(), rbTorsionIndices.size() ); (void) fprintf( getLog(), "%s number of bonds=%d\n", methodName.c_str(), rbTorsionIndices.size() );
} }
...@@ -752,13 +763,13 @@ int BrookBonded::_addRBTorsions( int *nbondeds, int *particles, float *params[], ...@@ -752,13 +763,13 @@ int BrookBonded::_addRBTorsions( int *nbondeds, int *particles, float *params[],
// to calculate the forces! // to calculate the forces!
index = 1; index = 1;
PARAMS( ibonded, 0, 0 ) = (BrookOpenMMFloat) rbParameters[index++]; PARAMS( ibonded, 0, 0 ) = static_cast<BrookOpenMMFloat>( rbParameters[index++] );
PARAMS( ibonded, 0, 1 ) = (BrookOpenMMFloat) rbParameters[index++]; PARAMS( ibonded, 0, 1 ) = static_cast<BrookOpenMMFloat>( rbParameters[index++] );
PARAMS( ibonded, 0, 2 ) = (BrookOpenMMFloat) rbParameters[index++]; PARAMS( ibonded, 0, 2 ) = static_cast<BrookOpenMMFloat>( rbParameters[index++] );
PARAMS( ibonded, 0, 3 ) = (BrookOpenMMFloat) rbParameters[index++]; PARAMS( ibonded, 0, 3 ) = static_cast<BrookOpenMMFloat>( rbParameters[index++] );
PARAMS( ibonded, 1, 0 ) = (BrookOpenMMFloat) rbParameters[index++]; PARAMS( ibonded, 1, 0 ) = static_cast<BrookOpenMMFloat>( rbParameters[index++] );
if( debug && getLog() ){ if( printOn && getLog() ){
(void) fprintf( getLog(), " %d [%d %d %d %d] %.3e %.3e %.3e %.3e\n", ibonded, i, j, k, l, (void) fprintf( getLog(), " %d [%d %d %d %d] %.3e %.3e %.3e %.3e\n", ibonded, i, j, k, l,
rbParameters[0], rbParameters[1], rbParameters[0], rbParameters[1],
rbParameters[2], rbParameters[3], rbParameters[4], rbParameters[5] ); rbParameters[2], rbParameters[3], rbParameters[4], rbParameters[5] );
...@@ -790,12 +801,12 @@ int BrookBonded::_addPTorsions( int *nbondeds, int *particles, BrookOpenMMFloat* ...@@ -790,12 +801,12 @@ int BrookBonded::_addPTorsions( int *nbondeds, int *particles, BrookOpenMMFloat*
static const BrookOpenMMFloat DEG2RAD = (BrookOpenMMFloat) (M_PI/180.0); static const BrookOpenMMFloat DEG2RAD = (BrookOpenMMFloat) (M_PI/180.0);
static const std::string methodName = "BrookBonded::_addPTorsion"; static const std::string methodName = "BrookBonded::_addPTorsion";
static const int debug = 0; static const int printOn = 0;
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
FILE* log = getLog(); FILE* log = getLog();
if( debug ){ if( printOn ){
log = log ? log : stderr; log = log ? log : stderr;
(void) fprintf( log, "%s npdih=%d\n", methodName.c_str(), periodicTorsionIndices.size() ); (void) fprintf( log, "%s npdih=%d\n", methodName.c_str(), periodicTorsionIndices.size() );
(void) fflush( log ); (void) fflush( log );
...@@ -825,11 +836,11 @@ int BrookBonded::_addPTorsions( int *nbondeds, int *particles, BrookOpenMMFloat* ...@@ -825,11 +836,11 @@ int BrookBonded::_addPTorsions( int *nbondeds, int *particles, BrookOpenMMFloat*
// note: parameters 0 & 2 switched // note: parameters 0 & 2 switched
PARAMS( ibonded, 1, 1 ) = (BrookOpenMMFloat) pTParameters[2]; PARAMS( ibonded, 1, 1 ) = static_cast<BrookOpenMMFloat>( pTParameters[2] );
PARAMS( ibonded, 1, 2 ) = (BrookOpenMMFloat) pTParameters[1]; PARAMS( ibonded, 1, 2 ) = static_cast<BrookOpenMMFloat>( pTParameters[1] );
PARAMS( ibonded, 1, 3 ) = (BrookOpenMMFloat) pTParameters[0]; PARAMS( ibonded, 1, 3 ) = static_cast<BrookOpenMMFloat>( pTParameters[0] );
if( debug ){ if( printOn ){
(void) fprintf( log, " %d [%d %d %d %d] %.3e %.3e %.3e\n", ibonded, i, j, k, l, (void) fprintf( log, " %d [%d %d %d %d] %.3e %.3e %.3e\n", ibonded, i, j, k, l,
