| 6 |
|
* redistribute this software in source and binary code form, provided |
| 7 |
|
* that the following conditions are met: |
| 8 |
|
* |
| 9 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
| 11 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
| 13 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
| 18 |
< |
* 2. Redistributions of source code must retain the above copyright |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
|
* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
|
* distribution. |
| 28 |
|
* arising out of the use of or inability to use software, even if the |
| 29 |
|
* University of Notre Dame has been advised of the possibility of |
| 30 |
|
* such damages. |
| 31 |
+ |
* |
| 32 |
+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
+ |
* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* work. Good starting points are: |
| 35 |
+ |
* |
| 36 |
+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
#include <fstream> |
| 43 |
|
#include <iostream> |
| 44 |
|
#include "integrators/LDForceManager.hpp" |
| 45 |
|
#include "math/CholeskyDecomposition.hpp" |
| 46 |
< |
#include "utils/OOPSEConstant.hpp" |
| 46 |
> |
#include "utils/PhysicalConstants.hpp" |
| 47 |
|
#include "hydrodynamics/Sphere.hpp" |
| 48 |
|
#include "hydrodynamics/Ellipsoid.hpp" |
| 49 |
< |
#include "openbabel/mol.hpp" |
| 49 |
> |
#include "utils/ElementsTable.hpp" |
| 50 |
> |
#include "types/LennardJonesAdapter.hpp" |
| 51 |
> |
#include "types/GayBerneAdapter.hpp" |
| 52 |
|
|
| 53 |
< |
using namespace OpenBabel; |
| 51 |
< |
namespace oopse { |
| 53 |
> |
namespace OpenMD { |
| 54 |
|
|
| 55 |
< |
LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info){ |
| 55 |
> |
LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info), |
| 56 |
> |
maxIterNum_(4), |
| 57 |
> |
forceTolerance_(1e-6) { |
| 58 |
|
simParams = info->getSimParams(); |
| 59 |
|
veloMunge = new Velocitizer(info); |
| 60 |
|
|
| 67 |
|
sprintf( painCave.errMsg, |
| 68 |
|
"langevinBufferRadius must be specified " |
| 69 |
|
"when useSphericalBoundaryConditions is turned on.\n"); |
| 70 |
< |
painCave.severity = OOPSE_ERROR; |
| 70 |
> |
painCave.severity = OPENMD_ERROR; |
| 71 |
|
painCave.isFatal = 1; |
| 72 |
|
simError(); |
| 73 |
|
} |
| 78 |
|
sprintf( painCave.errMsg, |
| 79 |
|
"frozenBufferRadius must be specified " |
| 80 |
|
"when useSphericalBoundaryConditions is turned on.\n"); |
| 81 |
< |
painCave.severity = OOPSE_ERROR; |
| 81 |
> |
painCave.severity = OPENMD_ERROR; |
| 82 |
|
painCave.isFatal = 1; |
| 83 |
|
simError(); |
| 84 |
|
} |
| 87 |
|
sprintf( painCave.errMsg, |
| 88 |
|
"frozenBufferRadius has been set smaller than the " |
| 89 |
|
"langevinBufferRadius. This is probably an error.\n"); |
| 90 |
< |
painCave.severity = OOPSE_WARNING; |
| 90 |
> |
painCave.severity = OPENMD_WARNING; |
| 91 |
|
painCave.isFatal = 0; |
| 92 |
|
simError(); |
| 93 |
|
} |
| 97 |
|
