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"platforms/cuda/tests/TestCudaMonteCarloBarostat.cpp" did not exist on "a138663d61116c35f1358ca0e6a49cf2782d1509"
Commit 73183c61 authored by ChayaSt's avatar ChayaSt
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resolved conflict

parents 0e218233 32e08b87
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plugins/amoeba/openmmapi/include/openmm/AmoebaStretchBendForce.h
View file @ 73183c61
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Mark Friedrichs, Peter Eastman *
* Contributors: *
* *
......@@ -119,20 +119,24 @@ public:
* in a term cannot be changed, nor can new terms be added.
*/
void updateParametersInContext(Context& context);
/**
* Set whether this force should apply periodic boundary conditions when calculating displacements.
* Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
*/
void setUsesPeriodicBoundaryConditions(bool periodic);
/**
* Returns whether or not this force makes use of periodic boundary
* conditions.
*
* @returns true if nonbondedMethod uses PBC and false otherwise
* @returns true if force uses PBC and false otherwise
*/
bool usesPeriodicBoundaryConditions() const {
return false;
}
bool usesPeriodicBoundaryConditions() const;
protected:
ForceImpl* createImpl() const;
private:
class StretchBendInfo;
std::vector<StretchBendInfo> stretchBends;
bool usePeriodic;
};
/**
......
plugins/amoeba/openmmapi/include/openmm/AmoebaTorsionTorsionForce.h
View file @ 73183c61
......@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2012 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Mark Friedrichs, Peter Eastman *
* Contributors: *
* *
......@@ -137,15 +137,18 @@ public:
* grid[x][y][5] = dEd(xy) value
*/
void setTorsionTorsionGrid(int index, const std::vector<std::vector<std::vector<double> > >& grid);
/**
* Set whether this force should apply periodic boundary conditions when calculating displacements.
* Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
*/
void setUsesPeriodicBoundaryConditions(bool periodic);
/**
* Returns whether or not this force makes use of periodic boundary
* conditions.
*
* @returns true if nonbondedMethod uses PBC and false otherwise
* @returns true if force uses PBC and false otherwise
*/
bool usesPeriodicBoundaryConditions() const {
return false;
}
bool usesPeriodicBoundaryConditions() const;
protected:
ForceImpl* createImpl() const;
private:
......@@ -153,6 +156,7 @@ private:
class TorsionTorsionGridInfo;
std::vector<TorsionTorsionInfo> torsionTorsions;
std::vector<TorsionTorsionGridInfo> torsionTorsionGrids;
bool usePeriodic;
};
/**
......
plugins/amoeba/openmmapi/src/AmoebaAngleForce.cpp
View file @ 73183c61
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
......@@ -36,7 +36,7 @@
using namespace OpenMM;
AmoebaAngleForce::AmoebaAngleForce() {
AmoebaAngleForce::AmoebaAngleForce() : usePeriodic(false) {
_globalCubicK = _globalQuarticK = _globalPenticK = _globalSexticK = 0.0;
}
......@@ -102,3 +102,11 @@ ForceImpl* AmoebaAngleForce::createImpl() const {
void AmoebaAngleForce::updateParametersInContext(Context& context) {
dynamic_cast<AmoebaAngleForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
}
void AmoebaAngleForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool AmoebaAngleForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
plugins/amoeba/openmmapi/src/AmoebaBondForce.cpp
View file @ 73183c61
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
......@@ -36,7 +36,7 @@
using namespace OpenMM;
AmoebaBondForce::AmoebaBondForce() {
AmoebaBondForce::AmoebaBondForce() : usePeriodic(false) {
_globalCubicK = _globalQuarticK = 0.0;
}
......@@ -82,3 +82,11 @@ ForceImpl* AmoebaBondForce::createImpl() const {
void AmoebaBondForce::updateParametersInContext(Context& context) {
dynamic_cast<AmoebaBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
}
void AmoebaBondForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool AmoebaBondForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
plugins/amoeba/openmmapi/src/AmoebaInPlaneAngleForce.cpp
View file @ 73183c61
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
......@@ -36,7 +36,7 @@
using namespace OpenMM;
AmoebaInPlaneAngleForce::AmoebaInPlaneAngleForce() {
AmoebaInPlaneAngleForce::AmoebaInPlaneAngleForce() : usePeriodic(false) {
_globalCubicK = _globalQuarticK = _globalPenticK = _globalSexticK = 0.0;
}
......@@ -104,3 +104,11 @@ ForceImpl* AmoebaInPlaneAngleForce::createImpl() const {
void AmoebaInPlaneAngleForce::updateParametersInContext(Context& context) {
dynamic_cast<AmoebaInPlaneAngleForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
}
void AmoebaInPlaneAngleForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool AmoebaInPlaneAngleForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
plugins/amoeba/openmmapi/src/AmoebaOutOfPlaneBendForce.cpp
View file @ 73183c61
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
......@@ -36,7 +36,7 @@
using namespace OpenMM;
AmoebaOutOfPlaneBendForce::AmoebaOutOfPlaneBendForce() {
AmoebaOutOfPlaneBendForce::AmoebaOutOfPlaneBendForce() : usePeriodic(false) {
_globalCubicK = -0.1400000E-01;
_globalQuarticK = 0.5600000E-04;
_globalPenticK = -0.7000000E-06;
......@@ -106,3 +106,11 @@ ForceImpl* AmoebaOutOfPlaneBendForce::createImpl() const {
void AmoebaOutOfPlaneBendForce::updateParametersInContext(Context& context) {
dynamic_cast<AmoebaOutOfPlaneBendForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
}
void AmoebaOutOfPlaneBendForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool AmoebaOutOfPlaneBendForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
plugins/amoeba/openmmapi/src/AmoebaPiTorsionForce.cpp
View file @ 73183c61
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
......@@ -36,7 +36,7 @@
using namespace OpenMM;
AmoebaPiTorsionForce::AmoebaPiTorsionForce() {
AmoebaPiTorsionForce::AmoebaPiTorsionForce() : usePeriodic(false) {
}
