Skip to content

GitLab

"platforms/hip/vscode:/vscode.git/clone" did not exist on "d2a5d7e40990be7c8b9764aa0366da05443badc9"
Commit f51a85b9 authored by Peter Eastman's avatar Peter Eastman
Browse files

Converted more forces to use OpenCLBondedUtilities

parent 42b9d891
Expand all Show whitespace changes
Inline Side-by-side
Showing with 225 additions and 557 deletions
platforms/opencl/src/OpenCLKernels.cpp
View file @ f51a85b9
This diff is collapsed.
platforms/opencl/src/OpenCLKernels.h
View file @ f51a85b9
......@@ -217,7 +217,7 @@ private:
class OpenCLCalcCustomBondForceKernel : public CalcCustomBondForceKernel {
public:
OpenCLCalcCustomBondForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, System& system) : CalcCustomBondForceKernel(name, platform),
hasInitializedKernel(false), cl(cl), system(system), params(NULL), indices(NULL), globals(NULL) {
hasInitializedKernel(false), cl(cl), system(system), params(NULL), globals(NULL) {
}
~OpenCLCalcCustomBondForceKernel();
/**
......@@ -242,11 +242,9 @@ private:
OpenCLContext& cl;
System& system;
OpenCLParameterSet* params;
OpenCLArray<mm_int4>* indices;
OpenCLArray<cl_float>* globals;
std::vector<std::string> globalParamNames;
std::vector<cl_float> globalParamValues;
cl::Kernel kernel;
};
/**
......@@ -288,7 +286,7 @@ private:
class OpenCLCalcCustomAngleForceKernel : public CalcCustomAngleForceKernel {
public:
OpenCLCalcCustomAngleForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, System& system) : CalcCustomAngleForceKernel(name, platform),
hasInitializedKernel(false), cl(cl), system(system), params(NULL), indices(NULL), globals(NULL) {
hasInitializedKernel(false), cl(cl), system(system), params(NULL), globals(NULL) {
}
~OpenCLCalcCustomAngleForceKernel();
/**
......@@ -313,11 +311,9 @@ private:
OpenCLContext& cl;
System& system;
OpenCLParameterSet* params;
OpenCLArray<mm_int8>* indices;
OpenCLArray<cl_float>* globals;
std::vector<std::string> globalParamNames;
std::vector<cl_float> globalParamValues;
cl::Kernel kernel;
};
/**
......@@ -392,7 +388,7 @@ private:
class OpenCLCalcCMAPTorsionForceKernel : public CalcCMAPTorsionForceKernel {
public:
OpenCLCalcCMAPTorsionForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, System& system) : CalcCMAPTorsionForceKernel(name, platform),
hasInitializedKernel(false), cl(cl), system(system), coefficients(NULL), mapPositions(NULL), torsionIndices(NULL), torsionMaps(NULL) {
hasInitializedKernel(false), cl(cl), system(system), coefficients(NULL), mapPositions(NULL), torsionMaps(NULL) {
}
~OpenCLCalcCMAPTorsionForceKernel();
/**
......@@ -418,9 +414,7 @@ private:
System& system;
OpenCLArray<mm_float4>* coefficients;
OpenCLArray<mm_int2>* mapPositions;
OpenCLArray<mm_int16>* torsionIndices;
OpenCLArray<cl_int>* torsionMaps;
cl::Kernel kernel;
};
/**
......@@ -429,7 +423,7 @@ private:
class OpenCLCalcCustomTorsionForceKernel : public CalcCustomTorsionForceKernel {
public:
OpenCLCalcCustomTorsionForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, System& system) : CalcCustomTorsionForceKernel(name, platform),
hasInitializedKernel(false), cl(cl), system(system), params(NULL), indices(NULL), globals(NULL) {
hasInitializedKernel(false), cl(cl), system(system), params(NULL), globals(NULL) {
}
~OpenCLCalcCustomTorsionForceKernel();
/**
......@@ -454,11 +448,9 @@ private:
OpenCLContext& cl;
System& system;
OpenCLParameterSet* params;
OpenCLArray<mm_int8>* indices;
OpenCLArray<cl_float>* globals;
std::vector<std::string> globalParamNames;
std::vector<cl_float> globalParamValues;
cl::Kernel kernel;
};
/**
......@@ -651,7 +643,7 @@ private:
class OpenCLCalcCustomExternalForceKernel : public CalcCustomExternalForceKernel {
public:
OpenCLCalcCustomExternalForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, System& system) : CalcCustomExternalForceKernel(name, platform),
hasInitializedKernel(false), cl(cl), system(system), params(NULL), indices(NULL), globals(NULL) {
hasInitializedKernel(false), cl(cl), system(system), params(NULL), globals(NULL) {
}
~OpenCLCalcCustomExternalForceKernel();
/**
......@@ -676,11 +668,9 @@ private:
OpenCLContext& cl;
System& system;
OpenCLParameterSet* params;
OpenCLArray<cl_int>* indices;
OpenCLArray<cl_float>* globals;
std::vector<std::string> globalParamNames;
std::vector<cl_float> globalParamValues;
cl::Kernel kernel;
};
/**
......
