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Commit 0827ad50 authored by peastman's avatar peastman Committed by GitHub
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Merge pull request #1858 from peastman/localcoordinates 

LocalCoordinatesSite can depend on arbitary number of particles
parents 15b9fb48 ea7f44b2
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docs-source/usersguide/application.rst
View file @ 0827ad50
...@@ -2051,10 +2051,9 @@ be represented with a virtual site. The :code:`type` attribute may equal ...@@ -2051,10 +2051,9 @@ be represented with a virtual site. The :code:`type` attribute may equal
:code:`"localCoords"`\ , which correspond to the TwoParticleAverageSite, ThreeParticleAverageSite, :code:`"localCoords"`\ , which correspond to the TwoParticleAverageSite, ThreeParticleAverageSite,
OutOfPlaneSite, and LocalCoordinatesSite classes respectively. The :code:`siteName` OutOfPlaneSite, and LocalCoordinatesSite classes respectively. The :code:`siteName`
attribute gives the name of the atom to represent with a virtual site. The atoms attribute gives the name of the atom to represent with a virtual site. The atoms
it is calculated based on are specified by :code:`atomName1`\ , :code:`atomName2`\ , it is calculated based on are specified by :code:`atomName1`\ , :code:`atomName2`\ , etc.
and (for virtual site classes that involve three atoms) :code:`atomName3`\ .
(Some old force fields use the deprecated tags :code:`index`, :code:`atom1`, (Some old force fields use the deprecated tags :code:`index`, :code:`atom1`,
:code:`atom2`, and :code:`atom3` to refer to them by index instead of name.) :code:`atom2`, etc. to refer to them by index instead of name.)
The remaining attributes are specific to the virtual site class, and specify the The remaining attributes are specific to the virtual site class, and specify the
parameters for calculating the site position. For a TwoParticleAverageSite, parameters for calculating the site position. For a TwoParticleAverageSite,
...@@ -2062,9 +2061,10 @@ they are :code:`weight1` and :code:`weight2`\ . For a ...@@ -2062,9 +2061,10 @@ they are :code:`weight1` and :code:`weight2`\ . For a
ThreeParticleAverageSite, they are :code:`weight1`\ , :code:`weight2`\ , and ThreeParticleAverageSite, they are :code:`weight1`\ , :code:`weight2`\ , and
\ :code:`weight3`\ . For an OutOfPlaneSite, they are :code:`weight12`\ , \ :code:`weight3`\ . For an OutOfPlaneSite, they are :code:`weight12`\ ,
:code:`weight13`\ , and :code:`weightCross`\ . For a LocalCoordinatesSite, they :code:`weight13`\ , and :code:`weightCross`\ . For a LocalCoordinatesSite, they
are :code:`wo1`\ , :code:`wo2`\ , :code:`wo3`\ , :code:`wx1`\ , :code:`wx2`\ , are :code:`p1`\ , :code:`p2`\ , and :code:`p3` (giving the x, y, and z coordinates
:code:`wx3`\ , :code:`wy1`\ , :code:`wy2`\ , :code:`wy3`\ , :code:`p1`\ , of the site position in the local coordinate system), and :code:`wo1`\ ,
:code:`p2`\ , and :code:`p3`\ . :code:`wx1`\ , :code:`wy1`\ , :code:`wo2`\ , :code:`wx2`\ , :code:`wy2`\ , ...
(giving the weights for computing the origin, x axis, and y axis).
<Patches> <Patches>
========= =========
......
docs-source/usersguide/theory.rst
View file @ 0827ad50
...@@ -1572,17 +1572,18 @@ specific types of rules. They are: ...@@ -1572,17 +1572,18 @@ specific types of rules. They are:
:math:`\mathbf{r}_{13} = \mathbf{r}_{3}-\mathbf{r}_{1}`\ . This allows :math:`\mathbf{r}_{13} = \mathbf{r}_{3}-\mathbf{r}_{1}`\ . This allows
the virtual site to be located outside the plane of the three particles. the virtual site to be located outside the plane of the three particles.
* LocalCoordinatesSite: The locations of three other particles are used to compute a local * LocalCoordinatesSite: The locations of several other particles are used to compute a local
coordinate system, and the virtual site is placed at a fixed location in that coordinate coordinate system, and the virtual site is placed at a fixed location in that coordinate
system. The origin of the coordinate system and the directions of its x and y axes system. The number of particles used to define the coordinate system is user defined.
are each specified as a weighted sum of the locations of the three particles: The origin of the coordinate system and the directions of its x and y axes
are each specified as a weighted sum of the locations of the other particles:
.. math:: .. math::
\mathbf{o}={w}^{o}_{1}\mathbf{r}_{1} + {w}^{o}_{2}\mathbf{r}_{2} + {w}^{o}_{3}\mathbf{r}_{3} \mathbf{o}={w}^{o}_{1}\mathbf{r}_{1} + {w}^{o}_{2}\mathbf{r}_{2} + ...
\mathbf{dx}={w}^{x}_{1}\mathbf{r}_{1} + {w}^{x}_{2}\mathbf{r}_{2} + {w}^{x}_{3}\mathbf{r}_{3} \mathbf{dx}={w}^{x}_{1}\mathbf{r}_{1} + {w}^{x}_{2}\mathbf{r}_{2} + ...
\mathbf{dy}={w}^{y}_{1}\mathbf{r}_{1} + {w}^{y}_{2}\mathbf{r}_{2} + {w}^{y}_{3}\mathbf{r}_{3} \mathbf{dy}={w}^{y}_{1}\mathbf{r}_{1} + {w}^{y}_{2}\mathbf{r}_{2} + ...
\mathbf{dz}=\mathbf{dx}\times \mathbf{dy} \mathbf{dz}=\mathbf{dx}\times \mathbf{dy}
.. ..
......
openmmapi/include/openmm/VirtualSite.h
View file @ 0827ad50
...@@ -9,7 +9,7 @@ ...@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2012-2014 Stanford University and the Authors. * * Portions copyright (c) 2012-2017 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -168,21 +168,21 @@ private: ...@@ -168,21 +168,21 @@ private:
}; };
/** /**
* This is a VirtualSite that uses the locations of three other particles to compute a local * This is a VirtualSite that uses the locations of several other particles to compute a local
* coordinate system, then places the virtual site at a fixed location in that coordinate * coordinate system, then places the virtual site at a fixed location in that coordinate
* system. The origin of the coordinate system and the directions of its x and y axes * system. The origin of the coordinate system and the directions of its x and y axes
* are each specified as a weighted sum of the locations of the three particles: * are each specified as a weighted sum of the locations of the other particles:
* *
* origin = w<sup>o</sup><sub>1</sub>r<sub>1</sub> + w<sup>o</sup><sub>2</sub>r<sub>2</sub> + w<sup>o</sup><sub>3</sub>r<sub>3</sub> * origin = w<sup>o</sup><sub>1</sub>r<sub>1</sub> + w<sup>o</sup><sub>2</sub>r<sub>2</sub> + w<sup>o</sup><sub>3</sub>r<sub>3</sub> + ...
* *
* xdir = w<sup>x</sup><sub>1</sub>r<sub>1</sub> + w<sup>x</sup><sub>2</sub>r<sub>2</sub> + w<sup>x</sup><sub>3</sub>r<sub>3</sub> * xdir = w<sup>x</sup><sub>1</sub>r<sub>1</sub> + w<sup>x</sup><sub>2</sub>r<sub>2</sub> + w<sup>x</sup><sub>3</sub>r<sub>3</sub> + ...
* *
* ydir = w<sup>y</sup><sub>1</sub>r<sub>1</sub> + w<sup>y</sup><sub>2</sub>r<sub>2</sub> + w<sup>y</sup><sub>3</sub>r<sub>3</sub> * ydir = w<sup>y</sup><sub>1</sub>r<sub>1</sub> + w<sup>y</sup><sub>2</sub>r<sub>2</sub> + w<sup>y</sup><sub>3</sub>r<sub>3</sub> + ...
* *
* For the origin, the three weights must add to one. For example if * For the origin, the weights must add to one. For example if
* (w<sup>o</sup><sub>1</sub>, w<sup>o</sup><sub>2</sub>, w<sup>o</sup><sub>3</sub>) = (1.0, 0.0, 0.0), * (w<sup>o</sup><sub>1</sub>, w<sup>o</sup><sub>2</sub>, w<sup>o</sup><sub>3</sub>) = (1.0, 0.0, 0.0),
* the origin of the local coordinate system is at the location of particle 1. For xdir and ydir, * the origin of the local coordinate system is at the location of particle 1. For xdir and ydir,
* the weights must add to zero. For excample, if * the weights must add to zero. For example, if
* (w<sup>x</sup><sub>1</sub>, w<sup>x</sup><sub>2</sub>, w<sup>x</sup><sub>3</sub>) = (-1.0, 0.5, 0.5), * (w<sup>x</sup><sub>1</sub>, w<sup>x</sup><sub>2</sub>, w<sup>x</sup><sub>3</sub>) = (-1.0, 0.5, 0.5),
* the x axis points from particle 1 toward the midpoint between particles 2 and 3. * the x axis points from particle 1 toward the midpoint between particles 2 and 3.
* *
...@@ -197,6 +197,17 @@ public: ...@@ -197,6 +197,17 @@ public:
/** /**
* Create a new LocalCoordinatesSite virtual site. * Create a new LocalCoordinatesSite virtual site.
* *
* @param particles the indices of the particle the site depends on
* @param originWeights the weight factors for the particles when computing the origin location
* @param xWeights the weight factors for the particles when computing xdir
* @param yWeights the weight factors for the particles when computing ydir
* @param localPosition the position of the virtual site in the local coordinate system
*/
LocalCoordinatesSite(const std::vector<int>& particles, const std::vector<double>& originWeights, const std::vector<double>& xWeights, const std::vector<double>& yWeights, const Vec3& localPosition);
/**
* Create a new LocalCoordinatesSite virtual site. This constructor assumes the site depends on
* exactly three other particles.
*
* @param particle1 the index of the first particle * @param particle1 the index of the first particle
* @param particle2 the index of the second particle * @param particle2 the index of the second particle
* @param particle3 the index of the third particle * @param particle3 the index of the third particle
...@@ -207,23 +218,42 @@ public: ...@@ -207,23 +218,42 @@ public:
*/ */
LocalCoordinatesSite(int particle1, int particle2, int particle3, const Vec3& originWeights, const Vec3& xWeights, const Vec3& yWeights, const Vec3& localPosition); LocalCoordinatesSite(int particle1, int particle2, int particle3, const Vec3& originWeights, const Vec3& xWeights, const Vec3& yWeights, const Vec3& localPosition);
/** /**
* Get the weight factors for the three particles when computing the origin location. * Get the weight factors for the particles when computing the origin location.
*/
void getOriginWeights(std::vector<double>& weights) const;
/**
* Get the weight factors for the particles when computing the origin location.
* This version assumes the site depends on exactly three other particles, and
* throws an exception if that is not the case.
*/
Vec3 getOriginWeights() const;
/**
* Get the weight factors for the particles when computing xdir.
*/
void getXWeights(std::vector<double>& weights) const;
/**
* Get the weight factors for the particles when computing xdir.
* This version assumes the site depends on exactly three other particles, and
* throws an exception if that is not the case.
*/ */
const Vec3& getOriginWeights() const; Vec3 getXWeights() const;
/** /**
* Get the weight factors for the three particles when computing xdir. * Get the weight factors for the particles when computing ydir.
*/ */
const Vec3& getXWeights() const; void getYWeights(std::vector<double>& weights) const;
/** /**
* Get the weight factors for the three particles when computing ydir. * Get the weight factors for the particles when computing ydir.
* This version assumes the site depends on exactly three other particles, and
* throws an exception if that is not the case.
*/ */
const Vec3& getYWeights() const; Vec3 getYWeights() const;
/** /**
* Get the position of the virtual site in the local coordinate system. * Get the position of the virtual site in the local coordinate system.
*/ */
const Vec3& getLocalPosition() const; const Vec3& getLocalPosition() const;
private: private:
Vec3 originWeights, xWeights, yWeights, localPosition; std::vector<double> originWeights, xWeights, yWeights;
Vec3 localPosition;
}; };
} // namespace OpenMM } // namespace OpenMM
......
openmmapi/src/VirtualSite.cpp
View file @ 0827ad50
...@@ -6,7 +6,7 @@ ...@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2012-2014 Stanford University and the Authors. * * Portions copyright (c) 2012-2017 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -105,8 +105,30 @@ double OutOfPlaneSite::getWeightCross() const { ...@@ -105,8 +105,30 @@ double OutOfPlaneSite::getWeightCross() const {
return weightCross; return weightCross;
} }
LocalCoordinatesSite::LocalCoordinatesSite(int particle1, int particle2, int particle3, const Vec3& originWeights, const Vec3& xWeights, const Vec3& yWeights, const Vec3& localPosition) : LocalCoordinatesSite::LocalCoordinatesSite(const vector<int>& particles, const vector<double>& originWeights, const vector<double>& xWeights, const vector<double>& yWeights, const Vec3& localPosition) :
originWeights(originWeights), xWeights(xWeights), yWeights(yWeights), localPosition(localPosition) { originWeights(originWeights), xWeights(xWeights), yWeights(yWeights), localPosition(localPosition) {
int numParticles = particles.size();
if (numParticles < 2)
throw OpenMMException("LocalCoordinatesSite: Must depend on at least two other particles");
if (originWeights.size() != numParticles || xWeights.size() != numParticles || yWeights.size() != numParticles)
throw OpenMMException("LocalCoordinatesSite: Number of weights does not match number of particles");
double originSum = 0, xSum = 0, ySum = 0;
for (int i = 0; i < numParticles; i++) {
originSum += originWeights[i];
xSum += xWeights[i];
ySum += yWeights[i];
}
if (fabs(originSum-1.0) > 1e-6)
throw OpenMMException("LocalCoordinatesSite: Weights for computing origin must add to 1");
if (fabs(xSum) > 1e-6)
throw OpenMMException("LocalCoordinatesSite: Weights for computing x axis must add to 0");
if (fabs(ySum) > 1e-6)
throw OpenMMException("LocalCoordinatesSite: Weights for computing y axis must add to 0");
setParticles(particles);
}
LocalCoordinatesSite::LocalCoordinatesSite(int particle1, int particle2, int particle3, const Vec3& originWeights, const Vec3& xWeights, const Vec3& yWeights, const Vec3& localPosition) :
localPosition(localPosition) {
if (fabs(originWeights[0]+originWeights[1]+originWeights[2]-1.0) > 1e-6) if (fabs(originWeights[0]+originWeights[1]+originWeights[2]-1.0) > 1e-6)
throw OpenMMException("LocalCoordinatesSite: Weights for computing origin must add to 1"); throw OpenMMException("LocalCoordinatesSite: Weights for computing origin must add to 1");
if (fabs(xWeights[0]+xWeights[1]+xWeights[2]) > 1e-6) if (fabs(xWeights[0]+xWeights[1]+xWeights[2]) > 1e-6)
...@@ -118,18 +140,45 @@ LocalCoordinatesSite::LocalCoordinatesSite(int particle1, int particle2, int par ...@@ -118,18 +140,45 @@ LocalCoordinatesSite::LocalCoordinatesSite(int particle1, int particle2, int par
particles[1] = particle2; particles[1] = particle2;
particles[2] = particle3; particles[2] = particle3;
setParticles(particles); setParticles(particles);
this->originWeights.push_back(originWeights[0]);
this->originWeights.push_back(originWeights[1]);
this->originWeights.push_back(originWeights[2]);
this->xWeights.push_back(xWeights[0]);
this->xWeights.push_back(xWeights[1]);
this->xWeights.push_back(xWeights[2]);
this->yWeights.push_back(yWeights[0]);
this->yWeights.push_back(yWeights[1]);
this->yWeights.push_back(yWeights[2]);
}
void LocalCoordinatesSite::getOriginWeights(vector<double>& weights) const {
weights = originWeights;
}
Vec3 LocalCoordinatesSite::getOriginWeights() const {
if (originWeights.size() != 3)
throw OpenMMException("LocalCoordinatesSite: This version of getOriginWeights() requires the site to depend on three particles");
return Vec3(originWeights[0], originWeights[1], originWeights[2]);
}
void LocalCoordinatesSite::getXWeights(vector<double>& weights) const {
weights = xWeights;
} }
const Vec3& LocalCoordinatesSite::getOriginWeights() const { Vec3 LocalCoordinatesSite::getXWeights() const {
return originWeights; if (xWeights.size() != 3)
throw OpenMMException("LocalCoordinatesSite: This version of getXWeights() requires the site to depend on three particles");
return Vec3(xWeights[0], xWeights[1], xWeights[2]);
} }
const Vec3& LocalCoordinatesSite::getXWeights() const { void LocalCoordinatesSite::getYWeights(vector<double>& weights) const {
return xWeights; weights = yWeights;
} }
const Vec3& LocalCoordinatesSite::getYWeights() const { Vec3 LocalCoordinatesSite::getYWeights() const {
return yWeights; if (yWeights.size() != 3)
throw OpenMMException("LocalCoordinatesSite: This version of getYWeights() requires the site to depend on three particles");
return Vec3(yWeights[0], yWeights[1], yWeights[2]);
} }
const Vec3& LocalCoordinatesSite::getLocalPosition() const { const Vec3& LocalCoordinatesSite::getLocalPosition() const {
......
platforms/cuda/include/CudaIntegrationUtilities.h
View file @ 0827ad50
...@@ -9,7 +9,7 @@ ...@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2009-2014 Stanford University and the Authors. * * Portions copyright (c) 2009-2017 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -158,8 +158,11 @@ private: ...@@ -158,8 +158,11 @@ private:
CudaArray* vsite3AvgWeights; CudaArray* vsite3AvgWeights;
CudaArray* vsiteOutOfPlaneAtoms; CudaArray* vsiteOutOfPlaneAtoms;
CudaArray* vsiteOutOfPlaneWeights; CudaArray* vsiteOutOfPlaneWeights;
CudaArray* vsiteLocalCoordsIndex;
CudaArray* vsiteLocalCoordsAtoms; CudaArray* vsiteLocalCoordsAtoms;
CudaArray* vsiteLocalCoordsParams; CudaArray* vsiteLocalCoordsWeights;
CudaArray* vsiteLocalCoordsPos;
CudaArray* vsiteLocalCoordsStartIndex;
int randomPos; int randomPos;
int lastSeed, numVsites; int lastSeed, numVsites;
double2 lastStepSize; double2 lastStepSize;
......
