int ReferenceLincsAlgorithm::apply( int numberOfAtoms, vector<RealVec>& atomCoordinates,
vector<RealVec>& atomCoordinatesP,
vector<RealOpenMM>& inverseMasses ){
// ---------------------------------------------------------------------------------------
static const char* methodName = "\nReferenceLincsAlgorithm::apply";
static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0;
static const RealOpenMM two = 2.0;
// ---------------------------------------------------------------------------------------
if (_numberOfConstraints == 0)
return SimTKOpenMMCommon::DefaultReturn;
if( !_hasInitialized )
initialize(numberOfAtoms, inverseMasses);
// Calculate the direction of each constraint, along with the initial RHS and solution vectors.
for (int i = 0; i < _numberOfConstraints; i++) {
int atom1 = _atomIndices[i][0];
int atom2 = _atomIndices[i][1];
_constraintDir[i] = RealVec(atomCoordinatesP[atom1][0]-atomCoordinatesP[atom2][0],
atomCoordinatesP[atom1][1]-atomCoordinatesP[atom2][1],
atomCoordinatesP[atom1][2]-atomCoordinatesP[atom2][2]);
RealOpenMM invLength = (RealOpenMM)(1/SQRT((RealOpenMM)_constraintDir[i].dot(_constraintDir[i])));
_constraintDir[i][0] *= invLength;
_constraintDir[i][1] *= invLength;
_constraintDir[i][2] *= invLength;
_rhs1[i] = _solution[i] = _sMatrix[i]*(one/invLength-_distance[i]);
}
// Build the coupling matrix.
for (int c1 = 0; c1 < (int)_couplingMatrix.size(); c1++) {
RealVec& dir1 = _constraintDir[c1];
for (int j = 0; j < (int)_couplingMatrix[c1].size(); j++) {
int c2 = _linkedConstraints[c1][j];
RealVec& dir2 = _constraintDir[c2];
if (_atomIndices[c1][0] == _atomIndices[c2][0] || _atomIndices[c1][1] == _atomIndices[c2][1])
_couplingMatrix[c1][j] = (RealOpenMM)(-inverseMasses[_atomIndices[c1][0]]*_sMatrix[c1]*dir1.dot(dir2)*_sMatrix[c2]);
else
_couplingMatrix[c1][j] = (RealOpenMM)(inverseMasses[_atomIndices[c1][1]]*_sMatrix[c1]*dir1.dot(dir2)*_sMatrix[c2]);
}
}
// Solve the matrix equation and update the positions.
solveMatrix();
updateAtomPositions(numberOfAtoms, atomCoordinatesP, inverseMasses);
// Correct for rotational lengthening.
for (int i = 0; i < _numberOfConstraints; i++) {
int atom1 = _atomIndices[i][0];
int atom2 = _atomIndices[i][1];
RealVec delta(atomCoordinatesP[atom1][0]-atomCoordinatesP[atom2][0],
atomCoordinatesP[atom1][1]-atomCoordinatesP[atom2][1],
atomCoordinatesP[atom1][2]-atomCoordinatesP[atom2][2]);
RealOpenMM p2 = (RealOpenMM)(two*_distance[i]*_distance[i]-delta.dot(delta));
if (p2 < zero)
p2 = zero;
_rhs1[i] = _solution[i] = _sMatrix[i]*(_distance[i]-SQRT(p2));
}
solveMatrix();
updateAtomPositions(numberOfAtoms, atomCoordinatesP, inverseMasses);
return SimTKOpenMMCommon::DefaultReturn;
}
// -----------------------------------------------------------------------------
// INITIALIZE OpenMM DATA STRUCTURES
// -----------------------------------------------------------------------------
// We take these actions here:
// (1) Load any available OpenMM plugins, e.g. Cuda and Brook.
// (2) Allocate a MyOpenMMData structure to hang on to OpenMM data structures
// in a manner which is opaque to the caller.