platforms/opencl/src/kernels/cmapTorsionForce.cl
View file @ f51a85b9
/**
* Compute CNAP torsion forces.
*/
const float PI = 3.14159265358979323846f;
__kernel void computeCMAPTorsionForces(int numAtoms, int numTorsions, __global float4* forceBuffers, __global float* energyBuffer,
__global float4* posq, __global float4* coeff, __global int2* mapPositions, __global int16* indices, __global int* maps) {
const float PI = 3.14159265358979323846f;
float energy = 0.0f;
for (int index = get_global_id(0); index < numTorsions; index += get_global_size(0)) {
int16 atoms = indices[index];
float4 a1 = posq[atoms.s0];
float4 a2 = posq[atoms.s1];
float4 a3 = posq[atoms.s2];
float4 a4 = posq[atoms.s3];
float4 b1 = posq[atoms.s4];
float4 b2 = posq[atoms.s5];
float4 b3 = posq[atoms.s6];
float4 b4 = posq[atoms.s7];
// Compute the first angle.
// Compute the first angle.
float4 v0a = (float4) (a1.xyz-a2.xyz, 0.0f);
float4 v1a = (float4) (a3.xyz-a2.xyz, 0.0f);
float4 v2a = (float4) (a3.xyz-a4.xyz, 0.0f);
float4 cp0a = cross(v0a, v1a);
float4 cp1a = cross(v1a, v2a);
float cosangle = dot(normalize(cp0a), normalize(cp1a));
float angleA;
if (cosangle > 0.99f || cosangle < -0.99f) {
float4 v0a = (float4) (pos1.xyz-pos2.xyz, 0.0f);
float4 v1a = (float4) (pos3.xyz-pos2.xyz, 0.0f);
float4 v2a = (float4) (pos3.xyz-pos4.xyz, 0.0f);
float4 cp0a = cross(v0a, v1a);
float4 cp1a = cross(v1a, v2a);
float cosangle = dot(normalize(cp0a), normalize(cp1a));
float angleA;
if (cosangle > 0.99f || cosangle < -0.99f) {
// We're close to the singularity in acos(), so take the cross product and use asin() instead.
float4 cross_prod = cross(cp0a, cp1a);
......@@ -34,22 +17,22 @@ __kernel void computeCMAPTorsionForces(int numAtoms, int numTorsions, __global f
angleA = asin(SQRT(dot(cross_prod, cross_prod)/scale));
if (cosangle < 0.0f)
angleA = PI-angleA;
}
else
}
else
angleA = acos(cosangle);
angleA = (dot(v0a, cp1a) >= 0 ? angleA : -angleA);
angleA = fmod(angleA+2.0f*PI, 2.0f*PI);
angleA = (dot(v0a, cp1a) >= 0 ? angleA : -angleA);
angleA = fmod(angleA+2.0f*PI, 2.0f*PI);
// Compute the second angle.