platforms/cuda/src/CudaIntegrationUtilities.cpp
View file @ 0827ad50
...@@ -6,7 +6,7 @@ ...@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2009-2015 Stanford University and the Authors. * * Portions copyright (c) 2009-2017 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -103,7 +103,8 @@ CudaIntegrationUtilities::CudaIntegrationUtilities(CudaContext& context, const S ...@@ -103,7 +103,8 @@ CudaIntegrationUtilities::CudaIntegrationUtilities(CudaContext& context, const S
ccmaReducedMass(NULL), ccmaAtomConstraints(NULL), ccmaNumAtomConstraints(NULL), ccmaConstraintMatrixColumn(NULL), ccmaReducedMass(NULL), ccmaAtomConstraints(NULL), ccmaNumAtomConstraints(NULL), ccmaConstraintMatrixColumn(NULL),
ccmaConstraintMatrixValue(NULL), ccmaDelta1(NULL), ccmaDelta2(NULL), ccmaConverged(NULL), ccmaConvergedMemory(NULL), ccmaConstraintMatrixValue(NULL), ccmaDelta1(NULL), ccmaDelta2(NULL), ccmaConverged(NULL), ccmaConvergedMemory(NULL),
vsite2AvgAtoms(NULL), vsite2AvgWeights(NULL), vsite3AvgAtoms(NULL), vsite3AvgWeights(NULL), vsite2AvgAtoms(NULL), vsite2AvgWeights(NULL), vsite3AvgAtoms(NULL), vsite3AvgWeights(NULL),
vsiteOutOfPlaneAtoms(NULL), vsiteOutOfPlaneWeights(NULL), vsiteLocalCoordsAtoms(NULL), vsiteLocalCoordsParams(NULL) { vsiteOutOfPlaneAtoms(NULL), vsiteOutOfPlaneWeights(NULL), vsiteLocalCoordsIndex(NULL), vsiteLocalCoordsAtoms(NULL),
vsiteLocalCoordsWeights(NULL), vsiteLocalCoordsPos(NULL), vsiteLocalCoordsStartIndex(NULL) {
// Create workspace arrays. // Create workspace arrays.
lastStepSize = make_double2(0.0, 0.0); lastStepSize = make_double2(0.0, 0.0);
...@@ -454,8 +455,11 @@ CudaIntegrationUtilities::CudaIntegrationUtilities(CudaContext& context, const S ...@@ -454,8 +455,11 @@ CudaIntegrationUtilities::CudaIntegrationUtilities(CudaContext& context, const S
vector<double4> vsite3AvgWeightVec; vector<double4> vsite3AvgWeightVec;
vector<int4> vsiteOutOfPlaneAtomVec; vector<int4> vsiteOutOfPlaneAtomVec;
vector<double4> vsiteOutOfPlaneWeightVec; vector<double4> vsiteOutOfPlaneWeightVec;
vector<int4> vsiteLocalCoordsAtomVec; vector<int> vsiteLocalCoordsIndexVec;
vector<double> vsiteLocalCoordsParamVec; vector<int> vsiteLocalCoordsAtomVec;
vector<int> vsiteLocalCoordsStartVec;
vector<double> vsiteLocalCoordsWeightVec;
vector<double4> vsiteLocalCoordsPosVec;
for (int i = 0; i < numAtoms; i++) { for (int i = 0; i < numAtoms; i++) {
if (system.isVirtualSite(i)) { if (system.isVirtualSite(i)) {
if (dynamic_cast<const TwoParticleAverageSite*>(&system.getVirtualSite(i)) != NULL) { if (dynamic_cast<const TwoParticleAverageSite*>(&system.getVirtualSite(i)) != NULL) {
...@@ -480,64 +484,72 @@ CudaIntegrationUtilities::CudaIntegrationUtilities(CudaContext& context, const S ...@@ -480,64 +484,72 @@ CudaIntegrationUtilities::CudaIntegrationUtilities(CudaContext& context, const S
vsiteOutOfPlaneWeightVec.push_back(make_double4(site.getWeight12(), site.getWeight13(), site.getWeightCross(), 0.0)); vsiteOutOfPlaneWeightVec.push_back(make_double4(site.getWeight12(), site.getWeight13(), site.getWeightCross(), 0.0));
} }
else if (dynamic_cast<const LocalCoordinatesSite*>(&system.getVirtualSite(i)) != NULL) { else if (dynamic_cast<const LocalCoordinatesSite*>(&system.getVirtualSite(i)) != NULL) {
// An out of plane site. // A local coordinates site.
const LocalCoordinatesSite& site = dynamic_cast<const LocalCoordinatesSite&>(system.getVirtualSite(i)); const LocalCoordinatesSite& site = dynamic_cast<const LocalCoordinatesSite&>(system.getVirtualSite(i));
vsiteLocalCoordsAtomVec.push_back(make_int4(i, site.getParticle(0), site.getParticle(1), site.getParticle(2))); int numParticles = site.getNumParticles();
Vec3 origin = site.getOriginWeights(); vector<double> origin, x, y;
Vec3 x = site.getXWeights(); site.getOriginWeights(origin);
Vec3 y = site.getYWeights(); site.getXWeights(x);
site.getYWeights(y);
vsiteLocalCoordsIndexVec.push_back(i);
vsiteLocalCoordsStartVec.push_back(vsiteLocalCoordsAtomVec.size());
for (int j = 0; j < numParticles; j++) {
vsiteLocalCoordsAtomVec.push_back(site.getParticle(j));
vsiteLocalCoordsWeightVec.push_back(origin[j]);
vsiteLocalCoordsWeightVec.push_back(x[j]);
vsiteLocalCoordsWeightVec.push_back(y[j]);
}
Vec3 pos = site.getLocalPosition(); Vec3 pos = site.getLocalPosition();
vsiteLocalCoordsParamVec.push_back(origin[0]); vsiteLocalCoordsPosVec.push_back(make_double4(pos[0], pos[1], pos[2], 0.0));
vsiteLocalCoordsParamVec.push_back(origin[1]);
vsiteLocalCoordsParamVec.push_back(origin[2]);
vsiteLocalCoordsParamVec.push_back(x[0]);
vsiteLocalCoordsParamVec.push_back(x[1]);
vsiteLocalCoordsParamVec.push_back(x[2]);
vsiteLocalCoordsParamVec.push_back(y[0]);
vsiteLocalCoordsParamVec.push_back(y[1]);
vsiteLocalCoordsParamVec.push_back(y[2]);
vsiteLocalCoordsParamVec.push_back(pos[0]);
vsiteLocalCoordsParamVec.push_back(pos[1]);
vsiteLocalCoordsParamVec.push_back(pos[2]);
} }
} }
} }
vsiteLocalCoordsStartVec.push_back(vsiteLocalCoordsAtomVec.size());
int num2Avg = vsite2AvgAtomVec.size(); int num2Avg = vsite2AvgAtomVec.size();
int num3Avg = vsite3AvgAtomVec.size(); int num3Avg = vsite3AvgAtomVec.size();
int numOutOfPlane = vsiteOutOfPlaneAtomVec.size(); int numOutOfPlane = vsiteOutOfPlaneAtomVec.size();
int numLocalCoords = vsiteLocalCoordsAtomVec.size(); int numLocalCoords = vsiteLocalCoordsPosVec.size();
vsite2AvgAtoms = CudaArray::create<int4>(context, max(1, num2Avg), "vsite2AvgAtoms"); vsite2AvgAtoms = CudaArray::create<int4>(context, max(1, num2Avg), "vsite2AvgAtoms");
vsite3AvgAtoms = CudaArray::create<int4>(context, max(1, num3Avg), "vsite3AvgAtoms"); vsite3AvgAtoms = CudaArray::create<int4>(context, max(1, num3Avg), "vsite3AvgAtoms");
vsiteOutOfPlaneAtoms = CudaArray::create<int4>(context, max(1, numOutOfPlane), "vsiteOutOfPlaneAtoms"); vsiteOutOfPlaneAtoms = CudaArray::create<int4>(context, max(1, numOutOfPlane), "vsiteOutOfPlaneAtoms");
vsiteLocalCoordsAtoms = CudaArray::create<int4>(context, max(1, numLocalCoords), "vsiteLocalCoordinatesAtoms"); vsiteLocalCoordsIndex = CudaArray::create<int>(context, max(1, (int) vsiteLocalCoordsIndexVec.size()), "vsiteLocalCoordsIndex");
vsiteLocalCoordsAtoms = CudaArray::create<int>(context, max(1, (int) vsiteLocalCoordsAtomVec.size()), "vsiteLocalCoordsAtoms");
vsiteLocalCoordsStartIndex = CudaArray::create<int>(context, max(1, (int) vsiteLocalCoordsStartVec.size()), "vsiteLocalCoordsStartIndex");
if (num2Avg > 0) if (num2Avg > 0)
vsite2AvgAtoms->upload(vsite2AvgAtomVec); vsite2AvgAtoms->upload(vsite2AvgAtomVec);
if (num3Avg > 0) if (num3Avg > 0)
vsite3AvgAtoms->upload(vsite3AvgAtomVec); vsite3AvgAtoms->upload(vsite3AvgAtomVec);
if (numOutOfPlane > 0) if (numOutOfPlane > 0)
vsiteOutOfPlaneAtoms->upload(vsiteOutOfPlaneAtomVec); vsiteOutOfPlaneAtoms->upload(vsiteOutOfPlaneAtomVec);
if (numLocalCoords > 0) if (numLocalCoords > 0) {
vsiteLocalCoordsIndex->upload(vsiteLocalCoordsIndexVec);
vsiteLocalCoordsAtoms->upload(vsiteLocalCoordsAtomVec); vsiteLocalCoordsAtoms->upload(vsiteLocalCoordsAtomVec);
vsiteLocalCoordsStartIndex->upload(vsiteLocalCoordsStartVec);
}
if (context.getUseDoublePrecision()) { if (context.getUseDoublePrecision()) {
vsite2AvgWeights = CudaArray::create<double2>(context, max(1, num2Avg), "vsite2AvgWeights"); vsite2AvgWeights = CudaArray::create<double2>(context, max(1, num2Avg), "vsite2AvgWeights");
vsite3AvgWeights = CudaArray::create<double4>(context, max(1, num3Avg), "vsite3AvgWeights"); vsite3AvgWeights = CudaArray::create<double4>(context, max(1, num3Avg), "vsite3AvgWeights");
vsiteOutOfPlaneWeights = CudaArray::create<double4>(context, max(1, numOutOfPlane), "vsiteOutOfPlaneWeights"); vsiteOutOfPlaneWeights = CudaArray::create<double4>(context, max(1, numOutOfPlane), "vsiteOutOfPlaneWeights");
vsiteLocalCoordsParams = CudaArray::create<double>(context, max(1, 12*numLocalCoords), "vsiteLocalCoordinatesParams"); vsiteLocalCoordsWeights = CudaArray::create<double>(context, max(1, (int) vsiteLocalCoordsWeightVec.size()), "vsiteLocalCoordsWeights");
vsiteLocalCoordsPos = CudaArray::create<double4>(context, max(1, (int) vsiteLocalCoordsPosVec.size()), "vsiteLocalCoordsPos");
if (num2Avg > 0) if (num2Avg > 0)
vsite2AvgWeights->upload(vsite2AvgWeightVec); vsite2AvgWeights->upload(vsite2AvgWeightVec);
if (num3Avg > 0) if (num3Avg > 0)
vsite3AvgWeights->upload(vsite3AvgWeightVec); vsite3AvgWeights->upload(vsite3AvgWeightVec);
if (numOutOfPlane > 0) if (numOutOfPlane > 0)
vsiteOutOfPlaneWeights->upload(vsiteOutOfPlaneWeightVec); vsiteOutOfPlaneWeights->upload(vsiteOutOfPlaneWeightVec);
if (numLocalCoords > 0) if (numLocalCoords > 0) {
vsiteLocalCoordsParams->upload(vsiteLocalCoordsParamVec); vsiteLocalCoordsWeights->upload(vsiteLocalCoordsWeightVec);
vsiteLocalCoordsPos->upload(vsiteLocalCoordsPosVec);
}
} }
else { else {
vsite2AvgWeights = CudaArray::create<float2>(context, max(1, num2Avg), "vsite2AvgWeights"); vsite2AvgWeights = CudaArray::create<float2>(context, max(1, num2Avg), "vsite2AvgWeights");
vsite3AvgWeights = CudaArray::create<float4>(context, max(1, num3Avg), "vsite3AvgWeights"); vsite3AvgWeights = CudaArray::create<float4>(context, max(1, num3Avg), "vsite3AvgWeights");
vsiteOutOfPlaneWeights = CudaArray::create<float4>(context, max(1, numOutOfPlane), "vsiteOutOfPlaneWeights"); vsiteOutOfPlaneWeights = CudaArray::create<float4>(context, max(1, numOutOfPlane), "vsiteOutOfPlaneWeights");
vsiteLocalCoordsParams = CudaArray::create<float>(context, max(1, 12*numLocalCoords), "vsiteLocalCoordinatesParams"); vsiteLocalCoordsWeights = CudaArray::create<float>(context, max(1, (int) vsiteLocalCoordsWeightVec.size()), "vsiteLocalCoordsWeights");
vsiteLocalCoordsPos = CudaArray::create<float4>(context, max(1, (int) vsiteLocalCoordsPosVec.size()), "vsiteLocalCoordsPos");
if (num2Avg > 0) { if (num2Avg > 0) {
vector<float2> floatWeights(num2Avg); vector<float2> floatWeights(num2Avg);
for (int i = 0; i < num2Avg; i++) for (int i = 0; i < num2Avg; i++)
...@@ -557,10 +569,14 @@ CudaIntegrationUtilities::CudaIntegrationUtilities(CudaContext& context, const S ...@@ -557,10 +569,14 @@ CudaIntegrationUtilities::CudaIntegrationUtilities(CudaContext& context, const S
vsiteOutOfPlaneWeights->upload(floatWeights); vsiteOutOfPlaneWeights->upload(floatWeights);
} }
if (numLocalCoords > 0) { if (numLocalCoords > 0) {
vector<float> floatParams(vsiteLocalCoordsParamVec.size()); vector<float> floatWeights(vsiteLocalCoordsWeightVec.size());
for (int i = 0; i < (int) vsiteLocalCoordsParamVec.size(); i++) for (int i = 0; i < (int) vsiteLocalCoordsWeightVec.size(); i++)
floatParams[i] = (float) vsiteLocalCoordsParamVec[i]; floatWeights[i] = (float) vsiteLocalCoordsWeightVec[i];
vsiteLocalCoordsParams->upload(floatParams); vsiteLocalCoordsWeights->upload(floatWeights);
vector<float4> floatPos(vsiteLocalCoordsPosVec.size());
for (int i = 0; i < (int) vsiteLocalCoordsPosVec.size(); i++)
floatPos[i] = make_float4((float) vsiteLocalCoordsPosVec[i].x, (float) vsiteLocalCoordsPosVec[i].y, (float) vsiteLocalCoordsPosVec[i].z, 0.0f);
vsiteLocalCoordsPos->upload(floatPos);
} }
} }
...@@ -644,10 +660,16 @@ CudaIntegrationUtilities::~CudaIntegrationUtilities() { ...@@ -644,10 +660,16 @@ CudaIntegrationUtilities::~CudaIntegrationUtilities() {
delete vsiteOutOfPlaneAtoms; delete vsiteOutOfPlaneAtoms;
if (vsiteOutOfPlaneWeights != NULL) if (vsiteOutOfPlaneWeights != NULL)
delete vsiteOutOfPlaneWeights; delete vsiteOutOfPlaneWeights;
if (vsiteLocalCoordsIndex != NULL)
delete vsiteLocalCoordsIndex;
if (vsiteLocalCoordsAtoms != NULL) if (vsiteLocalCoordsAtoms != NULL)
delete vsiteLocalCoordsAtoms; delete vsiteLocalCoordsAtoms;
if (vsiteLocalCoordsParams != NULL) if (vsiteLocalCoordsWeights != NULL)
delete vsiteLocalCoordsParams; delete vsiteLocalCoordsWeights;
if (vsiteLocalCoordsPos != NULL)
delete vsiteLocalCoordsPos;
if (vsiteLocalCoordsStartIndex != NULL)
delete vsiteLocalCoordsStartIndex;
} }
void CudaIntegrationUtilities::setNextStepSize(double size) { void CudaIntegrationUtilities::setNextStepSize(double size) {
...@@ -747,7 +769,9 @@ void CudaIntegrationUtilities::computeVirtualSites() { ...@@ -747,7 +769,9 @@ void CudaIntegrationUtilities::computeVirtualSites() {
void* args[] = {&context.getPosq().getDevicePointer(), &posCorrection, &vsite2AvgAtoms->getDevicePointer(), &vsite2AvgWeights->getDevicePointer(), void* args[] = {&context.getPosq().getDevicePointer(), &posCorrection, &vsite2AvgAtoms->getDevicePointer(), &vsite2AvgWeights->getDevicePointer(),
&vsite3AvgAtoms->getDevicePointer(), &vsite3AvgWeights->getDevicePointer(), &vsite3AvgAtoms->getDevicePointer(), &vsite3AvgWeights->getDevicePointer(),
&vsiteOutOfPlaneAtoms->getDevicePointer(), &vsiteOutOfPlaneWeights->getDevicePointer(), &vsiteOutOfPlaneAtoms->getDevicePointer(), &vsiteOutOfPlaneWeights->getDevicePointer(),
&vsiteLocalCoordsAtoms->getDevicePointer(), &vsiteLocalCoordsParams->getDevicePointer()}; &vsiteLocalCoordsIndex->getDevicePointer(), &vsiteLocalCoordsAtoms->getDevicePointer(),
&vsiteLocalCoordsWeights->getDevicePointer(), &vsiteLocalCoordsPos->getDevicePointer(),
&vsiteLocalCoordsStartIndex->getDevicePointer()};
context.executeKernel(vsitePositionKernel, args, numVsites); context.executeKernel(vsitePositionKernel, args, numVsites);
} }
} }
...@@ -759,7 +783,9 @@ void CudaIntegrationUtilities::distributeForcesFromVirtualSites() { ...@@ -759,7 +783,9 @@ void CudaIntegrationUtilities::distributeForcesFromVirtualSites() {
&vsite2AvgAtoms->getDevicePointer(), &vsite2AvgWeights->getDevicePointer(), &vsite2AvgAtoms->getDevicePointer(), &vsite2AvgWeights->getDevicePointer(),
&vsite3AvgAtoms->getDevicePointer(), &vsite3AvgWeights->getDevicePointer(), &vsite3AvgAtoms->getDevicePointer(), &vsite3AvgWeights->getDevicePointer(),
&vsiteOutOfPlaneAtoms->getDevicePointer(), &vsiteOutOfPlaneWeights->getDevicePointer(), &vsiteOutOfPlaneAtoms->getDevicePointer(), &vsiteOutOfPlaneWeights->getDevicePointer(),
&vsiteLocalCoordsAtoms->getDevicePointer(), &vsiteLocalCoordsParams->getDevicePointer()}; &vsiteLocalCoordsIndex->getDevicePointer(), &vsiteLocalCoordsAtoms->getDevicePointer(),
&vsiteLocalCoordsWeights->getDevicePointer(), &vsiteLocalCoordsPos->getDevicePointer(),
&vsiteLocalCoordsStartIndex->getDevicePointer()};
context.executeKernel(vsiteForceKernel, args, numVsites); context.executeKernel(vsiteForceKernel, args, numVsites);
} }
} }
......
platforms/cuda/src/kernels/integrationUtilities.cu
View file @ 0827ad50
...@@ -680,7 +680,9 @@ extern "C" __global__ void updateCCMAAtomPositions(const int* __restrict__ numAt ...@@ -680,7 +680,9 @@ extern "C" __global__ void updateCCMAAtomPositions(const int* __restrict__ numAt
extern "C" __global__ void computeVirtualSites(real4* __restrict__ posq, real4* __restrict__ posqCorrection, const int4* __restrict__ avg2Atoms, const real2* __restrict__ avg2Weights, extern "C" __global__ void computeVirtualSites(real4* __restrict__ posq, real4* __restrict__ posqCorrection, const int4* __restrict__ avg2Atoms, const real2* __restrict__ avg2Weights,
const int4* __restrict__ avg3Atoms, const real4* __restrict__ avg3Weights, const int4* __restrict__ avg3Atoms, const real4* __restrict__ avg3Weights,
const int4* __restrict__ outOfPlaneAtoms, const real4* __restrict__ outOfPlaneWeights, const int4* __restrict__ outOfPlaneAtoms, const real4* __restrict__ outOfPlaneWeights,
const int4* __restrict__ localCoordsAtoms, const real* __restrict__ localCoordsParams) { const int* __restrict__ localCoordsIndex, const int* __restrict__ localCoordsAtoms,
const real* __restrict__ localCoordsWeights, const real4* __restrict__ localCoordsPos,
const int* __restrict__ localCoordsStartIndex) {
// Two particle average sites. // Two particle average sites.