std::map<std::string, HydroProp*> hydroPropMap; |
| 98 |
|
|
| 99 |
|
Molecule* mol; |
| 100 |
< |
StuntDouble* integrableObject; |
| 100 |
> |
StuntDouble* sd; |
| 101 |
|
SimInfo::MoleculeIterator i; |
| 102 |
|
Molecule::IntegrableObjectIterator j; |
| 103 |
|
bool needHydroPropFile = false; |
| 104 |
|
|
| 105 |
|
for (mol = info->beginMolecule(i); mol != NULL; |
| 106 |
|
mol = info->nextMolecule(i)) { |
| 107 |
< |
for (integrableObject = mol->beginIntegrableObject(j); |
| 108 |
< |
integrableObject != NULL; |
| 109 |
< |
integrableObject = mol->nextIntegrableObject(j)) { |
| 107 |
> |
|
| 108 |
> |
for (sd = mol->beginIntegrableObject(j); sd != NULL; |
| 109 |
> |
sd = mol->nextIntegrableObject(j)) { |
| 110 |
|
|
| 111 |
< |
if (integrableObject->isRigidBody()) { |
| 112 |
< |
RigidBody* rb = static_cast<RigidBody*>(integrableObject); |
| 111 |
> |
if (sd->isRigidBody()) { |
| 112 |
> |
RigidBody* rb = static_cast<RigidBody*>(sd); |
| 113 |
|
if (rb->getNumAtoms() > 1) needHydroPropFile = true; |
| 114 |
|
} |
| 115 |
|
|
| 122 |
|
hydroPropMap = parseFrictionFile(simParams->getHydroPropFile()); |
| 123 |
|
} else { |
| 124 |
|
sprintf( painCave.errMsg, |
| 125 |
< |
"HydroPropFile must be set to a file name if Langevin\n" |
| 126 |
< |
"\tDynamics is specified for rigidBodies which contain more\n" |
| 127 |
< |
"\tthan one atom. To create a HydroPropFile, run \"Hydro\".\n"); |
| 128 |
< |
painCave.severity = OOPSE_ERROR; |
| 125 |
> |
"HydroPropFile must be set to a file name if Langevin Dynamics\n" |
| 126 |
> |
"\tis specified for rigidBodies which contain more than one atom\n" |
| 127 |
> |
"\tTo create a HydroPropFile, run the \"Hydro\" program.\n"); |
| 128 |
> |
painCave.severity = OPENMD_ERROR; |
| 129 |
|
painCave.isFatal = 1; |
| 130 |
|
simError(); |
| 131 |
|
} |
| 132 |
|
|
| 133 |
|
for (mol = info->beginMolecule(i); mol != NULL; |
| 134 |
|
mol = info->nextMolecule(i)) { |
| 131 |
– |
for (integrableObject = mol->beginIntegrableObject(j); |
| 132 |
– |
integrableObject != NULL; |
| 133 |
– |
integrableObject = mol->nextIntegrableObject(j)) { |
| 135 |
|
|
| 136 |
< |
std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType()); |
| 136 |
> |
for (sd = mol->beginIntegrableObject(j); sd != NULL; |
| 137 |
> |
sd = mol->nextIntegrableObject(j)) { |
| 138 |
> |
|
| 139 |
> |
std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(sd->getType()); |
| 140 |
|
if (iter != hydroPropMap.end()) { |
| 141 |
|
hydroProps_.push_back(iter->second); |
| 142 |
|
} else { |
| 143 |
|
sprintf( painCave.errMsg, |
| 144 |
< |
"Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str()); |
| 145 |
< |
painCave.severity = OOPSE_ERROR; |
| 144 |
> |
"Can not find resistance tensor for atom [%s]\n", sd->getType().c_str()); |
| 145 |
> |
painCave.severity = OPENMD_ERROR; |
| 146 |
|
painCave.isFatal = 1; |
| 147 |
|
simError(); |
| 148 |
|
} |
| 153 |
|
std::map<std::string, HydroProp*> hydroPropMap; |