// Compute the second angle.
float4 v0b = (float4) (b1.xyz-b2.xyz, 0.0f);
float4 v1b = (float4) (b3.xyz-b2.xyz, 0.0f);
float4 v2b = (float4) (b3.xyz-b4.xyz, 0.0f);
float4 cp0b = cross(v0b, v1b);
float4 cp1b = cross(v1b, v2b);
cosangle = dot(normalize(cp0b), normalize(cp1b));
float angleB;
if (cosangle > 0.99f || cosangle < -0.99f) {
float4 v0b = (float4) (pos5.xyz-pos6.xyz, 0.0f);
float4 v1b = (float4) (pos7.xyz-pos6.xyz, 0.0f);
float4 v2b = (float4) (pos7.xyz-pos8.xyz, 0.0f);
float4 cp0b = cross(v0b, v1b);
float4 cp1b = cross(v1b, v2b);
cosangle = dot(normalize(cp0b), normalize(cp1b));
float angleB;
if (cosangle > 0.99f || cosangle < -0.99f) {
// We're close to the singularity in acos(), so take the cross product and use asin() instead.
float4 cross_prod = cross(cp0b, cp1b);
......@@ -57,98 +40,73 @@ __kernel void computeCMAPTorsionForces(int numAtoms, int numTorsions, __global f
angleB = asin(SQRT(dot(cross_prod, cross_prod)/scale));
if (cosangle < 0.0f)
angleB = PI-angleB;
}
else
}
else
angleB = acos(cosangle);
angleB = (dot(v0b, cp1b) >= 0 ? angleB : -angleB);
angleB = fmod(angleB+2.0f*PI, 2.0f*PI);
angleB = (dot(v0b, cp1b) >= 0 ? angleB : -angleB);
angleB = fmod(angleB+2.0f*PI, 2.0f*PI);
// Identify which patch this is in.
// Identify which patch this is in.
int2 pos = mapPositions[maps[index]];
int size = pos.y;
float delta = 2*PI/size;
int s = (int) (angleA/delta);
int t = (int) (angleB/delta);
float4 c[4];
int coeffIndex = pos.x+4*(s+size*t);
c[0] = coeff[coeffIndex];
c[1] = coeff[coeffIndex+1];
c[2] = coeff[coeffIndex+2];
c[3] = coeff[coeffIndex+3];
float da = angleA/delta-s;
float db = angleB/delta-t;
int2 pos = MAP_POS[MAPS[index]];
int size = pos.y;
float delta = 2*PI/size;
int s = (int) (angleA/delta);
int t = (int) (angleB/delta);
float4 c[4];
int coeffIndex = pos.x+4*(s+size*t);
c[0] = COEFF[coeffIndex];
c[1] = COEFF[coeffIndex+1];
c[2] = COEFF[coeffIndex+2];
c[3] = COEFF[coeffIndex+3];
float da = angleA/delta-s;
float db = angleB/delta-t;
// Evaluate the spline to determine the energy and gradients.
// Evaluate the spline to determine the energy and gradients.