...@@ -732,30 +734,31 @@ extern "C" __global__ void computeVirtualSites(real4* __restrict__ posq, real4* ...@@ -732,30 +734,31 @@ extern "C" __global__ void computeVirtualSites(real4* __restrict__ posq, real4*
// Local coordinates sites. // Local coordinates sites.
for (int index = blockIdx.x*blockDim.x+threadIdx.x; index < NUM_LOCAL_COORDS; index += blockDim.x*gridDim.x) { for (int index = blockIdx.x*blockDim.x+threadIdx.x; index < NUM_LOCAL_COORDS; index += blockDim.x*gridDim.x) {
int4 atoms = localCoordsAtoms[index]; int siteAtomIndex = localCoordsIndex[index];
const real* params = &localCoordsParams[12*index]; int start = localCoordsStartIndex[index];
mixed4 pos = loadPos(posq, posqCorrection, atoms.x); int end = localCoordsStartIndex[index+1];
mixed4 pos1_4 = loadPos(posq, posqCorrection, atoms.y); mixed3 origin = make_mixed3(0), xdir = make_mixed3(0), ydir = make_mixed3(0);
mixed4 pos2_4 = loadPos(posq, posqCorrection, atoms.z); for (int j = start; j < end; j++) {
mixed4 pos3_4 = loadPos(posq, posqCorrection, atoms.w); mixed3 pos = trimTo3(loadPos(posq, posqCorrection, localCoordsAtoms[j]));
mixed3 pos1 = make_mixed3(pos1_4.x, pos1_4.y, pos1_4.z); origin += pos*localCoordsWeights[3*j];
mixed3 pos2 = make_mixed3(pos2_4.x, pos2_4.y, pos2_4.z); xdir += pos*localCoordsWeights[3*j+1];
mixed3 pos3 = make_mixed3(pos3_4.x, pos3_4.y, pos3_4.z); ydir += pos*localCoordsWeights[3*j+2];
mixed3 originWeights = make_mixed3(params[0], params[1], params[2]); }
mixed3 xWeights = make_mixed3(params[3], params[4], params[5]);
mixed3 yWeights = make_mixed3(params[6], params[7], params[8]);
mixed3 localPosition = make_mixed3(params[9], params[10], params[11]);
mixed3 origin = pos1*originWeights.x + pos2*originWeights.y + pos3*originWeights.z;
mixed3 xdir = pos1*xWeights.x + pos2*xWeights.y + pos3*xWeights.z;
mixed3 ydir = pos1*yWeights.x + pos2*yWeights.y + pos3*yWeights.z;
mixed3 zdir = cross(xdir, ydir); mixed3 zdir = cross(xdir, ydir);
xdir *= rsqrt(xdir.x*xdir.x+xdir.y*xdir.y+xdir.z*xdir.z); mixed normXdir = sqrt(xdir.x*xdir.x+xdir.y*xdir.y+xdir.z*xdir.z);
zdir *= rsqrt(zdir.x*zdir.x+zdir.y*zdir.y+zdir.z*zdir.z); mixed normZdir = sqrt(zdir.x*zdir.x+zdir.y*zdir.y+zdir.z*zdir.z);
mixed invNormXdir = (normXdir > 0 ? 1/normXdir : 0);
mixed invNormZdir = (normZdir > 0 ? 1/normZdir : 0);
xdir *= invNormXdir;
zdir *= invNormZdir;
ydir = cross(zdir, xdir); ydir = cross(zdir, xdir);
real4 localPosition_4 = localCoordsPos[index];
mixed3 localPosition = make_mixed3(localPosition_4.x, localPosition_4.y, localPosition_4.z);
mixed4 pos = loadPos(posq, posqCorrection, siteAtomIndex);
pos.x = origin.x + xdir.x*localPosition.x + ydir.x*localPosition.y + zdir.x*localPosition.z; pos.x = origin.x + xdir.x*localPosition.x + ydir.x*localPosition.y + zdir.x*localPosition.z;
pos.y = origin.y + xdir.y*localPosition.x + ydir.y*localPosition.y + zdir.y*localPosition.z; pos.y = origin.y + xdir.y*localPosition.x + ydir.y*localPosition.y + zdir.y*localPosition.z;
pos.z = origin.z + xdir.z*localPosition.x + ydir.z*localPosition.y + zdir.z*localPosition.z; pos.z = origin.z + xdir.z*localPosition.x + ydir.z*localPosition.y + zdir.z*localPosition.z;
storePos(posq, posqCorrection, atoms.x, pos); storePos(posq, posqCorrection, siteAtomIndex, pos);
} }
} }
...@@ -778,7 +781,9 @@ extern "C" __global__ void distributeVirtualSiteForces(const real4* __restrict__ ...@@ -778,7 +781,9 @@ extern "C" __global__ void distributeVirtualSiteForces(const real4* __restrict__
const int4* __restrict__ avg2Atoms, const real2* __restrict__ avg2Weights, const int4* __restrict__ avg2Atoms, const real2* __restrict__ avg2Weights,
const int4* __restrict__ avg3Atoms, const real4* __restrict__ avg3Weights, const int4* __restrict__ avg3Atoms, const real4* __restrict__ avg3Weights,
const int4* __restrict__ outOfPlaneAtoms, const real4* __restrict__ outOfPlaneWeights, const int4* __restrict__ outOfPlaneAtoms, const real4* __restrict__ outOfPlaneWeights,
const int4* __restrict__ localCoordsAtoms, const real* __restrict__ localCoordsParams) { const int* __restrict__ localCoordsIndex, const int* __restrict__ localCoordsAtoms,
const real* __restrict__ localCoordsWeights, const real4* __restrict__ localCoordsPos,
const int* __restrict__ localCoordsStartIndex) {
// Two particle average sites. // Two particle average sites.
...@@ -826,87 +831,56 @@ extern "C" __global__ void distributeVirtualSiteForces(const real4* __restrict__ ...@@ -826,87 +831,56 @@ extern "C" __global__ void distributeVirtualSiteForces(const real4* __restrict__
// Local coordinates sites. // Local coordinates sites.
for (int index = blockIdx.x*blockDim.x+threadIdx.x; index < NUM_LOCAL_COORDS; index += blockDim.x*gridDim.x) { for (int index = blockIdx.x*blockDim.x+threadIdx.x; index < NUM_LOCAL_COORDS; index += blockDim.x*gridDim.x) {
int4 atoms = localCoordsAtoms[index]; int siteAtomIndex = localCoordsIndex[index];
const real* params = &localCoordsParams[12*index]; int start = localCoordsStartIndex[index];
mixed4 pos = loadPos(posq, posqCorrection, atoms.x); int end = localCoordsStartIndex[index+1];
mixed4 pos1_4 = loadPos(posq, posqCorrection, atoms.y); mixed3 origin = make_mixed3(0), xdir = make_mixed3(0), ydir = make_mixed3(0);
mixed4 pos2_4 = loadPos(posq, posqCorrection, atoms.z); for (int j = start; j < end; j++) {
mixed4 pos3_4 = loadPos(posq, posqCorrection, atoms.w); mixed3 pos = trimTo3(loadPos(posq, posqCorrection, localCoordsAtoms[j]));
mixed3 pos1 = make_mixed3(pos1_4.x, pos1_4.y, pos1_4.z); origin += pos*localCoordsWeights[3*j];
mixed3 pos2 = make_mixed3(pos2_4.x, pos2_4.y, pos2_4.z); xdir += pos*localCoordsWeights[3*j+1];
mixed3 pos3 = make_mixed3(pos3_4.x, pos3_4.y, pos3_4.z); ydir += pos*localCoordsWeights[3*j+2];
mixed3 originWeights = make_mixed3(params[0], params[1], params[2]); }
mixed3 wx = make_mixed3(params[3], params[4], params[5]);
mixed3 wy = make_mixed3(params[6], params[7], params[8]);
mixed3 localPosition = make_mixed3(params[9], params[10], params[11]);
mixed3 origin = pos1*originWeights.x + pos2*originWeights.y + pos3*originWeights.z;
mixed3 xdir = pos1*wx.x + pos2*wx.y + pos3*wx.z;
mixed3 ydir = pos1*wy.x + pos2*wy.y + pos3*wy.z;
mixed3 zdir = cross(xdir, ydir); mixed3 zdir = cross(xdir, ydir);
mixed invNormXdir = rsqrt(xdir.x*xdir.x+xdir.y*xdir.y+xdir.z*xdir.z); mixed normXdir = sqrt(xdir.x*xdir.x+xdir.y*xdir.y+xdir.z*xdir.z);
mixed invNormZdir = rsqrt(zdir.x*zdir.x+zdir.y*zdir.y+zdir.z*zdir.z); mixed normZdir = sqrt(zdir.x*zdir.x+zdir.y*zdir.y+zdir.z*zdir.z);
mixed invNormXdir = (normXdir > 0 ? 1/normXdir : 0);
mixed invNormZdir = (normZdir > 0 ? 1/normZdir : 0);
mixed3 dx = xdir*invNormXdir; mixed3 dx = xdir*invNormXdir;
mixed3 dz = zdir*invNormZdir; mixed3 dz = zdir*invNormZdir;
mixed3 dy = cross(dz, dx); mixed3 dy = cross(dz, dx);
real4 localPosition_4 = localCoordsPos[index];
mixed3 localPosition = make_mixed3(localPosition_4.x, localPosition_4.y, localPosition_4.z);
// The derivatives for this case are very complicated. They were computed with SymPy then simplified by hand. // The derivatives for this case are very complicated. They were computed with SymPy then simplified by hand.
mixed t11 = (wx.x*ydir.x-wy.x*xdir.x)*invNormZdir; real3 f = loadForce(siteAtomIndex, force);
mixed t12 = (wx.x*ydir.y-wy.x*xdir.y)*invNormZdir;
mixed t13 = (wx.x*ydir.z-wy.x*xdir.z)*invNormZdir;
mixed t21 = (wx.y*ydir.x-wy.y*xdir.x)*invNormZdir;
mixed t22 = (wx.y*ydir.y-wy.y*xdir.y)*invNormZdir;
mixed t23 = (wx.y*ydir.z-wy.y*xdir.z)*invNormZdir;
mixed t31 = (wx.z*ydir.x-wy.z*xdir.x)*invNormZdir;
mixed t32 = (wx.z*ydir.y-wy.z*xdir.y)*invNormZdir;
mixed t33 = (wx.z*ydir.z-wy.z*xdir.z)*invNormZdir;
mixed sx1 = t13*dz.y-t12*dz.z;
mixed sy1 = t11*dz.z-t13*dz.x;
mixed sz1 = t12*dz.x-t11*dz.y;
mixed sx2 = t23*dz.y-t22*dz.z;
mixed sy2 = t21*dz.z-t23*dz.x;
mixed sz2 = t22*dz.x-t21*dz.y;
mixed sx3 = t33*dz.y-t32*dz.z;
mixed sy3 = t31*dz.z-t33*dz.x;
mixed sz3 = t32*dz.x-t31*dz.y;
mixed3 wxScaled = wx*invNormXdir;
real3 f = loadForce(atoms.x, force);
mixed3 fp1 = localPosition*f.x; mixed3 fp1 = localPosition*f.x;
mixed3 fp2 = localPosition*f.y; mixed3 fp2 = localPosition*f.y;
mixed3 fp3 = localPosition*f.z; mixed3 fp3 = localPosition*f.z;
real3 f1 = make_real3(0); for (int j = start; j < end; j++) {
real3 f2 = make_real3(0); real originWeight = localCoordsWeights[3*j];
real3 f3 = make_real3(0); real wx = localCoordsWeights[3*j+1];
f1.x += fp1.x*wxScaled.x*(1-dx.x*dx.x) + fp1.z*(dz.x*sx1 ) + fp1.y*((-dx.x*dy.x )*wxScaled.x + dy.x*sx1 - dx.y*t12 - dx.z*t13) + f.x*originWeights.x; real wy = localCoordsWeights[3*j+2];
f1.y += fp1.x*wxScaled.x*( -dx.x*dx.y) + fp1.z*(dz.x*sy1+t13) + fp1.y*((-dx.y*dy.x-dz.z)*wxScaled.x + dy.x*sy1 + dx.y*t11); mixed wxScaled = wx*invNormXdir;
f1.z += fp1.x*wxScaled.x*( -dx.x*dx.z) + fp1.z*(dz.x*sz1-t12) + fp1.y*((-dx.z*dy.x+dz.y)*wxScaled.x + dy.x*sz1 + dx.z*t11); mixed t1 = (wx*ydir.x-wy*xdir.x)*invNormZdir;
f2.x += fp1.x*wxScaled.y*(1-dx.x*dx.x) + fp1.z*(dz.x*sx2 ) + fp1.y*((-dx.x*dy.x )*wxScaled.y + dy.x*sx2 - dx.y*t22 - dx.z*t23) + f.x*originWeights.y; mixed t2 = (wx*ydir.y-wy*xdir.y)*invNormZdir;
f2.y += fp1.x*wxScaled.y*( -dx.x*dx.y) + fp1.z*(dz.x*sy2+t23) + fp1.y*((-dx.y*dy.x-dz.z)*wxScaled.y + dy.x*sy2 + dx.y*t21); mixed t3 = (wx*ydir.z-wy*xdir.z)*invNormZdir;
f2.z += fp1.x*wxScaled.y*( -dx.x*dx.z) + fp1.z*(dz.x*sz2-t22) + fp1.y*((-dx.z*dy.x+dz.y)*wxScaled.y + dy.x*sz2 + dx.z*t21); mixed sx = t3*dz.y-t2*dz.z;
f3.x += fp1.x*wxScaled.z*(1-dx.x*dx.x) + fp1.z*(dz.x*sx3 ) + fp1.y*((-dx.x*dy.x )*wxScaled.z + dy.x*sx3 - dx.y*t32 - dx.z*t33) + f.x*originWeights.z; mixed sy = t1*dz.z-t3*dz.x;
f3.y += fp1.x*wxScaled.z*( -dx.x*dx.y) + fp1.z*(dz.x*sy3+t33) + fp1.y*((-dx.y*dy.x-dz.z)*wxScaled.z + dy.x*sy3 + dx.y*t31); mixed sz = t2*dz.x-t1*dz.y;
f3.z += fp1.x*wxScaled.z*( -dx.x*dx.z) + fp1.z*(dz.x*sz3-t32) + fp1.y*((-dx.z*dy.x+dz.y)*wxScaled.z + dy.x*sz3 + dx.z*t31); real3 fresult = make_real3(0);
f1.x += fp2.x*wxScaled.x*( -dx.y*dx.x) + fp2.z*(dz.y*sx1-t13) - fp2.y*(( dx.x*dy.y-dz.z)*wxScaled.x - dy.y*sx1 - dx.x*t12); fresult.x += fp1.x*wxScaled*(1-dx.x*dx.x) + fp1.z*(dz.x*sx ) + fp1.y*((-dx.x*dy.x )*wxScaled + dy.x*sx - dx.y*t2 - dx.z*t3) + f.x*originWeight;
f1.y += fp2.x*wxScaled.x*(1-dx.y*dx.y) + fp2.z*(dz.y*sy1 ) - fp2.y*(( dx.y*dy.y )*wxScaled.x - dy.y*sy1 + dx.x*t11 + dx.z*t13) + f.y*originWeights.x; fresult.y += fp1.x*wxScaled*( -dx.x*dx.y) + fp1.z*(dz.x*sy+t3) + fp1.y*((-dx.y*dy.x-dz.z)*wxScaled + dy.x*sy + dx.y*t1);
f1.z += fp2.x*wxScaled.x*( -dx.y*dx.z) + fp2.z*(dz.y*sz1+t11) - fp2.y*(( dx.z*dy.y+dz.x)*wxScaled.x - dy.y*sz1 - dx.z*t12); fresult.z += fp1.x*wxScaled*( -dx.x*dx.z) + fp1.z*(dz.x*sz-t2) + fp1.y*((-dx.z*dy.x+dz.y)*wxScaled + dy.x*sz + dx.z*t1);
f2.x += fp2.x*wxScaled.y*( -dx.y*dx.x) + fp2.z*(dz.y*sx2-t23) - fp2.y*(( dx.x*dy.y-dz.z)*wxScaled.y - dy.y*sx2 - dx.x*t22); fresult.x += fp2.x*wxScaled*( -dx.y*dx.x) + fp2.z*(dz.y*sx-t3) - fp2.y*(( dx.x*dy.y-dz.z)*wxScaled - dy.y*sx - dx.x*t2);
f2.y += fp2.x*wxScaled.y*(1-dx.y*dx.y) + fp2.z*(dz.y*sy2 ) - fp2.y*(( dx.y*dy.y )*wxScaled.y - dy.y*sy2 + dx.x*t21 + dx.z*t23) + f.y*originWeights.y; fresult.y += fp2.x*wxScaled*(1-dx.y*dx.y) + fp2.z*(dz.y*sy ) - fp2.y*(( dx.y*dy.y )*wxScaled - dy.y*sy + dx.x*t1 + dx.z*t3) + f.y*originWeight;
f2.z += fp2.x*wxScaled.y*( -dx.y*dx.z) + fp2.z*(dz.y*sz2+t21) - fp2.y*(( dx.z*dy.y+dz.x)*wxScaled.y - dy.y*sz2 - dx.z*t22); fresult.z += fp2.x*wxScaled*( -dx.y*dx.z) + fp2.z*(dz.y*sz+t1) - fp2.y*(( dx.z*dy.y+dz.x)*wxScaled - dy.y*sz - dx.z*t2);
f3.x += fp2.x*wxScaled.z*( -dx.y*dx.x) + fp2.z*(dz.y*sx3-t33) - fp2.y*(( dx.x*dy.y-dz.z)*wxScaled.z - dy.y*sx3 - dx.x*t32); fresult.x += fp3.x*wxScaled*( -dx.z*dx.x) + fp3.z*(dz.z*sx+t2) + fp3.y*((-dx.x*dy.z-dz.y)*wxScaled + dy.z*sx + dx.x*t3);
f3.y += fp2.x*wxScaled.z*(1-dx.y*dx.y) + fp2.z*(dz.y*sy3 ) - fp2.y*(( dx.y*dy.y )*wxScaled.z - dy.y*sy3 + dx.x*t31 + dx.z*t33) + f.y*originWeights.z; fresult.y += fp3.x*wxScaled*( -dx.z*dx.y) + fp3.z*(dz.z*sy-t1) + fp3.y*((-dx.y*dy.z+dz.x)*wxScaled + dy.z*sy + dx.y*t3);
f3.z += fp2.x*wxScaled.z*( -dx.y*dx.z) + fp2.z*(dz.y*sz3+t31) - fp2.y*(( dx.z*dy.y+dz.x)*wxScaled.z - dy.y*sz3 - dx.z*t32); fresult.z += fp3.x*wxScaled*(1-dx.z*dx.z) + fp3.z*(dz.z*sz ) + fp3.y*((-dx.z*dy.z )*wxScaled + dy.z*sz - dx.x*t1 - dx.y*t2) + f.z*originWeight;
f1.x += fp3.x*wxScaled.x*( -dx.z*dx.x) + fp3.z*(dz.z*sx1+t12) + fp3.y*((-dx.x*dy.z-dz.y)*wxScaled.x + dy.z*sx1 + dx.x*t13); addForce(localCoordsAtoms[j], force, fresult);
f1.y += fp3.x*wxScaled.x*( -dx.z*dx.y) + fp3.z*(dz.z*sy1-t11) + fp3.y*((-dx.y*dy.z+dz.x)*wxScaled.x + dy.z*sy1 + dx.y*t13); }
f1.z += fp3.x*wxScaled.x*(1-dx.z*dx.z) + fp3.z*(dz.z*sz1 ) + fp3.y*((-dx.z*dy.z )*wxScaled.x + dy.z*sz1 - dx.x*t11 - dx.y*t12) + f.z*originWeights.x;
f2.x += fp3.x*wxScaled.y*( -dx.z*dx.x) + fp3.z*(dz.z*sx2+t22) + fp3.y*((-dx.x*dy.z-dz.y)*wxScaled.y + dy.z*sx2 + dx.x*t23);
f2.y += fp3.x*wxScaled.y*( -dx.z*dx.y) + fp3.z*(dz.z*sy2-t21) + fp3.y*((-dx.y*dy.z+dz.x)*wxScaled.y + dy.z*sy2 + dx.y*t23);
f2.z += fp3.x*wxScaled.y*(1-dx.z*dx.z) + fp3.z*(dz.z*sz2 ) + fp3.y*((-dx.z*dy.z )*wxScaled.y + dy.z*sz2 - dx.x*t21 - dx.y*t22) + f.z*originWeights.y;
f3.x += fp3.x*wxScaled.z*( -dx.z*dx.x) + fp3.z*(dz.z*sx3+t32) + fp3.y*((-dx.x*dy.z-dz.y)*wxScaled.z + dy.z*sx3 + dx.x*t33);
f3.y += fp3.x*wxScaled.z*( -dx.z*dx.y) + fp3.z*(dz.z*sy3-t31) + fp3.y*((-dx.y*dy.z+dz.x)*wxScaled.z + dy.z*sy3 + dx.y*t33);
f3.z += fp3.x*wxScaled.z*(1-dx.z*dx.z) + fp3.z*(dz.z*sz3 ) + fp3.y*((-dx.z*dy.z )*wxScaled.z + dy.z*sz3 - dx.x*t31 - dx.y*t32) + f.z*originWeights.z;
addForce(atoms.y, force, f1);
addForce(atoms.z, force, f2);
addForce(atoms.w, force, f3);
} }
} }
......
