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Commit 0d1d98ce authored by Mark Friedrichs's avatar Mark Friedrichs
Browse files

Mods to output of forces

parent 132a94bc
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Showing with 144 additions and 100 deletions
plugins/amoeba/platforms/reference/src/AmoebaReferenceKernelFactory.cpp
View file @ 0d1d98ce
......@@ -37,7 +37,9 @@ extern "C" void OPENMM_EXPORT registerKernelFactories() {
for( int ii = 0; ii < Platform::getNumPlatforms(); ii++ ){
Platform& platform = Platform::getPlatform(ii);
if( platform.getName() == "Reference" ){
AmoebaReferenceKernelFactory* factory = new AmoebaReferenceKernelFactory();
platform.registerKernelFactory(CalcAmoebaHarmonicBondForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaUreyBradleyForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaHarmonicAngleForceKernel::Name(), factory);
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceHarmonicAngleForce.cpp
View file @ 0d1d98ce
......@@ -175,9 +175,9 @@ RealOpenMM AmoebaReferenceHarmonicAngleForce::calculateAngleIxn( const RealVec&
// accumulate forces
for( int jj = 0; jj < 3; jj++ ){
forces[jj][0] += deltaCrossP[jj][0];
forces[jj][1] += deltaCrossP[jj][1];
forces[jj][2] += deltaCrossP[jj][2];
forces[jj][0] = deltaCrossP[jj][0];
forces[jj][1] = deltaCrossP[jj][1];
forces[jj][2] = deltaCrossP[jj][2];
}
return energy;
......@@ -202,11 +202,14 @@ RealOpenMM AmoebaReferenceHarmonicAngleForce::calculateForceAndEnergy( int numAn
RealOpenMM idealAngle = angle[ii];
RealOpenMM angleK = kQuadratic[ii];
RealVec forces[3];
forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index];
forces[2] = forceData[particle3Index];
energy += calculateAngleIxn( posData[particle1Index], posData[particle2Index], posData[particle3Index],
idealAngle, angleK, angleCubic, angleQuartic, anglePentic, angleSextic, forces );
for( unsigned int jj = 0; jj < 3; jj++ ){
forceData[particle1Index][jj] += forces[0][jj];
forceData[particle2Index][jj] += forces[1][jj];
forceData[particle3Index][jj] += forces[2][jj];
}
}
return energy;
}
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceHarmonicBondForce.cpp
View file @ 0d1d98ce
......@@ -75,13 +75,14 @@ RealOpenMM AmoebaReferenceHarmonicBondForce::calculateBondIxn( const RealVec& po
dEdR *= two*bondK*deltaIdeal;
dEdR = r > zero ? (dEdR/r) : zero;
forces[0][0] += dEdR*deltaR[0];
forces[0][1] += dEdR*deltaR[1];
forces[0][2] += dEdR*deltaR[2];
forces[0][0] = dEdR*deltaR[0];
forces[0][1] = dEdR*deltaR[1];
forces[0][2] = dEdR*deltaR[2];
forces[1][0] -= dEdR*deltaR[0];
forces[1][1] -= dEdR*deltaR[1];
forces[1][2] -= dEdR*deltaR[2];
dEdR *= -1.0;
forces[1][0] = dEdR*deltaR[0];
forces[1][1] = dEdR*deltaR[1];
forces[1][2] = dEdR*deltaR[2];
RealOpenMM energy = bondK*deltaIdeal2*( one + bondCubic*deltaIdeal + bondQuartic*deltaIdeal2 );
return energy;
......@@ -103,11 +104,16 @@ RealOpenMM AmoebaReferenceHarmonicBondForce::calculateForceAndEnergy( int numBon
RealOpenMM bondLength = length[ii];
RealOpenMM bondK = kQuadratic[ii];
RealVec forces[2];
forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index];
energy += calculateBondIxn( particlePositions[particle1Index], particlePositions[particle2Index],
bondLength, bondK, globalHarmonicBondCubic, globalHarmonicBondQuartic,
forces );
for( int jj = 0; jj < 3; jj++ ){
forceData[particle1Index][jj] += forces[0][jj];
forceData[particle2Index][jj] += forces[1][jj];
}
}
return energy;
}
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceHarmonicInPlaneAngleForce.cpp
View file @ 0d1d98ce
