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Commit b3bab499 authored by peastman's avatar peastman
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Use templates to improve performance when not using triclinic boxes

parent f6aae604
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platforms/cpu/include/CpuNonbondedForceVec4.h
View file @ b3bab499
/* Portions copyright (c) 2006-2013 Stanford University and Simbios. /* Portions copyright (c) 2006-2014 Stanford University and Simbios.
* Contributors: Pande Group * Contributors: Pande Group
* *
* Permission is hereby granted, free of charge, to any person obtaining * Permission is hereby granted, free of charge, to any person obtaining
...@@ -52,6 +52,12 @@ protected: ...@@ -52,6 +52,12 @@ protected:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculateBlockIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize); void calculateBlockIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize);
/**
* Templatized implementation of calculateBlockIxn.
*/
template <bool TRICLINIC>
void calculateBlockIxnImpl(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -65,10 +71,17 @@ protected: ...@@ -65,10 +71,17 @@ protected:
void calculateBlockEwaldIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize); void calculateBlockEwaldIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize);
/**
* Templatized implementation of calculateBlockEwaldIxn.
*/
template <bool TRICLINIC>
void calculateBlockEwaldIxnImpl(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize);
/** /**
* Compute the displacement and squared distance between a collection of points, optionally using * Compute the displacement and squared distance between a collection of points, optionally using
* periodic boundary conditions. * periodic boundary conditions.
*/ */
template <bool TRICLINIC>
void getDeltaR(const float* posI, const fvec4& x, const fvec4& y, const fvec4& z, fvec4& dx, fvec4& dy, fvec4& dz, fvec4& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const; void getDeltaR(const float* posI, const fvec4& x, const fvec4& y, const fvec4& z, fvec4& dx, fvec4& dy, fvec4& dz, fvec4& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const;
/** /**
......
platforms/cpu/include/CpuNonbondedForceVec8.h
View file @ b3bab499
/* Portions copyright (c) 2006-2013 Stanford University and Simbios. /* Portions copyright (c) 2006-2014 Stanford University and Simbios.
* Contributors: Pande Group * Contributors: Pande Group
* *
* Permission is hereby granted, free of charge, to any person obtaining * Permission is hereby granted, free of charge, to any person obtaining
...@@ -51,6 +51,12 @@ protected: ...@@ -51,6 +51,12 @@ protected:
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void calculateBlockIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize); void calculateBlockIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize);
/**
* Templatized implementation of calculateBlockIxn.
*/
template <bool TRICLINIC>
void calculateBlockIxnImpl(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize);
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
...@@ -64,10 +70,17 @@ protected: ...@@ -64,10 +70,17 @@ protected:
void calculateBlockEwaldIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize); void calculateBlockEwaldIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize);
/**
* Templatized implementation of calculateBlockEwaldIxn.
*/
template <bool TRICLINIC>
void calculateBlockEwaldIxnImpl(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize);
/** /**
* Compute the displacement and squared distance between a collection of points, optionally using * Compute the displacement and squared distance between a collection of points, optionally using
* periodic boundary conditions. * periodic boundary conditions.
*/ */
template <bool TRICLINIC>
void getDeltaR(const float* posI, const fvec8& x, const fvec8& y, const fvec8& z, fvec8& dx, fvec8& dy, fvec8& dz, fvec8& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const; void getDeltaR(const float* posI, const fvec8& x, const fvec8& y, const fvec8& z, fvec8& dx, fvec8& dy, fvec8& dz, fvec8& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const;
/** /**
......
platforms/cpu/src/CpuNonbondedForceVec4.cpp
View file @ b3bab499
/* Portions copyright (c) 2006-2013 Stanford University and Simbios. /* Portions copyright (c) 2006-2014 Stanford University and Simbios.
