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Commit a381a3ab authored by peastman's avatar peastman
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Merge branch 'master' into gayberne

parents 5ecc8e00 1f7866ad
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Showing with 806 additions and 272 deletions
plugins/amoeba/platforms/cuda/src/kernels/pmeMultipoleElectrostatics.cu
View file @ a381a3ab
......@@ -555,6 +555,8 @@ extern "C" __global__ void computeElectrostatics(
#ifdef USE_CUTOFF
const unsigned int numTiles = interactionCount[0];
if (numTiles > maxTiles)
return; // There wasn't enough memory for the neighbor list.
int pos = (int) (numTiles > maxTiles ? startTileIndex+warp*(long long)numTileIndices/totalWarps : warp*(long long)numTiles/totalWarps);
int end = (int) (numTiles > maxTiles ? startTileIndex+(warp+1)*(long long)numTileIndices/totalWarps : (warp+1)*(long long)numTiles/totalWarps);
#else
......@@ -575,11 +577,8 @@ extern "C" __global__ void computeElectrostatics(
int x, y;
#ifdef USE_CUTOFF
if (numTiles <= maxTiles)
x = tiles[pos];
else
#endif
{
#else
y = (int) floor(NUM_BLOCKS+0.5f-SQRT((NUM_BLOCKS+0.5f)*(NUM_BLOCKS+0.5f)-2*pos));
x = (pos-y*NUM_BLOCKS+y*(y+1)/2);
if (x < y || x >= NUM_BLOCKS) { // Occasionally happens due to roundoff error.
......@@ -602,7 +601,7 @@ extern "C" __global__ void computeElectrostatics(
while (skipTiles[currentSkipIndex] < pos)
currentSkipIndex++;
includeTile = (skipTiles[currentSkipIndex] != pos);
}
#endif
if (includeTile) {
unsigned int atom1 = x*TILE_SIZE + tgx;
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaAngleForce.cpp
View file @ a381a3ab
......@@ -33,6 +33,9 @@
* This tests the CUDA implementation of CudaAmoebaAngleForce.
*/
#ifdef WIN32
#define _USE_MATH_DEFINES // Needed to get M_PI
#endif
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "openmm/CustomAngleForce.h"
......
plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaMultipoleForce.cpp
View file @ a381a3ab
......@@ -2666,6 +2666,76 @@ static void testParticleInducedDipoles() {
ASSERT_EQUAL_VEC(expectedDipole[i], dipole[i], 1e-4);
}
// test querying particle lab frame permanent dipoles
static void testParticleLabFramePermanentDipoles() {
int numberOfParticles = 8;
int inputPmeGridDimension = 0;
double cutoff = 9000000.0;
std::vector<Vec3> forces;
double energy;
System system;
AmoebaMultipoleForce* amoebaMultipoleForce = new AmoebaMultipoleForce();;
setupMultipoleAmmonia(system, amoebaMultipoleForce, AmoebaMultipoleForce::NoCutoff, AmoebaMultipoleForce::Mutual,
cutoff, inputPmeGridDimension);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
Context context(system, integrator, Platform::getPlatformByName("CUDA"));
getForcesEnergyMultipoleAmmonia(context, forces, energy);
std::vector<Vec3> dipole;
amoebaMultipoleForce->getLabFramePermanentDipoles(context, dipole);
// Compare to values calculated by TINKER.
std::vector<Vec3> expectedDipole(numberOfParticles);
expectedDipole[0] = Vec3(0.00876454250, -2.04310718E-06, -0.00227593519);
expectedDipole[1] = Vec3(0.000780382180, -0.00432882849, 0.00236926761);
expectedDipole[2] = Vec3(0.000801345883, 0.00431830946, 0.00238143437);
expectedDipole[3] = Vec3(-0.00109746996, 1.16087953e-5, -0.00487407492);
expectedDipole[4] = Vec3(0.00203814102, -2.26554196e-5, 0.00882284298);
expectedDipole[5] = Vec3(-0.00239443187, 0.00432388648, 0.000729303209);
expectedDipole[6] = Vec3(0.00491086743, 2.86430963e-6, -0.000918996348);
expectedDipole[7] = Vec3(-0.00239301946, -0.00432743976, 0.000712674115);
for (int i = 0; i < numberOfParticles; i++)
ASSERT_EQUAL_VEC(expectedDipole[i], dipole[i], 1e-4);
}
// test querying particle total dipoles (fixed + induced)
static void testParticleTotalDipoles() {
int numberOfParticles = 8;
int inputPmeGridDimension = 0;
double cutoff = 9000000.0;
std::vector<Vec3> forces;
double energy;
System system;
AmoebaMultipoleForce* amoebaMultipoleForce = new AmoebaMultipoleForce();;
setupMultipoleAmmonia(system, amoebaMultipoleForce, AmoebaMultipoleForce::NoCutoff, AmoebaMultipoleForce::Mutual,
cutoff, inputPmeGridDimension);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
Context context(system, integrator, Platform::getPlatformByName("CUDA"));
getForcesEnergyMultipoleAmmonia(context, forces, energy);
std::vector<Vec3> dipole;
amoebaMultipoleForce->getTotalDipoles(context, dipole);
// Compare to values calculated by TINKER.
std::vector<Vec3> expectedDipole(numberOfParticles);
expectedDipole[0] = Vec3(0.0119356307, -1.11302433e-6, -0.00296793872);
expectedDipole[1] = Vec3(8.60636211e-4, -0.00460821816, 0.00241705344);
expectedDipole[2] = Vec3(8.80646403e-4, 0.00459728769, 0.00243013245);
expectedDipole[3] = Vec3(-0.00123822377, 1.31555550e-5, -0.00558185336);
expectedDipole[4] = Vec3(0.00399455556, -2.27511931e-5, 0.00955607952);
expectedDipole[5] = Vec3(-0.00157302682, 0.00354892386, 3.40921137e-4);
expectedDipole[6] = Vec3(0.00952428069, 2.14171505e-6, -6.68945865e-4);
expectedDipole[7] = Vec3(-0.00157252460, -0.00355015528, 3.27055162e-4);
for (int i = 0; i < numberOfParticles; i++)
ASSERT_EQUAL_VEC(expectedDipole[i], dipole[i], 1e-4);
}
// test computation of system multipole moments
static void testSystemMultipoleMoments() {
......
plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.cpp
View file @ a381a3ab
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
......@@ -594,9 +594,9 @@ void ReferenceCalcAmoebaMultipoleForceKernel::initialize(const System& system, c
nonbondedMethod = force.getNonbondedMethod();
if (nonbondedMethod == AmoebaMultipoleForce::PME) {
usePme = true;
alphaEwald = force.getAEwald();
pmeGridDimension.resize(3);
force.getPMEParameters(alphaEwald, pmeGridDimension[0], pmeGridDimension[1], pmeGridDimension[2]);
cutoffDistance = force.getCutoffDistance();
force.getPmeGridDimensions(pmeGridDimension);
if (pmeGridDimension[0] == 0 || alphaEwald == 0.0) {
NonbondedForce nb;
nb.setEwaldErrorTolerance(force.getEwaldErrorTolerance());
......@@ -735,6 +735,48 @@ void ReferenceCalcAmoebaMultipoleForceKernel::getInducedDipoles(ContextImpl& con
delete amoebaReferenceMultipoleForce;
}
void ReferenceCalcAmoebaMultipoleForceKernel::getLabFramePermanentDipoles(ContextImpl& context, vector<Vec3>& outputDipoles) {
int numParticles = context.getSystem().getNumParticles();
outputDipoles.resize(numParticles);
// Create an AmoebaReferenceMultipoleForce to do the calculation.
AmoebaReferenceMultipoleForce* amoebaReferenceMultipoleForce = setupAmoebaReferenceMultipoleForce(context);
vector<RealVec>& posData = extractPositions(context);
// Retrieve the permanent dipoles in the lab frame.
vector<RealVec> labFramePermanentDipoles;
amoebaReferenceMultipoleForce->calculateLabFramePermanentDipoles(posData, charges, dipoles, quadrupoles, tholes,
dampingFactors, polarity, axisTypes, multipoleAtomZs, multipoleAtomXs, multipoleAtomYs, multipoleAtomCovalentInfo, labFramePermanentDipoles);
for (int i = 0; i < numParticles; i++)
outputDipoles[i] = labFramePermanentDipoles[i];
delete amoebaReferenceMultipoleForce;
}
void ReferenceCalcAmoebaMultipoleForceKernel::getTotalDipoles(ContextImpl& context, vector<Vec3>& outputDipoles) {
int numParticles = context.getSystem().getNumParticles();
outputDipoles.resize(numParticles);
// Create an AmoebaReferenceMultipoleForce to do the calculation.
AmoebaReferenceMultipoleForce* amoebaReferenceMultipoleForce = setupAmoebaReferenceMultipoleForce(context);
vector<RealVec>& posData = extractPositions(context);
// Retrieve the permanent dipoles in the lab frame.
vector<RealVec> totalDipoles;
amoebaReferenceMultipoleForce->calculateTotalDipoles(posData, charges, dipoles, quadrupoles, tholes,
dampingFactors, polarity, axisTypes, multipoleAtomZs, multipoleAtomXs, multipoleAtomYs, multipoleAtomCovalentInfo, totalDipoles);
for (int i = 0; i < numParticles; i++)
outputDipoles[i] = totalDipoles[i];
delete amoebaReferenceMultipoleForce;
}
void ReferenceCalcAmoebaMultipoleForceKernel::getElectrostaticPotential(ContextImpl& context, const std::vector< Vec3 >& inputGrid,
std::vector< double >& outputElectrostaticPotential) {
......@@ -996,7 +1038,7 @@ void ReferenceCalcAmoebaVdwForceKernel::initialize(const System& system, const A
epsilonCombiningRule = force.getEpsilonCombiningRule();
useCutoff = (force.getNonbondedMethod() != AmoebaVdwForce::NoCutoff);
usePBC = (force.getNonbondedMethod() == AmoebaVdwForce::CutoffPeriodic);
cutoff = force.getCutoff();
cutoff = force.getCutoffDistance();
neighborList = useCutoff ? new NeighborList() : NULL;
dispersionCoefficient = force.getUseDispersionCorrection() ? AmoebaVdwForceImpl::calcDispersionCorrection(system, force) : 0.0;
......
plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.h
View file @ a381a3ab
......@@ -381,6 +381,20 @@ public:
* @param dipoles the induced dipole moment of particle i is stored into the i'th element
*/
void getInducedDipoles(ContextImpl& context, std::vector<Vec3>& dipoles);
/**
* Get the fixed dipole moments of all particles in the global reference frame.
*
* @param context the Context for which to get the fixed dipoles
* @param dipoles the fixed dipole moment of particle i is stored into the i'th element
*/
void getLabFramePermanentDipoles(ContextImpl& context, std::vector<Vec3>& dipoles);
/**
* Get the total dipole moments of all particles in the global reference frame.
*
* @param context the Context for which to get the fixed dipoles
* @param dipoles the fixed dipole moment of particle i is stored into the i'th element
*/
void getTotalDipoles(ContextImpl& context, std::vector<Vec3>& dipoles);
/**
* Calculate the electrostatic potential given vector of grid coordinates.