......@@ -236,9 +236,9 @@ RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::calculateAngleIxn( const Re
// accumulate forces
for( int jj = 0; jj < 4; jj++ ){
forces[jj][0] -= forceTerm[jj][0];
forces[jj][1] -= forceTerm[jj][1];
forces[jj][2] -= forceTerm[jj][2];
forces[jj][0] = forceTerm[jj][0];
forces[jj][1] = forceTerm[jj][1];
forces[jj][2] = forceTerm[jj][2];
}
return energy;
......@@ -266,12 +266,18 @@ RealOpenMM AmoebaReferenceHarmonicInPlaneAngleForce::calculateForceAndEnergy( in
RealOpenMM idealAngle = angle[ii];
RealOpenMM angleK = kQuadratic[ii];
RealVec forces[4];
forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index];
forces[2] = forceData[particle3Index];
forces[3] = forceData[particle4Index];
energy += calculateAngleIxn( posData[particle1Index], posData[particle2Index], posData[particle3Index], posData[particle4Index],
idealAngle, angleK, angleCubic, angleQuartic, anglePentic, angleSextic, forces );
// accumulate forces
for( int jj = 0; jj < 3; jj++ ){
forceData[particle1Index][jj] -= forces[0][jj];
forceData[particle2Index][jj] -= forces[1][jj];
forceData[particle3Index][jj] -= forces[2][jj];
forceData[particle4Index][jj] -= forces[3][jj];
}
}
return energy;
}
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceOutOfPlaneBendForce.cpp
View file @ 0d1d98ce
......@@ -182,7 +182,7 @@ RealOpenMM AmoebaReferenceOutOfPlaneBendForce::calculateOutOfPlaneBendIxn( const
for( int jj = 0; jj < LastAtomIndex; jj++ ){
for( int ii = 0; ii < 3; ii++ ){
forces[jj][ii] -= subForce[jj][ii];
forces[jj][ii] = subForce[jj][ii];
}
}
......@@ -215,12 +215,15 @@ RealOpenMM AmoebaReferenceOutOfPlaneBendForce::calculateForceAndEnergy( int numO
int particle4Index = particle4[ii];
RealOpenMM kAngle = kQuadratic[ii];
RealVec forces[4];
forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index];
forces[2] = forceData[particle3Index];
forces[3] = forceData[particle4Index];
energy += calculateOutOfPlaneBendIxn( posData[particle1Index], posData[particle2Index], posData[particle3Index], posData[particle4Index],
kAngle, angleCubic, angleQuartic, anglePentic, angleSextic, forces );
for( int jj = 0; jj < 3; jj++ ){
forceData[particle1Index][jj] -= forces[0][jj];
forceData[particle2Index][jj] -= forces[1][jj];
forceData[particle3Index][jj] -= forces[2][jj];
forceData[particle4Index][jj] -= forces[3][jj];
}
}
return energy;
}
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferencePiTorsionForce.cpp
View file @ 0d1d98ce
......@@ -154,29 +154,29 @@ RealOpenMM AmoebaReferencePiTorsionForce::calculatePiTorsionIxn( const RealVec&
// add in forces
forces[0][0] -= d[0][0];
forces[0][1] -= d[0][1];
forces[0][2] -= d[0][2];
forces[0][0] = d[0][0];
forces[0][1] = d[0][1];
forces[0][2] = d[0][2];
forces[1][0] -= d[1][0];
forces[1][1] -= d[1][1];
forces[1][2] -= d[1][2];
forces[1][0] = d[1][0];
forces[1][1] = d[1][1];
forces[1][2] = d[1][2];
forces[2][0] -= d[2][0];
forces[2][1] -= d[2][1];
forces[2][2] -= d[2][2];
forces[2][0] = d[2][0];
forces[2][1] = d[2][1];
forces[2][2] = d[2][2];
forces[3][0] -= d[3][0];
forces[3][1] -= d[3][1];
forces[3][2] -= d[3][2];
forces[3][0] = d[3][0];
forces[3][1] = d[3][1];
forces[3][2] = d[3][2];
forces[4][0] -= d[4][0];
forces[4][1] -= d[4][1];
forces[4][2] -= d[4][2];
forces[4][0] = d[4][0];
forces[4][1] = d[4][1];
forces[4][2] = d[4][2];
forces[5][0] -= d[5][0];
forces[5][1] -= d[5][1];
forces[5][2] -= d[5][2];
forces[5][0] = d[5][0];
forces[5][1] = d[5][1];
forces[5][2] = d[5][2];
// ---------------------------------------------------------------------------------------