platforms/opencl/include/OpenCLIntegrationUtilities.h
View file @ 0827ad50
...@@ -9,7 +9,7 @@ ...@@ -9,7 +9,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2009-2014 Stanford University and the Authors. * * Portions copyright (c) 2009-2017 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -156,8 +156,11 @@ private: ...@@ -156,8 +156,11 @@ private:
OpenCLArray* vsite3AvgWeights; OpenCLArray* vsite3AvgWeights;
OpenCLArray* vsiteOutOfPlaneAtoms; OpenCLArray* vsiteOutOfPlaneAtoms;
OpenCLArray* vsiteOutOfPlaneWeights; OpenCLArray* vsiteOutOfPlaneWeights;
OpenCLArray* vsiteLocalCoordsIndex;
OpenCLArray* vsiteLocalCoordsAtoms; OpenCLArray* vsiteLocalCoordsAtoms;
OpenCLArray* vsiteLocalCoordsParams; OpenCLArray* vsiteLocalCoordsWeights;
OpenCLArray* vsiteLocalCoordsPos;
OpenCLArray* vsiteLocalCoordsStartIndex;
int randomPos; int randomPos;
int lastSeed, numVsites; int lastSeed, numVsites;
bool hasInitializedPosConstraintKernels, hasInitializedVelConstraintKernels, ccmaUseDirectBuffer, hasOverlappingVsites; bool hasInitializedPosConstraintKernels, hasInitializedVelConstraintKernels, ccmaUseDirectBuffer, hasOverlappingVsites;
......
platforms/opencl/src/OpenCLIntegrationUtilities.cpp
View file @ 0827ad50
...@@ -6,7 +6,7 @@ ...@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2009-2015 Stanford University and the Authors. * * Portions copyright (c) 2009-2017 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -102,7 +102,8 @@ OpenCLIntegrationUtilities::OpenCLIntegrationUtilities(OpenCLContext& context, c ...@@ -102,7 +102,8 @@ OpenCLIntegrationUtilities::OpenCLIntegrationUtilities(OpenCLContext& context, c
ccmaReducedMass(NULL), ccmaAtomConstraints(NULL), ccmaNumAtomConstraints(NULL), ccmaConstraintMatrixColumn(NULL), ccmaReducedMass(NULL), ccmaAtomConstraints(NULL), ccmaNumAtomConstraints(NULL), ccmaConstraintMatrixColumn(NULL),
ccmaConstraintMatrixValue(NULL), ccmaDelta1(NULL), ccmaDelta2(NULL), ccmaConverged(NULL), ccmaConvergedHostBuffer(NULL), ccmaConstraintMatrixValue(NULL), ccmaDelta1(NULL), ccmaDelta2(NULL), ccmaConverged(NULL), ccmaConvergedHostBuffer(NULL),
vsite2AvgAtoms(NULL), vsite2AvgWeights(NULL), vsite3AvgAtoms(NULL), vsite3AvgWeights(NULL), vsite2AvgAtoms(NULL), vsite2AvgWeights(NULL), vsite3AvgAtoms(NULL), vsite3AvgWeights(NULL),
vsiteOutOfPlaneAtoms(NULL), vsiteOutOfPlaneWeights(NULL), vsiteLocalCoordsAtoms(NULL), vsiteLocalCoordsParams(NULL), vsiteOutOfPlaneAtoms(NULL), vsiteOutOfPlaneWeights(NULL), vsiteLocalCoordsIndex(NULL), vsiteLocalCoordsAtoms(NULL),
vsiteLocalCoordsWeights(NULL), vsiteLocalCoordsPos(NULL), vsiteLocalCoordsStartIndex(NULL),
hasInitializedPosConstraintKernels(false), hasInitializedVelConstraintKernels(false), hasOverlappingVsites(false) { hasInitializedPosConstraintKernels(false), hasInitializedVelConstraintKernels(false), hasOverlappingVsites(false) {
// Create workspace arrays. // Create workspace arrays.
...@@ -497,8 +498,11 @@ OpenCLIntegrationUtilities::OpenCLIntegrationUtilities(OpenCLContext& context, c ...@@ -497,8 +498,11 @@ OpenCLIntegrationUtilities::OpenCLIntegrationUtilities(OpenCLContext& context, c
vector<mm_double4> vsite3AvgWeightVec; vector<mm_double4> vsite3AvgWeightVec;
vector<mm_int4> vsiteOutOfPlaneAtomVec; vector<mm_int4> vsiteOutOfPlaneAtomVec;
vector<mm_double4> vsiteOutOfPlaneWeightVec; vector<mm_double4> vsiteOutOfPlaneWeightVec;
vector<mm_int4> vsiteLocalCoordsAtomVec; vector<cl_int> vsiteLocalCoordsIndexVec;
vector<cl_double> vsiteLocalCoordsParamVec; vector<cl_int> vsiteLocalCoordsAtomVec;
vector<cl_int> vsiteLocalCoordsStartVec;
vector<cl_double> vsiteLocalCoordsWeightVec;
vector<mm_double4> vsiteLocalCoordsPosVec;
for (int i = 0; i < numAtoms; i++) { for (int i = 0; i < numAtoms; i++) {
if (system.isVirtualSite(i)) { if (system.isVirtualSite(i)) {
if (dynamic_cast<const TwoParticleAverageSite*>(&system.getVirtualSite(i)) != NULL) { if (dynamic_cast<const TwoParticleAverageSite*>(&system.getVirtualSite(i)) != NULL) {
...@@ -523,65 +527,73 @@ OpenCLIntegrationUtilities::OpenCLIntegrationUtilities(OpenCLContext& context, c ...@@ -523,65 +527,73 @@ OpenCLIntegrationUtilities::OpenCLIntegrationUtilities(OpenCLContext& context, c
vsiteOutOfPlaneWeightVec.push_back(mm_double4(site.getWeight12(), site.getWeight13(), site.getWeightCross(), 0.0)); vsiteOutOfPlaneWeightVec.push_back(mm_double4(site.getWeight12(), site.getWeight13(), site.getWeightCross(), 0.0));
} }
else if (dynamic_cast<const LocalCoordinatesSite*>(&system.getVirtualSite(i)) != NULL) { else if (dynamic_cast<const LocalCoordinatesSite*>(&system.getVirtualSite(i)) != NULL) {
// An out of plane site. // A local coordinates site.
const LocalCoordinatesSite& site = dynamic_cast<const LocalCoordinatesSite&>(system.getVirtualSite(i)); const LocalCoordinatesSite& site = dynamic_cast<const LocalCoordinatesSite&>(system.getVirtualSite(i));
vsiteLocalCoordsAtomVec.push_back(mm_int4(i, site.getParticle(0), site.getParticle(1), site.getParticle(2))); int numParticles = site.getNumParticles();
Vec3 origin = site.getOriginWeights(); vector<double> origin, x, y;
Vec3 x = site.getXWeights(); site.getOriginWeights(origin);
Vec3 y = site.getYWeights(); site.getXWeights(x);
site.getYWeights(y);
vsiteLocalCoordsIndexVec.push_back(i);
vsiteLocalCoordsStartVec.push_back(vsiteLocalCoordsAtomVec.size());
for (int j = 0; j < numParticles; j++) {
vsiteLocalCoordsAtomVec.push_back(site.getParticle(j));
vsiteLocalCoordsWeightVec.push_back(origin[j]);
vsiteLocalCoordsWeightVec.push_back(x[j]);
vsiteLocalCoordsWeightVec.push_back(y[j]);
}
Vec3 pos = site.getLocalPosition(); Vec3 pos = site.getLocalPosition();
vsiteLocalCoordsParamVec.push_back(origin[0]); vsiteLocalCoordsPosVec.push_back(mm_double4(pos[0], pos[1], pos[2], 0.0));
vsiteLocalCoordsParamVec.push_back(origin[1]);
vsiteLocalCoordsParamVec.push_back(origin[2]);
vsiteLocalCoordsParamVec.push_back(x[0]);
vsiteLocalCoordsParamVec.push_back(x[1]);
vsiteLocalCoordsParamVec.push_back(x[2]);
vsiteLocalCoordsParamVec.push_back(y[0]);
vsiteLocalCoordsParamVec.push_back(y[1]);
vsiteLocalCoordsParamVec.push_back(y[2]);
vsiteLocalCoordsParamVec.push_back(pos[0]);
vsiteLocalCoordsParamVec.push_back(pos[1]);
vsiteLocalCoordsParamVec.push_back(pos[2]);
} }
} }
} }
vsiteLocalCoordsStartVec.push_back(vsiteLocalCoordsAtomVec.size());
int num2Avg = vsite2AvgAtomVec.size(); int num2Avg = vsite2AvgAtomVec.size();
int num3Avg = vsite3AvgAtomVec.size(); int num3Avg = vsite3AvgAtomVec.size();
int numOutOfPlane = vsiteOutOfPlaneAtomVec.size(); int numOutOfPlane = vsiteOutOfPlaneAtomVec.size();
int numLocalCoords = vsiteLocalCoordsAtomVec.size(); int numLocalCoords = vsiteLocalCoordsPosVec.size();
numVsites = num2Avg+num3Avg+numOutOfPlane+numLocalCoords; numVsites = num2Avg+num3Avg+numOutOfPlane+numLocalCoords;
vsite2AvgAtoms = OpenCLArray::create<mm_int4>(context, max(1, num2Avg), "vsite2AvgAtoms"); vsite2AvgAtoms = OpenCLArray::create<mm_int4>(context, max(1, num2Avg), "vsite2AvgAtoms");
vsite3AvgAtoms = OpenCLArray::create<mm_int4>(context, max(1, num3Avg), "vsite3AvgAtoms"); vsite3AvgAtoms = OpenCLArray::create<mm_int4>(context, max(1, num3Avg), "vsite3AvgAtoms");
vsiteOutOfPlaneAtoms = OpenCLArray::create<mm_int4>(context, max(1, numOutOfPlane), "vsiteOutOfPlaneAtoms"); vsiteOutOfPlaneAtoms = OpenCLArray::create<mm_int4>(context, max(1, numOutOfPlane), "vsiteOutOfPlaneAtoms");
vsiteLocalCoordsAtoms = OpenCLArray::create<mm_int4>(context, max(1, numLocalCoords), "vsiteLocalCoordinatesAtoms"); vsiteLocalCoordsIndex = OpenCLArray::create<cl_int>(context, max(1, (int) vsiteLocalCoordsIndexVec.size()), "vsiteLocalCoordsIndex");
vsiteLocalCoordsAtoms = OpenCLArray::create<cl_int>(context, max(1, (int) vsiteLocalCoordsAtomVec.size()), "vsiteLocalCoordsAtoms");
vsiteLocalCoordsStartIndex = OpenCLArray::create<cl_int>(context, max(1, (int) vsiteLocalCoordsStartVec.size()), "vsiteLocalCoordsStartIndex");
if (num2Avg > 0) if (num2Avg > 0)
vsite2AvgAtoms->upload(vsite2AvgAtomVec); vsite2AvgAtoms->upload(vsite2AvgAtomVec);
if (num3Avg > 0) if (num3Avg > 0)
vsite3AvgAtoms->upload(vsite3AvgAtomVec); vsite3AvgAtoms->upload(vsite3AvgAtomVec);
if (numOutOfPlane > 0) if (numOutOfPlane > 0)
vsiteOutOfPlaneAtoms->upload(vsiteOutOfPlaneAtomVec); vsiteOutOfPlaneAtoms->upload(vsiteOutOfPlaneAtomVec);
if (numLocalCoords > 0) if (numLocalCoords > 0) {
vsiteLocalCoordsIndex->upload(vsiteLocalCoordsIndexVec);
vsiteLocalCoordsAtoms->upload(vsiteLocalCoordsAtomVec); vsiteLocalCoordsAtoms->upload(vsiteLocalCoordsAtomVec);
vsiteLocalCoordsStartIndex->upload(vsiteLocalCoordsStartVec);
}
if (context.getUseDoublePrecision()) { if (context.getUseDoublePrecision()) {
vsite2AvgWeights = OpenCLArray::create<mm_double2>(context, max(1, num2Avg), "vsite2AvgWeights"); vsite2AvgWeights = OpenCLArray::create<mm_double2>(context, max(1, num2Avg), "vsite2AvgWeights");
vsite3AvgWeights = OpenCLArray::create<mm_double4>(context, max(1, num3Avg), "vsite3AvgWeights"); vsite3AvgWeights = OpenCLArray::create<mm_double4>(context, max(1, num3Avg), "vsite3AvgWeights");
vsiteOutOfPlaneWeights = OpenCLArray::create<mm_double4>(context, max(1, numOutOfPlane), "vsiteOutOfPlaneWeights"); vsiteOutOfPlaneWeights = OpenCLArray::create<mm_double4>(context, max(1, numOutOfPlane), "vsiteOutOfPlaneWeights");
vsiteLocalCoordsParams = OpenCLArray::create<cl_double>(context, max(1, 12*numLocalCoords), "vsiteLocalCoordinatesParams"); vsiteLocalCoordsWeights = OpenCLArray::create<cl_double>(context, max(1, (int) vsiteLocalCoordsWeightVec.size()), "vsiteLocalCoordsWeights");
vsiteLocalCoordsPos = OpenCLArray::create<mm_double4>(context, max(1, (int) vsiteLocalCoordsPosVec.size()), "vsiteLocalCoordsPos");
if (num2Avg > 0) if (num2Avg > 0)
vsite2AvgWeights->upload(vsite2AvgWeightVec); vsite2AvgWeights->upload(vsite2AvgWeightVec);
if (num3Avg > 0) if (num3Avg > 0)
vsite3AvgWeights->upload(vsite3AvgWeightVec); vsite3AvgWeights->upload(vsite3AvgWeightVec);
if (numOutOfPlane > 0) if (numOutOfPlane > 0)
vsiteOutOfPlaneWeights->upload(vsiteOutOfPlaneWeightVec); vsiteOutOfPlaneWeights->upload(vsiteOutOfPlaneWeightVec);
if (numLocalCoords > 0) if (numLocalCoords > 0) {
vsiteLocalCoordsParams->upload(vsiteLocalCoordsParamVec); vsiteLocalCoordsWeights->upload(vsiteLocalCoordsWeightVec);
vsiteLocalCoordsPos->upload(vsiteLocalCoordsPosVec);
}
} }
else { else {
vsite2AvgWeights = OpenCLArray::create<mm_float2>(context, max(1, num2Avg), "vsite2AvgWeights"); vsite2AvgWeights = OpenCLArray::create<mm_float2>(context, max(1, num2Avg), "vsite2AvgWeights");
vsite3AvgWeights = OpenCLArray::create<mm_float4>(context, max(1, num3Avg), "vsite3AvgWeights"); vsite3AvgWeights = OpenCLArray::create<mm_float4>(context, max(1, num3Avg), "vsite3AvgWeights");
vsiteOutOfPlaneWeights = OpenCLArray::create<mm_float4>(context, max(1, numOutOfPlane), "vsiteOutOfPlaneWeights"); vsiteOutOfPlaneWeights = OpenCLArray::create<mm_float4>(context, max(1, numOutOfPlane), "vsiteOutOfPlaneWeights");
vsiteLocalCoordsParams = OpenCLArray::create<float>(context, max(1, 12*numLocalCoords), "vsiteLocalCoordinatesParams"); vsiteLocalCoordsWeights = OpenCLArray::create<cl_float>(context, max(1, (int) vsiteLocalCoordsWeightVec.size()), "vsiteLocalCoordsWeights");
vsiteLocalCoordsPos = OpenCLArray::create<mm_float4>(context, max(1, (int) vsiteLocalCoordsPosVec.size()), "vsiteLocalCoordsPos");
if (num2Avg > 0) { if (num2Avg > 0) {
vector<mm_float2> floatWeights(num2Avg); vector<mm_float2> floatWeights(num2Avg);
for (int i = 0; i < num2Avg; i++) for (int i = 0; i < num2Avg; i++)
...@@ -601,10 +613,14 @@ OpenCLIntegrationUtilities::OpenCLIntegrationUtilities(OpenCLContext& context, c ...@@ -601,10 +613,14 @@ OpenCLIntegrationUtilities::OpenCLIntegrationUtilities(OpenCLContext& context, c
vsiteOutOfPlaneWeights->upload(floatWeights); vsiteOutOfPlaneWeights->upload(floatWeights);
} }
if (numLocalCoords > 0) { if (numLocalCoords > 0) {
vector<cl_float> floatParams(vsiteLocalCoordsParamVec.size()); vector<cl_float> floatWeights(vsiteLocalCoordsWeightVec.size());
for (int i = 0; i < (int) vsiteLocalCoordsParamVec.size(); i++) for (int i = 0; i < (int) vsiteLocalCoordsWeightVec.size(); i++)
floatParams[i] = (cl_float) vsiteLocalCoordsParamVec[i]; floatWeights[i] = (cl_float) vsiteLocalCoordsWeightVec[i];
vsiteLocalCoordsParams->upload(floatParams); vsiteLocalCoordsWeights->upload(floatWeights);
vector<mm_float4> floatPos(vsiteLocalCoordsPosVec.size());
for (int i = 0; i < (int) vsiteLocalCoordsPosVec.size(); i++)
floatPos[i] = mm_float4((float) vsiteLocalCoordsPosVec[i].x, (float) vsiteLocalCoordsPosVec[i].y, (float) vsiteLocalCoordsPosVec[i].z, 0.0f);