*
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.cpp
View file @ a381a3ab
......@@ -1943,6 +1943,64 @@ void AmoebaReferenceMultipoleForce::calculateInducedDipoles(const vector<RealVec
outputInducedDipoles = _inducedDipole;
}
void AmoebaReferenceMultipoleForce::calculateLabFramePermanentDipoles(const vector<RealVec>& particlePositions,
const vector<RealOpenMM>& charges,
const vector<RealOpenMM>& dipoles,
const vector<RealOpenMM>& quadrupoles,
const vector<RealOpenMM>& tholes,
const vector<RealOpenMM>& dampingFactors,
const vector<RealOpenMM>& polarity,
const vector<int>& axisTypes,
const vector<int>& multipoleAtomZs,
const vector<int>& multipoleAtomXs,
const vector<int>& multipoleAtomYs,
const vector< vector< vector<int> > >& multipoleAtomCovalentInfo,
vector<RealVec>& outputRotatedPermanentDipoles) {
// setup, including calculating permanent dipoles
vector<MultipoleParticleData> particleData;
setup(particlePositions, charges, dipoles, quadrupoles, tholes,
dampingFactors, polarity, axisTypes, multipoleAtomZs, multipoleAtomXs, multipoleAtomYs,
multipoleAtomCovalentInfo, particleData);
outputRotatedPermanentDipoles.resize(_numParticles);
for (int i = 0; i < _numParticles; i++)
{
outputRotatedPermanentDipoles[i] = particleData[i].dipole;
}
}
void AmoebaReferenceMultipoleForce::calculateTotalDipoles(const vector<RealVec>& particlePositions,
const vector<RealOpenMM>& charges,
const vector<RealOpenMM>& dipoles,
const vector<RealOpenMM>& quadrupoles,
const vector<RealOpenMM>& tholes,
const vector<RealOpenMM>& dampingFactors,
const vector<RealOpenMM>& polarity,
const vector<int>& axisTypes,
const vector<int>& multipoleAtomZs,
const vector<int>& multipoleAtomXs,
const vector<int>& multipoleAtomYs,
const vector< vector< vector<int> > >& multipoleAtomCovalentInfo,
vector<RealVec>& outputTotalDipoles) {
// setup, including calculating permanent dipoles
vector<MultipoleParticleData> particleData;
setup(particlePositions, charges, dipoles, quadrupoles, tholes,
dampingFactors, polarity, axisTypes, multipoleAtomZs, multipoleAtomXs, multipoleAtomYs,
multipoleAtomCovalentInfo, particleData);
outputTotalDipoles.resize(_numParticles);
for (int i = 0; i < _numParticles; i++)
{
for (int j = 0; j < 3; j++)
{
outputTotalDipoles[i][j] = particleData[i].dipole[j] + _inducedDipole[i][j];
}
}
}
void AmoebaReferenceMultipoleForce::calculateAmoebaSystemMultipoleMoments(const vector<RealOpenMM>& masses,
const vector<RealVec>& particlePositions,
const vector<RealOpenMM>& charges,
......
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.h
View file @ a381a3ab
......@@ -533,6 +533,75 @@ public:
const std::vector< std::vector< std::vector<int> > >& multipoleAtomCovalentInfo,
std::vector<RealVec>& outputInducedDipoles);
/**
* Calculate particle permanent dipoles rotated in the lab frame.
*
* @param masses particle masses
* @param particlePositions Cartesian coordinates of particles
* @param charges scalar charges for each particle
* @param dipoles molecular frame dipoles for each particle
* @param quadrupoles molecular frame quadrupoles for each particle
* @param tholes Thole factors for each particle
* @param dampingFactors dampling factors for each particle
* @param polarity polarity for each particle
* @param axisTypes axis type (Z-then-X, ...) for each particle
* @param multipoleAtomZs indicies of particle specifying the molecular frame z-axis for each particle
* @param multipoleAtomXs indicies of particle specifying the molecular frame x-axis for each particle
* @param multipoleAtomYs indicies of particle specifying the molecular frame y-axis for each particle
* @param multipoleAtomCovalentInfo covalent info needed to set scaling factors
* @param outputMultipoleMoments output multipole moments
*/
void calculateLabFramePermanentDipoles(const std::vector<RealVec>& particlePositions,
const std::vector<RealOpenMM>& charges,
const std::vector<RealOpenMM>& dipoles,
const std::vector<RealOpenMM>& quadrupoles,
const std::vector<RealOpenMM>& tholes,
const std::vector<RealOpenMM>& dampingFactors,
const std::vector<RealOpenMM>& polarity,
const std::vector<int>& axisTypes,
const std::vector<int>& multipoleAtomZs,
const std::vector<int>& multipoleAtomXs,
const std::vector<int>& multipoleAtomYs,
const std::vector< vector< vector<int> > >& multipoleAtomCovalentInfo,
std::vector<RealVec>& outputRotatedPermanentDipoles);
/**
* Calculate particle total dipoles.
*
* @param masses particle masses
* @param particlePositions Cartesian coordinates of particles
* @param charges scalar charges for each particle
* @param dipoles molecular frame dipoles for each particle
* @param quadrupoles molecular frame quadrupoles for each particle
* @param tholes Thole factors for each particle
* @param dampingFactors dampling factors for each particle
* @param polarity polarity for each particle
* @param axisTypes axis type (Z-then-X, ...) for each particle
* @param multipoleAtomZs indicies of particle specifying the molecular frame z-axis for each particle
* @param multipoleAtomXs indicies of particle specifying the molecular frame x-axis for each particle
* @param multipoleAtomYs indicies of particle specifying the molecular frame y-axis for each particle
* @param multipoleAtomCovalentInfo covalent info needed to set scaling factors
* @param outputMultipoleMoments output multipole moments
*/
void calculateTotalDipoles(const std::vector<RealVec>& particlePositions,
const std::vector<RealOpenMM>& charges,
const std::vector<RealOpenMM>& dipoles,
const std::vector<RealOpenMM>& quadrupoles,
const std::vector<RealOpenMM>& tholes,
const std::vector<RealOpenMM>& dampingFactors,
const std::vector<RealOpenMM>& polarity,
const std::vector<int>& axisTypes,
const std::vector<int>& multipoleAtomZs,
const std::vector<int>& multipoleAtomXs,
const std::vector<int>& multipoleAtomYs,
const std::vector< vector< vector<int> > >& multipoleAtomCovalentInfo,
std::vector<RealVec>& outputRotatedPermanentDipoles);
/**
* Calculate system multipole moments.
