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Commit edbe6a87 authored by Peter Eastman's avatar Peter Eastman
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Continuing converting AMOEBA to the new CUDA platform:... 

Continuing converting AMOEBA to the new CUDA platform: AmoebaOutOfPlaneBendForce, AmoebaStretchBendForce, AmoebaTorsionTorsionForce
parent f5980599
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Showing with 4241 additions and 281 deletions
plugins/amoeba/platforms/cuda2/src/AmoebaCudaKernelFactory.cpp
View file @ edbe6a87
...@@ -88,15 +88,15 @@ KernelImpl* AmoebaCudaKernelFactory::createKernelImpl(std::string name, const Pl ...@@ -88,15 +88,15 @@ KernelImpl* AmoebaCudaKernelFactory::createKernelImpl(std::string name, const Pl
if (name == CalcAmoebaPiTorsionForceKernel::Name()) if (name == CalcAmoebaPiTorsionForceKernel::Name())
return new CudaCalcAmoebaPiTorsionForceKernel(name, platform, cu, context.getSystem()); return new CudaCalcAmoebaPiTorsionForceKernel(name, platform, cu, context.getSystem());
// if (name == CalcAmoebaStretchBendForceKernel::Name()) if (name == CalcAmoebaStretchBendForceKernel::Name())
// return new CudaCalcAmoebaStretchBendForceKernel(name, platform, cu, context.getSystem()); return new CudaCalcAmoebaStretchBendForceKernel(name, platform, cu, context.getSystem());
//
// if (name == CalcAmoebaOutOfPlaneBendForceKernel::Name()) if (name == CalcAmoebaOutOfPlaneBendForceKernel::Name())
// return new CudaCalcAmoebaOutOfPlaneBendForceKernel(name, platform, cu, context.getSystem()); return new CudaCalcAmoebaOutOfPlaneBendForceKernel(name, platform, cu, context.getSystem());
//
// if (name == CalcAmoebaTorsionTorsionForceKernel::Name()) if (name == CalcAmoebaTorsionTorsionForceKernel::Name())
// return new CudaCalcAmoebaTorsionTorsionForceKernel(name, platform, cu, context.getSystem()); return new CudaCalcAmoebaTorsionTorsionForceKernel(name, platform, cu, context.getSystem());
//
// if (name == CalcAmoebaMultipoleForceKernel::Name()) // if (name == CalcAmoebaMultipoleForceKernel::Name())
// return new CudaCalcAmoebaMultipoleForceKernel(name, platform, cu, context.getSystem()); // return new CudaCalcAmoebaMultipoleForceKernel(name, platform, cu, context.getSystem());
// //
......
plugins/amoeba/platforms/cuda2/src/AmoebaCudaKernels.h
View file @ edbe6a87
...@@ -253,6 +253,7 @@ private: ...@@ -253,6 +253,7 @@ private:
int numStretchBends; int numStretchBends;
CudaContext& cu; CudaContext& cu;
System& system; System& system;
CudaArray* params;
}; };
/** /**
...@@ -283,6 +284,7 @@ private: ...@@ -283,6 +284,7 @@ private:
int numOutOfPlaneBends; int numOutOfPlaneBends;
CudaContext& cu; CudaContext& cu;
System& system; System& system;
CudaArray* params;
}; };
/** /**
...@@ -314,6 +316,9 @@ private: ...@@ -314,6 +316,9 @@ private:
int numTorsionTorsionGrids; int numTorsionTorsionGrids;
CudaContext& cu; CudaContext& cu;
System& system; System& system;
CudaArray* gridValues;
CudaArray* gridParams;
CudaArray* torsionParams;
}; };
/** /**
......