| 154 |
|
for (mol = info->beginMolecule(i); mol != NULL; |
| 155 |
|
mol = info->nextMolecule(i)) { |
| 156 |
< |
for (integrableObject = mol->beginIntegrableObject(j); |
| 157 |
< |
integrableObject != NULL; |
| 158 |
< |
integrableObject = mol->nextIntegrableObject(j)) { |
| 156 |
> |
|
| 157 |
> |
for (sd = mol->beginIntegrableObject(j); sd != NULL; |
| 158 |
> |
sd = mol->nextIntegrableObject(j)) { |
| 159 |
> |
|
| 160 |
|
Shape* currShape = NULL; |
| 161 |
|
|
| 162 |
< |
if (integrableObject->isAtom()){ |
| 163 |
< |
Atom* atom = static_cast<Atom*>(integrableObject); |
| 162 |
> |
if (sd->isAtom()){ |
| 163 |
> |
Atom* atom = static_cast<Atom*>(sd); |
| 164 |
|
AtomType* atomType = atom->getAtomType(); |
| 165 |
< |
if (atomType->isGayBerne()) { |
| 166 |
< |
DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType); |
| 167 |
< |
GenericData* data = dAtomType->getPropertyByName("GayBerne"); |
| 168 |
< |
if (data != NULL) { |
| 169 |
< |
GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data); |
| 165 |
< |
|
| 166 |
< |
if (gayBerneData != NULL) { |
| 167 |
< |
GayBerneParam gayBerneParam = gayBerneData->getData(); |
| 168 |
< |
currShape = new Ellipsoid(V3Zero, |
| 169 |
< |
gayBerneParam.GB_l / 2.0, |
| 170 |
< |
gayBerneParam.GB_d / 2.0, |
| 171 |
< |
Mat3x3d::identity()); |
| 172 |
< |
} else { |
| 173 |
< |
sprintf( painCave.errMsg, |
| 174 |
< |
"Can not cast GenericData to GayBerneParam\n"); |
| 175 |
< |
painCave.severity = OOPSE_ERROR; |
| 176 |
< |
painCave.isFatal = 1; |
| 177 |
< |
simError(); |
| 178 |
< |
} |
| 179 |
< |
} else { |
| 180 |
< |
sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n"); |
| 181 |
< |
painCave.severity = OOPSE_ERROR; |
| 182 |
< |
painCave.isFatal = 1; |
| 183 |
< |
simError(); |
| 184 |
< |
} |
| 165 |
> |
GayBerneAdapter gba = GayBerneAdapter(atomType); |
| 166 |
> |
if (gba.isGayBerne()) { |
| 167 |
> |
currShape = new Ellipsoid(V3Zero, gba.getL() / 2.0, |
| 168 |
> |
gba.getD() / 2.0, |
| 169 |
> |
Mat3x3d::identity()); |
| 170 |
|
} else { |
| 171 |
< |
if (atomType->isLennardJones()){ |
| 172 |
< |
GenericData* data = atomType->getPropertyByName("LennardJones"); |
| 173 |
< |
if (data != NULL) { |
| 189 |
< |
LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data); |
| 190 |
< |
if (ljData != NULL) { |
| 191 |
< |
LJParam ljParam = ljData->getData(); |
| 192 |
< |
currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0); |
| 193 |
< |
} else { |
| 194 |
< |
sprintf( painCave.errMsg, |
| 195 |
< |
"Can not cast GenericData to LJParam\n"); |
| 196 |
< |
painCave.severity = OOPSE_ERROR; |
| 197 |
< |
painCave.isFatal = 1; |
| 198 |
< |
simError(); |
| 199 |
< |
} |
| 200 |
< |
} |
| 171 |
> |
LennardJonesAdapter lja = LennardJonesAdapter(atomType); |
| 172 |
> |
if (lja.isLennardJones()){ |
| 173 |
> |
currShape = new Sphere(atom->getPos(), lja.getSigma()/2.0); |
| 174 |
|
} else { |
| 175 |
< |