*
......
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaAngleForce.cpp
View file @ a381a3ab
......@@ -33,6 +33,9 @@
* This tests the Cuda implementation of CudaAmoebaAngleForce.
*/
#ifdef WIN32
#define _USE_MATH_DEFINES // Needed to get M_PI
#endif
#include "openmm/internal/AssertionUtilities.h"
#include "openmm/Context.h"
#include "openmm/CustomAngleForce.h"
......
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaMultipoleForce.cpp
View file @ a381a3ab
......@@ -2587,6 +2587,76 @@ static void testParticleInducedDipoles() {
ASSERT_EQUAL_VEC(expectedDipole[i], dipole[i], 1e-4);
}
// test querying particle lab frame permanent dipoles
static void testParticleLabFramePermanentDipoles() {
int numberOfParticles = 8;
int inputPmeGridDimension = 0;
double cutoff = 9000000.0;
std::vector<Vec3> forces;
double energy;
System system;
AmoebaMultipoleForce* amoebaMultipoleForce = new AmoebaMultipoleForce();;
setupMultipoleAmmonia(system, amoebaMultipoleForce, AmoebaMultipoleForce::NoCutoff, AmoebaMultipoleForce::Mutual,
cutoff, inputPmeGridDimension);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
Context context(system, integrator, Platform::getPlatformByName("Reference"));
getForcesEnergyMultipoleAmmonia(context, forces, energy);
std::vector<Vec3> dipole;
amoebaMultipoleForce->getLabFramePermanentDipoles(context, dipole);
// Compare to values calculated by TINKER.
std::vector<Vec3> expectedDipole(numberOfParticles);
expectedDipole[0] = Vec3(0.00876454250, -2.04310718E-06, -0.00227593519);
expectedDipole[1] = Vec3(0.000780382180, -0.00432882849, 0.00236926761);
expectedDipole[2] = Vec3(0.000801345883, 0.00431830946, 0.00238143437);
expectedDipole[3] = Vec3(-0.00109746996, 1.16087953e-5, -0.00487407492);
expectedDipole[4] = Vec3(0.00203814102, -2.26554196e-5, 0.00882284298);
expectedDipole[5] = Vec3(-0.00239443187, 0.00432388648, 0.000729303209);
expectedDipole[6] = Vec3(0.00491086743, 2.86430963e-6, -0.000918996348);
expectedDipole[7] = Vec3(-0.00239301946, -0.00432743976, 0.000712674115);
for (int i = 0; i < numberOfParticles; i++)
ASSERT_EQUAL_VEC(expectedDipole[i], dipole[i], 1e-4);
}
// test querying particle total dipoles (fixed + induced)
static void testParticleTotalDipoles() {
int numberOfParticles = 8;
int inputPmeGridDimension = 0;
double cutoff = 9000000.0;
std::vector<Vec3> forces;
double energy;
System system;
AmoebaMultipoleForce* amoebaMultipoleForce = new AmoebaMultipoleForce();;
setupMultipoleAmmonia(system, amoebaMultipoleForce, AmoebaMultipoleForce::NoCutoff, AmoebaMultipoleForce::Mutual,
cutoff, inputPmeGridDimension);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
Context context(system, integrator, Platform::getPlatformByName("Reference"));
getForcesEnergyMultipoleAmmonia(context, forces, energy);
std::vector<Vec3> dipole;
amoebaMultipoleForce->getTotalDipoles(context, dipole);
// Compare to values calculated by TINKER.
std::vector<Vec3> expectedDipole(numberOfParticles);
expectedDipole[0] = Vec3(0.0119356307, -1.11302433e-6, -0.00296793872);
expectedDipole[1] = Vec3(8.60636211e-4, -0.00460821816, 0.00241705344);
expectedDipole[2] = Vec3(8.80646403e-4, 0.00459728769, 0.00243013245);
expectedDipole[3] = Vec3(-0.00123822377, 1.31555550e-5, -0.00558185336);
expectedDipole[4] = Vec3(0.00399455556, -2.27511931e-5, 0.00955607952);
expectedDipole[5] = Vec3(-0.00157302682, 0.00354892386, 3.40921137e-4);
expectedDipole[6] = Vec3(0.00952428069, 2.14171505e-6, -6.68945865e-4);
expectedDipole[7] = Vec3(-0.00157252460, -0.00355015528, 3.27055162e-4);
for (int i = 0; i < numberOfParticles; i++)
ASSERT_EQUAL_VEC(expectedDipole[i], dipole[i], 1e-4);
}
// test computation of system multipole moments
static void testSystemMultipoleMoments() {
......