* Contributors: Pande Group * Contributors: Pande Group
* *
* Permission is hereby granted, free of charge, to any person obtaining * Permission is hereby granted, free of charge, to any person obtaining
...@@ -46,6 +46,14 @@ CpuNonbondedForceVec4::CpuNonbondedForceVec4() { ...@@ -46,6 +46,14 @@ CpuNonbondedForceVec4::CpuNonbondedForceVec4() {
} }
void CpuNonbondedForceVec4::calculateBlockIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) { void CpuNonbondedForceVec4::calculateBlockIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) {
if (triclinic)
calculateBlockIxnImpl<true>(blockIndex, forces, totalEnergy, boxSize, invBoxSize);
else
calculateBlockIxnImpl<false>(blockIndex, forces, totalEnergy, boxSize, invBoxSize);
}
template <bool TRICLINIC>
void CpuNonbondedForceVec4::calculateBlockIxnImpl(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) {
// Load the positions and parameters of the atoms in the block. // Load the positions and parameters of the atoms in the block.
const int* blockAtom = &neighborList->getSortedAtoms()[4*blockIndex]; const int* blockAtom = &neighborList->getSortedAtoms()[4*blockIndex];
...@@ -75,7 +83,7 @@ void CpuNonbondedForceVec4::calculateBlockIxn(int blockIndex, float* forces, dou ...@@ -75,7 +83,7 @@ void CpuNonbondedForceVec4::calculateBlockIxn(int blockIndex, float* forces, dou
// Compute the distances to the block atoms. // Compute the distances to the block atoms.
fvec4 dx, dy, dz, r2; fvec4 dx, dy, dz, r2;
getDeltaR(posq+4*atom, blockAtomX, blockAtomY, blockAtomZ, dx, dy, dz, r2, needPeriodic, boxSize, invBoxSize); getDeltaR<TRICLINIC>(posq+4*atom, blockAtomX, blockAtomY, blockAtomZ, dx, dy, dz, r2, needPeriodic, boxSize, invBoxSize);
ivec4 include; ivec4 include;
char excl = exclusions[i]; char excl = exclusions[i];
if (excl == 0) if (excl == 0)
...@@ -155,6 +163,14 @@ void CpuNonbondedForceVec4::calculateBlockIxn(int blockIndex, float* forces, dou ...@@ -155,6 +163,14 @@ void CpuNonbondedForceVec4::calculateBlockIxn(int blockIndex, float* forces, dou
} }
void CpuNonbondedForceVec4::calculateBlockEwaldIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) { void CpuNonbondedForceVec4::calculateBlockEwaldIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) {
if (triclinic)
calculateBlockEwaldIxnImpl<true>(blockIndex, forces, totalEnergy, boxSize, invBoxSize);
else
calculateBlockEwaldIxnImpl<false>(blockIndex, forces, totalEnergy, boxSize, invBoxSize);
}
template <bool TRICLINIC>
void CpuNonbondedForceVec4::calculateBlockEwaldIxnImpl(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) {
// Load the positions and parameters of the atoms in the block. // Load the positions and parameters of the atoms in the block.
const int* blockAtom = &neighborList->getSortedAtoms()[4*blockIndex]; const int* blockAtom = &neighborList->getSortedAtoms()[4*blockIndex];
...@@ -184,7 +200,7 @@ void CpuNonbondedForceVec4::calculateBlockEwaldIxn(int blockIndex, float* forces ...@@ -184,7 +200,7 @@ void CpuNonbondedForceVec4::calculateBlockEwaldIxn(int blockIndex, float* forces
// Compute the distances to the block atoms. // Compute the distances to the block atoms.