int obanum = etab.GetAtomicNum((atom->getType()).c_str()); |
| 176 |
< |
if (obanum != 0) { |
| 177 |
< |
currShape = new Sphere(atom->getPos(), etab.GetVdwRad(obanum)); |
| 175 |
> |
int aNum = etab.GetAtomicNum((atom->getType()).c_str()); |
| 176 |
> |
if (aNum != 0) { |
| 177 |
> |
currShape = new Sphere(atom->getPos(), etab.GetVdwRad(aNum)); |
| 178 |
|
} else { |
| 179 |
|
sprintf( painCave.errMsg, |
| 180 |
|
"Could not find atom type in default element.txt\n"); |
| 181 |
< |
painCave.severity = OOPSE_ERROR; |
| 181 |
> |
painCave.severity = OPENMD_ERROR; |
| 182 |
|
painCave.isFatal = 1; |
| 183 |
|
simError(); |
| 184 |
|
} |
| 185 |
|
} |
| 186 |
|
} |
| 187 |
|
} |
| 188 |
+ |
|
| 189 |
+ |
if (!simParams->haveTargetTemp()) { |
| 190 |
+ |
sprintf(painCave.errMsg, "You can't use LangevinDynamics without a targetTemp!\n"); |
| 191 |
+ |
painCave.isFatal = 1; |
| 192 |
+ |
painCave.severity = OPENMD_ERROR; |
| 193 |
+ |
simError(); |
| 194 |
+ |
} |
| 195 |
+ |
|
| 196 |
+ |
if (!simParams->haveViscosity()) { |
| 197 |
+ |
sprintf(painCave.errMsg, "You can't use LangevinDynamics without a viscosity!\n"); |
| 198 |
+ |
painCave.isFatal = 1; |
| 199 |
+ |
painCave.severity = OPENMD_ERROR; |
| 200 |
+ |
simError(); |
| 201 |
+ |
} |
| 202 |
+ |
|
| 203 |
+ |
|
| 204 |
|
HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp()); |
| 205 |
< |
std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType()); |
| 205 |
> |
std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(sd->getType()); |
| 206 |
|
if (iter != hydroPropMap.end()) |
| 207 |
|
hydroProps_.push_back(iter->second); |
| 208 |
|
else { |
| 209 |
|
currHydroProp->complete(); |
| 210 |
< |
hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(integrableObject->getType(), currHydroProp)); |
| 210 |
> |
hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(sd->getType(), currHydroProp)); |
| 211 |
|
hydroProps_.push_back(currHydroProp); |
| 212 |
|
} |
| 213 |
+ |
delete currShape; |
| 214 |
|
} |
| 215 |
|
} |
| 216 |
|
} |
| 217 |
< |
variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt(); |
| 217 |
> |
variance_ = 2.0 * PhysicalConstants::kb*simParams->getTargetTemp()/simParams->getDt(); |
| 218 |
|
} |
| 219 |
|
|
| 220 |
|
std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) { |
| 234 |
|
return props; |
| 235 |
|
} |
| 236 |
|
|
| 237 |
< |
void LDForceManager::postCalculation(bool needStress){ |
| 237 |
> |
void LDForceManager::postCalculation(){ |
| 238 |
|
SimInfo::MoleculeIterator i; |
| 239 |
|
Molecule::IntegrableObjectIterator j; |
| 240 |
|
Molecule* mol; |
| 241 |
< |
StuntDouble* integrableObject; |
| 241 |
> |
StuntDouble* sd; |
| 242 |
|
RealType mass; |
| 253 |
– |
Vector3d vel; |
| 243 |
|
Vector3d pos; |
| 244 |
|
Vector3d frc; |
| 245 |
|
Mat3x3d A; |
| 251 |
|
bool freezeMolecule; |
| 252 |
|
int fdf; |
| 253 |
|
|
| 265 |
– |
|
| 266 |
– |
|
| 254 |
|
fdf = 0; |
| 255 |
|
|
| 256 |
|