plugins/amoeba/serialization/src/AmoebaMultipoleForceProxy.cpp
View file @ a381a3ab
......@@ -74,20 +74,18 @@ void AmoebaMultipoleForceProxy::serialize(const void* object, SerializationNode&
node.setIntProperty("forceGroup", force.getForceGroup());
node.setIntProperty("nonbondedMethod", force.getNonbondedMethod());
node.setIntProperty("polarizationType", force.getPolarizationType());
//node.setIntProperty("pmeBSplineOrder", force.getPmeBSplineOrder());
//node.setIntProperty("mutualInducedIterationMethod", force.getMutualInducedIterationMethod());
node.setIntProperty("mutualInducedMaxIterations", force.getMutualInducedMaxIterations());
node.setDoubleProperty("cutoffDistance", force.getCutoffDistance());
node.setDoubleProperty("aEwald", force.getAEwald());
double alpha;
int nx, ny, nz;
force.getPMEParameters(alpha, nx, ny, nz);
node.setDoubleProperty("aEwald", alpha);
node.setDoubleProperty("mutualInducedTargetEpsilon", force.getMutualInducedTargetEpsilon());
//node.setDoubleProperty("electricConstant", force.getElectricConstant());
node.setDoubleProperty("ewaldErrorTolerance", force.getEwaldErrorTolerance());
std::vector<int> gridDimensions;
force.getPmeGridDimensions(gridDimensions);
SerializationNode& gridDimensionsNode = node.createChildNode("MultipoleParticleGridDimension");
gridDimensionsNode.setIntProperty("d0", gridDimensions[0]).setIntProperty("d1", gridDimensions[1]).setIntProperty("d2", gridDimensions[2]);
gridDimensionsNode.setIntProperty("d0", nx).setIntProperty("d1", ny).setIntProperty("d2", nz);
SerializationNode& coefficients = node.createChildNode("ExtrapolationCoefficients");
vector<double> coeff = force.getExtrapolationCoefficients();
......@@ -144,22 +142,14 @@ void* AmoebaMultipoleForceProxy::deserialize(const SerializationNode& node) cons
force->setNonbondedMethod(static_cast<AmoebaMultipoleForce::NonbondedMethod>(node.getIntProperty("nonbondedMethod")));
if (version >= 2)
force->setPolarizationType(static_cast<AmoebaMultipoleForce::PolarizationType>(node.getIntProperty("polarizationType")));
//force->setPmeBSplineOrder(node.getIntProperty("pmeBSplineOrder"));
//force->setMutualInducedIterationMethod(static_cast<AmoebaMultipoleForce::MutualInducedIterationMethod>(node.getIntProperty("mutualInducedIterationMethod")));
force->setMutualInducedMaxIterations(node.getIntProperty("mutualInducedMaxIterations"));
force->setCutoffDistance(node.getDoubleProperty("cutoffDistance"));
force->setAEwald(node.getDoubleProperty("aEwald"));
force->setMutualInducedTargetEpsilon(node.getDoubleProperty("mutualInducedTargetEpsilon"));
//force->setElectricConstant(node.getDoubleProperty("electricConstant"));
force->setEwaldErrorTolerance(node.getDoubleProperty("ewaldErrorTolerance"));
std::vector<int> gridDimensions;
const SerializationNode& gridDimensionsNode = node.getChildNode("MultipoleParticleGridDimension");
gridDimensions.push_back(gridDimensionsNode.getIntProperty("d0"));
gridDimensions.push_back(gridDimensionsNode.getIntProperty("d1"));
gridDimensions.push_back(gridDimensionsNode.getIntProperty("d2"));
force->setPmeGridDimensions(gridDimensions);
force->setPMEParameters(node.getDoubleProperty("aEwald"), gridDimensionsNode.getIntProperty("d0"), gridDimensionsNode.getIntProperty("d1"), gridDimensionsNode.getIntProperty("d2"));
if (version >= 3) {
const SerializationNode& coefficients = node.getChildNode("ExtrapolationCoefficients");
......
plugins/amoeba/serialization/src/AmoebaVdwForceProxy.cpp
View file @ a381a3ab
......@@ -48,7 +48,7 @@ void AmoebaVdwForceProxy::serialize(const void* object, SerializationNode& node)
node.setIntProperty("forceGroup", force.getForceGroup());
node.setStringProperty("SigmaCombiningRule", force.getSigmaCombiningRule());
node.setStringProperty("EpsilonCombiningRule", force.getEpsilonCombiningRule());
node.setDoubleProperty("VdwCutoff", force.getCutoff());
node.setDoubleProperty("VdwCutoff", force.getCutoffDistance());
node.setIntProperty("method", (int) force.getNonbondedMethod());
......@@ -82,7 +82,7 @@ void* AmoebaVdwForceProxy::deserialize(const SerializationNode& node) const {
force->setForceGroup(node.getIntProperty("forceGroup", 0));
force->setSigmaCombiningRule(node.getStringProperty("SigmaCombiningRule"));
force->setEpsilonCombiningRule(node.getStringProperty("EpsilonCombiningRule"));
force->setCutoff(node.getDoubleProperty("VdwCutoff"));
force->setCutoffDistance(node.getDoubleProperty("VdwCutoff"));
force->setNonbondedMethod((AmoebaVdwForce::NonbondedMethod) node.getIntProperty("method"));
const SerializationNode& particles = node.getChildNode("VdwParticles");
......
plugins/amoeba/serialization/tests/TestSerializeAmoebaMultipoleForce.cpp
View file @ a381a3ab
......@@ -116,11 +116,8 @@ void testSerialization() {
ASSERT_EQUAL(force1.getCutoffDistance(), force2.getCutoffDistance());
ASSERT_EQUAL(force1.getNonbondedMethod(), force2.getNonbondedMethod());
ASSERT_EQUAL(force1.getAEwald(), force2.getAEwald());
//ASSERT_EQUAL(force1.getPmeBSplineOrder(), force2.getPmeBSplineOrder());
//ASSERT_EQUAL(force1.getMutualInducedIterationMethod(), force2.getMutualInducedIterationMethod());
ASSERT_EQUAL(force1.getMutualInducedMaxIterations(), force2.getMutualInducedMaxIterations());
ASSERT_EQUAL(force1.getMutualInducedTargetEpsilon(), force2.getMutualInducedTargetEpsilon());
//ASSERT_EQUAL(force1.getElectricConstant(), force2.getElectricConstant());
ASSERT_EQUAL(force1.getEwaldErrorTolerance(), force2.getEwaldErrorTolerance());
......
plugins/drude/platforms/cuda/src/CudaDrudeKernels.cpp
View file @ a381a3ab
......@@ -364,9 +364,11 @@ void CudaIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const D
// Apply hard wall constraints.
if (maxDrudeDistance > 0) {
void* hardwallArgs[] = {&cu.getPosq().getDevicePointer(), &posCorrection, &cu.getVelm().getDevicePointer(),
&pairParticles->getDevicePointer(), &integration.getStepSize().getDevicePointer(), maxDrudeDistancePtr, hardwallscaleDrudePtr};
cu.executeKernel(hardwallKernel, hardwallArgs, pairParticles->getSize());
}
integration.computeVirtualSites();
// Update the time and step count.