vsiteLocalCoordsPos->upload(floatPos);
} }
} }
...@@ -645,8 +661,11 @@ OpenCLIntegrationUtilities::OpenCLIntegrationUtilities(OpenCLContext& context, c ...@@ -645,8 +661,11 @@ OpenCLIntegrationUtilities::OpenCLIntegrationUtilities(OpenCLContext& context, c
vsitePositionKernel.setArg<cl::Buffer>(index++, vsite3AvgWeights->getDeviceBuffer()); vsitePositionKernel.setArg<cl::Buffer>(index++, vsite3AvgWeights->getDeviceBuffer());
vsitePositionKernel.setArg<cl::Buffer>(index++, vsiteOutOfPlaneAtoms->getDeviceBuffer()); vsitePositionKernel.setArg<cl::Buffer>(index++, vsiteOutOfPlaneAtoms->getDeviceBuffer());
vsitePositionKernel.setArg<cl::Buffer>(index++, vsiteOutOfPlaneWeights->getDeviceBuffer()); vsitePositionKernel.setArg<cl::Buffer>(index++, vsiteOutOfPlaneWeights->getDeviceBuffer());
vsitePositionKernel.setArg<cl::Buffer>(index++, vsiteLocalCoordsIndex->getDeviceBuffer());
vsitePositionKernel.setArg<cl::Buffer>(index++, vsiteLocalCoordsAtoms->getDeviceBuffer()); vsitePositionKernel.setArg<cl::Buffer>(index++, vsiteLocalCoordsAtoms->getDeviceBuffer());
vsitePositionKernel.setArg<cl::Buffer>(index++, vsiteLocalCoordsParams->getDeviceBuffer()); vsitePositionKernel.setArg<cl::Buffer>(index++, vsiteLocalCoordsWeights->getDeviceBuffer());
vsitePositionKernel.setArg<cl::Buffer>(index++, vsiteLocalCoordsPos->getDeviceBuffer());
vsitePositionKernel.setArg<cl::Buffer>(index++, vsiteLocalCoordsStartIndex->getDeviceBuffer());
vsiteForceKernel = cl::Kernel(vsiteProgram, "distributeForces"); vsiteForceKernel = cl::Kernel(vsiteProgram, "distributeForces");
index = 0; index = 0;
vsiteForceKernel.setArg<cl::Buffer>(index++, context.getPosq().getDeviceBuffer()); vsiteForceKernel.setArg<cl::Buffer>(index++, context.getPosq().getDeviceBuffer());
...@@ -661,8 +680,11 @@ OpenCLIntegrationUtilities::OpenCLIntegrationUtilities(OpenCLContext& context, c ...@@ -661,8 +680,11 @@ OpenCLIntegrationUtilities::OpenCLIntegrationUtilities(OpenCLContext& context, c
vsiteForceKernel.setArg<cl::Buffer>(index++, vsite3AvgWeights->getDeviceBuffer()); vsiteForceKernel.setArg<cl::Buffer>(index++, vsite3AvgWeights->getDeviceBuffer());
vsiteForceKernel.setArg<cl::Buffer>(index++, vsiteOutOfPlaneAtoms->getDeviceBuffer()); vsiteForceKernel.setArg<cl::Buffer>(index++, vsiteOutOfPlaneAtoms->getDeviceBuffer());
vsiteForceKernel.setArg<cl::Buffer>(index++, vsiteOutOfPlaneWeights->getDeviceBuffer()); vsiteForceKernel.setArg<cl::Buffer>(index++, vsiteOutOfPlaneWeights->getDeviceBuffer());
vsiteForceKernel.setArg<cl::Buffer>(index++, vsiteLocalCoordsIndex->getDeviceBuffer());
vsiteForceKernel.setArg<cl::Buffer>(index++, vsiteLocalCoordsAtoms->getDeviceBuffer()); vsiteForceKernel.setArg<cl::Buffer>(index++, vsiteLocalCoordsAtoms->getDeviceBuffer());
vsiteForceKernel.setArg<cl::Buffer>(index++, vsiteLocalCoordsParams->getDeviceBuffer()); vsiteForceKernel.setArg<cl::Buffer>(index++, vsiteLocalCoordsWeights->getDeviceBuffer());
vsiteForceKernel.setArg<cl::Buffer>(index++, vsiteLocalCoordsPos->getDeviceBuffer());
vsiteForceKernel.setArg<cl::Buffer>(index++, vsiteLocalCoordsStartIndex->getDeviceBuffer());
if (hasOverlappingVsites && context.getSupports64BitGlobalAtomics()) if (hasOverlappingVsites && context.getSupports64BitGlobalAtomics())
vsiteAddForcesKernel = cl::Kernel(vsiteProgram, "addDistributedForces"); vsiteAddForcesKernel = cl::Kernel(vsiteProgram, "addDistributedForces");
} }
...@@ -718,10 +740,16 @@ OpenCLIntegrationUtilities::~OpenCLIntegrationUtilities() { ...@@ -718,10 +740,16 @@ OpenCLIntegrationUtilities::~OpenCLIntegrationUtilities() {
delete vsiteOutOfPlaneAtoms; delete vsiteOutOfPlaneAtoms;
if (vsiteOutOfPlaneWeights != NULL) if (vsiteOutOfPlaneWeights != NULL)
delete vsiteOutOfPlaneWeights; delete vsiteOutOfPlaneWeights;
if (vsiteLocalCoordsIndex != NULL)
delete vsiteLocalCoordsIndex;
if (vsiteLocalCoordsAtoms != NULL) if (vsiteLocalCoordsAtoms != NULL)
delete vsiteLocalCoordsAtoms; delete vsiteLocalCoordsAtoms;
if (vsiteLocalCoordsParams != NULL) if (vsiteLocalCoordsWeights != NULL)
delete vsiteLocalCoordsParams; delete vsiteLocalCoordsWeights;
if (vsiteLocalCoordsPos != NULL)
delete vsiteLocalCoordsPos;
if (vsiteLocalCoordsStartIndex != NULL)
delete vsiteLocalCoordsStartIndex;
} }
void OpenCLIntegrationUtilities::setNextStepSize(double size) { void OpenCLIntegrationUtilities::setNextStepSize(double size) {
......
platforms/opencl/src/kernels/virtualSites.cl
View file @ 0827ad50
...@@ -33,7 +33,9 @@ __kernel void computeVirtualSites(__global real4* restrict posq, ...@@ -33,7 +33,9 @@ __kernel void computeVirtualSites(__global real4* restrict posq,
__global const int4* restrict avg2Atoms, __global const real2* restrict avg2Weights, __global const int4* restrict avg2Atoms, __global const real2* restrict avg2Weights,
__global const int4* restrict avg3Atoms, __global const real4* restrict avg3Weights, __global const int4* restrict avg3Atoms, __global const real4* restrict avg3Weights,
__global const int4* restrict outOfPlaneAtoms, __global const real4* restrict outOfPlaneWeights, __global const int4* restrict outOfPlaneAtoms, __global const real4* restrict outOfPlaneWeights,
__global const int4* restrict localCoordsAtoms, __global const real* restrict localCoordsParams) { __global const int* restrict localCoordsIndex, __global const int* restrict localCoordsAtoms,
__global const real* restrict localCoordsWeights, __global const real4* restrict localCoordsPos,
__global const int* restrict localCoordsStartIndex) {
#ifndef USE_MIXED_PRECISION #ifndef USE_MIXED_PRECISION
__global real4* posqCorrection = 0; __global real4* posqCorrection = 0;
#endif #endif
...@@ -81,30 +83,30 @@ __kernel void computeVirtualSites(__global real4* restrict posq, ...@@ -81,30 +83,30 @@ __kernel void computeVirtualSites(__global real4* restrict posq,
// Local coordinates sites. // Local coordinates sites.
for (int index = get_global_id(0); index < NUM_LOCAL_COORDS; index += get_global_size(0)) { for (int index = get_global_id(0); index < NUM_LOCAL_COORDS; index += get_global_size(0)) {
int4 atoms = localCoordsAtoms[index]; int siteAtomIndex = localCoordsIndex[index];
__global const real* params = &localCoordsParams[12*index]; int start = localCoordsStartIndex[index];
mixed4 pos = loadPos(posq, posqCorrection, atoms.x); int end = localCoordsStartIndex[index+1];
mixed4 pos1_4 = loadPos(posq, posqCorrection, atoms.y); mixed3 origin = 0, xdir = 0, ydir = 0;
mixed4 pos2_4 = loadPos(posq, posqCorrection, atoms.z); for (int j = start; j < end; j++) {
mixed4 pos3_4 = loadPos(posq, posqCorrection, atoms.w); mixed3 pos = loadPos(posq, posqCorrection, localCoordsAtoms[j]).xyz;
mixed4 pos1 = (mixed4) (pos1_4.x, pos1_4.y, pos1_4.z, 0); origin += pos*localCoordsWeights[3*j];
mixed4 pos2 = (mixed4) (pos2_4.x, pos2_4.y, pos2_4.z, 0); xdir += pos*localCoordsWeights[3*j+1];
mixed4 pos3 = (mixed4) (pos3_4.x, pos3_4.y, pos3_4.z, 0); ydir += pos*localCoordsWeights[3*j+2];
mixed4 originWeights = (mixed4) (params[0], params[1], params[2], 0); }
mixed4 xWeights = (mixed4) (params[3], params[4], params[5], 0); mixed3 zdir = cross(xdir, ydir);
mixed4 yWeights = (mixed4) (params[6], params[7], params[8], 0); mixed normXdir = sqrt(xdir.x*xdir.x+xdir.y*xdir.y+xdir.z*xdir.z);
mixed4 localPosition = (mixed4) (params[9], params[10], params[11], 0); mixed normZdir = sqrt(zdir.x*zdir.x+zdir.y*zdir.y+zdir.z*zdir.z);
mixed4 origin = pos1*originWeights.x + pos2*originWeights.y + pos3*originWeights.z; mixed invNormXdir = (normXdir > 0 ? 1/normXdir : 0);
mixed4 xdir = pos1*xWeights.x + pos2*xWeights.y + pos3*xWeights.z; mixed invNormZdir = (normZdir > 0 ? 1/normZdir : 0);
mixed4 ydir = pos1*yWeights.x + pos2*yWeights.y + pos3*yWeights.z; xdir *= invNormXdir;
mixed4 zdir = cross(xdir, ydir); zdir *= invNormZdir;
xdir *= rsqrt(xdir.x*xdir.x+xdir.y*xdir.y+xdir.z*xdir.z);
zdir *= rsqrt(zdir.x*zdir.x+zdir.y*zdir.y+zdir.z*zdir.z);
ydir = cross(zdir, xdir); ydir = cross(zdir, xdir);
mixed3 localPosition = convert_mixed4(localCoordsPos[index]).xyz;
mixed4 pos = loadPos(posq, posqCorrection, siteAtomIndex);
pos.x = origin.x + xdir.x*localPosition.x + ydir.x*localPosition.y + zdir.x*localPosition.z; pos.x = origin.x + xdir.x*localPosition.x + ydir.x*localPosition.y + zdir.x*localPosition.z;
pos.y = origin.y + xdir.y*localPosition.x + ydir.y*localPosition.y + zdir.y*localPosition.z; pos.y = origin.y + xdir.y*localPosition.x + ydir.y*localPosition.y + zdir.y*localPosition.z;
pos.z = origin.z + xdir.z*localPosition.x + ydir.z*localPosition.y + zdir.z*localPosition.z; pos.z = origin.z + xdir.z*localPosition.x + ydir.z*localPosition.y + zdir.z*localPosition.z;
storePos(posq, posqCorrection, atoms.x, pos); storePos(posq, posqCorrection, siteAtomIndex, pos);
} }
} }
...@@ -174,7 +176,9 @@ __kernel void distributeForces(__global const real4* restrict posq, __global rea ...@@ -174,7 +176,9 @@ __kernel void distributeForces(__global const real4* restrict posq, __global rea
__global const int4* restrict avg2Atoms, __global const real2* restrict avg2Weights, __global const int4* restrict avg2Atoms, __global const real2* restrict avg2Weights,
__global const int4* restrict avg3Atoms, __global const real4* restrict avg3Weights, __global const int4* restrict avg3Atoms, __global const real4* restrict avg3Weights,
__global const int4* restrict outOfPlaneAtoms, __global const real4* restrict outOfPlaneWeights, __global const int4* restrict outOfPlaneAtoms, __global const real4* restrict outOfPlaneWeights,
__global const int4* restrict localCoordsAtoms, __global const real* restrict localCoordsParams) { __global const int* restrict localCoordsIndex, __global const int* restrict localCoordsAtoms,
__global const real* restrict localCoordsWeights, __global const real4* restrict localCoordsPos,
__global const int* restrict localCoordsStartIndex) {
#ifndef USE_MIXED_PRECISION #ifndef USE_MIXED_PRECISION
__global real4* posqCorrection = 0; __global real4* posqCorrection = 0;
#endif #endif
...@@ -225,86 +229,54 @@ __kernel void distributeForces(__global const real4* restrict posq, __global rea ...@@ -225,86 +229,54 @@ __kernel void distributeForces(__global const real4* restrict posq, __global rea
// Local coordinates sites. // Local coordinates sites.
for (int index = get_global_id(0); index < NUM_LOCAL_COORDS; index += get_global_size(0)) { for (int index = get_global_id(0); index < NUM_LOCAL_COORDS; index += get_global_size(0)) {
int4 atoms = localCoordsAtoms[index]; int siteAtomIndex = localCoordsIndex[index];
__global const real* params = &localCoordsParams[12*index]; int start = localCoordsStartIndex[index];
mixed4 pos = loadPos(posq, posqCorrection, atoms.x); int end = localCoordsStartIndex[index+1];
mixed4 pos1_4 = loadPos(posq, posqCorrection, atoms.y); mixed3 origin = 0, xdir = 0, ydir = 0;
mixed4 pos2_4 = loadPos(posq, posqCorrection, atoms.z); for (int j = start; j < end; j++) {
mixed4 pos3_4 = loadPos(posq, posqCorrection, atoms.w); mixed3 pos = loadPos(posq, posqCorrection, localCoordsAtoms[j]).xyz;
mixed4 pos1 = (mixed4) (pos1_4.x, pos1_4.y, pos1_4.z, 0); origin += pos*localCoordsWeights[3*j];
mixed4 pos2 = (mixed4) (pos2_4.x, pos2_4.y, pos2_4.z, 0); xdir += pos*localCoordsWeights[3*j+1];
mixed4 pos3 = (mixed4) (pos3_4.x, pos3_4.y, pos3_4.z, 0); ydir += pos*localCoordsWeights[3*j+2];
mixed4 originWeights = (mixed4) (params[0], params[1], params[2], 0); }
mixed4 wx = (mixed4) (params[3], params[4], params[5], 0); mixed3 zdir = cross(xdir, ydir);
mixed4 wy = (mixed4) (params[6], params[7], params[8], 0); mixed normXdir = sqrt(xdir.x*xdir.x+xdir.y*xdir.y+xdir.z*xdir.z);
mixed4 localPosition = (mixed4) (params[9], params[10], params[11], 0); mixed normZdir = sqrt(zdir.x*zdir.x+zdir.y*zdir.y+zdir.z*zdir.z);
mixed4 origin = pos1*originWeights.x + pos2*originWeights.y + pos3*originWeights.z; mixed invNormXdir = (normXdir > 0 ? 1/normXdir : 0);
mixed4 xdir = pos1*wx.x + pos2*wx.y + pos3*wx.z; mixed invNormZdir = (normZdir > 0 ? 1/normZdir : 0);
mixed4 ydir = pos1*wy.x + pos2*wy.y + pos3*wy.z; mixed3 dx = xdir*invNormXdir;
mixed4 zdir = cross(xdir, ydir); mixed3 dz = zdir*invNormZdir;
mixed invNormXdir = rsqrt(xdir.x*xdir.x+xdir.y*xdir.y+xdir.z*xdir.z); mixed3 dy = cross(dz, dx);
mixed invNormZdir = rsqrt(zdir.x*zdir.x+zdir.y*zdir.y+zdir.z*zdir.z); mixed3 localPosition = convert_mixed4(localCoordsPos[index]).xyz;
mixed4 dx = xdir*invNormXdir;
mixed4 dz = zdir*invNormZdir;
mixed4 dy = cross(dz, dx);
// The derivatives for this case are very complicated. They were computed with SymPy then simplified by hand. // The derivatives for this case are very complicated. They were computed with SymPy then simplified by hand.