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
| 275 |
|
} |
| 276 |
|
} |
| 277 |
|
|
| 278 |
< |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 279 |
< |
integrableObject = mol->nextIntegrableObject(j)) { |
| 278 |
> |
for (sd = mol->beginIntegrableObject(j); sd != NULL; |
| 279 |
> |
sd = mol->nextIntegrableObject(j)) { |
| 280 |
|
|
| 281 |
|
if (freezeMolecule) |
| 282 |
< |
fdf += integrableObject->freeze(); |
| 282 |
> |
fdf += sd->freeze(); |
| 283 |
|
|
| 284 |
|
if (doLangevinForces) { |
| 285 |
< |
vel =integrableObject->getVel(); |
| 286 |
< |
mass = integrableObject->getMass(); |
| 287 |
< |
if (integrableObject->isDirectional()){ |
| 288 |
< |
//calculate angular velocity in lab frame |
| 302 |
< |
Mat3x3d I = integrableObject->getI(); |
| 303 |
< |
Vector3d angMom = integrableObject->getJ(); |
| 304 |
< |
Vector3d omega; |
| 305 |
< |
|
| 306 |
< |
if (integrableObject->isLinear()) { |
| 307 |
< |
int linearAxis = integrableObject->linearAxis(); |
| 308 |
< |
int l = (linearAxis +1 )%3; |
| 309 |
< |
int m = (linearAxis +2 )%3; |
| 310 |
< |
omega[l] = angMom[l] /I(l, l); |
| 311 |
< |
omega[m] = angMom[m] /I(m, m); |
| 312 |
< |
|
| 313 |
< |
} else { |
| 314 |
< |
omega[0] = angMom[0] /I(0, 0); |
| 315 |
< |
omega[1] = angMom[1] /I(1, 1); |
| 316 |
< |
omega[2] = angMom[2] /I(2, 2); |
| 317 |
< |
} |
| 285 |
> |
mass = sd->getMass(); |
| 286 |
> |
if (sd->isDirectional()){ |
| 287 |
> |
|
| 288 |
> |
// preliminaries for directional objects: |
| 289 |
|
|
| 290 |
< |
//std::cerr << "I = " << I(0,0) << "\t" << I(1,1) << "\t" << I(2,2) << "\n\n"; |
| 320 |
< |
|
| 321 |
< |
//apply friction force and torque at center of resistance |
| 322 |
< |
A = integrableObject->getA(); |
| 290 |
> |
A = sd->getA(); |
| 291 |
|
Atrans = A.transpose(); |
| 292 |
< |
//std::cerr << "A = " << integrableObject->getA() << "\n"; |
| 325 |
< |
//std::cerr << "Atrans = " << A.transpose() << "\n\n"; |
| 326 |
< |
Vector3d rcr = Atrans * hydroProps_[index]->getCOR(); |
| 327 |
< |
//std::cerr << "cor = " << hydroProps_[index]->getCOR() << "\n\n\n\n"; |
| 328 |
< |
//std::cerr << "rcr = " << rcr << "\n\n"; |
| 329 |
< |
Vector3d vcdLab = vel + cross(omega, rcr); |
| 330 |
< |
|
| 331 |
< |
//std::cerr << "velL = " << vel << "\n\n"; |
| 332 |
< |
//std::cerr << "vcdL = " << vcdLab << "\n\n"; |
| 333 |
< |
Vector3d vcdBody = A* vcdLab; |
| 334 |
< |
//std::cerr << "vcdB = " << vcdBody << "\n\n"; |
| 335 |
< |
Vector3d frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omega); |
| 292 |
> |
Vector3d rcrLab = Atrans * hydroProps_[index]->getCOR(); |
| 293 |
|
|
| 337 |
– |
//std::cerr << "xitt = " << hydroProps_[index]->getXitt() << "\n\n"; |
| 338 |
– |
//std::cerr << "ffB = " << frictionForceBody << "\n\n"; |
| 339 |
– |
Vector3d frictionForceLab = Atrans*frictionForceBody; |
| 340 |
– |
//std::cerr << "ffL = " << frictionForceLab << "\n\n"; |
| 341 |
– |