......
plugins/drude/platforms/cuda/tests/TestCudaDrudeLangevinIntegrator.cpp
View file @ a381a3ab
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2013-2015 Stanford University and the Authors. *
* Portions copyright (c) 2013-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -179,6 +179,66 @@ void testWater() {
ASSERT_USUALLY_EQUAL_TOL(expectedTemp, ke/(0.5*numDof*BOLTZ), 0.02);
}
void testForceEnergyConsistency() {
// Create a box of polarizable particles.
const int gridSize = 3;
const int numAtoms = gridSize*gridSize*gridSize;
const double spacing = 0.6;
const double boxSize = spacing*(gridSize+1);
const double temperature = 300.0;
const double temperatureDrude = 10.0;
System system;
vector<Vec3> positions;
NonbondedForce* nonbonded = new NonbondedForce();
DrudeForce* drude = new DrudeForce();
system.addForce(nonbonded);
system.addForce(drude);
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
nonbonded->setNonbondedMethod(NonbondedForce::PME);
nonbonded->setCutoffDistance(1.0);
nonbonded->setUseSwitchingFunction(true);
nonbonded->setSwitchingDistance(0.9);
nonbonded->setEwaldErrorTolerance(5e-5);
for (int i = 0; i < numAtoms; i++) {
int startIndex = system.getNumParticles();
system.addParticle(1.0);
system.addParticle(1.0);
nonbonded->addParticle(1.0, 0.3, 1.0);
nonbonded->addParticle(-1.0, 0.3, 1.0);
nonbonded->addException(startIndex, startIndex+1, 0, 1, 0);
drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.0, 0.001, 1, 1);
}
for (int i = 0; i < gridSize; i++)
for (int j = 0; j < gridSize; j++)
for (int k = 0; k < gridSize; k++) {
Vec3 pos(i*spacing, j*spacing, k*spacing);
positions.push_back(pos);
positions.push_back(pos);
}
// Simulate it and check that force and energy remain consistent.
DrudeLangevinIntegrator integ(temperature, 50.0, temperatureDrude, 50.0, 0.001);
Platform& platform = Platform::getPlatformByName("CUDA");
Context context(system, integ, platform);
context.setPositions(positions);
State prevState;
for (int i = 0; i < 100; i++) {
State state = context.getState(State::Energy | State::Forces | State::Positions);
if (i > 0) {
double expectedEnergyChange = 0;
for (int j = 0; j < system.getNumParticles(); j++) {
Vec3 delta = state.getPositions()[j]-prevState.getPositions()[j];
expectedEnergyChange -= 0.5*(state.getForces()[j]+prevState.getForces()[j]).dot(delta);
}
ASSERT_EQUAL_TOL(expectedEnergyChange, state.getPotentialEnergy()-prevState.getPotentialEnergy(), 0.05);
}
prevState = state;
integ.step(1);
}
}
int main(int argc, char* argv[]) {
try {
registerDrudeCudaKernelFactories();
......@@ -186,6 +246,7 @@ int main(int argc, char* argv[]) {
Platform::getPlatformByName("CUDA").setPropertyDefaultValue("Precision", string(argv[1]));
testSinglePair();
testWater();
testForceEnergyConsistency();
}
catch(const std::exception& e) {
std::cout << "exception: " << e.what() << std::endl;
......
plugins/drude/platforms/opencl/src/OpenCLDrudeKernels.cpp
View file @ a381a3ab
......@@ -376,6 +376,7 @@ void OpenCLIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const
// Apply hard wall constraints.
if (maxDrudeDistance > 0)
cl.executeKernel(hardwallKernel, pairParticles->getSize());
integration.computeVirtualSites();
......
plugins/drude/platforms/opencl/tests/TestOpenCLDrudeLangevinIntegrator.cpp
View file @ a381a3ab
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2013-2015 Stanford University and the Authors. *
* Portions copyright (c) 2013-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -179,6 +179,66 @@ void testWater() {
ASSERT_USUALLY_EQUAL_TOL(expectedTemp, ke/(0.5*numDof*BOLTZ), 0.02);
}
void testForceEnergyConsistency() {
// Create a box of polarizable particles.
const int gridSize = 3;
const int numAtoms = gridSize*gridSize*gridSize;
const double spacing = 0.6;
const double boxSize = spacing*(gridSize+1);
const double temperature = 300.0;
const double temperatureDrude = 10.0;
System system;
vector<Vec3> positions;
NonbondedForce* nonbonded = new NonbondedForce();
DrudeForce* drude = new DrudeForce();
system.addForce(nonbonded);
system.addForce(drude);
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
nonbonded->setNonbondedMethod(NonbondedForce::PME);
nonbonded->setCutoffDistance(1.0);
nonbonded->setUseSwitchingFunction(true);
nonbonded->setSwitchingDistance(0.9);
nonbonded->setEwaldErrorTolerance(5e-5);
for (int i = 0; i < numAtoms; i++) {
int startIndex = system.getNumParticles();
system.addParticle(1.0);
system.addParticle(1.0);
nonbonded->addParticle(1.0, 0.3, 1.0);
nonbonded->addParticle(-1.0, 0.3, 1.0);
nonbonded->addException(startIndex, startIndex+1, 0, 1, 0);
drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.0, 0.001, 1, 1);
}
for (int i = 0; i < gridSize; i++)
for (int j = 0; j < gridSize; j++)
for (int k = 0; k < gridSize; k++) {
Vec3 pos(i*spacing, j*spacing, k*spacing);
positions.push_back(pos);
positions.push_back(pos);
}
// Simulate it and check that force and energy remain consistent.