fvec4 dx, dy, dz, r2; fvec4 dx, dy, dz, r2;
getDeltaR(posq+4*atom, blockAtomX, blockAtomY, blockAtomZ, dx, dy, dz, r2, needPeriodic, boxSize, invBoxSize); getDeltaR<TRICLINIC>(posq+4*atom, blockAtomX, blockAtomY, blockAtomZ, dx, dy, dz, r2, needPeriodic, boxSize, invBoxSize);
ivec4 include; ivec4 include;
char excl = exclusions[i]; char excl = exclusions[i];
if (excl == 0) if (excl == 0)
...@@ -257,12 +273,13 @@ void CpuNonbondedForceVec4::calculateBlockEwaldIxn(int blockIndex, float* forces ...@@ -257,12 +273,13 @@ void CpuNonbondedForceVec4::calculateBlockEwaldIxn(int blockIndex, float* forces
(fvec4(forces+4*blockAtom[j])+f[j]).store(forces+4*blockAtom[j]); (fvec4(forces+4*blockAtom[j])+f[j]).store(forces+4*blockAtom[j]);
} }
template <bool TRICLINIC>
void CpuNonbondedForceVec4::getDeltaR(const float* posI, const fvec4& x, const fvec4& y, const fvec4& z, fvec4& dx, fvec4& dy, fvec4& dz, fvec4& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const { void CpuNonbondedForceVec4::getDeltaR(const float* posI, const fvec4& x, const fvec4& y, const fvec4& z, fvec4& dx, fvec4& dy, fvec4& dz, fvec4& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const {
dx = x-posI[0]; dx = x-posI[0];
dy = y-posI[1]; dy = y-posI[1];
dz = z-posI[2]; dz = z-posI[2];
if (periodic) { if (periodic) {
if (triclinic) { if (TRICLINIC) {
fvec4 scale3 = floor(dz*recipBoxSize[2]+0.5f); fvec4 scale3 = floor(dz*recipBoxSize[2]+0.5f);
dx -= scale3*periodicBoxVectors[2][0]; dx -= scale3*periodicBoxVectors[2][0];
dy -= scale3*periodicBoxVectors[2][1]; dy -= scale3*periodicBoxVectors[2][1];
......
platforms/cpu/src/CpuNonbondedForceVec8.cpp
View file @ b3bab499
/* Portions copyright (c) 2006-2013 Stanford University and Simbios. /* Portions copyright (c) 2006-2014 Stanford University and Simbios.
* Contributors: Pande Group * Contributors: Pande Group
* *
* Permission is hereby granted, free of charge, to any person obtaining * Permission is hereby granted, free of charge, to any person obtaining
...@@ -78,6 +78,14 @@ CpuNonbondedForceVec8::CpuNonbondedForceVec8() { ...@@ -78,6 +78,14 @@ CpuNonbondedForceVec8::CpuNonbondedForceVec8() {
} }
void CpuNonbondedForceVec8::calculateBlockIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) { void CpuNonbondedForceVec8::calculateBlockIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) {
if (triclinic)
calculateBlockIxnImpl<true>(blockIndex, forces, totalEnergy, boxSize, invBoxSize);
else
calculateBlockIxnImpl<false>(blockIndex, forces, totalEnergy, boxSize, invBoxSize);
}
template <bool TRICLINIC>
void CpuNonbondedForceVec8::calculateBlockIxnImpl(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) {
// Load the positions and parameters of the atoms in the block. // Load the positions and parameters of the atoms in the block.
const int* blockAtom = &neighborList->getSortedAtoms()[8*blockIndex]; const int* blockAtom = &neighborList->getSortedAtoms()[8*blockIndex];
...@@ -106,7 +114,7 @@ void CpuNonbondedForceVec8::calculateBlockIxn(int blockIndex, float* forces, dou ...@@ -106,7 +114,7 @@ void CpuNonbondedForceVec8::calculateBlockIxn(int blockIndex, float* forces, dou
// Compute the distances to the block atoms. // Compute the distances to the block atoms.