//std::cerr << "frc = " << integrableObject->getFrc() << "\n\n"; |
| 342 |
– |
integrableObject->addFrc(frictionForceLab); |
| 343 |
– |
//std::cerr << "frc = " << integrableObject->getFrc() << "\n\n"; |
| 344 |
– |
//std::cerr << "ome = " << omega << "\n\n"; |
| 345 |
– |
Vector3d frictionTorqueBody = - (hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omega); |
| 346 |
– |
//std::cerr << "ftB = " << frictionTorqueBody << "\n\n"; |
| 347 |
– |
Vector3d frictionTorqueLab = Atrans*frictionTorqueBody; |
| 348 |
– |
//std::cerr << "ftL = " << frictionTorqueLab << "\n\n"; |
| 349 |
– |
//std::cerr << "ftL2 = " << frictionTorqueLab+cross(rcr,frictionForceLab) << "\n\n"; |
| 350 |
– |
//std::cerr << "trq = " << integrableObject->getTrq() << "\n\n"; |
| 351 |
– |
integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab)); |
| 352 |
– |
//std::cerr << "trq = " << integrableObject->getTrq() << "\n\n"; |
| 353 |
– |
|
| 294 |
|
//apply random force and torque at center of resistance |
| 295 |
+ |
|
| 296 |
|
Vector3d randomForceBody; |
| 297 |
|
Vector3d randomTorqueBody; |
| 298 |
|
genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_); |
| 299 |
< |
//std::cerr << "rfB = " << randomForceBody << "\n\n"; |
| 300 |
< |
//std::cerr << "rtB = " << randomTorqueBody << "\n\n"; |
| 301 |
< |
Vector3d randomForceLab = Atrans*randomForceBody; |
| 302 |
< |
Vector3d randomTorqueLab = Atrans* randomTorqueBody; |
| 303 |
< |
integrableObject->addFrc(randomForceLab); |
| 304 |
< |
//std::cerr << "rfL = " << randomForceLab << "\n\n"; |
| 305 |
< |
//std::cerr << "rtL = " << randomTorqueLab << "\n\n"; |
| 306 |
< |
//std::cerr << "rtL2 = " << randomTorqueLab + cross(rcr, randomForceLab) << "\n\n"; |
| 307 |
< |
integrableObject->addTrq(randomTorqueLab + cross(rcr, randomForceLab )); |
| 299 |
> |
Vector3d randomForceLab = Atrans * randomForceBody; |
| 300 |
> |
Vector3d randomTorqueLab = Atrans * randomTorqueBody; |
| 301 |
> |
sd->addFrc(randomForceLab); |
| 302 |
> |
sd->addTrq(randomTorqueLab + cross(rcrLab, randomForceLab )); |
| 303 |
> |
|
| 304 |
> |
Mat3x3d I = sd->getI(); |
| 305 |
> |
Vector3d omegaBody; |
| 306 |
> |
|
| 307 |
> |
// What remains contains velocity explicitly, but the velocity required |
| 308 |
> |
// is at the full step: v(t + h), while we have initially the velocity |
| 309 |
> |
// at the half step: v(t + h/2). We need to iterate to converge the |
| 310 |
> |
// friction force and friction torque vectors. |
| 311 |
> |
|
| 312 |
> |
// this is the velocity at the half-step: |
| 313 |
|
|
| 314 |
+ |
Vector3d vel =sd->getVel(); |
| 315 |
+ |
Vector3d angMom = sd->getJ(); |
| 316 |
+ |
|
| 317 |
+ |
//estimate velocity at full-step using everything but friction forces: |
| 318 |
+ |
|
| 319 |
+ |
frc = sd->getFrc(); |
| 320 |
+ |
Vector3d velStep = vel + (dt2_ /mass * PhysicalConstants::energyConvert) * frc; |
| 321 |
+ |
|
| 322 |
+ |
Tb = sd->lab2Body(sd->getTrq()); |
| 323 |
+ |