DrudeLangevinIntegrator integ(temperature, 50.0, temperatureDrude, 50.0, 0.001);
Platform& platform = Platform::getPlatformByName("OpenCL");
Context context(system, integ, platform);
context.setPositions(positions);
State prevState;
for (int i = 0; i < 100; i++) {
State state = context.getState(State::Energy | State::Forces | State::Positions);
if (i > 0) {
double expectedEnergyChange = 0;
for (int j = 0; j < system.getNumParticles(); j++) {
Vec3 delta = state.getPositions()[j]-prevState.getPositions()[j];
expectedEnergyChange -= 0.5*(state.getForces()[j]+prevState.getForces()[j]).dot(delta);
}
ASSERT_EQUAL_TOL(expectedEnergyChange, state.getPotentialEnergy()-prevState.getPotentialEnergy(), 0.05);
}
prevState = state;
integ.step(1);
}
}
int main(int argc, char* argv[]) {
try {
registerDrudeOpenCLKernelFactories();
......@@ -186,6 +246,7 @@ int main(int argc, char* argv[]) {
Platform::getPlatformByName("OpenCL").setPropertyDefaultValue("Precision", string(argv[1]));
testSinglePair();
testWater();
testForceEnergyConsistency();
}
catch(const std::exception& e) {
std::cout << "exception: " << e.what() << std::endl;
......
plugins/drude/platforms/reference/tests/TestReferenceDrudeLangevinIntegrator.cpp
View file @ a381a3ab
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2013-2015 Stanford University and the Authors. *
* Portions copyright (c) 2013-2016 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -179,11 +179,72 @@ void testWater() {
ASSERT_USUALLY_EQUAL_TOL(expectedTemp, ke/(0.5*numDof*BOLTZ), 0.03);
}
void testForceEnergyConsistency() {
// Create a box of polarizable particles.
const int gridSize = 3;
const int numAtoms = gridSize*gridSize*gridSize;
const double spacing = 0.6;
const double boxSize = spacing*(gridSize+1);
const double temperature = 300.0;
const double temperatureDrude = 10.0;
System system;
vector<Vec3> positions;
NonbondedForce* nonbonded = new NonbondedForce();
DrudeForce* drude = new DrudeForce();
system.addForce(nonbonded);
system.addForce(drude);
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
nonbonded->setNonbondedMethod(NonbondedForce::PME);
nonbonded->setCutoffDistance(1.0);
nonbonded->setUseSwitchingFunction(true);
nonbonded->setSwitchingDistance(0.9);
nonbonded->setEwaldErrorTolerance(5e-5);
for (int i = 0; i < numAtoms; i++) {
int startIndex = system.getNumParticles();
system.addParticle(1.0);
system.addParticle(1.0);
nonbonded->addParticle(1.0, 0.3, 1.0);
nonbonded->addParticle(-1.0, 0.3, 1.0);
nonbonded->addException(startIndex, startIndex+1, 0, 1, 0);
drude->addParticle(startIndex+1, startIndex, -1, -1, -1, -1.0, 0.001, 1, 1);
}
for (int i = 0; i < gridSize; i++)
for (int j = 0; j < gridSize; j++)
for (int k = 0; k < gridSize; k++) {
Vec3 pos(i*spacing, j*spacing, k*spacing);
positions.push_back(pos);
positions.push_back(pos);
}
// Simulate it and check that force and energy remain consistent.
DrudeLangevinIntegrator integ(temperature, 50.0, temperatureDrude, 50.0, 0.001);
Platform& platform = Platform::getPlatformByName("Reference");
Context context(system, integ, platform);
context.setPositions(positions);
State prevState;
for (int i = 0; i < 100; i++) {
State state = context.getState(State::Energy | State::Forces | State::Positions);
if (i > 0) {
double expectedEnergyChange = 0;
for (int j = 0; j < system.getNumParticles(); j++) {
Vec3 delta = state.getPositions()[j]-prevState.getPositions()[j];
expectedEnergyChange -= 0.5*(state.getForces()[j]+prevState.getForces()[j]).dot(delta);
}
ASSERT_EQUAL_TOL(expectedEnergyChange, state.getPotentialEnergy()-prevState.getPotentialEnergy(), 0.05);
}
prevState = state;
integ.step(1);
}
}
int main() {
try {
registerDrudeReferenceKernelFactories();
testSinglePair();
testWater();
testForceEnergyConsistency();
}
catch(const std::exception& e) {
std::cout << "exception: " << e.what() << std::endl;
......
serialization/src/CustomAngleForceProxy.cpp
View file @ a381a3ab
......@@ -42,7 +42,7 @@ CustomAngleForceProxy::CustomAngleForceProxy() : SerializationProxy("CustomAngle
}
void CustomAngleForceProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 2);
node.setIntProperty("version", 3);
const CustomAngleForce& force = *reinterpret_cast<const CustomAngleForce*>(object);
node.setIntProperty("forceGroup", force.getForceGroup());
node.setBoolProperty("usesPeriodic", force.usesPeriodicBoundaryConditions());
......@@ -55,6 +55,10 @@ void CustomAngleForceProxy::serialize(const void* object, SerializationNode& nod
for (int i = 0; i < force.getNumGlobalParameters(); i++) {
globalParams.createChildNode("Parameter").setStringProperty("name", force.getGlobalParameterName(i)).setDoubleProperty("default", force.getGlobalParameterDefaultValue(i));
}
SerializationNode& energyDerivs = node.createChildNode("EnergyParameterDerivatives");
for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
energyDerivs.createChildNode("Parameter").setStringProperty("name", force.getEnergyParameterDerivativeName(i));
}
SerializationNode& angles = node.createChildNode("Angles");
for (int i = 0; i < force.getNumAngles(); i++) {
int p1, p2, p3;
......@@ -72,7 +76,7 @@ void CustomAngleForceProxy::serialize(const void* object, SerializationNode& nod
void* CustomAngleForceProxy::deserialize(const SerializationNode& node) const {
int version = node.getIntProperty("version");
if (version < 1 || version > 2)
if (version < 1 || version > 3)
throw OpenMMException("Unsupported version number");
CustomAngleForce* force = NULL;
try {
......@@ -90,6 +94,13 @@ void* CustomAngleForceProxy::deserialize(const SerializationNode& node) const {
const SerializationNode& parameter = globalParams.getChildren()[i];
force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
}
if (version > 2) {
const SerializationNode& energyDerivs = node.getChildNode("EnergyParameterDerivatives");
for (int i = 0; i < (int) energyDerivs.getChildren().size(); i++) {
const SerializationNode& parameter = energyDerivs.getChildren()[i];
force->addEnergyParameterDerivative(parameter.getStringProperty("name"));
}
}
const SerializationNode& angles = node.getChildNode("Angles");
vector<double> params(force->getNumPerAngleParameters());
for (int i = 0; i < (int) angles.getChildren().size(); i++) {
......