pTParameters[0], pTParameters[1], pTParameters[2] ); pTParameters[0], pTParameters[1], pTParameters[2] );
(void) fflush( log ); (void) fflush( log );
...@@ -858,11 +869,11 @@ int BrookBonded::_addAngles( int *nbondeds, int *particles, float *params[], con ...@@ -858,11 +869,11 @@ int BrookBonded::_addAngles( int *nbondeds, int *particles, float *params[], con
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
static const std::string methodName = "BrookBonded::_addAngles"; static const std::string methodName = "BrookBonded::_addAngles";
static const int debug = 0; static const int printOn = 0;
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
if( debug && getLog() ){ if( printOn && getLog() ){
(void) fprintf( getLog(), "%s nang=%d\n", methodName.c_str(), angleIndices.size() ); (void) fprintf( getLog(), "%s nang=%d\n", methodName.c_str(), angleIndices.size() );
} }
...@@ -888,10 +899,10 @@ int BrookBonded::_addAngles( int *nbondeds, int *particles, float *params[], con ...@@ -888,10 +899,10 @@ int BrookBonded::_addAngles( int *nbondeds, int *particles, float *params[], con
flag = 0; flag = 0;
(*nbondeds)++; (*nbondeds)++;
} }
PARAMS( ibonded, 2, flag*2 ) = (BrookOpenMMFloat) angParameters[0]; PARAMS( ibonded, 2, flag*2 ) = static_cast<BrookOpenMMFloat>( angParameters[0] );
PARAMS( ibonded, 2, flag*2 + 1 ) = (BrookOpenMMFloat) angParameters[1]; PARAMS( ibonded, 2, flag*2 + 1 ) = static_cast<BrookOpenMMFloat>( angParameters[1] );
if( debug && getLog() ){ if( printOn && getLog() ){
(void) fprintf( getLog(), " %d [%d %d %d ] %.6e %.6e\n", ibonded, i, j, k, (void) fprintf( getLog(), " %d [%d %d %d ] %.6e %.6e\n", ibonded, i, j, k,
angParameters[0], angParameters[1] ); angParameters[0], angParameters[1] );
} }
...@@ -919,11 +930,11 @@ int BrookBonded::_addBonds( int *nbondeds, int *particles, float *params[], cons ...@@ -919,11 +930,11 @@ int BrookBonded::_addBonds( int *nbondeds, int *particles, float *params[], cons
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
static const std::string methodName = "BrookBonded::_addBonds"; static const std::string methodName = "BrookBonded::_addBonds";
static const int debug = 0; static const int printOn = 0;
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
if( debug && getLog() ){ if( printOn && getLog() ){
(void) fprintf( getLog(), "%s nbonds=%d\n", methodName.c_str(), bondIndices.size() ); (void) fprintf( getLog(), "%s nbonds=%d\n", methodName.c_str(), bondIndices.size() );
} }
...@@ -958,14 +969,14 @@ int saveIbond = ibonded; ...@@ -958,14 +969,14 @@ int saveIbond = ibonded;
} }
if( flag < 2 ){ if( flag < 2 ){
PARAMS( ibonded, 3, flag*2 ) = (BrookOpenMMFloat) bndParameters[0]; PARAMS( ibonded, 3, flag*2 ) = static_cast<BrookOpenMMFloat>( bndParameters[0] );
PARAMS( ibonded, 3, flag*2 + 1 ) = (BrookOpenMMFloat) bndParameters[1]; PARAMS( ibonded, 3, flag*2 + 1 ) = static_cast<BrookOpenMMFloat>( bndParameters[1] );
} else { } else {
PARAMS( ibonded, 4, 0 ) = (BrookOpenMMFloat) bndParameters[0]; PARAMS( ibonded, 4, 0 ) = static_cast<BrookOpenMMFloat>( bndParameters[0] );
PARAMS( ibonded, 4, 1 ) = (BrookOpenMMFloat) bndParameters[1]; PARAMS( ibonded, 4, 1 ) = static_cast<BrookOpenMMFloat>( bndParameters[1] );
} }
if( debug && getLog() ){ if( printOn && getLog() ){
(void) fprintf( getLog(), " %d (%5d) [%6d %6d ] flag=%2d %.3e %.3e\n", ibonded, saveIbond, i, j, flag, (void) fprintf( getLog(), " %d (%5d) [%6d %6d ] flag=%2d %.3e %.3e\n", ibonded, saveIbond, i, j, flag,