Vector3d angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * Tb; |
| 324 |
+ |
|
| 325 |
+ |
Vector3d omegaLab; |
| 326 |
+ |
Vector3d vcdLab; |
| 327 |
+ |
Vector3d vcdBody; |
| 328 |
+ |
Vector3d frictionForceBody; |
| 329 |
+ |
Vector3d frictionForceLab(0.0); |
| 330 |
+ |
Vector3d oldFFL; // used to test for convergence |
| 331 |
+ |
Vector3d frictionTorqueBody(0.0); |
| 332 |
+ |
Vector3d oldFTB; // used to test for convergence |
| 333 |
+ |
Vector3d frictionTorqueLab; |
| 334 |
+ |
RealType fdot; |
| 335 |
+ |
RealType tdot; |
| 336 |
+ |
|
| 337 |
+ |
//iteration starts here: |
| 338 |
+ |
|
| 339 |
+ |
for (int k = 0; k < maxIterNum_; k++) { |
| 340 |
+ |
|
| 341 |
+ |
if (sd->isLinear()) { |
| 342 |
+ |
int linearAxis = sd->linearAxis(); |
| 343 |
+ |
int l = (linearAxis +1 )%3; |
| 344 |
+ |
int m = (linearAxis +2 )%3; |
| 345 |
+ |
omegaBody[l] = angMomStep[l] /I(l, l); |
| 346 |
+ |
omegaBody[m] = angMomStep[m] /I(m, m); |
| 347 |
+ |
|
| 348 |
+ |
} else { |
| 349 |
+ |
omegaBody[0] = angMomStep[0] /I(0, 0); |
| 350 |
+ |
omegaBody[1] = angMomStep[1] /I(1, 1); |
| 351 |
+ |
omegaBody[2] = angMomStep[2] /I(2, 2); |
| 352 |
+ |
} |
| 353 |
+ |
|
| 354 |
+ |
omegaLab = Atrans * omegaBody; |
| 355 |
+ |
|
| 356 |
+ |
// apply friction force and torque at center of resistance |
| 357 |
+ |
|
| 358 |
+ |
vcdLab = velStep + cross(omegaLab, rcrLab); |
| 359 |
+ |
vcdBody = A * vcdLab; |
| 360 |
+ |
frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omegaBody); |
| 361 |
+ |
oldFFL = frictionForceLab; |
| 362 |
+ |
frictionForceLab = Atrans * frictionForceBody; |
| 363 |
+ |
oldFTB = frictionTorqueBody; |
| 364 |
+ |
frictionTorqueBody = -(hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omegaBody); |
| 365 |
+ |
frictionTorqueLab = Atrans * frictionTorqueBody; |
| 366 |
+ |
|
| 367 |
+ |
// re-estimate velocities at full-step using friction forces: |
| 368 |
+ |
|
| 369 |
+ |
velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForceLab); |
| 370 |
+ |
angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * (Tb + frictionTorqueBody); |
| 371 |
+ |
|
| 372 |
+ |
// check for convergence (if the vectors have converged, fdot and tdot will both be 1.0): |
| 373 |
+ |
|
| 374 |
+ |
fdot = dot(frictionForceLab, oldFFL) / frictionForceLab.lengthSquare(); |
| 375 |
+ |
tdot = dot(frictionTorqueBody, oldFTB) / frictionTorqueBody.lengthSquare(); |
| 376 |
+ |
|
| 377 |
+ |
if (fabs(1.0 - fdot) <= forceTolerance_ && fabs(1.0 - tdot) <= forceTolerance_) |
| 378 |
+ |
break; // iteration ends here |
| 379 |
+ |
} |
| 380 |
+ |
|
| 381 |
+ |
sd->addFrc(frictionForceLab); |
| 382 |
+ |
sd->addTrq(frictionTorqueLab + cross(rcrLab, frictionForceLab)); |
| 383 |
+ |
|
| 384 |
+ |
|
| 385 |
|
} else { |
| 386 |
|
//spherical atom |
| 387 |
< |
Vector3d frictionForce = -(hydroProps_[index]->getXitt() * vel); |
| 371 |
< |
//std::cerr << "xitt = " << hydroProps_[index]->getXitt() << "\n\n"; |