int AmoebaPiTorsionForce::addPiTorsion(int particle1, int particle2, int particle3, int particle4, int particle5, int particle6, double k) {
......@@ -71,3 +71,11 @@ ForceImpl* AmoebaPiTorsionForce::createImpl() const {
void AmoebaPiTorsionForce::updateParametersInContext(Context& context) {
dynamic_cast<AmoebaPiTorsionForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
}
void AmoebaPiTorsionForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool AmoebaPiTorsionForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
plugins/amoeba/openmmapi/src/AmoebaStretchBendForce.cpp
View file @ 73183c61
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
......@@ -36,7 +36,7 @@
using namespace OpenMM;
AmoebaStretchBendForce::AmoebaStretchBendForce() {
AmoebaStretchBendForce::AmoebaStretchBendForce() : usePeriodic(false) {
}
int AmoebaStretchBendForce::addStretchBend(int particle1, int particle2, int particle3,
......@@ -76,3 +76,11 @@ ForceImpl* AmoebaStretchBendForce::createImpl() const {
void AmoebaStretchBendForce::updateParametersInContext(Context& context) {
dynamic_cast<AmoebaStretchBendForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
}
void AmoebaStretchBendForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool AmoebaStretchBendForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
plugins/amoeba/openmmapi/src/AmoebaTorsionTorsionForce.cpp
View file @ 73183c61
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2014 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
......@@ -38,7 +38,7 @@
using namespace OpenMM;
using namespace std;
AmoebaTorsionTorsionForce::AmoebaTorsionTorsionForce() {
AmoebaTorsionTorsionForce::AmoebaTorsionTorsionForce() : usePeriodic(false) {
}
int AmoebaTorsionTorsionForce::addTorsionTorsion(int particle1, int particle2, int particle3,
......@@ -183,3 +183,11 @@ AmoebaTorsionTorsionForce::TorsionTorsionGridInfo::TorsionTorsionGridInfo(const
}
}
}
void AmoebaTorsionTorsionForce::setUsesPeriodicBoundaryConditions(bool periodic) {
usePeriodic = periodic;
}
bool AmoebaTorsionTorsionForce::usesPeriodicBoundaryConditions() const {
return usePeriodic;
}
plugins/amoeba/platforms/cuda/src/AmoebaCudaKernels.cpp
View file @ 73183c61
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2015 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Peter Eastman, Mark Friedrichs *
* Contributors: *
* *
......@@ -117,6 +117,7 @@ void CudaCalcAmoebaBondForceKernel::initialize(const System& system, const Amoeb
}
params->upload(paramVector);
map<string, string> replacements;
replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
replacements["COMPUTE_FORCE"] = CudaAmoebaKernelSources::amoebaBondForce;
replacements["PARAMS"] = cu.getBondedUtilities().addArgument(params->getDevicePointer(), "float2");
replacements["CUBIC_K"] = cu.doubleToString(force.getAmoebaGlobalBondCubic());
......@@ -214,6 +215,7 @@ void CudaCalcAmoebaAngleForceKernel::initialize(const System& system, const Amoe
}
params->upload(paramVector);
map<string, string> replacements;
replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
replacements["COMPUTE_FORCE"] = CudaAmoebaKernelSources::amoebaAngleForce;
replacements["PARAMS"] = cu.getBondedUtilities().addArgument(params->getDevicePointer(), "float2");
replacements["CUBIC_K"] = cu.doubleToString(force.getAmoebaGlobalAngleCubic());
......@@ -315,6 +317,7 @@ void CudaCalcAmoebaInPlaneAngleForceKernel::initialize(const System& system, con
}
params->upload(paramVector);
map<string, string> replacements;
replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
replacements["PARAMS"] = cu.getBondedUtilities().addArgument(params->getDevicePointer(), "float2");
replacements["CUBIC_K"] = cu.doubleToString(force.getAmoebaGlobalInPlaneAngleCubic());
replacements["QUARTIC_K"] = cu.doubleToString(force.getAmoebaGlobalInPlaneAngleQuartic());
......@@ -417,6 +420,7 @@ void CudaCalcAmoebaPiTorsionForceKernel::initialize(const System& system, const
}
params->upload(paramVector);
map<string, string> replacements;
replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
replacements["PARAMS"] = cu.getBondedUtilities().addArgument(params->getDevicePointer(), "float");
cu.getBondedUtilities().addInteraction(atoms, cu.replaceStrings(CudaAmoebaKernelSources::amoebaPiTorsionForce, replacements), force.getForceGroup());
cu.addForce(new ForceInfo(force));
......@@ -517,6 +521,7 @@ void CudaCalcAmoebaStretchBendForceKernel::initialize(const System& system, cons
params1->upload(paramVector);
params2->upload(paramVectorK);
map<string, string> replacements;
replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
replacements["PARAMS"] = cu.getBondedUtilities().addArgument(params1->getDevicePointer(), "float3");
replacements["FORCE_CONSTANTS"] = cu.getBondedUtilities().addArgument(params2->getDevicePointer(), "float2");
replacements["RAD_TO_DEG"] = cu.doubleToString(180/M_PI);
......@@ -617,6 +622,7 @@ void CudaCalcAmoebaOutOfPlaneBendForceKernel::initialize(const System& system, c
}
params->upload(paramVector);
map<string, string> replacements;
replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
replacements["PARAMS"] = cu.getBondedUtilities().addArgument(params->getDevicePointer(), "float");
replacements["CUBIC_K"] = cu.doubleToString(force.getAmoebaGlobalOutOfPlaneBendCubic());
replacements["QUARTIC_K"] = cu.doubleToString(force.getAmoebaGlobalOutOfPlaneBendQuartic());
......@@ -748,6 +754,7 @@ void CudaCalcAmoebaTorsionTorsionForceKernel::initialize(const System& system, c
gridValues->upload(gridValuesVec);
gridParams->upload(gridParamsVec);
map<string, string> replacements;
replacements["APPLY_PERIODIC"] = (force.usesPeriodicBoundaryConditions() ? "1" : "0");
replacements["GRID_VALUES"] = cu.getBondedUtilities().addArgument(gridValues->getDevicePointer(), "float4");
replacements["GRID_PARAMS"] = cu.getBondedUtilities().addArgument(gridParams->getDevicePointer(), "float4");
replacements["TORSION_PARAMS"] = cu.getBondedUtilities().addArgument(torsionParams->getDevicePointer(), "int2");
......