bndParameters[0], bndParameters[1] ); bndParameters[0], bndParameters[1] );
} }
...@@ -999,11 +1010,11 @@ int BrookBonded::_addPairs( int *nbondeds, int *particles, BrookOpenMMFloat* par ...@@ -999,11 +1010,11 @@ int BrookBonded::_addPairs( int *nbondeds, int *particles, BrookOpenMMFloat* par
static const std::string methodName = "BrookBonded::_addPairs"; static const std::string methodName = "BrookBonded::_addPairs";
static const double oneSixth = 1.0/6.0; static const double oneSixth = 1.0/6.0;
static const int debug = 0; static const int printOn = 0;
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
if( debug && getLog() ){ if( printOn && getLog() ){
(void) fprintf( getLog(), "%s npairs=%d sz=%u %u\n", methodName.c_str(), bonded14Indices.size(), bonded14Indices.size(), nonbondedParameters.size() ); fflush( getLog() ); (void) fprintf( getLog(), "%s npairs=%d sz=%u %u\n", methodName.c_str(), bonded14Indices.size(), bonded14Indices.size(), nonbondedParameters.size() ); fflush( getLog() );
} }
...@@ -1020,32 +1031,16 @@ int BrookBonded::_addPairs( int *nbondeds, int *particles, BrookOpenMMFloat* par ...@@ -1020,32 +1031,16 @@ int BrookBonded::_addPairs( int *nbondeds, int *particles, BrookOpenMMFloat* par
(*nbondeds)++; (*nbondeds)++;
} }
//(void) fprintf( getLog(), "%s %d %ibonded=%d done\n", methodName.c_str(), ii, ibonded ); fflush( getLog() );
vector<double> iParameters = nonbondedParameters[ii]; vector<double> iParameters = nonbondedParameters[ii];
/*
double c6 = iParameters[1];
double c12 = 4.0*iParameters[2];
double sig, eps;
if( c12 != 0.0 ){
//eps = c6*c6/c12;
//sig = pow( c12/c6, oneSixth );
eps = c12;
sig = c6;
} else {
eps = 0.0;
sig = 1.0;
}
*/
PARAMS( ibonded, 4, 2 ) = (BrookOpenMMFloat) iParameters[1]; PARAMS( ibonded, 4, 2 ) = static_cast<BrookOpenMMFloat>( iParameters[1] );
PARAMS( ibonded, 4, 3 ) = (BrookOpenMMFloat) (4.0*iParameters[2]); PARAMS( ibonded, 4, 3 ) = static_cast<BrookOpenMMFloat>( (4.0*iParameters[2]) );
// a little wasteful, but ... // a little wasteful, but ...
charges[ibonded] = (BrookOpenMMFloat) iParameters[0]; charges[ibonded] = (BrookOpenMMFloat) iParameters[0];
if( debug ){ if( printOn ){
(void) fprintf( getLog(), " %d [%d %d ] %.3e %.3e q=%.4f\n", ibonded, i, j, iParameters[1], iParameters[2], charges[ibonded] ); (void) fprintf( getLog(), " %d [%d %d ] %.3e %.3e q=%.4f\n", ibonded, i, j, iParameters[1], iParameters[2], charges[ibonded] );
} }
} }
...@@ -1379,7 +1374,7 @@ int BrookBonded::setup( int numberOfParticles, ...@@ -1379,7 +1374,7 @@ int BrookBonded::setup( int numberOfParticles,
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
// debug stuff // printOn stuff
if( printOn ){ if( printOn ){
...@@ -1851,7 +1846,11 @@ void BrookBonded::computeForces( BrookStreamImpl& positionStream, BrookStreamImp ...@@ -1851,7 +1846,11 @@ void BrookBonded::computeForces( BrookStreamImpl& positionStream, BrookStreamImp
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
printOn = (printOn && getLog()) ? printOn : 0; if( printOn && getLog() ){
log = getLog();
} else {
printOn = 0;
}
// bonded // bonded
...@@ -1888,7 +1887,6 @@ void BrookBonded::computeForces( BrookStreamImpl& positionStream, BrookStreamImp ...@@ -1888,7 +1887,6 @@ void BrookBonded::computeForces( BrookStreamImpl& positionStream, BrookStreamImp
// diagnostics // diagnostics
if( printOn ){ if( printOn ){
log = getLog();
//FILE* log = stderr; //FILE* log = stderr;
int countPrintInvMap[4] = { 3, 5, 2, 4 }; int countPrintInvMap[4] = { 3, 5, 2, 4 };
......