fvec8 dx, dy, dz, r2; fvec8 dx, dy, dz, r2;
getDeltaR(&posq[4*atom], blockAtomX, blockAtomY, blockAtomZ, dx, dy, dz, r2, needPeriodic, boxSize, invBoxSize); getDeltaR<TRICLINIC>(&posq[4*atom], blockAtomX, blockAtomY, blockAtomZ, dx, dy, dz, r2, needPeriodic, boxSize, invBoxSize);
ivec8 include; ivec8 include;
char excl = exclusions[i]; char excl = exclusions[i];
if (excl == 0) if (excl == 0)
...@@ -186,6 +194,14 @@ void CpuNonbondedForceVec8::calculateBlockIxn(int blockIndex, float* forces, dou ...@@ -186,6 +194,14 @@ void CpuNonbondedForceVec8::calculateBlockIxn(int blockIndex, float* forces, dou
} }
void CpuNonbondedForceVec8::calculateBlockEwaldIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) { void CpuNonbondedForceVec8::calculateBlockEwaldIxn(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) {
if (triclinic)
calculateBlockEwaldIxnImpl<true>(blockIndex, forces, totalEnergy, boxSize, invBoxSize);
else
calculateBlockEwaldIxnImpl<false>(blockIndex, forces, totalEnergy, boxSize, invBoxSize);
}
template <bool TRICLINIC>
void CpuNonbondedForceVec8::calculateBlockEwaldIxnImpl(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize) {
// Load the positions and parameters of the atoms in the block. // Load the positions and parameters of the atoms in the block.
const int* blockAtom = &neighborList->getSortedAtoms()[8*blockIndex]; const int* blockAtom = &neighborList->getSortedAtoms()[8*blockIndex];
...@@ -214,7 +230,7 @@ void CpuNonbondedForceVec8::calculateBlockEwaldIxn(int blockIndex, float* forces ...@@ -214,7 +230,7 @@ void CpuNonbondedForceVec8::calculateBlockEwaldIxn(int blockIndex, float* forces
// Compute the distances to the block atoms. // Compute the distances to the block atoms.
fvec8 dx, dy, dz, r2; fvec8 dx, dy, dz, r2;
getDeltaR(&posq[4*atom], blockAtomX, blockAtomY, blockAtomZ, dx, dy, dz, r2, needPeriodic, boxSize, invBoxSize); getDeltaR<TRICLINIC>(&posq[4*atom], blockAtomX, blockAtomY, blockAtomZ, dx, dy, dz, r2, needPeriodic, boxSize, invBoxSize);
ivec8 include; ivec8 include;
char excl = exclusions[i]; char excl = exclusions[i];
if (excl == 0) if (excl == 0)
...@@ -287,12 +303,13 @@ void CpuNonbondedForceVec8::calculateBlockEwaldIxn(int blockIndex, float* forces ...@@ -287,12 +303,13 @@ void CpuNonbondedForceVec8::calculateBlockEwaldIxn(int blockIndex, float* forces
(fvec4(forces+4*blockAtom[j])+f[j]).store(forces+4*blockAtom[j]); (fvec4(forces+4*blockAtom[j])+f[j]).store(forces+4*blockAtom[j]);
} }
template <bool TRICLINIC>
void CpuNonbondedForceVec8::getDeltaR(const float* posI, const fvec8& x, const fvec8& y, const fvec8& z, fvec8& dx, fvec8& dy, fvec8& dz, fvec8& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const { void CpuNonbondedForceVec8::getDeltaR(const float* posI, const fvec8& x, const fvec8& y, const fvec8& z, fvec8& dx, fvec8& dy, fvec8& dz, fvec8& r2, bool periodic, const fvec4& boxSize, const fvec4& invBoxSize) const {
dx = x-posI[0]; dx = x-posI[0];
dy = y-posI[1]; dy = y-posI[1];
dz = z-posI[2]; dz = z-posI[2];
if (periodic) { if (periodic) {
if (triclinic) { if (TRICLINIC) {
fvec8 scale3 = floor(dz*recipBoxSize[2]+0.5f); fvec8 scale3 = floor(dz*recipBoxSize[2]+0.5f);
dx -= scale3*periodicBoxVectors[2][0]; dx -= scale3*periodicBoxVectors[2][0];
dy -= scale3*periodicBoxVectors[2][1]; dy -= scale3*periodicBoxVectors[2][1];
......
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