plugins/amoeba/platforms/cuda/src/kernels/amoebaInPlaneForce.cu
View file @ 73183c61
float2 angleParams = PARAMS[index];
real xad = pos1.x - pos4.x;
real yad = pos1.y - pos4.y;
real zad = pos1.z - pos4.z;
real3 ad = make_real3(pos1.x-pos4.x, pos1.y-pos4.y, pos1.z-pos4.z);
real3 bd = make_real3(pos2.x-pos4.x, pos2.y-pos4.y, pos2.z-pos4.z);
real3 cd = make_real3(pos3.x-pos4.x, pos3.y-pos4.y, pos3.z-pos4.z);
real xbd = pos2.x - pos4.x;
real ybd = pos2.y - pos4.y;
real zbd = pos2.z - pos4.z;
#if APPLY_PERIODIC
APPLY_PERIODIC_TO_DELTA(ad)
APPLY_PERIODIC_TO_DELTA(bd)
APPLY_PERIODIC_TO_DELTA(cd)
#endif
real xcd = pos3.x - pos4.x;
real ycd = pos3.y - pos4.y;
real zcd = pos3.z - pos4.z;
real xt = yad*zcd - zad*ycd;
real yt = zad*xcd - xad*zcd;
real zt = xad*ycd - yad*xcd;
real xt = ad.y*cd.z - ad.z*cd.y;
real yt = ad.z*cd.x - ad.x*cd.z;
real zt = ad.x*cd.y - ad.y*cd.x;
real rt2 = xt*xt + yt*yt + zt*zt;
real delta = -(xt*xbd + yt*ybd + zt*zbd) / rt2;
real delta = -(xt*bd.x + yt*bd.y + zt*bd.z) / rt2;
real xip = pos2.x + xt*delta;
real yip = pos2.y + yt*delta;
real zip = pos2.z + zt*delta;
real xap = pos1.x - xip;
real yap = pos1.y - yip;
real zap = pos1.z - zip;
real3 ap = make_real3(pos1.x-xip, pos1.y-yip, pos1.z-zip);
real3 cp = make_real3(pos3.x-xip, pos3.y-yip, pos3.z-zip);
real xcp = pos3.x - xip;
real ycp = pos3.y - yip;
real zcp = pos3.z - zip;
#if APPLY_PERIODIC
APPLY_PERIODIC_TO_DELTA(ap)
APPLY_PERIODIC_TO_DELTA(cp)
#endif
real rap2 = xap*xap + yap*yap + zap*zap;
real rcp2 = xcp*xcp + ycp*ycp + zcp*zcp;
real rap2 = ap.x*ap.x + ap.y*ap.y + ap.z*ap.z;
real rcp2 = cp.x*cp.x + cp.y*cp.y + cp.z*cp.z;
real xm = ycp*zap - zcp*yap;
real ym = zcp*xap - xcp*zap;
real zm = xcp*yap - ycp*xap;
real xm = cp.y*ap.z - cp.z*ap.y;
real ym = cp.z*ap.x - cp.x*ap.z;
real zm = cp.x*ap.y - cp.y*ap.x;
real rm = max(SQRT(xm*xm + ym*ym + zm*zm), (real) 1e-6f);
real dotp = xap*xcp + yap*ycp + zap*zcp;
real dotp = ap.x*cp.x + ap.y*cp.y + ap.z*cp.z;
real product = SQRT(rap2*rcp2);
real cosine = (product > 0 ? (dotp/product) : 0);
cosine = max(min(cosine, (real) 1), (real) -1);
real angle;
if (cosine > 0.99f || cosine < -0.99f) {
real3 cross_prod = cross(make_real3(xap, yap, zap), make_real3(xcp, ycp, zcp));
real3 cross_prod = cross(ap, cp);
angle = ASIN(SQRT(dot(cross_prod, cross_prod)/(rap2*rcp2)))*RAD_TO_DEG;
if (cosine < 0.0f)
angle = 180-angle;
......@@ -67,13 +65,13 @@ dEdAngle *= RAD_TO_DEG;
real terma = -dEdAngle/(rap2*rm);
real termc = dEdAngle/(rcp2*rm);
real dedxia = terma * (yap*zm-zap*ym);
real dedyia = terma * (zap*xm-xap*zm);
real dedzia = terma * (xap*ym-yap*xm);
real dedxia = terma * (ap.y*zm-ap.z*ym);
real dedyia = terma * (ap.z*xm-ap.x*zm);
real dedzia = terma * (ap.x*ym-ap.y*xm);
real dedxic = termc * (ycp*zm-zcp*ym);
real dedyic = termc * (zcp*xm-xcp*zm);
real dedzic = termc * (xcp*ym-ycp*xm);
real dedxic = termc * (cp.y*zm-cp.z*ym);
real dedyic = termc * (cp.z*xm-cp.x*zm);
real dedzic = termc * (cp.x*ym-cp.y*xm);
real dedxip = -dedxia - dedxic;
real dedyip = -dedyia - dedyic;
......@@ -82,23 +80,23 @@ real dedzip = -dedzia - dedzic;
real delta2 = 2.0f*delta;
real ptrt2 = (dedxip*xt + dedyip*yt + dedzip*zt) / rt2;
real term = (zcd*ybd-ycd*zbd) + delta2*(yt*zcd-zt*ycd);
real dpdxia = delta*(ycd*dedzip-zcd*dedyip) + term*ptrt2;
real term = (cd.z*bd.y-cd.y*bd.z) + delta2*(yt*cd.z-zt*cd.y);
real dpdxia = delta*(cd.y*dedzip-cd.z*dedyip) + term*ptrt2;
term = (xcd*zbd-zcd*xbd) + delta2*(zt*xcd-xt*zcd);
real dpdyia = delta*(zcd*dedxip-xcd*dedzip) + term*ptrt2;
term = (cd.x*bd.z-cd.z*bd.x) + delta2*(zt*cd.x-xt*cd.z);
real dpdyia = delta*(cd.z*dedxip-cd.x*dedzip) + term*ptrt2;
term = (ycd*xbd-xcd*ybd) + delta2*(xt*ycd-yt*xcd);
real dpdzia = delta*(xcd*dedyip-ycd*dedxip) + term*ptrt2;
term = (cd.y*bd.x-cd.x*bd.y) + delta2*(xt*cd.y-yt*cd.x);
real dpdzia = delta*(cd.x*dedyip-cd.y*dedxip) + term*ptrt2;
term = (yad*zbd-zad*ybd) + delta2*(zt*yad-yt*zad);
real dpdxic = delta*(zad*dedyip-yad*dedzip) + term*ptrt2;
term = (ad.y*bd.z-ad.z*bd.y) + delta2*(zt*ad.y-yt*ad.z);
real dpdxic = delta*(ad.z*dedyip-ad.y*dedzip) + term*ptrt2;
term = (zad*xbd-xad*zbd) + delta2*(xt*zad-zt*xad);
real dpdyic = delta*(xad*dedzip-zad*dedxip) + term*ptrt2;
term = (ad.z*bd.x-ad.x*bd.z) + delta2*(xt*ad.z-zt*ad.x);
real dpdyic = delta*(ad.x*dedzip-ad.z*dedxip) + term*ptrt2;
term = (xad*ybd-yad*xbd) + delta2*(yt*xad-xt*yad);
real dpdzic = delta*(yad*dedxip-xad*dedyip) + term*ptrt2;
term = (ad.x*bd.y-ad.y*bd.x) + delta2*(yt*ad.x-xt*ad.y);
real dpdzic = delta*(ad.y*dedxip-ad.x*dedyip) + term*ptrt2;
dedxia = dedxia + dpdxia;
dedyia = dedyia + dpdyia;
......