plugins/amoeba/platforms/cuda2/src/kernels/amoebaOutOfPlaneBendForce.cu 0 → 100644
View file @ edbe6a87
// compute the value of the bond angle
real xab = pos1.x - pos2.x;
real yab = pos1.y - pos2.y;
real zab = pos1.z - pos2.z;
real xcb = pos3.x - pos2.x;
real ycb = pos3.y - pos2.y;
real zcb = pos3.z - pos2.z;
// compute the out-of-plane bending angle
real xdb = pos4.x - pos2.x;
real ydb = pos4.y - pos2.y;
real zdb = pos4.z - pos2.z;
real xad = pos1.x - pos4.x;
real yad = pos1.y - pos4.y;
real zad = pos1.z - pos4.z;
real xcd = pos3.x - pos4.x;
real ycd = pos3.y - pos4.y;
real zcd = pos3.z - pos4.z;
real rdb2 = xdb*xdb + ydb*ydb + zdb*zdb;
real rad2 = xad*xad + yad*yad + zad*zad;
real rcd2 = xcd*xcd + ycd*ycd + zcd*zcd;
real ee = xab*(ycb*zdb-zcb*ydb) + yab*(zcb*xdb-xcb*zdb) + zab*(xcb*ydb-ycb*xdb);
real dot = xad*xcd + yad*ycd + zad*zcd;
real cc = rad2*rcd2 - dot*dot;
real bkk2 = (cc != 0 ? (ee*ee)/(cc) : (real) 0);
bkk2 = rdb2 - bkk2;
real adXcd_0 = yad*zcd - zad*ycd;
real adXcd_1 = zad*xcd - xad*zcd;
real adXcd_2 = xad*ycd - yad*xcd;
real adXcd_nrm2 = adXcd_0*adXcd_0 + adXcd_1*adXcd_1 + adXcd_2*adXcd_2;
real adXcd_dot_db = xdb*adXcd_0 + ydb*adXcd_1 + zdb*adXcd_2;
adXcd_dot_db /= SQRT(rdb2*adXcd_nrm2);
real angle = abs(ASIN(adXcd_dot_db));
// find the out-of-plane energy and master chain rule terms
real dt = RAD_TO_DEG*angle;
real dt2 = dt * dt;
real dt3 = dt2 * dt;
real dt4 = dt2 * dt2;
float k = (rdb2 != 0 && cc != 0) ? PARAMS[index] : 0.0f;
energy += k*dt2*(1.0f + CUBIC_K*dt + QUARTIC_K*dt2 + PENTIC_K*dt3 + SEXTIC_K*dt4);
real deddt = k*dt*RAD_TO_DEG*(2.0f + 3.0f*CUBIC_K*dt + 4.0f*QUARTIC_K*dt2 + 5.0f*PENTIC_K*dt3 + 6.0f*SEXTIC_K*dt4);
real eeSign = (ee >= 0 ? 1 : -1);
real dedcos = -deddt*eeSign/SQRT(cc*bkk2);
// chain rule terms for first derivative components
real term = ee / cc;
real dccdxia = (xad*rcd2-xcd*dot) * term;
real dccdyia = (yad*rcd2-ycd*dot) * term;
real dccdzia = (zad*rcd2-zcd*dot) * term;
real dccdxic = (xcd*rad2-xad*dot) * term;
real dccdyic = (ycd*rad2-yad*dot) * term;
real dccdzic = (zcd*rad2-zad*dot) * term;
real dccdxid = -dccdxia - dccdxic;
real dccdyid = -dccdyia - dccdyic;
real dccdzid = -dccdzia - dccdzic;
term = ee / rdb2;
real deedxia = ydb*zcb - zdb*ycb;
real deedyia = zdb*xcb - xdb*zcb;
real deedzia = xdb*ycb - ydb*xcb;
real deedxic = yab*zdb - zab*ydb;
real deedyic = zab*xdb - xab*zdb;
real deedzic = xab*ydb - yab*xdb;
real deedxid = ycb*zab - zcb*yab + xdb*term;
real deedyid = zcb*xab - xcb*zab + ydb*term;
real deedzid = xcb*yab - ycb*xab + zdb*term;
// compute first derivative components for this angle
real3 force1 = make_real3(-dedcos*(dccdxia+deedxia), -dedcos*(dccdyia+deedyia), -dedcos*(dccdzia+deedzia));
real3 force3 = make_real3(-dedcos*(dccdxic+deedxic), -dedcos*(dccdyic+deedyic), -dedcos*(dccdzic+deedzic));
real3 force4 = make_real3(-dedcos*(dccdxid+deedxid), -dedcos*(dccdyid+deedyid), -dedcos*(dccdzid+deedzid));
real3 force2 = make_real3(-force1.x-force3.x-force4.x, -force1.y-force3.y-force4.y, -force1.z-force3.z-force4.z);