platforms/brook/src/BrookLangevinDynamics.cpp
View file @ 7a51ccf6
...@@ -1532,11 +1532,11 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI ...@@ -1532,11 +1532,11 @@ int BrookLangevinDynamics::update( BrookStreamImpl& positionStream, BrookStreamI
nans[1] = brookRandomNumberGenerator.getRandomNumberStream( 1 )->checkForNans(); nans[1] = brookRandomNumberGenerator.getRandomNumberStream( 1 )->checkForNans();
(void) fprintf( log1, "Aborting: Nans rng: active index=%d %d %d\n", brookRandomNumberGenerator.getRvStreamIndex(), nans[0], nans[1] ); (void) fprintf( log1, "Aborting: Nans rng: active index=%d %d %d\n", brookRandomNumberGenerator.getRvStreamIndex(), nans[0], nans[1] );
brookStreamInternalPos->printToFile( log ); brookStreamInternalPos->printToFile( log1 );
brookStreamInternalVel->printToFile( log ); brookStreamInternalVel->printToFile( log1 );
brookStreamInternalFrc->printToFile( log ); brookStreamInternalFrc->printToFile( log1 );
brookRandomNumberGenerator.getRandomNumberStream( brookRandomNumberGenerator.getRvStreamIndex() )->printToFile( log ); brookRandomNumberGenerator.getRandomNumberStream( brookRandomNumberGenerator.getRvStreamIndex() )->printToFile( log1 );
exit(1); exit(1);
} }
......
platforms/brook/src/BrookVerletDynamics.cpp
View file @ 7a51ccf6
...@@ -677,6 +677,67 @@ int BrookVerletDynamics::update( BrookStreamImpl& positionStream, BrookStreamImp ...@@ -677,6 +677,67 @@ int BrookVerletDynamics::update( BrookStreamImpl& positionStream, BrookStreamImp
positionStream.getBrookStream() ); positionStream.getBrookStream() );
} }
// diagnostics
if( (_internalStepCount % 1) == 0 ){
FILE* log1 = stderr;
float epsilon = 1.0e-01f;
BrookStreamInternal* brookStreamInternalPos = positionStream.getBrookStreamInternal();
BrookStreamInternal* brookStreamInternalVel = velocityStream.getBrookStreamInternal();
BrookStreamInternal* brookStreamInternalFrc = forceStream.getBrookStreamInternal();
// check for nan and infinities
int coordinateNans = brookStreamInternalPos->checkForNans( );
int velocityNans = brookStreamInternalVel->checkForNans( );
int forceNans = brookStreamInternalFrc->checkForNans( );
int abort = abs( coordinateNans ) + abs( velocityNans ) + abs( forceNans );
// Shake violations
std::string violationString;
int constraintViolations = brookShakeAlgorithm.checkConstraints( brookStreamInternalPos, violationString, 0.0001f );
abort += abs( constraintViolations );
// force sums ~ 0?
std::vector<float> sums;
brookStreamInternalFrc->sumColumns( sums );
// check if should abort
(void) fprintf( log1, "%d Nans: x=%d v=%d f=%d ", _internalStepCount, coordinateNans, velocityNans, forceNans );
(void) fprintf( log1, " Fsum[" );
for( int ii = 0; ii < 3; ii++ ){
if( fabsf( sums[ii] ) > epsilon ){
abort++;
}
(void) fprintf( log1, "%12.4e ", sums[ii] );
}
(void) fprintf( log1, "] %s abort=%d\n", violationString.c_str(), abort );
(void) fflush( log1 );
if( abort ){
(void) fprintf( log1, "Aborting:\n" );
brookStreamInternalPos->printToFile( log1 );
brookStreamInternalVel->printToFile( log1 );
brookStreamInternalFrc->printToFile( log1 );
exit(1);
}
/*
std::vector<std::vector<double> > velocityStatistics;
brookStreamInternalPos->getStatistics( velocityStatistics, getNumberOfParticles() );
std::stringstream tagV;
tagV << _internalStepCount << " Vxx ";
std::string stats = brookStreamInternalPos->printStatistics( tagV.str(), velocityStatistics );
(void) fprintf( log1, "\nStep %d Velocity stats:\n%s", _internalStepCount, stats.c_str() );
*/
//removeCom( brookStreamInternalPos, getInverseMassStream() );
}
//_brookVelocityCenterOfMassRemoval->removeVelocityCenterOfMass( velocities ); //_brookVelocityCenterOfMassRemoval->removeVelocityCenterOfMass( velocities );
return DefaultReturnValue; return DefaultReturnValue;
......
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