plugins/amoeba/platforms/cuda/src/kernels/amoebaOutOfPlaneBendForce.cu
View file @ 73183c61
// 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;
real3 ab = make_real3(pos1.x-pos2.x, pos1.y-pos2.y, pos1.z-pos2.z);
real3 cb = make_real3(pos3.x-pos2.x, pos3.y-pos2.y, pos3.z-pos2.z);
real3 db = make_real3(pos4.x-pos2.x, pos4.y-pos2.y, pos4.z-pos2.z);
real3 ad = make_real3(pos1.x-pos4.x, pos1.y-pos4.y, pos1.z-pos4.z);
real3 cd = make_real3(pos3.x-pos4.x, pos3.y-pos4.y, pos3.z-pos4.z);
#if APPLY_PERIODIC
APPLY_PERIODIC_TO_DELTA(ab)
APPLY_PERIODIC_TO_DELTA(cb)
APPLY_PERIODIC_TO_DELTA(db)
APPLY_PERIODIC_TO_DELTA(ad)
APPLY_PERIODIC_TO_DELTA(cd)
#endif
real rdb2 = db.x*db.x + db.y*db.y + db.z*db.z;
real rad2 = ad.x*ad.x + ad.y*ad.y + ad.z*ad.z;
real rcd2 = cd.x*cd.x + cd.y*cd.y + cd.z*cd.z;
real ee = ab.x*(cb.y*db.z-cb.z*db.y) + ab.y*(cb.z*db.x-cb.x*db.z) + ab.z*(cb.x*db.y-cb.y*db.x);
real dot = ad.x*cd.x + ad.y*cd.y + ad.z*cd.z;
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_0 = ad.y*cd.z - ad.z*cd.y;
real adXcd_1 = ad.z*cd.x - ad.x*cd.z;
real adXcd_2 = ad.x*cd.y - ad.y*cd.x;
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;
real adXcd_dot_db = db.x*adXcd_0 + db.y*adXcd_1 + db.z*adXcd_2;
adXcd_dot_db /= SQRT(rdb2*adXcd_nrm2);
real angle = abs(ASIN(adXcd_dot_db));
......@@ -62,13 +54,13 @@ real dedcos = -deddt*eeSign/SQRT(cc*bkk2);
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 dccdxia = (ad.x*rcd2-cd.x*dot) * term;
real dccdyia = (ad.y*rcd2-cd.y*dot) * term;
real dccdzia = (ad.z*rcd2-cd.z*dot) * term;
real dccdxic = (xcd*rad2-xad*dot) * term;
real dccdyic = (ycd*rad2-yad*dot) * term;
real dccdzic = (zcd*rad2-zad*dot) * term;
real dccdxic = (cd.x*rad2-ad.x*dot) * term;
real dccdyic = (cd.y*rad2-ad.y*dot) * term;
real dccdzic = (cd.z*rad2-ad.z*dot) * term;
real dccdxid = -dccdxia - dccdxic;
real dccdyid = -dccdyia - dccdyic;
......@@ -76,17 +68,17 @@ 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 deedxia = db.y*cb.z - db.z*cb.y;
real deedyia = db.z*cb.x - db.x*cb.z;
real deedzia = db.x*cb.y - db.y*cb.x;
real deedxic = yab*zdb - zab*ydb;
real deedyic = zab*xdb - xab*zdb;
real deedzic = xab*ydb - yab*xdb;
real deedxic = ab.y*db.z - ab.z*db.y;
real deedyic = ab.z*db.x - ab.x*db.z;
real deedzic = ab.x*db.y - ab.y*db.x;
real deedxid = ycb*zab - zcb*yab + xdb*term;
real deedyid = zcb*xab - xcb*zab + ydb*term;
real deedzid = xcb*yab - ycb*xab + zdb*term;
real deedxid = cb.y*ab.z - cb.z*ab.y + db.x*term;
real deedyid = cb.z*ab.x - cb.x*ab.z + db.y*term;
real deedzid = cb.x*ab.y - cb.y*ab.x + db.z*term;
// compute first derivative components for this angle
......