plugins/amoeba/platforms/cuda2/src/kernels/amoebaStretchBendForce.cu 0 → 100644
View file @ edbe6a87
// compute the value of the bond angle
real xab = pos1.x - pos2.x;
real yab = pos1.y - pos2.y;
real zab = pos1.z - pos2.z;
real xcb = pos3.x - pos2.x;
real ycb = pos3.y - pos2.y;
real zcb = pos3.z - pos2.z;
real rab = SQRT(xab*xab + yab*yab + zab*zab);
real rcb = SQRT(xcb*xcb + ycb*ycb + zcb*zcb);
real xp = ycb*zab - zcb*yab;
real yp = zcb*xab - xcb*zab;
real zp = xcb*yab - ycb*xab;
real rp = SQRT(xp*xp + yp*yp + zp*zp);
real dot = xab*xcb + yab*ycb + zab*zcb;
real cosine = rab*rcb > 0 ? (dot / (rab*rcb)) : (real) 1;
cosine = (cosine > 1 ? (real) 1 : cosine);
cosine = (cosine < -1 ? -(real) 1 : cosine);
real angle = ACOS(cosine);
// find chain rule terms for the bond angle deviation
float4 parameters = PARAMS[index];
real dt = RAD_TO_DEG*(angle - parameters.z);
real terma = rab*rp != 0 ? (-RAD_TO_DEG/(rab*rab*rp)) : (real) 0;
real termc = rcb*rp != 0 ? (RAD_TO_DEG/(rcb*rcb*rp)) : (real) 0;
real ddtdxia = terma * (yab*zp-zab*yp);
real ddtdyia = terma * (zab*xp-xab*zp);
real ddtdzia = terma * (xab*yp-yab*xp);
real ddtdxic = termc * (ycb*zp-zcb*yp);
real ddtdyic = termc * (zcb*xp-xcb*zp);
real ddtdzic = termc * (xcb*yp-ycb*xp);
// find chain rule terms for the bond length deviations
real dr = (parameters.x > 0 ? (rab - parameters.x) : (real) 0);
terma = (parameters.x > 0 ? RECIP(rab) : (real) 0);
dr += (parameters.y > 0 ? (rcb - parameters.y) : (real) 0);
termc = (parameters.y > 0 ? RECIP(rcb) : (real) 0);
real ddrdxia = terma * xab;
real ddrdyia = terma * yab;
real ddrdzia = terma * zab;
real ddrdxic = termc * xcb;
real ddrdyic = termc * ycb;
real ddrdzic = termc * zcb;
// get the energy and master chain rule terms for derivatives
real term = ((rp != 0) ? parameters.w : (real) 0);
energy += term*dt*dr;
real3 force1 = make_real3(-term*(dt*ddrdxia+ddtdxia*dr), -term*(dt*ddrdyia+ddtdyia*dr), -term*(dt*ddrdzia+ddtdzia*dr));
real3 force3 = make_real3(-term*(dt*ddrdxic+ddtdxic*dr), -term*(dt*ddrdyic+ddtdyic*dr), -term*(dt*ddrdzic+ddtdzic*dr));
real3 force2 = make_real3(-force1.x-force3.x, -force1.y-force3.y, -force1.z-force3.z);
plugins/amoeba/platforms/cuda2/src/kernels/amoebaTorsionTorsionForce.cu 0 → 100644
View file @ edbe6a87
int2 torsionParams = TORSION_PARAMS[index];
real xba = pos2.x - pos1.x;
real yba = pos2.y - pos1.y;
real zba = pos2.z - pos1.z;
real xcb = pos3.x - pos2.x;
real ycb = pos3.y - pos2.y;
real zcb = pos3.z - pos2.z;
real xdc = pos4.x - pos3.x;
real ydc = pos4.y - pos3.y;
real zdc = pos4.z - pos3.z;
real xed = pos5.x - pos4.x;
real yed = pos5.y - pos4.y;
real zed = pos5.z - pos4.z;
real xt = yba*zcb - ycb*zba;
real yt = zba*xcb - zcb*xba;
real zt = xba*ycb - xcb*yba;
real xu = ycb*zdc - ydc*zcb;
real yu = zcb*xdc - zdc*xcb;
real zu = xcb*ydc - xdc*ycb;
real rt2 = xt*xt + yt*yt + zt*zt;
real ru2 = xu*xu + yu*yu + zu*zu;
real rtru = SQRT(rt2 * ru2);
real xv = ydc*zed - yed*zdc;