mixed t11 = (wx.x*ydir.x-wy.x*xdir.x)*invNormZdir; real4 f = force[siteAtomIndex];
mixed t12 = (wx.x*ydir.y-wy.x*xdir.y)*invNormZdir; mixed3 fp1 = localPosition*f.x;
mixed t13 = (wx.x*ydir.z-wy.x*xdir.z)*invNormZdir; mixed3 fp2 = localPosition*f.y;
mixed t21 = (wx.y*ydir.x-wy.y*xdir.x)*invNormZdir; mixed3 fp3 = localPosition*f.z;
mixed t22 = (wx.y*ydir.y-wy.y*xdir.y)*invNormZdir; for (int j = start; j < end; j++) {
mixed t23 = (wx.y*ydir.z-wy.y*xdir.z)*invNormZdir; real originWeight = localCoordsWeights[3*j];
mixed t31 = (wx.z*ydir.x-wy.z*xdir.x)*invNormZdir; real wx = localCoordsWeights[3*j+1];
mixed t32 = (wx.z*ydir.y-wy.z*xdir.y)*invNormZdir; real wy = localCoordsWeights[3*j+2];
mixed t33 = (wx.z*ydir.z-wy.z*xdir.z)*invNormZdir; mixed wxScaled = wx*invNormXdir;
mixed sx1 = t13*dz.y-t12*dz.z; mixed t1 = (wx*ydir.x-wy*xdir.x)*invNormZdir;
mixed sy1 = t11*dz.z-t13*dz.x; mixed t2 = (wx*ydir.y-wy*xdir.y)*invNormZdir;
mixed sz1 = t12*dz.x-t11*dz.y; mixed t3 = (wx*ydir.z-wy*xdir.z)*invNormZdir;
mixed sx2 = t23*dz.y-t22*dz.z; mixed sx = t3*dz.y-t2*dz.z;
mixed sy2 = t21*dz.z-t23*dz.x; mixed sy = t1*dz.z-t3*dz.x;
mixed sz2 = t22*dz.x-t21*dz.y; mixed sz = t2*dz.x-t1*dz.y;
mixed sx3 = t33*dz.y-t32*dz.z; real4 fresult = 0;
mixed sy3 = t31*dz.z-t33*dz.x; fresult.x += fp1.x*wxScaled*(1-dx.x*dx.x) + fp1.z*(dz.x*sx ) + fp1.y*((-dx.x*dy.x )*wxScaled + dy.x*sx - dx.y*t2 - dx.z*t3) + f.x*originWeight;
mixed sz3 = t32*dz.x-t31*dz.y; fresult.y += fp1.x*wxScaled*( -dx.x*dx.y) + fp1.z*(dz.x*sy+t3) + fp1.y*((-dx.y*dy.x-dz.z)*wxScaled + dy.x*sy + dx.y*t1);
mixed4 wxScaled = wx*invNormXdir; fresult.z += fp1.x*wxScaled*( -dx.x*dx.z) + fp1.z*(dz.x*sz-t2) + fp1.y*((-dx.z*dy.x+dz.y)*wxScaled + dy.x*sz + dx.z*t1);
real4 f = force[atoms.x]; fresult.x += fp2.x*wxScaled*( -dx.y*dx.x) + fp2.z*(dz.y*sx-t3) - fp2.y*(( dx.x*dy.y-dz.z)*wxScaled - dy.y*sx - dx.x*t2);
real4 f1 = 0; fresult.y += fp2.x*wxScaled*(1-dx.y*dx.y) + fp2.z*(dz.y*sy ) - fp2.y*(( dx.y*dy.y )*wxScaled - dy.y*sy + dx.x*t1 + dx.z*t3) + f.y*originWeight;
real4 f2 = 0; fresult.z += fp2.x*wxScaled*( -dx.y*dx.z) + fp2.z*(dz.y*sz+t1) - fp2.y*(( dx.z*dy.y+dz.x)*wxScaled - dy.y*sz - dx.z*t2);
real4 f3 = 0; fresult.x += fp3.x*wxScaled*( -dx.z*dx.x) + fp3.z*(dz.z*sx+t2) + fp3.y*((-dx.x*dy.z-dz.y)*wxScaled + dy.z*sx + dx.x*t3);
mixed4 fp1 = localPosition*f.x; fresult.y += fp3.x*wxScaled*( -dx.z*dx.y) + fp3.z*(dz.z*sy-t1) + fp3.y*((-dx.y*dy.z+dz.x)*wxScaled + dy.z*sy + dx.y*t3);
mixed4 fp2 = localPosition*f.y; fresult.z += fp3.x*wxScaled*(1-dx.z*dx.z) + fp3.z*(dz.z*sz ) + fp3.y*((-dx.z*dy.z )*wxScaled + dy.z*sz - dx.x*t1 - dx.y*t2) + f.z*originWeight;
mixed4 fp3 = localPosition*f.z; ADD_FORCE(localCoordsAtoms[j], fresult);
f1.x += fp1.x*wxScaled.x*(1-dx.x*dx.x) + fp1.z*(dz.x*sx1 ) + fp1.y*((-dx.x*dy.x )*wxScaled.x + dy.x*sx1 - dx.y*t12 - dx.z*t13) + f.x*originWeights.x; }
f1.y += fp1.x*wxScaled.x*( -dx.x*dx.y) + fp1.z*(dz.x*sy1+t13) + fp1.y*((-dx.y*dy.x-dz.z)*wxScaled.x + dy.x*sy1 + dx.y*t11);
f1.z += fp1.x*wxScaled.x*( -dx.x*dx.z) + fp1.z*(dz.x*sz1-t12) + fp1.y*((-dx.z*dy.x+dz.y)*wxScaled.x + dy.x*sz1 + dx.z*t11);
f2.x += fp1.x*wxScaled.y*(1-dx.x*dx.x) + fp1.z*(dz.x*sx2 ) + fp1.y*((-dx.x*dy.x )*wxScaled.y + dy.x*sx2 - dx.y*t22 - dx.z*t23) + f.x*originWeights.y;
f2.y += fp1.x*wxScaled.y*( -dx.x*dx.y) + fp1.z*(dz.x*sy2+t23) + fp1.y*((-dx.y*dy.x-dz.z)*wxScaled.y + dy.x*sy2 + dx.y*t21);
f2.z += fp1.x*wxScaled.y*( -dx.x*dx.z) + fp1.z*(dz.x*sz2-t22) + fp1.y*((-dx.z*dy.x+dz.y)*wxScaled.y + dy.x*sz2 + dx.z*t21);
f3.x += fp1.x*wxScaled.z*(1-dx.x*dx.x) + fp1.z*(dz.x*sx3 ) + fp1.y*((-dx.x*dy.x )*wxScaled.z + dy.x*sx3 - dx.y*t32 - dx.z*t33) + f.x*originWeights.z;
f3.y += fp1.x*wxScaled.z*( -dx.x*dx.y) + fp1.z*(dz.x*sy3+t33) + fp1.y*((-dx.y*dy.x-dz.z)*wxScaled.z + dy.x*sy3 + dx.y*t31);
f3.z += fp1.x*wxScaled.z*( -dx.x*dx.z) + fp1.z*(dz.x*sz3-t32) + fp1.y*((-dx.z*dy.x+dz.y)*wxScaled.z + dy.x*sz3 + dx.z*t31);
f1.x += fp2.x*wxScaled.x*( -dx.y*dx.x) + fp2.z*(dz.y*sx1-t13) - fp2.y*(( dx.x*dy.y-dz.z)*wxScaled.x - dy.y*sx1 - dx.x*t12);
f1.y += fp2.x*wxScaled.x*(1-dx.y*dx.y) + fp2.z*(dz.y*sy1 ) - fp2.y*(( dx.y*dy.y )*wxScaled.x - dy.y*sy1 + dx.x*t11 + dx.z*t13) + f.y*originWeights.x;
f1.z += fp2.x*wxScaled.x*( -dx.y*dx.z) + fp2.z*(dz.y*sz1+t11) - fp2.y*(( dx.z*dy.y+dz.x)*wxScaled.x - dy.y*sz1 - dx.z*t12);
f2.x += fp2.x*wxScaled.y*( -dx.y*dx.x) + fp2.z*(dz.y*sx2-t23) - fp2.y*(( dx.x*dy.y-dz.z)*wxScaled.y - dy.y*sx2 - dx.x*t22);
f2.y += fp2.x*wxScaled.y*(1-dx.y*dx.y) + fp2.z*(dz.y*sy2 ) - fp2.y*(( dx.y*dy.y )*wxScaled.y - dy.y*sy2 + dx.x*t21 + dx.z*t23) + f.y*originWeights.y;
f2.z += fp2.x*wxScaled.y*( -dx.y*dx.z) + fp2.z*(dz.y*sz2+t21) - fp2.y*(( dx.z*dy.y+dz.x)*wxScaled.y - dy.y*sz2 - dx.z*t22);
f3.x += fp2.x*wxScaled.z*( -dx.y*dx.x) + fp2.z*(dz.y*sx3-t33) - fp2.y*(( dx.x*dy.y-dz.z)*wxScaled.z - dy.y*sx3 - dx.x*t32);
f3.y += fp2.x*wxScaled.z*(1-dx.y*dx.y) + fp2.z*(dz.y*sy3 ) - fp2.y*(( dx.y*dy.y )*wxScaled.z - dy.y*sy3 + dx.x*t31 + dx.z*t33) + f.y*originWeights.z;
f3.z += fp2.x*wxScaled.z*( -dx.y*dx.z) + fp2.z*(dz.y*sz3+t31) - fp2.y*(( dx.z*dy.y+dz.x)*wxScaled.z - dy.y*sz3 - dx.z*t32);
f1.x += fp3.x*wxScaled.x*( -dx.z*dx.x) + fp3.z*(dz.z*sx1+t12) + fp3.y*((-dx.x*dy.z-dz.y)*wxScaled.x + dy.z*sx1 + dx.x*t13);
f1.y += fp3.x*wxScaled.x*( -dx.z*dx.y) + fp3.z*(dz.z*sy1-t11) + fp3.y*((-dx.y*dy.z+dz.x)*wxScaled.x + dy.z*sy1 + dx.y*t13);
f1.z += fp3.x*wxScaled.x*(1-dx.z*dx.z) + fp3.z*(dz.z*sz1 ) + fp3.y*((-dx.z*dy.z )*wxScaled.x + dy.z*sz1 - dx.x*t11 - dx.y*t12) + f.z*originWeights.x;
f2.x += fp3.x*wxScaled.y*( -dx.z*dx.x) + fp3.z*(dz.z*sx2+t22) + fp3.y*((-dx.x*dy.z-dz.y)*wxScaled.y + dy.z*sx2 + dx.x*t23);
f2.y += fp3.x*wxScaled.y*( -dx.z*dx.y) + fp3.z*(dz.z*sy2-t21) + fp3.y*((-dx.y*dy.z+dz.x)*wxScaled.y + dy.z*sy2 + dx.y*t23);
f2.z += fp3.x*wxScaled.y*(1-dx.z*dx.z) + fp3.z*(dz.z*sz2 ) + fp3.y*((-dx.z*dy.z )*wxScaled.y + dy.z*sz2 - dx.x*t21 - dx.y*t22) + f.z*originWeights.y;
f3.x += fp3.x*wxScaled.z*( -dx.z*dx.x) + fp3.z*(dz.z*sx3+t32) + fp3.y*((-dx.x*dy.z-dz.y)*wxScaled.z + dy.z*sx3 + dx.x*t33);
f3.y += fp3.x*wxScaled.z*( -dx.z*dx.y) + fp3.z*(dz.z*sy3-t31) + fp3.y*((-dx.y*dy.z+dz.x)*wxScaled.z + dy.z*sy3 + dx.y*t33);
f3.z += fp3.x*wxScaled.z*(1-dx.z*dx.z) + fp3.z*(dz.z*sz3 ) + fp3.y*((-dx.z*dy.z )*wxScaled.z + dy.z*sz3 - dx.x*t31 - dx.y*t32) + f.z*originWeights.z;
ADD_FORCE(atoms.y, f1);
ADD_FORCE(atoms.z, f2);
ADD_FORCE(atoms.w, f3);
} }
} }
platforms/reference/src/SimTKReference/ReferenceVirtualSites.cpp
View file @ 0827ad50
...@@ -6,7 +6,7 @@ ...@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2012-2014 Stanford University and the Authors. * * Portions copyright (c) 2012-2017 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -70,22 +70,30 @@ void ReferenceVirtualSites::computePositions(const OpenMM::System& system, vecto ...@@ -70,22 +70,30 @@ void ReferenceVirtualSites::computePositions(const OpenMM::System& system, vecto
// A local coordinates site. // A local coordinates site.
const LocalCoordinatesSite& site = dynamic_cast<const LocalCoordinatesSite&>(system.getVirtualSite(i)); const LocalCoordinatesSite& site = dynamic_cast<const LocalCoordinatesSite&>(system.getVirtualSite(i));
int p1 = site.getParticle(0), p2 = site.getParticle(1), p3 = site.getParticle(2); int numParticles = site.getNumParticles();
Vec3 originWeights = site.getOriginWeights(); vector<double> originWeights, xWeights, yWeights;
Vec3 xWeights = site.getXWeights(); site.getOriginWeights(originWeights);
Vec3 yWeights = site.getYWeights(); site.getXWeights(xWeights);
site.getYWeights(yWeights);
Vec3 origin, xdir, ydir;
for (int j = 0; j < numParticles; j++) {
Vec3 pos = atomCoordinates[site.getParticle(j)];
origin += pos*originWeights[j];
xdir += pos*xWeights[j];
ydir += pos*yWeights[j];
}
Vec3 localPosition = site.getLocalPosition(); Vec3 localPosition = site.getLocalPosition();
Vec3 origin = atomCoordinates[p1]*originWeights[0] + atomCoordinates[p2]*originWeights[1] + atomCoordinates[p3]*originWeights[2];
Vec3 xdir = atomCoordinates[p1]*xWeights[0] + atomCoordinates[p2]*xWeights[1] + atomCoordinates[p3]*xWeights[2];
Vec3 ydir = atomCoordinates[p1]*yWeights[0] + atomCoordinates[p2]*yWeights[1] + atomCoordinates[p3]*yWeights[2];
Vec3 zdir = xdir.cross(ydir); Vec3 zdir = xdir.cross(ydir);
xdir /= sqrt(xdir.dot(xdir)); double normXdir = sqrt(xdir.dot(xdir));
zdir /= sqrt(zdir.dot(zdir)); double normZdir = sqrt(zdir.dot(zdir));
if (normXdir > 0.0)
xdir /= normXdir;
if (normZdir > 0.0)
zdir /= normZdir;
ydir = zdir.cross(xdir); ydir = zdir.cross(xdir);
atomCoordinates[i] = origin + xdir*localPosition[0] + ydir*localPosition[1] + zdir*localPosition[2]; atomCoordinates[i] = origin + xdir*localPosition[0] + ydir*localPosition[1] + zdir*localPosition[2];
} }
} }
} }
void ReferenceVirtualSites::distributeForces(const OpenMM::System& system, const vector<OpenMM::Vec3>& atomCoordinates, vector<OpenMM::Vec3>& forces) { void ReferenceVirtualSites::distributeForces(const OpenMM::System& system, const vector<OpenMM::Vec3>& atomCoordinates, vector<OpenMM::Vec3>& forces) {
...@@ -133,71 +141,53 @@ void ReferenceVirtualSites::distributeForces(const OpenMM::System& system, const ...@@ -133,71 +141,53 @@ void ReferenceVirtualSites::distributeForces(const OpenMM::System& system, const
// A local coordinates site. // A local coordinates site.
const LocalCoordinatesSite& site = dynamic_cast<const LocalCoordinatesSite&>(system.getVirtualSite(i)); const LocalCoordinatesSite& site = dynamic_cast<const LocalCoordinatesSite&>(system.getVirtualSite(i));
int p1 = site.getParticle(0), p2 = site.getParticle(1), p3 = site.getParticle(2); int numParticles = site.getNumParticles();
Vec3 originWeights = site.getOriginWeights(); vector<double> originWeights, wx, wy;
Vec3 wx = site.getXWeights(); site.getOriginWeights(originWeights);
Vec3 wy = site.getYWeights(); site.getXWeights(wx);
site.getYWeights(wy);
Vec3 xdir, ydir;
for (int j = 0; j < numParticles; j++) {
Vec3 pos = atomCoordinates[site.getParticle(j)];
xdir += pos*wx[j];
ydir += pos*wy[j];
}
Vec3 localPosition = site.getLocalPosition(); Vec3 localPosition = site.getLocalPosition();
Vec3 xdir = atomCoordinates[p1]*wx[0] + atomCoordinates[p2]*wx[1] + atomCoordinates[p3]*wx[2];
Vec3 ydir = atomCoordinates[p1]*wy[0] + atomCoordinates[p2]*wy[1] + atomCoordinates[p3]*wy[2];
Vec3 zdir = xdir.cross(ydir); Vec3 zdir = xdir.cross(ydir);
double invNormXdir = 1.0/sqrt(xdir.dot(xdir)); double normXdir = sqrt(xdir.dot(xdir));
double invNormZdir = 1.0/sqrt(zdir.dot(zdir)); double normZdir = sqrt(zdir.dot(zdir));
double invNormXdir = (normXdir > 0.0 ? 1.0/normXdir : 0.0);
double invNormZdir = (normZdir > 0.0 ? 1.0/normZdir : 0.0);
Vec3 dx = xdir*invNormXdir; Vec3 dx = xdir*invNormXdir;
Vec3 dz = zdir*invNormZdir; Vec3 dz = zdir*invNormZdir;
Vec3 dy = dz.cross(dx); Vec3 dy = dz.cross(dx);
// The derivatives for this case are very complicated. They were computed with SymPy then simplified by hand. // The derivatives for this case are very complicated. They were computed with SymPy then simplified by hand.