plugins/amoeba/platforms/cuda/src/kernels/amoebaPiTorsionForce.cu
View file @ 73183c61
// compute the value of the pi-orbital torsion angle
real xad = pos1.x - pos4.x;
real yad = pos1.y - pos4.y;
real zad = pos1.z - pos4.z;
real xbd = pos2.x - pos4.x;
real ybd = pos2.y - pos4.y;
real zbd = pos2.z - pos4.z;
real xec = pos5.x - pos3.x;
real yec = pos5.y - pos3.y;
real zec = pos5.z - pos3.z;
real xgc = pos6.x - pos3.x;
real ygc = pos6.y - pos3.y;
real zgc = pos6.z - pos3.z;
real xip = yad*zbd - ybd*zad + pos3.x;
real yip = zad*xbd - zbd*xad + pos3.y;
real zip = xad*ybd - xbd*yad + pos3.z;
real xiq = yec*zgc - ygc*zec + pos4.x;
real yiq = zec*xgc - zgc*xec + pos4.y;
real ziq = xec*ygc - xgc*yec + pos4.z;
real3 ad = make_real3(pos1.x-pos4.x, pos1.y-pos4.y, pos1.z-pos4.z);
real3 bd = make_real3(pos2.x-pos4.x, pos2.y-pos4.y, pos2.z-pos4.z);
real3 ec = make_real3(pos5.x-pos3.x, pos5.y-pos3.y, pos5.z-pos3.z);
real3 gc = make_real3(pos6.x-pos3.x, pos6.y-pos3.y, pos6.z-pos3.z);
#if APPLY_PERIODIC
APPLY_PERIODIC_TO_DELTA(ad)
APPLY_PERIODIC_TO_DELTA(bd)
APPLY_PERIODIC_TO_DELTA(ec)
APPLY_PERIODIC_TO_DELTA(gc)
#endif
real xip = ad.y*bd.z - bd.y*ad.z + pos3.x;
real yip = ad.z*bd.x - bd.z*ad.x + pos3.y;
real zip = ad.x*bd.y - bd.x*ad.y + pos3.z;
real xiq = ec.y*gc.z - gc.y*ec.z + pos4.x;
real yiq = ec.z*gc.x - gc.z*ec.x + pos4.y;
real ziq = ec.x*gc.y - gc.x*ec.y + pos4.z;
real xcp = pos3.x - xip;
real ycp = pos3.y - yip;
......@@ -112,21 +108,21 @@ real dedziq = ydc*dedxu - xdc*dedyu;
// compute first derivative components for individual atoms
real dedxia = ybd*dedzip - zbd*dedyip;
real dedyia = zbd*dedxip - xbd*dedzip;
real dedzia = xbd*dedyip - ybd*dedxip;
real dedxia = bd.y*dedzip - bd.z*dedyip;
real dedyia = bd.z*dedxip - bd.x*dedzip;
real dedzia = bd.x*dedyip - bd.y*dedxip;
real dedxib = zad*dedyip - yad*dedzip;
real dedyib = xad*dedzip - zad*dedxip;
real dedzib = yad*dedxip - xad*dedyip;
real dedxib = ad.z*dedyip - ad.y*dedzip;
real dedyib = ad.x*dedzip - ad.z*dedxip;
real dedzib = ad.y*dedxip - ad.x*dedyip;
real dedxie = ygc*dedziq - zgc*dedyiq;
real dedyie = zgc*dedxiq - xgc*dedziq;
real dedzie = xgc*dedyiq - ygc*dedxiq;
real dedxie = gc.y*dedziq - gc.z*dedyiq;
real dedyie = gc.z*dedxiq - gc.x*dedziq;
real dedzie = gc.x*dedyiq - gc.y*dedxiq;
real dedxig = zec*dedyiq - yec*dedziq;
real dedyig = xec*dedziq - zec*dedxiq;
real dedzig = yec*dedxiq - xec*dedyiq;
real dedxig = ec.z*dedyiq - ec.y*dedziq;
real dedyig = ec.x*dedziq - ec.z*dedxiq;
real dedzig = ec.y*dedxiq - ec.x*dedyiq;
dedxic = dedxic + dedxip - dedxie - dedxig;
dedyic = dedyic + dedyip - dedyie - dedyig;
......
plugins/amoeba/platforms/cuda/src/kernels/amoebaStretchBendForce.cu
View file @ 73183c61
// 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;
real3 ab = make_real3(pos1.x-pos2.x, pos1.y-pos2.y, pos1.z-pos2.z);
real3 cb = make_real3(pos3.x-pos2.x, pos3.y-pos2.y, pos3.z-pos2.z);
real xcb = pos3.x - pos2.x;
real ycb = pos3.y - pos2.y;
real zcb = pos3.z - pos2.z;
#if APPLY_PERIODIC
APPLY_PERIODIC_TO_DELTA(ab)
APPLY_PERIODIC_TO_DELTA(cb)
#endif
real rab = SQRT(xab*xab + yab*yab + zab*zab);
real rcb = SQRT(xcb*xcb + ycb*ycb + zcb*zcb);
real rab = SQRT(ab.x*ab.x + ab.y*ab.y + ab.z*ab.z);
real rcb = SQRT(cb.x*cb.x + cb.y*cb.y + cb.z*cb.z);
real xp = ycb*zab - zcb*yab;
real yp = zcb*xab - xcb*zab;
real zp = xcb*yab - ycb*xab;
real xp = cb.y*ab.z - cb.z*ab.y;
real yp = cb.z*ab.x - cb.x*ab.z;
real zp = cb.x*ab.y - cb.y*ab.x;
real rp = SQRT(xp*xp + yp*yp + zp*zp);
real dotp = xab*xcb + yab*ycb + zab*zcb;
real dotp = ab.x*cb.x + ab.y*cb.y + ab.z*cb.z;
real cosine = rab*rcb > 0 ? (dotp / (rab*rcb)) : (real) 1;
cosine = (cosine > 1 ? (real) 1 : cosine);
cosine = (cosine < -1 ? -(real) 1 : cosine);
real angle;
if (cosine > 0.99f || cosine < -0.99f) {
// Highly unlikely a stretch-bend angle will be near 0 or 180, but just in case...
real3 cross_prod = cross(make_real3(xab, yab, zab), make_real3(xcb, ycb, zcb));
real3 cross_prod = cross(make_real3(ab.x, ab.y, ab.z), make_real3(cb.x, cb.y, cb.z));
angle = ASIN(SQRT(dot(cross_prod, cross_prod))/(rab*rcb))*RAD_TO_DEG;
if (cosine < 0.0f)
angle = 180-angle;
......@@ -41,13 +41,13 @@ real dt = angle - RAD_TO_DEG*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 ddtdxia = terma * (ab.y*zp-ab.z*yp);
real ddtdyia = terma * (ab.z*xp-ab.x*zp);
real ddtdzia = terma * (ab.x*yp-ab.y*xp);
real ddtdxic = termc * (ycb*zp-zcb*yp);
real ddtdyic = termc * (zcb*xp-xcb*zp);
real ddtdzic = termc * (xcb*yp-ycb*xp);
real ddtdxic = termc * (cb.y*zp-cb.z*yp);
real ddtdyic = termc * (cb.z*xp-cb.x*zp);
real ddtdzic = termc * (cb.x*yp-cb.y*xp);
// find chain rule terms for the bond length deviations
......@@ -61,13 +61,13 @@ real frc2 = ((rp != 0) ? force_constants.y : (real) 0);
real drkk = dr1*frc1 + dr2*frc2;
real ddrdxia = terma * xab;
real ddrdyia = terma * yab;
real ddrdzia = terma * zab;
real ddrdxia = terma * ab.x;
real ddrdyia = terma * ab.y;
real ddrdzia = terma * ab.z;
real ddrdxic = termc * xcb;
real ddrdyic = termc * ycb;
real ddrdzic = termc * zcb;
real ddrdxic = termc * cb.x;
real ddrdyic = termc * cb.y;
real ddrdzic = termc * cb.z;
// get the energy and master chain rule terms for derivatives
......