real yv = zdc*xed - zed*xdc;
real zv = xdc*yed - xed*ydc;
real rv2 = xv*xv + yv*yv + zv*zv;
real rurv = SQRT(ru2 * rv2);
real rcb = SQRT(xcb*xcb + ycb*ycb + zcb*zcb);
real cosine1 = (rtru != 0 ? (xt*xu+yt*yu+zt*zu)/rtru : (real) 0);
cosine1 = (cosine1 > 1 ? (real) 1 : cosine1);
cosine1 = (cosine1 < -1 ? (real) -1 : cosine1);
real angle1 = RAD_TO_DEG * ACOS(cosine1);
real sign = xba*xu + yba*yu + zba*zu;
angle1 = (sign < 0 ? -angle1 : angle1);
real value1 = angle1;
real rdc = SQRT(xdc*xdc + ydc*ydc + zdc*zdc);
real cosine2 = (xu*xv + yu*yv + zu*zv) / rurv;
cosine2 = (cosine2 > 1 ? (real) 1 : cosine2);
cosine2 = (cosine2 < -1 ? (real) -1 : cosine2);
real angle2 = RAD_TO_DEG * ACOS(cosine2);
sign = xcb*xv + ycb*yv + zcb*zv;
angle2 = (sign < 0 ? -angle2 : angle2);
real value2 = angle2;
// check for inverted chirality at the central atom
// if atom2.y < 0, then no chiral check required
// sign is set to 1.0 in this case
// use atom5 for the atom index to avoid warp divergence
int chiralAtomIndex = (torsionParams.x > -1 ? torsionParams.x : atom5);
real4 pos6 = posq[chiralAtomIndex];
real xac = pos6.x - pos3.x;
real yac = pos6.y - pos3.y;
real zac = pos6.z - pos3.z;
real xbc = pos2.x - pos3.x;
real ybc = pos2.y - pos3.y;
real zbc = pos2.z - pos3.z;
// xdc, ydc, zdc appear above
real xdc1 = pos4.x - pos3.x;
real ydc1 = pos4.y - pos3.y;
real zdc1 = pos4.z - pos3.z;
real c1 = ybc*zdc1 - zbc*ydc1;
real c2 = ydc1*zac - zdc1*yac;
real c3 = yac*zbc - zac*ybc;
real vol = xac*c1 + xbc*c2 + xdc1*c3;
sign = (vol > 0 ? (real) 1 : (real) -1);
sign = (torsionParams.x < 0 ? (real) 1 : sign);
value1 *= sign;
value2 *= sign;
// use bicubic interpolation to compute spline values
// compute indices into grid based on angles
float4 gridParams = GRID_PARAMS[torsionParams.y];
int index1 = (int) ((value1 - gridParams.y)/gridParams.z + 1.0e-05f);
real fIndex = (real) index1;
real x1l = gridParams.z*fIndex + gridParams.y;
real x1u = x1l + gridParams.z;
int index2 = (int) ((value2 - gridParams.y)/gridParams.z + 1.0e-05f);
fIndex = (real) index2;
real x2l = gridParams.z*fIndex + gridParams.y;
real x2u = x2l + gridParams.z;
int posIndex1 = index2 + index1*(int) gridParams.w;
posIndex1 += (int) gridParams.x;
int posIndex2 = index2 + (index1+1)*(int) gridParams.w;
posIndex2 += (int) gridParams.x;
// load grid points surrounding angle
real4 y;
real4 y1;
real4 y2;
real4 y12;
int localIndex = posIndex1;
y.x = GRID_VALUES[localIndex].x;
y1.x = GRID_VALUES[localIndex].y;
y2.x = GRID_VALUES[localIndex].z;
y12.x = GRID_VALUES[localIndex].w;
localIndex = posIndex2;
y.y = GRID_VALUES[localIndex].x;
y1.y = GRID_VALUES[localIndex].y;
y2.y = GRID_VALUES[localIndex].z;
y12.y = GRID_VALUES[localIndex].w;
localIndex = posIndex2 + 1;
y.z = GRID_VALUES[localIndex].x;
y1.z = GRID_VALUES[localIndex].y;
y2.z = GRID_VALUES[localIndex].z;
y12.z = GRID_VALUES[localIndex].w;
localIndex = posIndex1 + 1;
y.w = GRID_VALUES[localIndex].x;
y1.w = GRID_VALUES[localIndex].y;