serialization/src/CustomBondForceProxy.cpp
View file @ a381a3ab
......@@ -42,7 +42,7 @@ CustomBondForceProxy::CustomBondForceProxy() : SerializationProxy("CustomBondFor
}
void CustomBondForceProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 2);
node.setIntProperty("version", 3);
const CustomBondForce& force = *reinterpret_cast<const CustomBondForce*>(object);
node.setIntProperty("forceGroup", force.getForceGroup());
node.setBoolProperty("usesPeriodic", force.usesPeriodicBoundaryConditions());
......@@ -55,6 +55,10 @@ void CustomBondForceProxy::serialize(const void* object, SerializationNode& node
for (int i = 0; i < force.getNumGlobalParameters(); i++) {
globalParams.createChildNode("Parameter").setStringProperty("name", force.getGlobalParameterName(i)).setDoubleProperty("default", force.getGlobalParameterDefaultValue(i));
}
SerializationNode& energyDerivs = node.createChildNode("EnergyParameterDerivatives");
for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
energyDerivs.createChildNode("Parameter").setStringProperty("name", force.getEnergyParameterDerivativeName(i));
}
SerializationNode& bonds = node.createChildNode("Bonds");
for (int i = 0; i < force.getNumBonds(); i++) {
int p1, p2;
......@@ -72,7 +76,7 @@ void CustomBondForceProxy::serialize(const void* object, SerializationNode& node
void* CustomBondForceProxy::deserialize(const SerializationNode& node) const {
int version = node.getIntProperty("version");
if (version < 1 || version > 2)
if (version < 1 || version > 3)
throw OpenMMException("Unsupported version number");
CustomBondForce* force = NULL;
try {
......@@ -90,6 +94,13 @@ void* CustomBondForceProxy::deserialize(const SerializationNode& node) const {
const SerializationNode& parameter = globalParams.getChildren()[i];
force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
}
if (version > 2) {
const SerializationNode& energyDerivs = node.getChildNode("EnergyParameterDerivatives");
for (int i = 0; i < (int) energyDerivs.getChildren().size(); i++) {
const SerializationNode& parameter = energyDerivs.getChildren()[i];
force->addEnergyParameterDerivative(parameter.getStringProperty("name"));
}
}
const SerializationNode& bonds = node.getChildNode("Bonds");
vector<double> params(force->getNumPerBondParameters());
for (int i = 0; i < (int) bonds.getChildren().size(); i++) {
......
serialization/src/CustomCentroidBondForceProxy.cpp
View file @ a381a3ab
......@@ -42,7 +42,7 @@ CustomCentroidBondForceProxy::CustomCentroidBondForceProxy() : SerializationProx
}
void CustomCentroidBondForceProxy::serialize(const void* object, SerializationNode& node) const {
node.setIntProperty("version", 2);
node.setIntProperty("version", 3);
const CustomCentroidBondForce& force = *reinterpret_cast<const CustomCentroidBondForce*>(object);
node.setIntProperty("forceGroup", force.getForceGroup());
node.setBoolProperty("usesPeriodic", force.usesPeriodicBoundaryConditions());
......@@ -56,6 +56,10 @@ void CustomCentroidBondForceProxy::serialize(const void* object, SerializationNo
for (int i = 0; i < force.getNumGlobalParameters(); i++) {
globalParams.createChildNode("Parameter").setStringProperty("name", force.getGlobalParameterName(i)).setDoubleProperty("default", force.getGlobalParameterDefaultValue(i));
}
SerializationNode& energyDerivs = node.createChildNode("EnergyParameterDerivatives");
for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
energyDerivs.createChildNode("Parameter").setStringProperty("name", force.getEnergyParameterDerivativeName(i));
}
SerializationNode& groups = node.createChildNode("Groups");
for (int i = 0; i < force.getNumGroups(); i++) {
vector<int> particles;
......@@ -95,7 +99,7 @@ void CustomCentroidBondForceProxy::serialize(const void* object, SerializationNo
void* CustomCentroidBondForceProxy::deserialize(const SerializationNode& node) const {
int version = node.getIntProperty("version");
if (version < 1 || version > 2)
if (version < 1 || version > 3)
throw OpenMMException("Unsupported version number");
CustomCentroidBondForce* force = NULL;
try {
......@@ -113,6 +117,13 @@ void* CustomCentroidBondForceProxy::deserialize(const SerializationNode& node) c
const SerializationNode& parameter = globalParams.getChildren()[i];
force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
}
if (version > 2) {
const SerializationNode& energyDerivs = node.getChildNode("EnergyParameterDerivatives");
for (int i = 0; i < (int) energyDerivs.getChildren().size(); i++) {
const SerializationNode& parameter = energyDerivs.getChildren()[i];
force->addEnergyParameterDerivative(parameter.getStringProperty("name"));
}
}
const SerializationNode& groups = node.getChildNode("Groups");
for (int i = 0; i < (int) groups.getChildren().size(); i++) {
const SerializationNode& group = groups.getChildren()[i];
......
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