float torsionEnergy = 0.0f;
float dEdA = 0.0f;
float dEdB = 0.0f;
torsionEnergy = da*torsionEnergy + ((c[3].w*db + c[3].z)*db + c[3].y)*db + c[3].x;
dEdA = db*dEdA + (3.0f*c[3].w*da + 2.0f*c[2].w)*da + c[1].w;
dEdB = da*dEdB + (3.0f*c[3].w*db + 2.0f*c[3].z)*db + c[3].y;
torsionEnergy = da*torsionEnergy + ((c[2].w*db + c[2].z)*db + c[2].y)*db + c[2].x;
dEdA = db*dEdA + (3.0f*c[3].z*da + 2.0f*c[2].z)*da + c[1].z;
dEdB = da*dEdB + (3.0f*c[2].w*db + 2.0f*c[2].z)*db + c[2].y;
torsionEnergy = da*torsionEnergy + ((c[1].w*db + c[1].z)*db + c[1].y)*db + c[1].x;
dEdA = db*dEdA + (3.0f*c[3].y*da + 2.0f*c[2].y)*da + c[1].y;
dEdB = da*dEdB + (3.0f*c[1].w*db + 2.0f*c[1].z)*db + c[1].y;
torsionEnergy = da*torsionEnergy + ((c[0].w*db + c[0].z)*db + c[0].y)*db + c[0].x;
dEdA = db*dEdA + (3.0f*c[3].x*da + 2.0f*c[2].x)*da + c[1].x;
dEdB = da*dEdB + (3.0f*c[0].w*db + 2.0f*c[0].z)*db + c[0].y;
dEdA /= delta;
dEdB /= delta;
energy += torsionEnergy;
float torsionEnergy = 0.0f;
float dEdA = 0.0f;
float dEdB = 0.0f;
torsionEnergy = da*torsionEnergy + ((c[3].w*db + c[3].z)*db + c[3].y)*db + c[3].x;
dEdA = db*dEdA + (3.0f*c[3].w*da + 2.0f*c[2].w)*da + c[1].w;
dEdB = da*dEdB + (3.0f*c[3].w*db + 2.0f*c[3].z)*db + c[3].y;
torsionEnergy = da*torsionEnergy + ((c[2].w*db + c[2].z)*db + c[2].y)*db + c[2].x;
dEdA = db*dEdA + (3.0f*c[3].z*da + 2.0f*c[2].z)*da + c[1].z;
dEdB = da*dEdB + (3.0f*c[2].w*db + 2.0f*c[2].z)*db + c[2].y;
torsionEnergy = da*torsionEnergy + ((c[1].w*db + c[1].z)*db + c[1].y)*db + c[1].x;
dEdA = db*dEdA + (3.0f*c[3].y*da + 2.0f*c[2].y)*da + c[1].y;
dEdB = da*dEdB + (3.0f*c[1].w*db + 2.0f*c[1].z)*db + c[1].y;
torsionEnergy = da*torsionEnergy + ((c[0].w*db + c[0].z)*db + c[0].y)*db + c[0].x;
dEdA = db*dEdA + (3.0f*c[3].x*da + 2.0f*c[2].x)*da + c[1].x;
dEdB = da*dEdB + (3.0f*c[0].w*db + 2.0f*c[0].z)*db + c[0].y;
dEdA /= delta;
dEdB /= delta;
energy += torsionEnergy;
// Apply the force to the first torsion.
// Apply the force to the first torsion.
float normCross1 = dot(cp0a, cp0a);
float normSqrBC = dot(v1a, v1a);
float normBC = SQRT(normSqrBC);
float normCross2 = dot(cp1a, cp1a);
float dp = 1.0f/normSqrBC;
float4 ff = (float4) ((-dEdA*normBC)/normCross1, dot(v0a, v1a)*dp, dot(v2a, v1a)*dp, (dEdA*normBC)/normCross2);
float4 internalF0 = ff.x*cp0a;
float4 internalF3 = ff.w*cp1a;
float4 d = ff.y*internalF0 - ff.z*internalF3;
int4 offset = atoms.lo.lo + numAtoms*atoms.hi.lo;
float4 forceA = forceBuffers[offset.x];
float4 forceB = forceBuffers[offset.y];
float4 forceC = forceBuffers[offset.z];
float4 forceD = forceBuffers[offset.w];
forceA.xyz += internalF0.xyz;
forceB.xyz += d.xyz-internalF0.xyz;
forceC.xyz += -d.xyz-internalF3.xyz;
forceD.xyz += internalF3.xyz;
forceBuffers[offset.x] = forceA;
forceBuffers[offset.y] = forceB;
forceBuffers[offset.z] = forceC;
forceBuffers[offset.w] = forceD;
float normCross1 = dot(cp0a, cp0a);
float normSqrBC = dot(v1a, v1a);
float normBC = SQRT(normSqrBC);
float normCross2 = dot(cp1a, cp1a);
float dp = 1.0f/normSqrBC;
float4 ff = (float4) ((-dEdA*normBC)/normCross1, dot(v0a, v1a)*dp, dot(v2a, v1a)*dp, (dEdA*normBC)/normCross2);
float4 force1 = ff.x*cp0a;
float4 force4 = ff.w*cp1a;
float4 d = ff.y*force1 - ff.z*force4;
float4 force2 = d-force1;
float4 force3 = -d-force4;
// Apply the force to the second torsion.