// (3) Fill the OpenMM::System with the force field parameters we want to
// use and the particular set of atoms to be simulated.
// (4) Create an Integrator and a Context associating the Integrator with
// the System.
// (5) Select the OpenMM platform to be used.
// (6) Return the MyOpenMMData struct and the name of the Platform in use.
//
// Note that this function must understand the calling MD code's molecule and
// force field data structures so will need to be customized for each MD code.
static MyOpenMMData*
myInitializeOpenMM( int numWatersAlongEdge,
double temperature,
double frictionInPerPs,
double stepSizeInFs,
std::string& platformName)
{
// Load all available OpenMM plugins from their default location.
OpenMM::Platform::loadPluginsFromDirectory
(OpenMM::Platform::getDefaultPluginsDirectory());
// Allocate space to hold OpenMM objects while we're using them.
MyOpenMMData* omm = new MyOpenMMData();
// Create a System and Force objects within the System. Retain a reference
// to each force object so we can fill in the forces. Note: the System owns
// the force objects and will take care of deleting them; don't do it yourself!
OpenMM::System& system = *(omm->system = new OpenMM::System());
OpenMM::NonbondedForce& nonbond = *new OpenMM::NonbondedForce();
system.addForce(&nonbond);
OpenMM::HarmonicBondForce& bondStretch = *new OpenMM::HarmonicBondForce();
system.addForce(&bondStretch);
OpenMM::HarmonicAngleForce& bondBend = *new OpenMM::HarmonicAngleForce();
system.addForce(&bondBend);
OpenMM::AndersenThermostat& thermostat = *new OpenMM::AndersenThermostat(
temperature, // kelvins
frictionInPerPs); // collision frequency in 1/picoseconds
system.addForce(&thermostat);
// Volume of one water is 30 Angstroms cubed;
// Thus length in one dimension is cube-root of 30,
// or 3.107 Angstroms or 0.3107 nanometers
const double WaterSizeInNm = 0.3107; // edge of cube containing one water, in nanometers
// Place water molecules one at a time in an NxNxN rectilinear grid
const double boxEdgeLengthInNm = WaterSizeInNm * numWatersAlongEdge;
// Create periodic box
nonbond.setNonbondedMethod(OpenMM::NonbondedForce::PME);
nonbond.setUseDispersionCorrection(true);
nonbond.setCutoffDistance(CutoffDistanceInAng * OpenMM::NmPerAngstrom);
nonbond.setSwitchingDistance(SwitchDistanceInAng * OpenMM::NmPerAngstrom);
nonbond.setEwaldErrorTolerance(1e-6);
system.setDefaultPeriodicBoxVectors(Vec3(boxEdgeLengthInNm,0,0),
Vec3(0,boxEdgeLengthInNm,0),
Vec3(0,0,boxEdgeLengthInNm));
// Specify the atoms and their properties:
// (1) System needs to know the masses and constraints (if any).
// (2) NonbondedForce needs charges,van der Waals properties (in MD units!).
// (3) Collect starting positions for initializing the simulation later.
// Create data structures to hold lists of initial positions and bonds
std::vector<Vec3> initialPosInNm;
std::vector< std::pair<int,int> > bondPairs;
// Add water molecules one at a time in the NxNxN cubic lattice
for (int latticeX = 0; latticeX < numWatersAlongEdge; ++latticeX)
for (int latticeY = 0; latticeY < numWatersAlongEdge; ++latticeY)
for (int latticeZ = 0; latticeZ < numWatersAlongEdge; ++latticeZ)
{
// Add parameters for one water molecule
// Add atom masses to system
int oIndex = system.addParticle(O_mass); // O
int h1Index = system.addParticle(H_mass); // H1
int h2Index = system.addParticle(H_mass); // H2
// Add atom charge, sigma, and stiffness to nonbonded force
nonbond.addParticle( // Oxygen
O_charge,
O_vdwRadInAng * OpenMM::NmPerAngstrom * OpenMM::SigmaPerVdwRadius,
O_vdwEnergyInKcal * OpenMM::KJPerKcal);
nonbond.addParticle( // Hydrogen1
H_charge,
H_vdwRadInAng * OpenMM::NmPerAngstrom * OpenMM::SigmaPerVdwRadius,
H_vdwEnergyInKcal * OpenMM::KJPerKcal);
nonbond.addParticle( // Hydrogen2
H_charge,
H_vdwRadInAng * OpenMM::NmPerAngstrom * OpenMM::SigmaPerVdwRadius,
H_vdwEnergyInKcal * OpenMM::KJPerKcal);
// Constrain O-H bond lengths or use harmonic forces.