y2.w = GRID_VALUES[localIndex].z;
y12.w = GRID_VALUES[localIndex].w;
// perform interpolation
real e;
real dedang1;
real dedang2;
bicubic(y, y1, y2, y12, value1, x1l, x1u, value2, x2l, x2u, &e, &dedang1, &dedang2);
energy += e;
dedang1 *= sign * RAD_TO_DEG;
dedang2 *= sign * RAD_TO_DEG;
// chain rule terms for first angle derivative components
real xca = pos3.x - pos1.x;
real yca = pos3.y - pos1.y;
real zca = pos3.z - pos1.z;
real xdb = pos4.x - pos2.x;
real ydb = pos4.y - pos2.y;
real zdb = pos4.z - pos2.z;
real dedxt = dedang1 * (yt*zcb - ycb*zt) / (rt2*rcb);
real dedyt = dedang1 * (zt*xcb - zcb*xt) / (rt2*rcb);
real dedzt = dedang1 * (xt*ycb - xcb*yt) / (rt2*rcb);
real dedxu = -dedang1 * (yu*zcb - ycb*zu) / (ru2*rcb);
real dedyu = -dedang1 * (zu*xcb - zcb*xu) / (ru2*rcb);
real dedzu = -dedang1 * (xu*ycb - xcb*yu) / (ru2*rcb);
// compute first derivative components for first angle
real dedxia = zcb*dedyt - ycb*dedzt;
real dedyia = xcb*dedzt - zcb*dedxt;
real dedzia = ycb*dedxt - xcb*dedyt;
real dedxib = yca*dedzt - zca*dedyt + zdc*dedyu - ydc*dedzu;
real dedyib = zca*dedxt - xca*dedzt + xdc*dedzu - zdc*dedxu;
real dedzib = xca*dedyt - yca*dedxt + ydc*dedxu - xdc*dedyu;
real dedxic = zba*dedyt - yba*dedzt + ydb*dedzu - zdb*dedyu;
real dedyic = xba*dedzt - zba*dedxt + zdb*dedxu - xdb*dedzu;
real dedzic = yba*dedxt - xba*dedyt + xdb*dedyu - ydb*dedxu;
real dedxid = zcb*dedyu - ycb*dedzu;
real dedyid = xcb*dedzu - zcb*dedxu;
real dedzid = ycb*dedxu - xcb*dedyu;
// chain rule terms for second angle derivative components
real xec = pos5.x - pos3.x;
real yec = pos5.y - pos3.y;
real zec = pos5.z - pos3.z;
real dedxu2 = dedang2 * (yu*zdc - ydc*zu) / (ru2*rdc);
real dedyu2 = dedang2 * (zu*xdc - zdc*xu) / (ru2*rdc);
real dedzu2 = dedang2 * (xu*ydc - xdc*yu) / (ru2*rdc);
real dedxv2 = -dedang2 * (yv*zdc - ydc*zv) / (rv2*rdc);
real dedyv2 = -dedang2 * (zv*xdc - zdc*xv) / (rv2*rdc);
real dedzv2 = -dedang2 * (xv*ydc - xdc*yv) / (rv2*rdc);
// compute first derivative components for second angle
real dedxib2 = zdc*dedyu2 - ydc*dedzu2;
real dedyib2 = xdc*dedzu2 - zdc*dedxu2;
real dedzib2 = ydc*dedxu2 - xdc*dedyu2;
real dedxic2 = ydb*dedzu2 - zdb*dedyu2 + zed*dedyv2 - yed*dedzv2;
real dedyic2 = zdb*dedxu2 - xdb*dedzu2 + xed*dedzv2 - zed*dedxv2;
real dedzic2 = xdb*dedyu2 - ydb*dedxu2 + yed*dedxv2 - xed*dedyv2;
real dedxid2 = zcb*dedyu2 - ycb*dedzu2 + yec*dedzv2 - zec*dedyv2;
real dedyid2 = xcb*dedzu2 - zcb*dedxu2 + zec*dedxv2 - xec*dedzv2;
real dedzid2 = ycb*dedxu2 - xcb*dedyu2 + xec*dedyv2 - yec*dedxv2;
real dedxie2 = zdc*dedyv2 - ydc*dedzv2;
real dedyie2 = xdc*dedzv2 - zdc*dedxv2;
real dedzie2 = ydc*dedxv2 - xdc*dedyv2;
real3 force1 = make_real3(-dedxia, -dedyia, -dedzia);
real3 force2 = make_real3(-dedxib-dedxib2, -dedyib-dedyib2, -dedzib-dedzib2);
real3 force3 = make_real3(-dedxic-dedxic2, -dedyic-dedyic2, -dedzic-dedzic2);
real3 force4 = make_real3(-dedxid-dedxid2, -dedyid-dedyid2, -dedzid-dedzid2);
real3 force5 = make_real3(-dedxie2, -dedyie2, -dedzie2);