double t11 = (wx[0]*ydir[0]-wy[0]*xdir[0])*invNormZdir; vector<double> wxScaled(numParticles);
double t12 = (wx[0]*ydir[1]-wy[0]*xdir[1])*invNormZdir; for (int j = 0; j < numParticles; j++)
double t13 = (wx[0]*ydir[2]-wy[0]*xdir[2])*invNormZdir; wxScaled[j] = wx[j]*invNormXdir;
double t21 = (wx[1]*ydir[0]-wy[1]*xdir[0])*invNormZdir;
double t22 = (wx[1]*ydir[1]-wy[1]*xdir[1])*invNormZdir;
double t23 = (wx[1]*ydir[2]-wy[1]*xdir[2])*invNormZdir;
double t31 = (wx[2]*ydir[0]-wy[2]*xdir[0])*invNormZdir;
double t32 = (wx[2]*ydir[1]-wy[2]*xdir[1])*invNormZdir;
double t33 = (wx[2]*ydir[2]-wy[2]*xdir[2])*invNormZdir;
double sx1 = t13*dz[1]-t12*dz[2];
double sy1 = t11*dz[2]-t13*dz[0];
double sz1 = t12*dz[0]-t11*dz[1];
double sx2 = t23*dz[1]-t22*dz[2];
double sy2 = t21*dz[2]-t23*dz[0];
double sz2 = t22*dz[0]-t21*dz[1];
double sx3 = t33*dz[1]-t32*dz[2];
double sy3 = t31*dz[2]-t33*dz[0];
double sz3 = t32*dz[0]-t31*dz[1];
Vec3 wxScaled = wx*invNormXdir;
Vec3 fp1 = localPosition*f[0]; Vec3 fp1 = localPosition*f[0];
Vec3 fp2 = localPosition*f[1]; Vec3 fp2 = localPosition*f[1];
Vec3 fp3 = localPosition*f[2]; Vec3 fp3 = localPosition*f[2];
forces[p1][0] += fp1[0]*wxScaled[0]*(1-dx[0]*dx[0]) + fp1[2]*(dz[0]*sx1 ) + fp1[1]*((-dx[0]*dy[0] )*wxScaled[0] + dy[0]*sx1 - dx[1]*t12 - dx[2]*t13) + f[0]*originWeights[0]; for (int j = 0; j < numParticles; j++) {
forces[p1][1] += fp1[0]*wxScaled[0]*( -dx[0]*dx[1]) + fp1[2]*(dz[0]*sy1+t13) + fp1[1]*((-dx[1]*dy[0]-dz[2])*wxScaled[0] + dy[0]*sy1 + dx[1]*t11); double t1 = (wx[j]*ydir[0]-wy[j]*xdir[0])*invNormZdir;
forces[p1][2] += fp1[0]*wxScaled[0]*( -dx[0]*dx[2]) + fp1[2]*(dz[0]*sz1-t12) + fp1[1]*((-dx[2]*dy[0]+dz[1])*wxScaled[0] + dy[0]*sz1 + dx[2]*t11); double t2 = (wx[j]*ydir[1]-wy[j]*xdir[1])*invNormZdir;
forces[p2][0] += fp1[0]*wxScaled[1]*(1-dx[0]*dx[0]) + fp1[2]*(dz[0]*sx2 ) + fp1[1]*((-dx[0]*dy[0] )*wxScaled[1] + dy[0]*sx2 - dx[1]*t22 - dx[2]*t23) + f[0]*originWeights[1]; double t3 = (wx[j]*ydir[2]-wy[j]*xdir[2])*invNormZdir;
forces[p2][1] += fp1[0]*wxScaled[1]*( -dx[0]*dx[1]) + fp1[2]*(dz[0]*sy2+t23) + fp1[1]*((-dx[1]*dy[0]-dz[2])*wxScaled[1] + dy[0]*sy2 + dx[1]*t21); double sx = t3*dz[1]-t2*dz[2];
forces[p2][2] += fp1[0]*wxScaled[1]*( -dx[0]*dx[2]) + fp1[2]*(dz[0]*sz2-t22) + fp1[1]*((-dx[2]*dy[0]+dz[1])*wxScaled[1] + dy[0]*sz2 + dx[2]*t21); double sy = t1*dz[2]-t3*dz[0];
forces[p3][0] += fp1[0]*wxScaled[2]*(1-dx[0]*dx[0]) + fp1[2]*(dz[0]*sx3 ) + fp1[1]*((-dx[0]*dy[0] )*wxScaled[2] + dy[0]*sx3 - dx[1]*t32 - dx[2]*t33) + f[0]*originWeights[2]; double sz = t2*dz[0]-t1*dz[1];
forces[p3][1] += fp1[0]*wxScaled[2]*( -dx[0]*dx[1]) + fp1[2]*(dz[0]*sy3+t33) + fp1[1]*((-dx[1]*dy[0]-dz[2])*wxScaled[2] + dy[0]*sy3 + dx[1]*t31); int p = site.getParticle(j);
forces[p3][2] += fp1[0]*wxScaled[2]*( -dx[0]*dx[2]) + fp1[2]*(dz[0]*sz3-t32) + fp1[1]*((-dx[2]*dy[0]+dz[1])*wxScaled[2] + dy[0]*sz3 + dx[2]*t31); forces[p][0] += fp1[0]*wxScaled[j]*(1-dx[0]*dx[0]) + fp1[2]*(dz[0]*sx ) + fp1[1]*((-dx[0]*dy[0] )*wxScaled[j] + dy[0]*sx - dx[1]*t2 - dx[2]*t3) + f[0]*originWeights[j];
forces[p1][0] += fp2[0]*wxScaled[0]*( -dx[1]*dx[0]) + fp2[2]*(dz[1]*sx1-t13) - fp2[1]*(( dx[0]*dy[1]-dz[2])*wxScaled[0] - dy[1]*sx1 - dx[0]*t12); forces[p][1] += fp1[0]*wxScaled[j]*( -dx[0]*dx[1]) + fp1[2]*(dz[0]*sy+t3) + fp1[1]*((-dx[1]*dy[0]-dz[2])*wxScaled[j] + dy[0]*sy + dx[1]*t1);
forces[p1][1] += fp2[0]*wxScaled[0]*(1-dx[1]*dx[1]) + fp2[2]*(dz[1]*sy1 ) - fp2[1]*(( dx[1]*dy[1] )*wxScaled[0] - dy[1]*sy1 + dx[0]*t11 + dx[2]*t13) + f[1]*originWeights[0]; forces[p][2] += fp1[0]*wxScaled[j]*( -dx[0]*dx[2]) + fp1[2]*(dz[0]*sz-t2) + fp1[1]*((-dx[2]*dy[0]+dz[1])*wxScaled[j] + dy[0]*sz + dx[2]*t1);
forces[p1][2] += fp2[0]*wxScaled[0]*( -dx[1]*dx[2]) + fp2[2]*(dz[1]*sz1+t11) - fp2[1]*(( dx[2]*dy[1]+dz[0])*wxScaled[0] - dy[1]*sz1 - dx[2]*t12); forces[p][0] += fp2[0]*wxScaled[j]*( -dx[1]*dx[0]) + fp2[2]*(dz[1]*sx-t3) - fp2[1]*(( dx[0]*dy[1]-dz[2])*wxScaled[j] - dy[1]*sx - dx[0]*t2);
forces[p2][0] += fp2[0]*wxScaled[1]*( -dx[1]*dx[0]) + fp2[2]*(dz[1]*sx2-t23) - fp2[1]*(( dx[0]*dy[1]-dz[2])*wxScaled[1] - dy[1]*sx2 - dx[0]*t22); forces[p][1] += fp2[0]*wxScaled[j]*(1-dx[1]*dx[1]) + fp2[2]*(dz[1]*sy ) - fp2[1]*(( dx[1]*dy[1] )*wxScaled[j] - dy[1]*sy + dx[0]*t1 + dx[2]*t3) + f[1]*originWeights[j];
forces[p2][1] += fp2[0]*wxScaled[1]*(1-dx[1]*dx[1]) + fp2[2]*(dz[1]*sy2 ) - fp2[1]*(( dx[1]*dy[1] )*wxScaled[1] - dy[1]*sy2 + dx[0]*t21 + dx[2]*t23) + f[1]*originWeights[1]; forces[p][2] += fp2[0]*wxScaled[j]*( -dx[1]*dx[2]) + fp2[2]*(dz[1]*sz+t1) - fp2[1]*(( dx[2]*dy[1]+dz[0])*wxScaled[j] - dy[1]*sz - dx[2]*t2);
forces[p2][2] += fp2[0]*wxScaled[1]*( -dx[1]*dx[2]) + fp2[2]*(dz[1]*sz2+t21) - fp2[1]*(( dx[2]*dy[1]+dz[0])*wxScaled[1] - dy[1]*sz2 - dx[2]*t22); forces[p][0] += fp3[0]*wxScaled[j]*( -dx[2]*dx[0]) + fp3[2]*(dz[2]*sx+t2) + fp3[1]*((-dx[0]*dy[2]-dz[1])*wxScaled[j] + dy[2]*sx + dx[0]*t3);
forces[p3][0] += fp2[0]*wxScaled[2]*( -dx[1]*dx[0]) + fp2[2]*(dz[1]*sx3-t33) - fp2[1]*(( dx[0]*dy[1]-dz[2])*wxScaled[2] - dy[1]*sx3 - dx[0]*t32); forces[p][1] += fp3[0]*wxScaled[j]*( -dx[2]*dx[1]) + fp3[2]*(dz[2]*sy-t1) + fp3[1]*((-dx[1]*dy[2]+dz[0])*wxScaled[j] + dy[2]*sy + dx[1]*t3);
forces[p3][1] += fp2[0]*wxScaled[2]*(1-dx[1]*dx[1]) + fp2[2]*(dz[1]*sy3 ) - fp2[1]*(( dx[1]*dy[1] )*wxScaled[2] - dy[1]*sy3 + dx[0]*t31 + dx[2]*t33) + f[1]*originWeights[2]; forces[p][2] += fp3[0]*wxScaled[j]*(1-dx[2]*dx[2]) + fp3[2]*(dz[2]*sz ) + fp3[1]*((-dx[2]*dy[2] )*wxScaled[j] + dy[2]*sz - dx[0]*t1 - dx[1]*t2) + f[2]*originWeights[j];
forces[p3][2] += fp2[0]*wxScaled[2]*( -dx[1]*dx[2]) + fp2[2]*(dz[1]*sz3+t31) - fp2[1]*(( dx[2]*dy[1]+dz[0])*wxScaled[2] - dy[1]*sz3 - dx[2]*t32); }
forces[p1][0] += fp3[0]*wxScaled[0]*( -dx[2]*dx[0]) + fp3[2]*(dz[2]*sx1+t12) + fp3[1]*((-dx[0]*dy[2]-dz[1])*wxScaled[0] + dy[2]*sx1 + dx[0]*t13);
forces[p1][1] += fp3[0]*wxScaled[0]*( -dx[2]*dx[1]) + fp3[2]*(dz[2]*sy1-t11) + fp3[1]*((-dx[1]*dy[2]+dz[0])*wxScaled[0] + dy[2]*sy1 + dx[1]*t13);
forces[p1][2] += fp3[0]*wxScaled[0]*(1-dx[2]*dx[2]) + fp3[2]*(dz[2]*sz1 ) + fp3[1]*((-dx[2]*dy[2] )*wxScaled[0] + dy[2]*sz1 - dx[0]*t11 - dx[1]*t12) + f[2]*originWeights[0];
forces[p2][0] += fp3[0]*wxScaled[1]*( -dx[2]*dx[0]) + fp3[2]*(dz[2]*sx2+t22) + fp3[1]*((-dx[0]*dy[2]-dz[1])*wxScaled[1] + dy[2]*sx2 + dx[0]*t23);
forces[p2][1] += fp3[0]*wxScaled[1]*( -dx[2]*dx[1]) + fp3[2]*(dz[2]*sy2-t21) + fp3[1]*((-dx[1]*dy[2]+dz[0])*wxScaled[1] + dy[2]*sy2 + dx[1]*t23);
forces[p2][2] += fp3[0]*wxScaled[1]*(1-dx[2]*dx[2]) + fp3[2]*(dz[2]*sz2 ) + fp3[1]*((-dx[2]*dy[2] )*wxScaled[1] + dy[2]*sz2 - dx[0]*t21 - dx[1]*t22) + f[2]*originWeights[1];
forces[p3][0] += fp3[0]*wxScaled[2]*( -dx[2]*dx[0]) + fp3[2]*(dz[2]*sx3+t32) + fp3[1]*((-dx[0]*dy[2]-dz[1])*wxScaled[2] + dy[2]*sx3 + dx[0]*t33);
forces[p3][1] += fp3[0]*wxScaled[2]*( -dx[2]*dx[1]) + fp3[2]*(dz[2]*sy3-t31) + fp3[1]*((-dx[1]*dy[2]+dz[0])*wxScaled[2] + dy[2]*sy3 + dx[1]*t33);
forces[p3][2] += fp3[0]*wxScaled[2]*(1-dx[2]*dx[2]) + fp3[2]*(dz[2]*sz3 ) + fp3[1]*((-dx[2]*dy[2] )*wxScaled[2] + dy[2]*sz3 - dx[0]*t31 - dx[1]*t32) + f[2]*originWeights[2];
} }
} }
} }
serialization/src/SystemProxy.cpp
View file @ 0827ad50
...@@ -6,7 +6,7 @@ ...@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2010-2015 Stanford University and the Authors. * * Portions copyright (c) 2010-2017 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -71,15 +71,23 @@ void SystemProxy::serialize(const void* object, SerializationNode& node) const { ...@@ -71,15 +71,23 @@ void SystemProxy::serialize(const void* object, SerializationNode& node) const {
} }
else if (typeid(system.getVirtualSite(i)) == typeid(LocalCoordinatesSite)) { else if (typeid(system.getVirtualSite(i)) == typeid(LocalCoordinatesSite)) {
const LocalCoordinatesSite& site = dynamic_cast<const LocalCoordinatesSite&>(system.getVirtualSite(i)); const LocalCoordinatesSite& site = dynamic_cast<const LocalCoordinatesSite&>(system.getVirtualSite(i));
Vec3 wo = site.getOriginWeights(); int numParticles = site.getNumParticles();
Vec3 wx = site.getXWeights(); vector<double> wo, wx, wy;
Vec3 wy = site.getYWeights(); site.getOriginWeights(wo);
site.getXWeights(wx);
site.getYWeights(wy);
Vec3 p = site.getLocalPosition(); Vec3 p = site.getLocalPosition();
particle.createChildNode("LocalCoordinatesSite").setIntProperty("p1", site.getParticle(0)).setIntProperty("p2", site.getParticle(1)).setIntProperty("p3", site.getParticle(2)). SerializationNode& siteNode = particle.createChildNode("LocalCoordinatesSite");
setDoubleProperty("wo1", wo[0]).setDoubleProperty("wo2", wo[1]).setDoubleProperty("wo3", wo[2]). siteNode.setDoubleProperty("pos1", p[0]).setDoubleProperty("pos2", p[1]).setDoubleProperty("pos3", p[2]);
setDoubleProperty("wx1", wx[0]).setDoubleProperty("wx2", wx[1]).setDoubleProperty("wx3", wx[2]). for (int j = 0; j < numParticles; j++) {
setDoubleProperty("wy1", wy[0]).setDoubleProperty("wy2", wy[1]).setDoubleProperty("wy3", wy[2]). stringstream ss;
setDoubleProperty("pos1", p[0]).setDoubleProperty("pos2", p[1]).setDoubleProperty("pos3", p[2]); ss << (j+1);
string index = ss.str();
siteNode.setIntProperty("p"+index, site.getParticle(j));
siteNode.setDoubleProperty("wo"+index, wo[j]);
siteNode.setDoubleProperty("wx"+index, wx[j]);
siteNode.setDoubleProperty("wy"+index, wy[j]);
}
} }
} }
} }
...@@ -120,11 +128,21 @@ void* SystemProxy::deserialize(const SerializationNode& node) const { ...@@ -120,11 +128,21 @@ void* SystemProxy::deserialize(const SerializationNode& node) const {
else if (vsite.getName() == "OutOfPlaneSite") else if (vsite.getName() == "OutOfPlaneSite")
system->setVirtualSite(i, new OutOfPlaneSite(vsite.getIntProperty("p1"), vsite.getIntProperty("p2"), vsite.getIntProperty("p3"), vsite.getDoubleProperty("w12"), vsite.getDoubleProperty("w13"), vsite.getDoubleProperty("wc"))); system->setVirtualSite(i, new OutOfPlaneSite(vsite.getIntProperty("p1"), vsite.getIntProperty("p2"), vsite.getIntProperty("p3"), vsite.getDoubleProperty("w12"), vsite.getDoubleProperty("w13"), vsite.getDoubleProperty("wc")));
else if (vsite.getName() == "LocalCoordinatesSite") { else if (vsite.getName() == "LocalCoordinatesSite") {
Vec3 wo(vsite.getDoubleProperty("wo1"), vsite.getDoubleProperty("wo2"), vsite.getDoubleProperty("wo3")); vector<int> particles;
Vec3 wx(vsite.getDoubleProperty("wx1"), vsite.getDoubleProperty("wx2"), vsite.getDoubleProperty("wx3")); vector<double> wo, wx, wy;
Vec3 wy(vsite.getDoubleProperty("wy1"), vsite.getDoubleProperty("wy2"), vsite.getDoubleProperty("wy3")); for (int j = 0; ; j++) {
stringstream ss;
ss << (j+1);
string index = ss.str();
if (!vsite.hasProperty("p"+index))
break;
particles.push_back(vsite.getIntProperty("p"+index));
wo.push_back(vsite.getDoubleProperty("wo"+index));
wx.push_back(vsite.getDoubleProperty("wx"+index));
wy.push_back(vsite.getDoubleProperty("wy"+index));
}
Vec3 p(vsite.getDoubleProperty("pos1"), vsite.getDoubleProperty("pos2"), vsite.getDoubleProperty("pos3")); Vec3 p(vsite.getDoubleProperty("pos1"), vsite.getDoubleProperty("pos2"), vsite.getDoubleProperty("pos3"));
system->setVirtualSite(i, new LocalCoordinatesSite(vsite.getIntProperty("p1"), vsite.getIntProperty("p2"), vsite.getIntProperty("p3"), wo, wx, wy, p)); system->setVirtualSite(i, new LocalCoordinatesSite(particles, wo, wx, wy, p));
} }
} }
} }
......