if (UseConstraints) {
system.addConstraint(oIndex, h1Index,
OH_nominalLengthInAng * OpenMM::NmPerAngstrom);
system.addConstraint(oIndex, h2Index,
OH_nominalLengthInAng * OpenMM::NmPerAngstrom);
} else {
// Add stretch parameters for two covalent bonds
// Note factor of 2 for stiffness below because Amber specifies the constant
// as it is used in the harmonic energy term kx^2 with force 2kx; OpenMM wants
// it as used in the force term kx, with energy kx^2/2.
bondStretch.addBond(oIndex, h1Index,
OH_nominalLengthInAng * OpenMM::NmPerAngstrom,
OH_stiffnessInKcalPerAng2 * 2 * OpenMM::KJPerKcal
* OpenMM::AngstromsPerNm * OpenMM::AngstromsPerNm);
bondStretch.addBond(oIndex, h2Index,
OH_nominalLengthInAng * OpenMM::NmPerAngstrom,
OH_stiffnessInKcalPerAng2 * 2 * OpenMM::KJPerKcal
* OpenMM::AngstromsPerNm * OpenMM::AngstromsPerNm);
}
// Store bonds for exclusion list
bondPairs.push_back(std::make_pair(oIndex, h1Index));
bondPairs.push_back(std::make_pair(oIndex, h2Index));
// Add bond bend parameters for one angle.
// See note under bond stretch above regarding the factor of 2 here.
bondBend.addAngle(h1Index, oIndex, h2Index,
HOH_nominalAngleInDeg * OpenMM::RadiansPerDegree,
HOH_stiffnessInKcalPerRad2 * 2 * OpenMM::KJPerKcal);
// Location of this molecule in the lattice
Vec3 latticeVec(WaterSizeInNm * latticeX,
WaterSizeInNm * latticeY,
WaterSizeInNm * latticeZ);
// flip half the waters to prevent giant dipole
int flip = (rand() % 100) > 49 ? 1 : -1;
// place this water
initialPosInNm.push_back(Vec3(0,0,0) + latticeVec); // O
initialPosInNm.push_back(Vec3(0.09572*flip,0,0) + latticeVec); // H1
initialPosInNm.push_back(Vec3(-0.02397*flip,0.09267*flip,0) + latticeVec); // H2
}
// Populate nonbonded exclusions
nonbond.createExceptionsFromBonds(bondPairs, 1.0, 1.0);
// Choose an Integrator for advancing time, and a Context connecting the
// System with the Integrator for simulation. Let the Context choose the
// best available Platform. Initialize the configuration from the default
// positions we collected above. Initial velocities will be zero.
omm->integrator = new OpenMM::VerletIntegrator(StepSizeInFs * OpenMM::PsPerFs);
omm->context = new OpenMM::Context(*omm->system, *omm->integrator);
omm->context->setPositions(initialPosInNm);
platformName = omm->context->getPlatform().getName();
return omm;
}
MBPolReferenceDispersionForce::MBPolReferenceDispersionForce( ) : _nonbondedMethod(NoCutoff), _cutoff(1.0e+10) {
_periodicBoxDimensions = RealVec( 0.0, 0.0, 0.0 );
}