// Apply the force to the second torsion.
normCross1 = dot(cp0b, cp0b);
normSqrBC = dot(v1b, v1b);
normBC = SQRT(normSqrBC);
normCross2 = dot(cp1b, cp1b);
dp = 1.0f/normSqrBC;
ff = (float4) ((-dEdB*normBC)/normCross1, dot(v0b, v1b)*dp, dot(v2b, v1b)*dp, (dEdB*normBC)/normCross2);
internalF0 = ff.x*cp0b;
internalF3 = ff.w*cp1b;
d = ff.y*internalF0 - ff.z*internalF3;
offset = atoms.lo.hi + numAtoms*atoms.hi.hi;
forceA = forceBuffers[offset.x];
forceB = forceBuffers[offset.y];
forceC = forceBuffers[offset.z];
forceD = forceBuffers[offset.w];
forceA.xyz += internalF0.xyz;
forceB.xyz += d.xyz-internalF0.xyz;
forceC.xyz += -d.xyz-internalF3.xyz;
forceD.xyz += internalF3.xyz;
forceBuffers[offset.x] = forceA;
forceBuffers[offset.y] = forceB;
forceBuffers[offset.z] = forceC;
forceBuffers[offset.w] = forceD;
}
energyBuffer[get_global_id(0)] += energy;
}
normCross1 = dot(cp0b, cp0b);
normSqrBC = dot(v1b, v1b);
normBC = SQRT(normSqrBC);
normCross2 = dot(cp1b, cp1b);
dp = 1.0f/normSqrBC;
ff = (float4) ((-dEdB*normBC)/normCross1, dot(v0b, v1b)*dp, dot(v2b, v1b)*dp, (dEdB*normBC)/normCross2);
float4 force5 = ff.x*cp0b;
float4 force8 = ff.w*cp1b;
d = ff.y*force5 - ff.z*force8;
float4 force6 = d-force5;
float4 force7 = -d-force8;
platforms/opencl/src/kernels/customAngleForce.cl
View file @ f51a85b9
/**
* Compute custom angle forces.
*/
__kernel void computeCustomAngleForces(int numAtoms, int numAngles, __global float4* forceBuffers, __global float* energyBuffer,
__global float4* posq, __global int8* indices
EXTRA_ARGUMENTS) {
float energy = 0.0f;
for (int index = get_global_id(0); index < numAngles; index += get_global_size(0)) {
int8 atoms = indices[index];
float4 a1 = posq[atoms.s0];
float4 a2 = posq[atoms.s1];
float4 a3 = posq[atoms.s2];
// Compute the force.
float4 v0 = a2-a1;
float4 v1 = a2-a3;
float4 cp = cross(v0, v1);
float rp = cp.x*cp.x + cp.y*cp.y + cp.z*cp.z;
rp = max(sqrt(rp), 1.0e-06f);
float r21 = v0.x*v0.x + v0.y*v0.y + v0.z*v0.z;
float r23 = v1.x*v1.x + v1.y*v1.y + v1.z*v1.z;
float dot = v0.x*v1.x + v0.y*v1.y + v0.z*v1.z;
float cosine = clamp(dot/sqrt(r21*r23), -1.0f, 1.0f);
float theta = acos(cosine);
COMPUTE_FORCE
float4 c21 = cross(v0, cp)*(dEdAngle/(r21*rp));
float4 c23 = cross(cp, v1)*(dEdAngle/(r23*rp));
// Record the force on each of the three atoms.