| 387 |
> |
|
| 388 |
|
Vector3d randomForce; |
| 389 |
|
Vector3d randomTorque; |
| 390 |
|
genRandomForceAndTorque(randomForce, randomTorque, index, variance_); |
| 391 |
+ |
sd->addFrc(randomForce); |
| 392 |
+ |
|
| 393 |
+ |
// What remains contains velocity explicitly, but the velocity required |
| 394 |
+ |
// is at the full step: v(t + h), while we have initially the velocity |
| 395 |
+ |
// at the half step: v(t + h/2). We need to iterate to converge the |
| 396 |
+ |
// friction force vector. |
| 397 |
+ |
|
| 398 |
+ |
// this is the velocity at the half-step: |
| 399 |
|
|
| 400 |
< |
integrableObject->addFrc(frictionForce+randomForce); |
| 400 |
> |
Vector3d vel =sd->getVel(); |
| 401 |
> |
|
| 402 |
> |
//estimate velocity at full-step using everything but friction forces: |
| 403 |
> |
|
| 404 |
> |
frc = sd->getFrc(); |
| 405 |
> |
Vector3d velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * frc; |
| 406 |
> |
|
| 407 |
> |
Vector3d frictionForce(0.0); |
| 408 |
> |
Vector3d oldFF; // used to test for convergence |
| 409 |
> |
RealType fdot; |
| 410 |
> |
|
| 411 |
> |
//iteration starts here: |
| 412 |
> |
|
| 413 |
> |
for (int k = 0; k < maxIterNum_; k++) { |
| 414 |
> |
|
| 415 |
> |
oldFF = frictionForce; |
| 416 |
> |
frictionForce = -hydroProps_[index]->getXitt() * velStep; |
| 417 |
> |
|
| 418 |
> |
// re-estimate velocities at full-step using friction forces: |
| 419 |
> |
|
| 420 |
> |
velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForce); |
| 421 |
> |
|
| 422 |
> |
// check for convergence (if the vector has converged, fdot will be 1.0): |
| 423 |
> |
|
| 424 |
> |
fdot = dot(frictionForce, oldFF) / frictionForce.lengthSquare(); |
| 425 |
> |
|
| 426 |
> |
if (fabs(1.0 - fdot) <= forceTolerance_) |
| 427 |
> |
break; // iteration ends here |
| 428 |
> |
} |
| 429 |
> |
|
| 430 |
> |
sd->addFrc(frictionForce); |
| 431 |
> |
|
| 432 |
|
} |
| 433 |
|
} |
| 434 |
|
|
| 443 |
|
if(!simParams->getUsePeriodicBoundaryConditions()) |
| 444 |
|
veloMunge->removeAngularDrift(); |
| 445 |
|
|
| 446 |
< |
ForceManager::postCalculation(needStress); |
| 446 |
> |
ForceManager::postCalculation(); |
| 447 |
|
} |
| 448 |
|
|
| 449 |
|
void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) { |
| 455 |
|
Z[0] = randNumGen_.randNorm(0, variance); |
| 456 |
|
Z[1] = randNumGen_.randNorm(0, variance); |
| 457 |
|
Z[2] = randNumGen_.randNorm(0, variance); |
| 403 |
– |
//Z[3] = randNumGen_.randNorm(0, variance)*(2.0*M_PI); |
| 404 |
– |
//Z[4] = randNumGen_.randNorm(0, variance)*(2.0*M_PI); |
| 405 |
– |
//Z[5] = randNumGen_.randNorm(0, variance)*(2.0*M_PI); |
| 458 |
|
Z[3] = randNumGen_.randNorm(0, variance); |
| 459 |
|
Z[4] = randNumGen_.randNorm(0, variance); |
| 460 |
|
Z[5] = randNumGen_.randNorm(0, variance); |
| 461 |
|
|
| 410 |
– |
|
| 462 |
|
generalForce = hydroProps_[index]->getS()*Z; |
| 463 |
|
|
| 464 |
|
force[0] = generalForce[0]; |