plugins/amoeba/platforms/cuda/src/kernels/amoebaTorsionTorsionForce.cu
View file @ 73183c61
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;
real3 ba = make_real3(pos2.x-pos1.x, pos2.y-pos1.y, pos2.z-pos1.z);
real3 cb = make_real3(pos3.x-pos2.x, pos3.y-pos2.y, pos3.z-pos2.z);
real3 dc = make_real3(pos4.x-pos3.x, pos4.y-pos3.y, pos4.z-pos3.z);
real3 ed = make_real3(pos5.x-pos4.x, pos5.y-pos4.y, pos5.z-pos4.z);
#if APPLY_PERIODIC
APPLY_PERIODIC_TO_DELTA(ba)
APPLY_PERIODIC_TO_DELTA(cb)
APPLY_PERIODIC_TO_DELTA(dc)
APPLY_PERIODIC_TO_DELTA(ed)
#endif
real xt = ba.y*cb.z - cb.y*ba.z;
real yt = ba.z*cb.x - cb.z*ba.x;
real zt = ba.x*cb.y - cb.x*ba.y;
real xu = cb.y*dc.z - dc.y*cb.z;
real yu = cb.z*dc.x - dc.z*cb.x;
real zu = cb.x*dc.y - dc.x*cb.y;
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 xv = dc.y*ed.z - ed.y*dc.z;
real yv = dc.z*ed.x - ed.z*dc.x;
real zv = dc.x*ed.y - ed.x*dc.y;
real rv2 = xv*xv + yv*yv + zv*zv;
real rurv = SQRT(ru2 * rv2);
real rcb = SQRT(xcb*xcb + ycb*ycb + zcb*zcb);
real rcb = SQRT(cb.x*cb.x + cb.y*cb.y + cb.z*cb.z);
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);
......@@ -51,11 +47,11 @@ if (cosine1 > 0.99f || cosine1 < -0.99f) {
}
else
angle1 = RAD_TO_DEG*ACOS(cosine1);
real sign = xba*xu + yba*yu + zba*zu;
real sign = ba.x*xu + ba.y*yu + ba.z*zu;
angle1 = (sign < 0 ? -angle1 : angle1);
real value1 = angle1;
real rdc = SQRT(xdc*xdc + ydc*ydc + zdc*zdc);
real rdc = SQRT(dc.x*dc.x + dc.y*dc.y + dc.z*dc.z);
real cosine2 = (xu*xv + yu*yv + zu*zv) / rurv;
cosine2 = (cosine2 > 1 ? (real) 1 : cosine2);
cosine2 = (cosine2 < -1 ? (real) -1 : cosine2);
......@@ -70,7 +66,7 @@ if (cosine2 > 0.99f || cosine2 < -0.99f) {
}
else
angle2 = RAD_TO_DEG*ACOS(cosine2);
sign = xcb*xv + ycb*yv + zcb*zv;
sign = cb.x*xv + cb.y*yv + cb.z*zv;
angle2 = (sign < 0 ? -angle2 : angle2);
real value2 = angle2;
......@@ -83,24 +79,20 @@ real value2 = angle2;
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;
real3 ac = make_real3(pos6.x-pos3.x, pos6.y-pos3.y, pos6.z-pos3.z);
real3 bc = make_real3(pos2.x-pos3.x, pos2.y-pos3.y, pos2.z-pos3.z);
real3 dc1 = make_real3(pos4.x-pos3.x, pos4.y-pos3.y, pos4.z-pos3.z);
// xdc, ydc, zdc appear above
#if APPLY_PERIODIC
APPLY_PERIODIC_TO_DELTA(ac)
APPLY_PERIODIC_TO_DELTA(bc)
APPLY_PERIODIC_TO_DELTA(dc1)
#endif
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;
real c1 = bc.y*dc1.z - bc.z*dc1.y;
real c2 = dc1.y*ac.z - dc1.z*ac.y;
real c3 = ac.y*bc.z - ac.z*bc.y;
real vol = ac.x*c1 + bc.x*c2 + dc1.x*c3;
sign = (vol > 0 ? (real) 1 : (real) -1);
sign = (torsionParams.x < 0 ? (real) 1 : sign);
value1 *= sign;
......@@ -170,66 +162,68 @@ 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;
real3 ca = make_real3(pos3.x-pos1.x, pos3.y-pos1.y, pos3.z-pos1.z);
real3 db = make_real3(pos4.x-pos2.x, pos4.y-pos2.y, pos4.z-pos2.z);
real xdb = pos4.x - pos2.x;
real ydb = pos4.y - pos2.y;
real zdb = pos4.z - pos2.z;
#if APPLY_PERIODIC
APPLY_PERIODIC_TO_DELTA(ca)
APPLY_PERIODIC_TO_DELTA(db)
#endif
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);
real dedxt = dedang1 * (yt*cb.z - cb.y*zt) / (rt2*rcb);
real dedyt = dedang1 * (zt*cb.x - cb.z*xt) / (rt2*rcb);
real dedzt = dedang1 * (xt*cb.y - cb.x*yt) / (rt2*rcb);
real dedxu = -dedang1 * (yu*cb.z - cb.y*zu) / (ru2*rcb);
real dedyu = -dedang1 * (zu*cb.x - cb.z*xu) / (ru2*rcb);
real dedzu = -dedang1 * (xu*cb.y - cb.x*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 dedxia = cb.z*dedyt - cb.y*dedzt;
real dedyia = cb.x*dedzt - cb.z*dedxt;
real dedzia = cb.y*dedxt - cb.x*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 dedxib = ca.y*dedzt - ca.z*dedyt + dc.z*dedyu - dc.y*dedzu;
real dedyib = ca.z*dedxt - ca.x*dedzt + dc.x*dedzu - dc.z*dedxu;
real dedzib = ca.x*dedyt - ca.y*dedxt + dc.y*dedxu - dc.x*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 dedxic = ba.z*dedyt - ba.y*dedzt + db.y*dedzu - db.z*dedyu;
real dedyic = ba.x*dedzt - ba.z*dedxt + db.z*dedxu - db.x*dedzu;
real dedzic = ba.y*dedxt - ba.x*dedyt + db.x*dedyu - db.y*dedxu;
real dedxid = zcb*dedyu - ycb*dedzu;
real dedyid = xcb*dedzu - zcb*dedxu;
real dedzid = ycb*dedxu - xcb*dedyu;
real dedxid = cb.z*dedyu - cb.y*dedzu;
real dedyid = cb.x*dedzu - cb.z*dedxu;
real dedzid = cb.y*dedxu - cb.x*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;
real3 ec = make_real3(pos5.x-pos3.x, pos5.y-pos3.y, pos5.z-pos3.z);
#if APPLY_PERIODIC
APPLY_PERIODIC_TO_DELTA(ec)
#endif
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);
real dedxu2 = dedang2 * (yu*dc.z - dc.y*zu) / (ru2*rdc);
real dedyu2 = dedang2 * (zu*dc.x - dc.z*xu) / (ru2*rdc);
real dedzu2 = dedang2 * (xu*dc.y - dc.x*yu) / (ru2*rdc);
real dedxv2 = -dedang2 * (yv*dc.z - dc.y*zv) / (rv2*rdc);
real dedyv2 = -dedang2 * (zv*dc.x - dc.z*xv) / (rv2*rdc);
real dedzv2 = -dedang2 * (xv*dc.y - dc.x*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;
real dedxib2 = dc.z*dedyu2 - dc.y*dedzu2;
real dedyib2 = dc.x*dedzu2 - dc.z*dedxu2;
real dedzib2 = dc.y*dedxu2 - dc.x*dedyu2;