\ No newline at end of file
plugins/amoeba/platforms/cuda2/src/kernels/bicubic.cu 0 → 100644
View file @ edbe6a87
__device__ void bicubic(real4 y, real4 y1i, real4 y2i, real4 y12i, real x1, real x1l, real x1u,
real x2, real x2l, real x2u, real* energyOut, real* dang1Out, real* dang2Out) {
real c[4][4];
real d1 = x1u - x1l;
real d2 = x2u - x2l;
real d12 = d1*d2;
real4 y1 = d1*y1i;
real4 y2 = d2*y2i;
real4 y12 = d12*y12i;
c[0][0] = y.x;
c[0][1] = y2.x;
c[0][2] = 3.0f*(y.w - y.x) - (2.0f*y2.x + y2.w);
c[0][3] = 2.0f*(y.x - y.w) + y2.x + y2.w;
c[1][0] = y1.x;
c[1][1] = y12.x;
c[1][2] = 3.0f*(y1.w - y1.x) - (2.0f*y12.x + y12.w);
c[1][3] = 2.0f*(y1.x - y1.w) + y12.x + y12.w;
c[2][0] = 3.0f*(y.y - y.x) - (2.0f*y1.x + y1.y);
c[2][1] = 3.0f*(y2.y - y2.x) - (2.0f*y12.x + y12.y);
c[2][2] = 9.0f*(y.x - y.y + y.z - y.w) + 6.0f* y1.x + 3.0f* y1.y - 3.0f* y1.z - 6.0f* y1.w +
6.0f* y2.x - 6.0f* y2.y - 3.0f* y2.z + 3.0f* y2.w +
4.0f*y12.x + 2.0f*y12.y + y12.z + 2.0f*y12.w;
c[2][3] = 6.0f*(y.y - y.x + y.w - y.z) + -4.0f* y1.x - 2.0f* y1.y + 2.0f* y1.z + 4.0f* y1.w +
-3.0f* y2.x + 3.0f* y2.y + 3.0f* y2.z - 3.0f* y2.w
-2.0f*y12.x - y12.y - y12.z - 2.0f*y12.w;
c[3][0] = 2.0f*(y.x - y.y) + y1.x + y1.y;
c[3][1] = 2.0f*(y2.x - y2.y) + y12.x + y12.y;
c[3][2] = 6.0f*( y.y - y.x + y.w - y.z) +
3.0f*(y1.z + y1.w - y1.x - y1.y) +
2.0f*( 2.0f*(y2.y - y2.x) + y2.z - y2.w) +
-2.0f*(y12.x + y12.y) - y12.z - y12.w;
c[3][3] = 4.0f*( y.x - y.y + y.z - y.w) +
2.0f*( y1.x + y1.y - y1.z - y1.w) +
2.0f*( y2.x - y2.y - y2.z + y2.w) +
y12.x + y12.y + y12.z + y12.w;
real t = (x1-x1l) / (x1u-x1l);
real u = (x2-x2l) / (x2u-x2l);
real energy = ((c[3][3]*u + c[3][2])*u + c[3][1])*u + c[3][0];
energy = t*energy + ((c[2][3]*u + c[2][2])*u + c[2][1])*u + c[2][0];
energy = t*energy + ((c[1][3]*u + c[1][2])*u + c[1][1])*u + c[1][0];
energy = t*energy + ((c[0][3]*u + c[0][2])*u + c[0][1])*u + c[0][0];
real dang1 = (3.0f*c[3][3]*t + 2.0f*c[2][3])*t + c[1][3];
dang1 = u*dang1 + (3.0f*c[3][2]*t + 2.0f*c[2][2])*t + c[1][2];
dang1 = u*dang1 + (3.0f*c[3][1]*t + 2.0f*c[2][1])*t + c[1][1];
dang1 = u*dang1 + (3.0f*c[3][0]*t + 2.0f*c[2][0])*t + c[1][0];
real dang2 = (3.0f*c[3][3]*u + 2.0f*c[3][2])*u + c[3][1];
dang2 = t*dang2 + (3.0f*c[2][3]*u + 2.0f*c[2][2])*u + c[2][1];
dang2 = t*dang2 + (3.0f*c[1][3]*u + 2.0f*c[1][2])*u + c[1][1];
dang2 = t*dang2 + (3.0f*c[0][3]*u + 2.0f*c[0][2])*u + c[0][1];
dang1 = dang1 / (x1u-x1l);
dang2 = dang2 / (x2u-x2l);
*energyOut = energy;
*dang1Out = dang1;
*dang2Out = dang2;
}
\ No newline at end of file
plugins/amoeba/platforms/cuda2/tests/TestCudaAmoebaStretchBendForce.cpp 0 → 100644
View file @ edbe6a87
/* -------------------------------------------------------------------------- *
* OpenMMAmoeba *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008 Stanford University and the Authors. *
* Authors: Mark Friedrichs *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
/**
* This tests the CUDA implementation of CudaAmoebaStretchBendForce.