serialization/tests/TestSerializeSystem.cpp
View file @ 0827ad50
...@@ -6,7 +6,7 @@ ...@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for * * Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. * * Medical Research, grant U54 GM072970. See https://simtk.org. *
* * * *
* Portions copyright (c) 2010 Stanford University and the Authors. * * Portions copyright (c) 2010-2017 Stanford University and the Authors. *
* Authors: Peter Eastman * * Authors: Peter Eastman *
* Contributors: * * Contributors: *
* * * *
...@@ -82,6 +82,23 @@ void compareSystems(System& system, System& system2) { ...@@ -82,6 +82,23 @@ void compareSystems(System& system, System& system2) {
ASSERT_EQUAL(0.1, site7.getWeight12()); ASSERT_EQUAL(0.1, site7.getWeight12());
ASSERT_EQUAL(0.2, site7.getWeight13()); ASSERT_EQUAL(0.2, site7.getWeight13());
ASSERT_EQUAL(0.5, site7.getWeightCross()); ASSERT_EQUAL(0.5, site7.getWeightCross());
const LocalCoordinatesSite& site8 = dynamic_cast<const LocalCoordinatesSite&>(system2.getVirtualSite(8));
ASSERT_EQUAL(4, site8.getNumParticles());
ASSERT_EQUAL(4, site8.getParticle(0));
ASSERT_EQUAL(3, site8.getParticle(1));
ASSERT_EQUAL(2, site8.getParticle(2));
ASSERT_EQUAL(1, site8.getParticle(3));
ASSERT_EQUAL(Vec3(-0.5, 1.0, 1.5), site8.getLocalPosition());
vector<double> wo, wx, wy;
site8.getOriginWeights(wo);
site8.getXWeights(wx);
site8.getYWeights(wy);
vector<double> woExpected = {0.1, 0.2, 0.3, 0.4};
vector<double> wxExpected = {-1.0, 0.4, 0.4, 0.2};
vector<double> wyExpected = {0.3, 0.7, 0.0, -1.0};
ASSERT_EQUAL_CONTAINERS(woExpected, wo);
ASSERT_EQUAL_CONTAINERS(wxExpected, wx);
ASSERT_EQUAL_CONTAINERS(wyExpected, wy);
ASSERT_EQUAL(system.getNumForces(), system2.getNumForces()); ASSERT_EQUAL(system.getNumForces(), system2.getNumForces());
for (int i = 0; i < system.getNumForces(); i++) for (int i = 0; i < system.getNumForces(); i++)
ASSERT(typeid(system.getForce(i)) == typeid(system2.getForce(i))) ASSERT(typeid(system.getForce(i)) == typeid(system2.getForce(i)))
...@@ -93,7 +110,7 @@ void testSerialization() { ...@@ -93,7 +110,7 @@ void testSerialization() {
System system; System system;
for (int i = 0; i < 5; i++) for (int i = 0; i < 5; i++)
system.addParticle(0.1*i+1); system.addParticle(0.1*i+1);
for (int i = 0; i < 4; i++) for (int i = 0; i < 5; i++)
system.addParticle(0.0); system.addParticle(0.0);
system.addConstraint(0, 1, 3.0); system.addConstraint(0, 1, 3.0);
system.addConstraint(1, 2, 2.5); system.addConstraint(1, 2, 2.5);
...@@ -102,6 +119,7 @@ void testSerialization() { ...@@ -102,6 +119,7 @@ void testSerialization() {
system.setVirtualSite(5, new TwoParticleAverageSite(0, 1, 0.3, 0.7)); system.setVirtualSite(5, new TwoParticleAverageSite(0, 1, 0.3, 0.7));
system.setVirtualSite(6, new ThreeParticleAverageSite(2, 4, 3, 0.5, 0.2, 0.3)); system.setVirtualSite(6, new ThreeParticleAverageSite(2, 4, 3, 0.5, 0.2, 0.3));
system.setVirtualSite(7, new OutOfPlaneSite(0, 3, 1, 0.1, 0.2, 0.5)); system.setVirtualSite(7, new OutOfPlaneSite(0, 3, 1, 0.1, 0.2, 0.5));
system.setVirtualSite(8, new LocalCoordinatesSite({4, 3, 2, 1}, {0.1, 0.2, 0.3, 0.4}, {-1.0, 0.4, 0.4, 0.2}, {0.3, 0.7, 0.0, -1.0}, Vec3(-0.5, 1.0, 1.5)));
system.addForce(new HarmonicBondForce()); system.addForce(new HarmonicBondForce());
// Serialize and then deserialize it, then make sure the systems are identical. // Serialize and then deserialize it, then make sure the systems are identical.
......
tests/TestVirtualSites.h
View file @ 0827ad50
...@@ -206,30 +206,51 @@ void testOutOfPlane() { ...@@ -206,30 +206,51 @@ void testOutOfPlane() {
} }
} }
Vec3 computeWeightedPosition(const vector<Vec3>& positions, const vector<double>& weights) {
Vec3 sum;
for (int i = 0; i < weights.size(); i++)
sum += positions[i]*weights[i];
return sum;
}
/** /**
* Test a LocalCoordinatesSite virtual site. * Test a LocalCoordinatesSite virtual site.
*/ */
void testLocalCoordinates() { void testLocalCoordinates(int numSiteParticles) {
const Vec3 originWeights(0.2, 0.3, 0.5); vector<int> particles;
const Vec3 xWeights(-1.0, 0.5, 0.5); vector<double> originWeights, xWeights, yWeights;
const Vec3 yWeights(0.0, -1.0, 1.0); if (numSiteParticles == 2) {
particles = {0, 1};
originWeights = {0.4, 0.6};
xWeights = {-1.0, 1.0};
yWeights = {1.0, -1.0};
}
else if (numSiteParticles == 3) {
particles = {0, 1, 2};
originWeights = {0.2, 0.3, 0.5};
xWeights = {-1.0, 0.5, 0.5};
yWeights = {0.0, -1.0, 1.0};
}
else if (numSiteParticles == 4) {
particles = {0, 1, 2, 3};
originWeights = {0.2, 0.3, 0.1, 0.4};
xWeights = {-1.0, 0.3, 0.3, 0.4};
yWeights = {0.5, 0.5, -0.5, -0.5};
}
const Vec3 localPosition(0.4, 0.3, 0.2); const Vec3 localPosition(0.4, 0.3, 0.2);
System system; System system;
system.addParticle(1.0); for (int i = 0; i < numSiteParticles; i++)
system.addParticle(1.0);
system.addParticle(1.0); system.addParticle(1.0);
system.addParticle(0.0); system.addParticle(0.0);
system.setVirtualSite(3, new LocalCoordinatesSite(0, 1, 2, originWeights, xWeights, yWeights, localPosition)); system.setVirtualSite(numSiteParticles, new LocalCoordinatesSite(particles, originWeights, xWeights, yWeights, localPosition));
CustomExternalForce* forceField = new CustomExternalForce("2*x^2+3*y^2+4*z^2"); CustomExternalForce* forceField = new CustomExternalForce("2*x^2+3*y^2+4*z^2");
system.addForce(forceField); system.addForce(forceField);
vector<double> params; vector<double> params;
for (int i = 0; i < numSiteParticles+1; i++)
forceField->addParticle(0, params); forceField->addParticle(0, params);
forceField->addParticle(1, params);
forceField->addParticle(2, params);
forceField->addParticle(3, params);
LangevinIntegrator integrator(300.0, 0.1, 0.002); LangevinIntegrator integrator(300.0, 0.1, 0.002);
Context context(system, integrator, platform); Context context(system, integrator, platform);
vector<Vec3> positions(4), positions2(4), positions3(4); vector<Vec3> positions(numSiteParticles+1), positions2(numSiteParticles+1), positions3(numSiteParticles+1);
OpenMM_SFMT::SFMT sfmt; OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt); init_gen_rand(0, sfmt);
for (int i = 0; i < 100; i++) { for (int i = 0; i < 100; i++) {
...@@ -237,12 +258,12 @@ void testLocalCoordinates() { ...@@ -237,12 +258,12 @@ void testLocalCoordinates() {
Vec3 xdir, ydir, zdir; Vec3 xdir, ydir, zdir;
do { do {
for (int j = 0; j < 3; j++) for (int j = 0; j < numSiteParticles; j++)
positions[j] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt)); positions[j] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
xdir = positions[0]*xWeights[0] + positions[1]*xWeights[1] + positions[2]*xWeights[2]; xdir = computeWeightedPosition(positions, xWeights);
ydir = positions[0]*yWeights[0] + positions[1]*yWeights[1] + positions[2]*yWeights[2]; ydir = computeWeightedPosition(positions, yWeights);;
zdir = xdir.cross(ydir); zdir = xdir.cross(ydir);
if (sqrt(xdir.dot(xdir)) > 0.1 && sqrt(ydir.dot(ydir)) > 0.1 && sqrt(zdir.dot(zdir)) > 0.1) if (sqrt(xdir.dot(xdir)) > 0.1 && (numSiteParticles == 2 || (sqrt(ydir.dot(ydir)) > 0.1 && sqrt(zdir.dot(zdir)) > 0.1)))
break; // These positions give a reasonable coordinate system. break; // These positions give a reasonable coordinate system.
} while (true); } while (true);
context.setPositions(positions); context.setPositions(positions);
...@@ -252,23 +273,23 @@ void testLocalCoordinates() { ...@@ -252,23 +273,23 @@ void testLocalCoordinates() {
State state = context.getState(State::Positions | State::Forces); State state = context.getState(State::Positions | State::Forces);
const vector<Vec3>& pos = state.getPositions(); const vector<Vec3>& pos = state.getPositions();
Vec3 origin = pos[0]*originWeights[0] + pos[1]*originWeights[1] + pos[2]*originWeights[2]; Vec3 origin = computeWeightedPosition(pos, originWeights);;
xdir /= sqrt(xdir.dot(xdir)); xdir /= sqrt(xdir.dot(xdir));
zdir /= sqrt(zdir.dot(zdir)); zdir /= sqrt(zdir.dot(zdir));
ydir = zdir.cross(xdir); ydir = zdir.cross(xdir);
ASSERT_EQUAL_VEC(origin+xdir*localPosition[0]+ydir*localPosition[1]+zdir*localPosition[2], pos[3], 1e-5); ASSERT_EQUAL_VEC(origin+xdir*localPosition[0]+ydir*localPosition[1]+zdir*localPosition[2], pos[numSiteParticles], 1e-5);
// Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount. // Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
double norm = 0.0; double norm = 0.0;
for (int i = 0; i < 3; ++i) { for (int i = 0; i < numSiteParticles; ++i) {
Vec3 f = state.getForces()[i]; Vec3 f = state.getForces()[i];
norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2]; norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
} }
norm = std::sqrt(norm); norm = std::sqrt(norm);
const double delta = 1e-2; const double delta = 1e-2;
double step = 0.5*delta/norm; double step = 0.5*delta/norm;
for (int i = 0; i < 3; ++i) { for (int i = 0; i < numSiteParticles; ++i) {
Vec3 p = positions[i]; Vec3 p = positions[i];
Vec3 f = state.getForces()[i]; Vec3 f = state.getForces()[i];
positions2[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step); positions2[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
...@@ -469,7 +490,9 @@ int main(int argc, char* argv[]) { ...@@ -469,7 +490,9 @@ int main(int argc, char* argv[]) {
testTwoParticleAverage(); testTwoParticleAverage();
testThreeParticleAverage(); testThreeParticleAverage();
testOutOfPlane(); testOutOfPlane();
testLocalCoordinates(); testLocalCoordinates(2);
testLocalCoordinates(3);
testLocalCoordinates(4);
testConservationLaws(); testConservationLaws();
testOverlappingSites(); testOverlappingSites();
runPlatformTests(); runPlatformTests();
......
wrappers/generateWrappers.py
View file @ 0827ad50
...@@ -68,7 +68,15 @@ class WrapperGenerator: ...@@ -68,7 +68,15 @@ class WrapperGenerator:
def __init__(self, inputDirname, output): def __init__(self, inputDirname, output):
self.skipClasses = ['OpenMM::Vec3', 'OpenMM::XmlSerializer', 'OpenMM::Kernel', 'OpenMM::KernelImpl', 'OpenMM::KernelFactory', 'OpenMM::ContextImpl', 'OpenMM::SerializationNode', 'OpenMM::SerializationProxy'] self.skipClasses = ['OpenMM::Vec3', 'OpenMM::XmlSerializer', 'OpenMM::Kernel', 'OpenMM::KernelImpl', 'OpenMM::KernelFactory', 'OpenMM::ContextImpl', 'OpenMM::SerializationNode', 'OpenMM::SerializationProxy']
self.skipMethods = ['OpenMM::Context::getState', 'OpenMM::Platform::loadPluginsFromDirectory', 'OpenMM::Platform::getPluginLoadFailures', 'OpenMM::Context::createCheckpoint', 'OpenMM::Context::loadCheckpoint', 'OpenMM::Context::getMolecules'] self.skipMethods = ['State OpenMM::Context::getState',
'void OpenMM::Context::createCheckpoint',
'void OpenMM::Context::loadCheckpoint',
'const std::vector<std::vector<int> >& OpenMM::Context::getMolecules',
'static std::vector<std::string> OpenMM::Platform::getPluginLoadFailures',
'static std::vector<std::string> OpenMM::Platform::loadPluginsFromDirectory',
'Vec3 OpenMM::LocalCoordinatesSite::getOriginWeights',
'Vec3 OpenMM::LocalCoordinatesSite::getXWeights',
'Vec3 OpenMM::LocalCoordinatesSite::getYWeights']
self.hideClasses = ['Kernel', 'KernelImpl', 'KernelFactory', 'ContextImpl', 'SerializationNode', 'SerializationProxy'] self.hideClasses = ['Kernel', 'KernelImpl', 'KernelFactory', 'ContextImpl', 'SerializationNode', 'SerializationProxy']
self.nodeByID={} self.nodeByID={}
...@@ -119,9 +127,7 @@ class WrapperGenerator: ...@@ -119,9 +127,7 @@ class WrapperGenerator:
for section in findNodes(classNode, "sectiondef", kind="public-static-func")+findNodes(classNode, "sectiondef", kind="public-func"): for section in findNodes(classNode, "sectiondef", kind="public-static-func")+findNodes(classNode, "sectiondef", kind="public-func"):
for memberNode in findNodes(section, "memberdef", kind="function", prot="public"): for memberNode in findNodes(section, "memberdef", kind="function", prot="public"):
methodDefinition = getText("definition", memberNode) methodDefinition = getText("definition", memberNode)
shortMethodDefinition = stripOpenMMPrefix(methodDefinition) if methodDefinition in self.skipMethods:
methodName = shortMethodDefinition.split()[-1]
if className+'::'+methodName in self.skipMethods:
continue continue
methodList.append(memberNode) methodList.append(memberNode)
return methodList return methodList
......
wrappers/python/simtk/openmm/app/forcefield.py
View file @ 0827ad50
...@@ -647,10 +647,15 @@ class ForceField(object): ...@@ -647,10 +647,15 @@ class ForceField(object):
numAtoms = 3 numAtoms = 3
self.weights = [float(attrib['weight12']), float(attrib['weight13']), float(attrib['weightCross'])] self.weights = [float(attrib['weight12']), float(attrib['weight13']), float(attrib['weightCross'])]
elif self.type == 'localCoords': elif self.type == 'localCoords':
numAtoms = 3 numAtoms = 0
self.originWeights = [float(attrib['wo1']), float(attrib['wo2']), float(attrib['wo3'])] self.originWeights = []
self.xWeights = [float(attrib['wx1']), float(attrib['wx2']), float(attrib['wx3'])] self.xWeights = []
self.yWeights = [float(attrib['wy1']), float(attrib['wy2']), float(attrib['wy3'])] self.yWeights = []
while ('wo%d' % (numAtoms+1)) in attrib:
numAtoms += 1
self.originWeights.append(float(attrib['wo%d' % numAtoms]))
self.xWeights.append(float(attrib['wx%d' % numAtoms]))
self.yWeights.append(float(attrib['wy%d' % numAtoms]))
self.localPos = [float(attrib['p1']), float(attrib['p2']), float(attrib['p3'])] self.localPos = [float(attrib['p1']), float(attrib['p2']), float(attrib['p3'])]
else: else:
raise ValueError('Unknown virtual site type: %s' % self.type) raise ValueError('Unknown virtual site type: %s' % self.type)
...@@ -1255,11 +1260,7 @@ class ForceField(object): ...@@ -1255,11 +1260,7 @@ class ForceField(object):
elif site.type == 'outOfPlane': elif site.type == 'outOfPlane':
sys.setVirtualSite(index, mm.OutOfPlaneSite(atoms[0], atoms[1], atoms[2], site.weights[0], site.weights[1], site.weights[2])) sys.setVirtualSite(index, mm.OutOfPlaneSite(atoms[0], atoms[1], atoms[2], site.weights[0], site.weights[1], site.weights[2]))
elif site.type == 'localCoords': elif site.type == 'localCoords':
sys.setVirtualSite(index, mm.LocalCoordinatesSite(atoms[0], atoms[1], atoms[2], sys.setVirtualSite(index, mm.LocalCoordinatesSite(atoms, site.originWeights, site.xWeights, site.yWeights, site.localPos))
mm.Vec3(site.originWeights[0], site.originWeights[1], site.originWeights[2]),
mm.Vec3(site.xWeights[0], site.xWeights[1], site.xWeights[2]),
mm.Vec3(site.yWeights[0], site.yWeights[1], site.yWeights[2]),
mm.Vec3(site.localPos[0], site.localPos[1], site.localPos[2])))
# Add forces to the System # Add forces to the System
......
wrappers/python/src/swig_doxygen/swigInputConfig.py
View file @ 0827ad50
...@@ -108,6 +108,9 @@ SKIP_METHODS = [('State', 'getPositions'), ...@@ -108,6 +108,9 @@ SKIP_METHODS = [('State', 'getPositions'),
('IntegrateDrudeSCFStepKernel',), ('IntegrateDrudeSCFStepKernel',),
('XmlSerializer', 'serialize'), ('XmlSerializer', 'serialize'),
('XmlSerializer', 'deserialize'), ('XmlSerializer', 'deserialize'),
('LocalCoordinatesSite', 'getOriginWeights', 0),
('LocalCoordinatesSite', 'getXWeights', 0),
('LocalCoordinatesSite', 'getYWeights', 0),
] ]
# The build script assumes method args that are non-const references are # The build script assumes method args that are non-const references are
......
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