real dedxic2 = db.y*dedzu2 - db.z*dedyu2 + ed.z*dedyv2 - ed.y*dedzv2;
real dedyic2 = db.z*dedxu2 - db.x*dedzu2 + ed.x*dedzv2 - ed.z*dedxv2;
real dedzic2 = db.x*dedyu2 - db.y*dedxu2 + ed.y*dedxv2 - ed.x*dedyv2;
real dedxid2 = cb.z*dedyu2 - cb.y*dedzu2 + ec.y*dedzv2 - ec.z*dedyv2;
real dedyid2 = cb.x*dedzu2 - cb.z*dedxu2 + ec.z*dedxv2 - ec.x*dedzv2;
real dedzid2 = cb.y*dedxu2 - cb.x*dedyu2 + ec.x*dedyv2 - ec.y*dedxv2;
real dedxie2 = dc.z*dedyv2 - dc.y*dedzv2;
real dedyie2 = dc.x*dedzv2 - dc.z*dedxv2;
real dedzie2 = dc.y*dedxv2 - dc.x*dedyv2;
real3 force1 = make_real3(-dedxia, -dedyia, -dedzia);
real3 force2 = make_real3(-dedxib-dedxib2, -dedyib-dedyib2, -dedzib-dedzib2);
......
plugins/amoeba/platforms/cuda/src/kernels/multipoleElectrostatics.cu
View file @ 73183c61
......@@ -488,6 +488,8 @@ extern "C" __global__ void computeElectrostatics(
#ifdef USE_CUTOFF
const unsigned int numTiles = interactionCount[0];
if (numTiles > maxTiles)
return; // There wasn't enough memory for the neighbor list.
int pos = (int) (numTiles > maxTiles ? startTileIndex+warp*(long long)numTileIndices/totalWarps : warp*(long long)numTiles/totalWarps);
int end = (int) (numTiles > maxTiles ? startTileIndex+(warp+1)*(long long)numTileIndices/totalWarps : (warp+1)*(long long)numTiles/totalWarps);
#else
......@@ -508,34 +510,31 @@ extern "C" __global__ void computeElectrostatics(
int x, y;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles)
x = tiles[pos];
else
#endif
{
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = tiles[pos];
#else
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
}
// Skip over tiles that have exclusions, since they were already processed.
// Skip over tiles that have exclusions, since they were already processed.
while (skipTiles[tbx+TILE_SIZE-1] < pos) {
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[threadIdx.x] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
skipTiles[threadIdx.x] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
while (skipTiles[tbx+TILE_SIZE-1] < pos) {
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[threadIdx.x] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
else
skipTiles[threadIdx.x] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
}
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
#endif
if (includeTile) {
unsigned int atom1 = x*TILE_SIZE + tgx;
......
plugins/amoeba/platforms/cuda/src/kernels/multipoleFixedField.cu
View file @ 73183c61
......@@ -592,6 +592,8 @@ extern "C" __global__ void computeFixedField(
#ifdef USE_CUTOFF
const unsigned int numTiles = interactionCount[0];
if (numTiles > maxTiles)
return; // There wasn't enough memory for the neighbor list.
int pos = (int) (numTiles > maxTiles ? startTileIndex+warp*(long long)numTileIndices/totalWarps : warp*(long long)numTiles/totalWarps);
int end = (int) (numTiles > maxTiles ? startTileIndex+(warp+1)*(long long)numTileIndices/totalWarps : (warp+1)*(long long)numTiles/totalWarps);
#else
......@@ -612,34 +614,31 @@ extern "C" __global__ void computeFixedField(
int x, y;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles)
x = tiles[pos];
else
#endif
{
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = tiles[pos];
#else
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
}
// Skip over tiles that have exclusions, since they were already processed.
// Skip over tiles that have exclusions, since they were already processed.
while (skipTiles[tbx+TILE_SIZE-1] < pos) {
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[threadIdx.x] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
skipTiles[threadIdx.x] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
while (skipTiles[tbx+TILE_SIZE-1] < pos) {
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[threadIdx.x] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
else
skipTiles[threadIdx.x] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
}
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
#endif
if (includeTile) {
unsigned int atom1 = x*TILE_SIZE + tgx;
......
plugins/amoeba/platforms/cuda/src/kernels/multipoleInducedField.cu
View file @ 73183c61
......@@ -454,6 +454,8 @@ extern "C" __global__ void computeInducedField(
#ifdef USE_CUTOFF
const unsigned int numTiles = interactionCount[0];
if (numTiles > maxTiles)
return; // There wasn't enough memory for the neighbor list.
int pos = (int) (numTiles > maxTiles ? startTileIndex+warp*(long long)numTileIndices/totalWarps : warp*(long long)numTiles/totalWarps);
int end = (int) (numTiles > maxTiles ? startTileIndex+(warp+1)*(long long)numTileIndices/totalWarps : (warp+1)*(long long)numTiles/totalWarps);
#else
......@@ -474,34 +476,31 @@ extern "C" __global__ void computeInducedField(
int x, y;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles)
x = tiles[pos];
else
#endif
{
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = tiles[pos];
#else
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
}
// Skip over tiles that have exclusions, since they were already processed.