*/
#include "openmm/internal/AssertionUtilities.h"
#include "AmoebaTinkerParameterFile.h"
#include "openmm/Context.h"
#include "OpenMMAmoeba.h"
#include "openmm/System.h"
#include "openmm/LangevinIntegrator.h"
#include <iostream>
#include <vector>
using namespace OpenMM;
const double TOL = 1e-5;
#define PI_M 3.141592653589
#define RADIAN 57.29577951308
/* ---------------------------------------------------------------------------------------
Compute cross product of two 3-vectors and place in 3rd vector
vectorZ = vectorX x vectorY
@param vectorX x-vector
@param vectorY y-vector
@param vectorZ z-vector
@return vector is vectorZ
--------------------------------------------------------------------------------------- */
static void crossProductVector3( double* vectorX, double* vectorY, double* vectorZ ){
vectorZ[0] = vectorX[1]*vectorY[2] - vectorX[2]*vectorY[1];
vectorZ[1] = vectorX[2]*vectorY[0] - vectorX[0]*vectorY[2];
vectorZ[2] = vectorX[0]*vectorY[1] - vectorX[1]*vectorY[0];
return;
}
static double dotVector3( double* vectorX, double* vectorY ){
return vectorX[0]*vectorY[0] + vectorX[1]*vectorY[1] + vectorX[2]*vectorY[2];
}
static void computeAmoebaStretchBendForce(int bondIndex, std::vector<Vec3>& positions, AmoebaStretchBendForce& amoebaStretchBendForce,
std::vector<Vec3>& forces, double* energy, FILE* log ) {
int particle1, particle2, particle3;
double abBondLength, cbBondLength, angleStretchBend, kStretchBend;
amoebaStretchBendForce.getStretchBendParameters(bondIndex, particle1, particle2, particle3, abBondLength, cbBondLength, angleStretchBend, kStretchBend);
angleStretchBend *= RADIAN;
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaStretchBendForce: bond %d [%d %d %d] ab=%10.3e cb=%10.3e angle=%10.3e k=%10.3e\n",
bondIndex, particle1, particle2, particle3, abBondLength, cbBondLength, angleStretchBend, kStretchBend );
(void) fflush( log );
}
#endif
enum { A, B, C, LastAtomIndex };
enum { AB, CB, CBxAB, ABxP, CBxP, LastDeltaIndex };
// ---------------------------------------------------------------------------------------
// get deltaR between various combinations of the 3 atoms
// and various intermediate terms
double deltaR[LastDeltaIndex][3];
double rAB2 = 0.0;
double rCB2 = 0.0;
for( int ii = 0; ii < 3; ii++ ){
deltaR[AB][ii] = positions[particle1][ii] - positions[particle2][ii];
rAB2 += deltaR[AB][ii]*deltaR[AB][ii];
deltaR[CB][ii] = positions[particle3][ii] - positions[particle2][ii];
rCB2 += deltaR[CB][ii]*deltaR[CB][ii];
}
double rAB = sqrt( rAB2 );
double rCB = sqrt( rCB2 );
crossProductVector3( deltaR[CB], deltaR[AB], deltaR[CBxAB] );
double rP = dotVector3( deltaR[CBxAB], deltaR[CBxAB] );
rP = sqrt( rP );
if( rP <= 0.0 ){
return;
}
double dot = dotVector3( deltaR[CB], deltaR[AB] );
double cosine = dot/(rAB*rCB);
double angle;
if( cosine >= 1.0 ){
angle = 0.0;
} else if( cosine <= -1.0 ){
angle = PI_M;
} else {
angle = RADIAN*acos(cosine);
}
double termA = -RADIAN/(rAB2*rP);
double termC = RADIAN/(rCB2*rP);
// P = CBxAB
crossProductVector3( deltaR[AB], deltaR[CBxAB], deltaR[ABxP] );
crossProductVector3( deltaR[CB], deltaR[CBxAB], deltaR[CBxP] );
for( int ii = 0; ii < 3; ii++ ){
deltaR[ABxP][ii] *= termA;
deltaR[CBxP][ii] *= termC;
}
double dr = rAB - abBondLength + rCB - cbBondLength;
termA = 1.0/rAB;
termC = 1.0/rCB;
double term = kStretchBend;
// ---------------------------------------------------------------------------------------
// forces
// calculate forces for atoms a, b, c
// the force for b is then -( a + c)
double subForce[LastAtomIndex][3];
double dt = angle - angleStretchBend;
for( int jj = 0; jj < 3; jj++ ){
subForce[A][jj] = term*(dt*termA*deltaR[AB][jj] + dr*deltaR[ABxP][jj] );
subForce[C][jj] = term*(dt*termC*deltaR[CB][jj] + dr*deltaR[CBxP][jj] );
subForce[B][jj] = -( subForce[A][jj] + subForce[C][jj] );
}
// ---------------------------------------------------------------------------------------
// accumulate forces and energy
forces[particle1][0] -= subForce[0][0];
forces[particle1][1] -= subForce[0][1];
forces[particle1][2] -= subForce[0][2];
forces[particle2][0] -= subForce[1][0];
forces[particle2][1] -= subForce[1][1];
forces[particle2][2] -= subForce[1][2];