unsigned int offsetA = atoms.s0+atoms.s3*numAtoms;
unsigned int offsetB = atoms.s1+atoms.s4*numAtoms;
unsigned int offsetC = atoms.s2+atoms.s5*numAtoms;
float4 forceA = forceBuffers[offsetA];
float4 forceB = forceBuffers[offsetB];
float4 forceC = forceBuffers[offsetC];
forceA.xyz += c21.xyz;
forceB.xyz -= c21.xyz+c23.xyz;
forceC.xyz += c23.xyz;
forceBuffers[offsetA] = forceA;
forceBuffers[offsetB] = forceB;
forceBuffers[offsetC] = forceC;
}
energyBuffer[get_global_id(0)] += energy;
}
float4 v0 = pos2-pos1;
float4 v1 = pos2-pos3;
float4 cp = cross(v0, v1);
float rp = cp.x*cp.x + cp.y*cp.y + cp.z*cp.z;
rp = max(sqrt(rp), 1.0e-06f);
float r21 = v0.x*v0.x + v0.y*v0.y + v0.z*v0.z;
float r23 = v1.x*v1.x + v1.y*v1.y + v1.z*v1.z;
float dot = v0.x*v1.x + v0.y*v1.y + v0.z*v1.z;
float cosine = clamp(dot/sqrt(r21*r23), -1.0f, 1.0f);
float theta = acos(cosine);
COMPUTE_FORCE
float4 force1 = cross(v0, cp)*(dEdAngle/(r21*rp));
float4 force3 = cross(cp, v1)*(dEdAngle/(r23*rp));
float4 force2 = -force1-force3;
platforms/opencl/src/kernels/customBondForce.cl
View file @ f51a85b9
/**
* Compute custom bond forces.
*/
__kernel void computeCustomBondForces(int numAtoms, int numBonds, __global float4* forceBuffers, __global float* energyBuffer,
__global float4* posq, __global int4* indices
EXTRA_ARGUMENTS) {
float energy = 0.0f;
for (int index = get_global_id(0); index < numBonds; index += get_global_size(0)) {
// Look up the data for this bond.
int4 atoms = indices[index];
float4 delta = posq[atoms.y]-posq[atoms.x];
// Compute the force.
float r = SQRT(delta.x*delta.x + delta.y*delta.y + delta.z*delta.z);
COMPUTE_FORCE
delta.xyz *= -dEdR/r;
// Record the force on each of the two atoms.
unsigned int offsetA = atoms.x+atoms.z*numAtoms;
unsigned int offsetB = atoms.y+atoms.w*numAtoms;
float4 forceA = forceBuffers[offsetA];
float4 forceB = forceBuffers[offsetB];
forceA.xyz -= delta.xyz;
forceB.xyz += delta.xyz;
forceBuffers[offsetA] = forceA;
forceBuffers[offsetB] = forceB;
}
energyBuffer[get_global_id(0)] += energy;
}
float4 delta = pos2-pos1;
float r = SQRT(delta.x*delta.x + delta.y*delta.y + delta.z*delta.z);
COMPUTE_FORCE
delta.xyz *= -dEdR/r;
float4 force1 = -delta;
float4 force2 = delta;
platforms/opencl/src/kernels/customExternalForce.cl
View file @ f51a85b9
/**
* Compute custom external forces.
*/
__kernel void computeCustomExternalForces(int numTerms, __global float4* forceBuffers, __global float* energyBuffer,
__global float4* posq, __global int* indices
EXTRA_ARGUMENTS) {
float energy = 0.0f;
for (int index = get_global_id(0); index < numTerms; index += get_global_size(0)) {
// Look up the data for this particle.
int atom = indices[index];
float4 pos = posq[atom];
// Compute the force.
COMPUTE_FORCE
// Record the force on the atom.
float4 force = forceBuffers[atom];
force.x -= dEdX;
force.y -= dEdY;
force.z -= dEdZ;
forceBuffers[atom] = force;
}
energyBuffer[get_global_id(0)] += energy;
}
COMPUTE_FORCE
float4 force1 = (float4) (-dEdX, -dEdY, -dEdZ, 0.0f);
platforms/opencl/src/kernels/customTorsionForce.cl
View file @ f51a85b9
/**
* Compute custom torsion forces.