......@@ -206,16 +206,21 @@ RealOpenMM AmoebaReferencePiTorsionForce::calculateForceAndEnergy( int numPiTors
int particle6Index = particle6[ii];
RealVec forces[6];
forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index];
forces[2] = forceData[particle3Index];
forces[3] = forceData[particle4Index];
forces[4] = forceData[particle5Index];
forces[5] = forceData[particle6Index];
energy += calculatePiTorsionIxn( posData[particle1Index], posData[particle2Index],
posData[particle3Index], posData[particle4Index],
posData[particle5Index], posData[particle6Index],
kTorsion[ii], forces );
// accumulate forces
for( int jj = 0; jj < 3; jj++ ){
forceData[particle1Index][jj] -= forces[0][jj];
forceData[particle2Index][jj] -= forces[1][jj];
forceData[particle3Index][jj] -= forces[2][jj];
forceData[particle4Index][jj] -= forces[3][jj];
forceData[particle5Index][jj] -= forces[4][jj];
forceData[particle6Index][jj] -= forces[5][jj];
}
}
return energy;
}
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceStretchBendForce.cpp
View file @ 0d1d98ce
......@@ -137,9 +137,9 @@ RealOpenMM AmoebaReferenceStretchBendForce::calculateStretchBendIxn( const RealV
// add in forces
for( int jj = 0; jj < LastAtomIndex; jj++ ){
forces[jj][0] -= subForce[jj][0];
forces[jj][1] -= subForce[jj][1];
forces[jj][2] -= subForce[jj][2];
forces[jj][0] = subForce[jj][0];
forces[jj][1] = subForce[jj][1];
forces[jj][2] = subForce[jj][2];
}
// ---------------------------------------------------------------------------------------
......@@ -166,11 +166,16 @@ RealOpenMM AmoebaReferenceStretchBendForce::calculateForceAndEnergy( int numStre
RealOpenMM idealAngle = angle[ii];
RealOpenMM angleK = kQuadratic[ii];
RealVec forces[3];
forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index];
forces[2] = forceData[particle3Index];
energy += calculateStretchBendIxn( posData[particle1Index], posData[particle2Index], posData[particle3Index],
abLength, cbLength, idealAngle, angleK, forces );
// accumulate forces
for( int jj = 0; jj < 3; jj++ ){
forceData[particle1Index][jj] -= forces[0][jj];
forceData[particle2Index][jj] -= forces[1][jj];
forceData[particle3Index][jj] -= forces[2][jj];
}
}
return energy;
}
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceTorsionForce.cpp
View file @ 0d1d98ce
......@@ -185,21 +185,21 @@ RealOpenMM AmoebaReferenceTorsionForce::calculateTorsionIxn( const RealVec& posi
// forces
forces[0][0] -= tempVector[0][0];
forces[0][1] -= tempVector[0][1];
forces[0][2] -= tempVector[0][2];
forces[0][0] = tempVector[0][0];
forces[0][1] = tempVector[0][1];
forces[0][2] = tempVector[0][2];
forces[1][0] -= tempVector[1][0];
forces[1][1] -= tempVector[1][1];
forces[1][2] -= tempVector[1][2];
forces[1][0] = tempVector[1][0];
forces[1][1] = tempVector[1][1];
forces[1][2] = tempVector[1][2];
forces[2][0] -= tempVector[2][0];
forces[2][1] -= tempVector[2][1];
forces[2][2] -= tempVector[2][2];
forces[2][0] = tempVector[2][0];
forces[2][1] = tempVector[2][1];
forces[2][2] = tempVector[2][2];
forces[3][0] -= tempVector[3][0];
forces[3][1] -= tempVector[3][1];
forces[3][2] -= tempVector[3][2];
forces[3][0] = tempVector[3][0];
forces[3][1] = tempVector[3][1];
forces[3][2] = tempVector[3][2];
// ---------------------------------------------------------------------------------------
......@@ -228,12 +228,17 @@ RealOpenMM AmoebaReferenceTorsionForce::calculateForceAndEnergy( int numTorsions
int particle3Index = particle3[ii];
int particle4Index = particle4[ii];
RealVec forces[4];
forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index];
forces[2] = forceData[particle3Index];
forces[3] = forceData[particle4Index];
energy += calculateTorsionIxn( posData[particle1Index], posData[particle2Index], posData[particle3Index], posData[particle4Index],
torsionParameters1[ii], torsionParameters2[ii], torsionParameters3[ii], forces );
// accumulate forces
for( int jj = 0; jj < 3; jj++ ){
forceData[particle1Index][jj] -= forces[0][jj];
forceData[particle2Index][jj] -= forces[1][jj];
forceData[particle3Index][jj] -= forces[2][jj];
forceData[particle4Index][jj] -= forces[3][jj];
}
}
return energy;
}
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceTorsionTorsionForce.cpp
View file @ 0d1d98ce
......@@ -542,9 +542,9 @@ RealOpenMM AmoebaReferenceTorsionTorsionForce::calculateTorsionTorsionIxn( const
// add in forces
for( int jj = 0; jj < LastAtomIndex; jj++ ){
forces[jj][0] -= d[jj][0];
forces[jj][1] -= d[jj][1];
forces[jj][2] -= d[jj][2];
forces[jj][0] = d[jj][0];
forces[jj][1] = d[jj][1];
forces[jj][2] = d[jj][2];
}
// ---------------------------------------------------------------------------------------
......@@ -576,12 +576,6 @@ RealOpenMM AmoebaReferenceTorsionTorsionForce::calculateForceAndEnergy( int numT
int gridIndex = gridIndices[ii];
RealVec forces[5];
forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index];
forces[2] = forceData[particle3Index];
forces[3] = forceData[particle4Index];
forces[4] = forceData[particle5Index];
RealVec* chiralCheckAtom;
if( chiralCheckAtomIndex >= 0 ){
chiralCheckAtom = &posData[chiralCheckAtomIndex];
......@@ -593,6 +587,16 @@ RealOpenMM AmoebaReferenceTorsionTorsionForce::calculateForceAndEnergy( int numT
posData[particle5Index], chiralCheckAtom, torsionTorsionGrids[gridIndex],
forces );
// accumulate forces
for( int jj = 0; jj < 3; jj++ ){
forceData[particle1Index][jj] -= forces[0][jj];
forceData[particle2Index][jj] -= forces[1][jj];
forceData[particle3Index][jj] -= forces[2][jj];
forceData[particle4Index][jj] -= forces[3][jj];
forceData[particle5Index][jj] -= forces[4][jj];
}
}
return energy;
}
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceUreyBradleyForce.cpp
View file @ 0d1d98ce
......@@ -75,13 +75,13 @@ RealOpenMM AmoebaReferenceUreyBradleyForce::calculateUreyBradleyIxn( const RealV
dEdR *= two*kForceConstant*deltaIdeal;
dEdR = r > zero ? (dEdR/r) : zero;
forces[0][0] += dEdR*deltaR[0];
forces[0][1] += dEdR*deltaR[1];
forces[0][2] += dEdR*deltaR[2];
forces[0][0] = dEdR*deltaR[0];
forces[0][1] = dEdR*deltaR[1];
forces[0][2] = dEdR*deltaR[2];
forces[1][0] -= dEdR*deltaR[0];
forces[1][1] -= dEdR*deltaR[1];
forces[1][2] -= dEdR*deltaR[2];
forces[1][0] = dEdR*deltaR[0];
forces[1][1] = dEdR*deltaR[1];
forces[1][2] = dEdR*deltaR[2];
RealOpenMM energy = kForceConstant*deltaIdeal2*( one + cubicK*deltaIdeal + quarticK*deltaIdeal2 );
return energy;
......@@ -103,11 +103,16 @@ RealOpenMM AmoebaReferenceUreyBradleyForce::calculateForceAndEnergy( int numIxns
RealOpenMM idealLength = length[ii];
RealOpenMM kForceConstant = kQuadratic[ii];
RealVec forces[2];
forces[0] = forceData[particle1Index];
forces[1] = forceData[particle2Index];
energy += calculateUreyBradleyIxn( particlePositions[particle1Index], particlePositions[particle2Index],
idealLength, kForceConstant, globalUreyBradleyCubic, globalUreyBradleyQuartic,
forces );
// accumulate forces
for( int jj = 0; jj < 3; jj++ ){
forceData[particle1Index][jj] += forces[0][jj];
forceData[particle2Index][jj] -= forces[1][jj];
}
}
return energy;
}
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