forces[particle3][0] -= subForce[2][0];
forces[particle3][1] -= subForce[2][1];
forces[particle3][2] -= subForce[2][2];
*energy += term*dt*dr;
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaStretchBendForce: angle=%10.3e dt=%10.3e dr=%10.3e\n", angle, dt, dr );
(void) fflush( log );
}
#endif
return;
}
static void computeAmoebaStretchBendForces( Context& context, AmoebaStretchBendForce& amoebaStretchBendForce,
std::vector<Vec3>& expectedForces, double* expectedEnergy, FILE* log ) {
// get positions and zero forces
State state = context.getState(State::Positions);
std::vector<Vec3> positions = state.getPositions();
expectedForces.resize( positions.size() );
for( unsigned int ii = 0; ii < expectedForces.size(); ii++ ){
expectedForces[ii][0] = expectedForces[ii][1] = expectedForces[ii][2] = 0.0;
}
// calculates forces/energy
*expectedEnergy = 0.0;
for( int ii = 0; ii < amoebaStretchBendForce.getNumStretchBends(); ii++ ){
computeAmoebaStretchBendForce(ii, positions, amoebaStretchBendForce, expectedForces, expectedEnergy, log );
}
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaStretchBendForces: expected energy=%14.7e\n", *expectedEnergy );
for( unsigned int ii = 0; ii < positions.size(); ii++ ){
(void) fprintf( log, "%6u [%14.7e %14.7e %14.7e]\n", ii, expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2] );
}
(void) fflush( log );
}
#endif
return;
}
void compareWithExpectedForceAndEnergy( Context& context, AmoebaStretchBendForce& amoebaStretchBendForce,
double tolerance, const std::string& idString, FILE* log) {
std::vector<Vec3> expectedForces;
double expectedEnergy;
computeAmoebaStretchBendForces( context, amoebaStretchBendForce, expectedForces, &expectedEnergy, log );
State state = context.getState(State::Forces | State::Energy);
const std::vector<Vec3> forces = state.getForces();
#ifdef AMOEBA_DEBUG
if( log ){
(void) fprintf( log, "computeAmoebaStretchBendForces: expected energy=%14.7e %14.7e\n", expectedEnergy, state.getPotentialEnergy() );
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
(void) fprintf( log, "%6u [%14.7e %14.7e %14.7e] [%14.7e %14.7e %14.7e]\n", ii,
expectedForces[ii][0], expectedForces[ii][1], expectedForces[ii][2], forces[ii][0], forces[ii][1], forces[ii][2] );
}
(void) fflush( log );
}
#endif
for( unsigned int ii = 0; ii < forces.size(); ii++ ){
ASSERT_EQUAL_VEC( expectedForces[ii], forces[ii], tolerance );
}
ASSERT_EQUAL_TOL( expectedEnergy, state.getPotentialEnergy(), tolerance );
}
void testOneStretchBend( FILE* log ) {
System system;
int numberOfParticles = 3;
for( int ii = 0; ii < numberOfParticles; ii++ ){
system.addParticle(1.0);
}
LangevinIntegrator integrator(0.0, 0.1, 0.01);
AmoebaStretchBendForce* amoebaStretchBendForce = new AmoebaStretchBendForce();
double abLength = 0.144800000E+01;
double cbLength = 0.101500000E+01;
double angleStretchBend = 0.108500000E+03*DegreesToRadians;
//double kStretchBend = 0.750491578E-01;
double kStretchBend = 1.0;
amoebaStretchBendForce->addStretchBend(0, 1, 2, abLength, cbLength, angleStretchBend, kStretchBend );
system.addForce(amoebaStretchBendForce);
Context context(system, integrator, Platform::getPlatformByName( "CUDA"));
std::vector<Vec3> positions(numberOfParticles);
positions[0] = Vec3( 0.262660000E+02, 0.254130000E+02, 0.284200000E+01 );
positions[1] = Vec3( 0.273400000E+02, 0.244300000E+02, 0.261400000E+01 );
positions[2] = Vec3( 0.269573220E+02, 0.236108860E+02, 0.216376800E+01 );
context.setPositions(positions);
compareWithExpectedForceAndEnergy( context, *amoebaStretchBendForce, TOL, "testOneStretchBend", log );
}
int main( int numberOfArguments, char* argv[] ) {
try {
std::cout << "TestCudaAmoebaStretchBendForce running test..." << std::endl;
registerAmoebaCudaKernelFactories();
FILE* log = NULL;
testOneStretchBend( log );
} catch(const std::exception& e) {
std::cout << "exception: " << e.what() << std::endl;
std::cout << "FAIL - ERROR. Test failed." << std::endl;
return 1;
}
std::cout << "Done" << std::endl;
return 0;
}
plugins/amoeba/platforms/cuda2/tests/TestCudaAmoebaTorsionTorsionForce.cpp 0 → 100644
View file @ edbe6a87
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