// Skip over tiles that have exclusions, since they were already processed.
while (skipTiles[tbx+TILE_SIZE-1] < pos) {
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[threadIdx.x] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
skipTiles[threadIdx.x] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
while (skipTiles[tbx+TILE_SIZE-1] < pos) {
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[threadIdx.x] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
else
skipTiles[threadIdx.x] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
}
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
#endif
if (includeTile) {
unsigned int atom1 = x*TILE_SIZE + tgx;
......
plugins/amoeba/platforms/cuda/src/kernels/pmeMultipoleElectrostatics.cu
View file @ 73183c61
......@@ -555,6 +555,8 @@ extern "C" __global__ void computeElectrostatics(
#ifdef USE_CUTOFF
const unsigned int numTiles = interactionCount[0];
if (numTiles > maxTiles)
return; // There wasn't enough memory for the neighbor list.
int pos = (int) (numTiles > maxTiles ? startTileIndex+warp*(long long)numTileIndices/totalWarps : warp*(long long)numTiles/totalWarps);
int end = (int) (numTiles > maxTiles ? startTileIndex+(warp+1)*(long long)numTileIndices/totalWarps : (warp+1)*(long long)numTiles/totalWarps);
#else
......@@ -575,34 +577,31 @@ extern "C" __global__ void computeElectrostatics(
int x, y;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles)
x = tiles[pos];
else
#endif
{
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = tiles[pos];
#else
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
y += (x < y ? -1 : 1);
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
}
}
// Skip over tiles that have exclusions, since they were already processed.
// Skip over tiles that have exclusions, since they were already processed.
while (skipTiles[tbx+TILE_SIZE-1] < pos) {
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[threadIdx.x] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
else
skipTiles[threadIdx.x] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
while (skipTiles[tbx+TILE_SIZE-1] < pos) {
if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS) {
ushort2 tile = exclusionTiles[skipBase+tgx];
skipTiles[threadIdx.x] = tile.x + tile.y*NUM_BLOCKS - tile.y*(tile.y+1)/2;
}
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
else
skipTiles[threadIdx.x] = end;
skipBase += TILE_SIZE;
currentSkipIndex = tbx;
}
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
#endif
if (includeTile) {
unsigned int atom1 = x*TILE_SIZE + tgx;
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaAngleForce.cpp
View file @ 73183c61
......@@ -6,7 +6,7 @@
* 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. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: Mark Friedrichs *
* Contributors: *
* *
......@@ -35,6 +35,7 @@
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "openmm/CustomAngleForce.h"
#include "OpenMMAmoeba.h"
#include "openmm/System.h"
#include "openmm/LangevinIntegrator.h"
......@@ -273,13 +274,64 @@ void testOneAngle() {
compareWithExpectedForceAndEnergy(context, *amoebaAngleForce, TOL, "testOneAngle");
}
void testPeriodic() {
// Create a force that uses periodic boundary conditions, then compare to an identical custom force.
System system;
system.setDefaultPeriodicBoxVectors(Vec3(3, 0, 0), Vec3(0, 3, 0), Vec3(0, 0, 3));
int numParticles = 3;
for (int ii = 0; ii < numParticles; ii++)
system.addParticle(1.0);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
AmoebaAngleForce* amoebaAngleForce = new AmoebaAngleForce();
double angle = 100.0;
double quadraticK = 1.0;
double cubicK = 1.0e-01;
double quarticK = 1.0e-02;
double penticK = 1.0e-03;
double sexticK = 1.0e-04;
amoebaAngleForce->addAngle(0, 1, 2, angle, quadraticK);
amoebaAngleForce->setAmoebaGlobalAngleCubic(cubicK);
amoebaAngleForce->setAmoebaGlobalAngleQuartic(quarticK);
amoebaAngleForce->setAmoebaGlobalAnglePentic(penticK);
amoebaAngleForce->setAmoebaGlobalAngleSextic(sexticK);
amoebaAngleForce->setUsesPeriodicBoundaryConditions(true);
system.addForce(amoebaAngleForce);
CustomAngleForce* customForce = new CustomAngleForce("k2*delta^2 + k3*delta^3 + k4*delta^4 + k5*delta^5 + k6*delta^6; delta=theta-theta0");
customForce->addGlobalParameter("theta0", angle*M_PI/180);
customForce->addGlobalParameter("k2", quadraticK*pow(180/M_PI, 2.0));
customForce->addGlobalParameter("k3", cubicK*pow(180/M_PI, 3.0));
customForce->addGlobalParameter("k4", quarticK*pow(180/M_PI, 4.0));
customForce->addGlobalParameter("k5", penticK*pow(180/M_PI, 5.0));
customForce->addGlobalParameter("k6", sexticK*pow(180/M_PI, 6.0));
customForce->addAngle(0, 1, 2);
customForce->setUsesPeriodicBoundaryConditions(true);
customForce->setForceGroup(1);
system.addForce(customForce);
Context context(system, integrator, Platform::getPlatformByName("CUDA"));
std::vector<Vec3> positions(numParticles);
positions[0] = Vec3(0, 1, 0);
positions[1] = Vec3(0, 0, 0);
positions[2] = Vec3(0, 0, 2);
context.setPositions(positions);
State s1 = context.getState(State::Forces | State::Energy, true, 1);
State s2 = context.getState(State::Forces | State::Energy, true, 2);
ASSERT_EQUAL_TOL(s2.getPotentialEnergy(), s1.getPotentialEnergy(), 1e-5);
for (int i = 0; i < numParticles; i++)
ASSERT_EQUAL_VEC(s2.getForces()[i], s1.getForces()[i], 1e-5);
}
int main(int argc, char* argv[]) {
try {
std::cout << "TestCudaAmoebaAngleForce running test..." << std::endl;
registerAmoebaCudaKernelFactories();
if (argc > 1)
Platform::getPlatformByName("CUDA").setPropertyDefaultValue("CudaPrecision", std::string(argv[1]));
Platform::getPlatformByName("CUDA").setPropertyDefaultValue("Precision", std::string(argv[1]));
testOneAngle();
testPeriodic();
} catch(const std::exception& e) {
std::cout << "exception: " << e.what() << std::endl;
......
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