*/
__kernel void computeCustomTorsionForces(int numAtoms, int numTorsions, __global float4* forceBuffers, __global float* energyBuffer,
__global float4* posq, __global int8* indices
EXTRA_ARGUMENTS) {
float energy = 0.0f;
for (int index = get_global_id(0); index < numTorsions; index += get_global_size(0)) {
int8 atoms = indices[index];
float4 a1 = posq[atoms.s0];
float4 a2 = posq[atoms.s1];
float4 a3 = posq[atoms.s2];
float4 a4 = posq[atoms.s3];
// Compute the force.
float4 v0 = (float4) (a1.xyz-a2.xyz, 0.0f);
float4 v1 = (float4) (a3.xyz-a2.xyz, 0.0f);
float4 v2 = (float4) (a3.xyz-a4.xyz, 0.0f);
float4 cp0 = cross(v0, v1);
float4 cp1 = cross(v1, v2);
float cosangle = dot(normalize(cp0), normalize(cp1));
float theta;
if (cosangle > 0.99f || cosangle < -0.99f) {
float4 v0 = (float4) (pos1.xyz-pos2.xyz, 0.0f);
float4 v1 = (float4) (pos3.xyz-pos2.xyz, 0.0f);
float4 v2 = (float4) (pos3.xyz-pos4.xyz, 0.0f);
float4 cp0 = cross(v0, v1);
float4 cp1 = cross(v1, v2);
float cosangle = dot(normalize(cp0), normalize(cp1));
float theta;
if (cosangle > 0.99f || cosangle < -0.99f) {
// We're close to the singularity in acos(), so take the cross product and use asin() instead.
float4 cross_prod = cross(cp0, cp1);
......@@ -30,39 +13,19 @@ __kernel void computeCustomTorsionForces(int numAtoms, int numTorsions, __global
theta = asin(sqrt(dot(cross_prod, cross_prod)/scale));
if (cosangle < 0.0f)
theta = M_PI-theta;
}
else
theta = acos(cosangle);
theta = (dot(v0, cp1) >= 0 ? theta : -theta);
COMPUTE_FORCE
float normCross1 = dot(cp0, cp0);
float normSqrBC = dot(v1, v1);
float normBC = sqrt(normSqrBC);
float normCross2 = dot(cp1, cp1);
float dp = 1.0f/normSqrBC;
float4 ff = (float4) ((-dEdAngle*normBC)/normCross1, dot(v0, v1)*dp, dot(v2, v1)*dp, (dEdAngle*normBC)/normCross2);
float4 internalF0 = ff.x*cp0;
float4 internalF3 = ff.w*cp1;
float4 s = ff.y*internalF0 - ff.z*internalF3;
// Record the force on each of the four atoms.
unsigned int offsetA = atoms.s0+atoms.s4*numAtoms;
unsigned int offsetB = atoms.s1+atoms.s5*numAtoms;
unsigned int offsetC = atoms.s2+atoms.s6*numAtoms;
unsigned int offsetD = atoms.s3+atoms.s7*numAtoms;
float4 forceA = forceBuffers[offsetA];
float4 forceB = forceBuffers[offsetB];
float4 forceC = forceBuffers[offsetC];
float4 forceD = forceBuffers[offsetD];
forceA.xyz += internalF0.xyz;
forceB.xyz += s.xyz-internalF0.xyz;
forceC.xyz += -s.xyz-internalF3.xyz;
forceD.xyz += internalF3.xyz;
forceBuffers[offsetA] = forceA;
forceBuffers[offsetB] = forceB;
forceBuffers[offsetC] = forceC;
forceBuffers[offsetD] = forceD;
}
energyBuffer[get_global_id(0)] += energy;
}
else
theta = acos(cosangle);
theta = (dot(v0, cp1) >= 0 ? theta : -theta);
COMPUTE_FORCE
float normCross1 = dot(cp0, cp0);
float normSqrBC = dot(v1, v1);
float normBC = sqrt(normSqrBC);
float normCross2 = dot(cp1, cp1);
float dp = 1.0f/normSqrBC;
float4 ff = (float4) ((-dEdAngle*normBC)/normCross1, dot(v0, v1)*dp, dot(v2, v1)*dp, (dEdAngle*normBC)/normCross2);
float4 force1 = ff.x*cp0;
float4 force4 = ff.w*cp1;
float4 s = ff.y*force1 - ff.z*force4;
float4 force2 = s-force1;
float4 force3 = -s-force4;
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment