| 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; |
| 50 |
< |
namespace oopse { |
| 53 |
> |
namespace OpenMD { |
| 54 |
|
|
| 55 |
< |
LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info){ |
| 56 |
< |
Globals* simParams = info->getSimParams(); |
| 57 |
< |
|
| 55 |
> |
LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info), |
| 56 |
> |
maxIterNum_(4), |
| 57 |
> |
forceTolerance_(1e-6) { |
| 58 |
> |
simParams = info->getSimParams(); |
| 59 |
> |
veloMunge = new Velocitizer(info); |
| 60 |
> |
|
| 61 |
|
sphericalBoundaryConditions_ = false; |
| 62 |
|
if (simParams->getUseSphericalBoundaryConditions()) { |
| 63 |
|
sphericalBoundaryConditions_ = true; |
| 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 |
|
} |
| 94 |
|
} |
| 95 |
|
|
| 96 |
|
// Build the hydroProp map: |
| 97 |
< |
std::map<std::string, HydroProp> hydroPropMap; |
| 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 |
< |
std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType()); |
| 133 |
< |
if (iter != hydroPropMap.end()) { |
| 134 |
< |
hydroProps_.push_back(iter->second); |
| 135 |
< |
} else { |
| 136 |
< |
sprintf( painCave.errMsg, |
| 137 |
< |
"Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str()); |
| 138 |
< |
painCave.severity = OOPSE_ERROR; |
| 139 |
< |
painCave.isFatal = 1; |
| 140 |
< |
simError(); |
| 132 |
> |
|
| 133 |
> |
for (mol = info->beginMolecule(i); mol != NULL; |
| 134 |
> |
mol = info->nextMolecule(i)) { |
| 135 |
> |
|
| 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", sd->getType().c_str()); |
| 145 |
> |
painCave.severity = OPENMD_ERROR; |
| 146 |
> |
painCave.isFatal = 1; |
| 147 |
> |
simError(); |
| 148 |
> |
} |
| 149 |
> |
} |
| 150 |
|
} |
| 151 |
|
} else { |
| 152 |
< |
|
| 153 |
< |
std::map<std::string, HydroProp> hydroPropMap; |
| 152 |
> |
|
| 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 |
< |
if (integrableObject->isDirectionalAtom()) { |
| 162 |
< |
DirectionalAtom* dAtom = static_cast<DirectionalAtom*>(integrableObject); |
| 163 |
< |
AtomType* atomType = dAtom->getAtomType(); |
| 148 |
< |
if (atomType->isGayBerne()) { |
| 149 |
< |
DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType); |
| 150 |
< |
|
| 151 |
< |
GenericData* data = dAtomType->getPropertyByName("GayBerne"); |
| 152 |
< |
if (data != NULL) { |
| 153 |
< |
GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data); |
| 154 |
< |
|
| 155 |
< |
if (gayBerneData != NULL) { |
| 156 |
< |
GayBerneParam gayBerneParam = gayBerneData->getData(); |
| 157 |
< |
currShape = new Ellipsoid(V3Zero, |
| 158 |
< |
gayBerneParam.GB_sigma/2.0, |
| 159 |
< |
gayBerneParam.GB_l2b_ratio*gayBerneParam.GB_sigma/2.0, |
| 160 |
< |
Mat3x3d::identity()); |
| 161 |
< |
} else { |
| 162 |
< |
sprintf( painCave.errMsg, |
| 163 |
< |
"Can not cast GenericData to GayBerneParam\n"); |
| 164 |
< |
painCave.severity = OOPSE_ERROR; |
| 165 |
< |
painCave.isFatal = 1; |
| 166 |
< |
simError(); |
| 167 |
< |
} |
| 168 |
< |
} else { |
| 169 |
< |
sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n"); |
| 170 |
< |
painCave.severity = OOPSE_ERROR; |
| 171 |
< |
painCave.isFatal = 1; |
| 172 |
< |
simError(); |
| 173 |
< |
} |
| 174 |
< |
} |
| 175 |
< |
} else { |
| 176 |
< |
Atom* atom = static_cast<Atom*>(integrableObject); |
| 161 |
> |
|
| 162 |
> |
if (sd->isAtom()){ |
| 163 |
> |
Atom* atom = static_cast<Atom*>(sd); |
| 164 |
|
AtomType* atomType = atom->getAtomType(); |
| 165 |
< |
if (atomType->isLennardJones()){ |
| 166 |
< |
GenericData* data = atomType->getPropertyByName("LennardJones"); |
| 167 |
< |
if (data != NULL) { |
| 168 |
< |
LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data); |
| 169 |
< |
|
| 170 |
< |
if (ljData != NULL) { |
| 171 |
< |
LJParam ljParam = ljData->getData(); |
| 172 |
< |
currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0); |
| 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 |
> |
LennardJonesAdapter lja = LennardJonesAdapter(atomType); |
| 172 |
> |
if (lja.isLennardJones()){ |
| 173 |
> |
currShape = new Sphere(atom->getPos(), lja.getSigma()/2.0); |
| 174 |
> |
} else { |
| 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 |
< |
"Can not cast GenericData to LJParam\n"); |
| 181 |
< |
painCave.severity = OOPSE_ERROR; |
| 180 |
> |
"Could not find atom type in default element.txt\n"); |
| 181 |
> |
painCave.severity = OPENMD_ERROR; |
| 182 |
|
painCave.isFatal = 1; |
| 183 |
|
simError(); |
| 184 |
< |
} |
| 184 |
> |
} |
| 185 |
|
} |
| 194 |
– |
} else { |
| 195 |
– |
int obanum = etab.GetAtomicNum((atom->getType()).c_str()); |
| 196 |
– |
if (obanum != 0) { |
| 197 |
– |
currShape = new Sphere(atom->getPos(), etab.GetVdwRad(obanum)); |
| 198 |
– |
} else { |
| 199 |
– |
sprintf( painCave.errMsg, |
| 200 |
– |
"Could not find atom type in default element.txt\n"); |
| 201 |
– |
painCave.severity = OOPSE_ERROR; |
| 202 |
– |
painCave.isFatal = 1; |
| 203 |
– |
simError(); |
| 204 |
– |
} |
| 186 |
|
} |
| 187 |
|
} |
| 188 |
< |
HydroProps currHydroProp = currShape->getHydroProps(simParams->getViscosity(),simParams->getTargetTemp()); |
| 189 |
< |
std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType()); |
| 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(sd->getType()); |
| 206 |
|
if (iter != hydroPropMap.end()) |
| 207 |
|
hydroProps_.push_back(iter->second); |
| 208 |
|
else { |
| 209 |
< |
HydroProp myProp; |
| 210 |
< |
myProp.cor = V3Zero; |
| 211 |
< |
for (int i1 = 0; i1 < 3; i1++) { |
| 215 |
< |
for (int j1 = 0; j1 < 3; j1++) { |
| 216 |
< |
myProp.Xirtt(i1,j1) = currHydroProp.Xi(i1,j1); |
| 217 |
< |
myProp.Xirrt(i1,j1) = currHydroProp.Xi(i1,j1+3); |
| 218 |
< |
myProp.Xirtr(i1,j1) = currHydroProp.Xi(i1+3,j1); |
| 219 |
< |
myProp.Xirrr(i1,j1) = currHydroProp.Xi(i1+3,j1+3); |
| 220 |
< |
} |
| 221 |
< |
} |
| 222 |
< |
CholeskyDecomposition(currHydroProp.Xi, myProp.S); |
| 223 |
< |
hydroPropMap.insert(std::map<std::string, HydroProp>::value_type(integrableObject->getType(), myProp)); |
| 224 |
< |
hydroProps_.push_back(myProp); |
| 209 |
> |
currHydroProp->complete(); |
| 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(); |
| 218 |
< |
} |
| 231 |
< |
|
| 232 |
< |
|
| 217 |
> |
variance_ = 2.0 * PhysicalConstants::kb*simParams->getTargetTemp()/simParams->getDt(); |
| 218 |
> |
} |
| 219 |
|
|
| 220 |
< |
|
| 221 |
< |
|
| 236 |
< |
std::map<std::string, HydroProp> LDForceManager::parseFrictionFile(const std::string& filename) { |
| 237 |
< |
std::map<std::string, HydroProp> props; |
| 220 |
> |
std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) { |
| 221 |
> |
std::map<std::string, HydroProp*> props; |
| 222 |
|
std::ifstream ifs(filename.c_str()); |
| 223 |
|
if (ifs.is_open()) { |
| 224 |
|
|
| 227 |
|
const unsigned int BufferSize = 65535; |
| 228 |
|
char buffer[BufferSize]; |
| 229 |
|
while (ifs.getline(buffer, BufferSize)) { |
| 230 |
< |
StringTokenizer tokenizer(buffer); |
| 231 |
< |
HydroProp currProp; |
| 248 |
< |
if (tokenizer.countTokens() >= 40) { |
| 249 |
< |
std::string atomName = tokenizer.nextToken(); |
| 250 |
< |
currProp.cor[0] = tokenizer.nextTokenAsDouble(); |
| 251 |
< |
currProp.cor[1] = tokenizer.nextTokenAsDouble(); |
| 252 |
< |
currProp.cor[2] = tokenizer.nextTokenAsDouble(); |
| 253 |
< |
|
| 254 |
< |
currProp.Xirtt(0,0) = tokenizer.nextTokenAsDouble(); |
| 255 |
< |
currProp.Xirtt(0,1) = tokenizer.nextTokenAsDouble(); |
| 256 |
< |
currProp.Xirtt(0,2) = tokenizer.nextTokenAsDouble(); |
| 257 |
< |
currProp.Xirtt(1,0) = tokenizer.nextTokenAsDouble(); |
| 258 |
< |
currProp.Xirtt(1,1) = tokenizer.nextTokenAsDouble(); |
| 259 |
< |
currProp.Xirtt(1,2) = tokenizer.nextTokenAsDouble(); |
| 260 |
< |
currProp.Xirtt(2,0) = tokenizer.nextTokenAsDouble(); |
| 261 |
< |
currProp.Xirtt(2,1) = tokenizer.nextTokenAsDouble(); |
| 262 |
< |
currProp.Xirtt(2,2) = tokenizer.nextTokenAsDouble(); |
| 263 |
< |
|
| 264 |
< |
currProp.Xirrt(0,0) = tokenizer.nextTokenAsDouble(); |
| 265 |
< |
currProp.Xirrt(0,1) = tokenizer.nextTokenAsDouble(); |
| 266 |
< |
currProp.Xirrt(0,2) = tokenizer.nextTokenAsDouble(); |
| 267 |
< |
currProp.Xirrt(1,0) = tokenizer.nextTokenAsDouble(); |
| 268 |
< |
currProp.Xirrt(1,1) = tokenizer.nextTokenAsDouble(); |
| 269 |
< |
currProp.Xirrt(1,2) = tokenizer.nextTokenAsDouble(); |
| 270 |
< |
currProp.Xirrt(2,0) = tokenizer.nextTokenAsDouble(); |
| 271 |
< |
currProp.Xirrt(2,1) = tokenizer.nextTokenAsDouble(); |
| 272 |
< |
currProp.Xirrt(2,2) = tokenizer.nextTokenAsDouble(); |
| 273 |
< |
|
| 274 |
< |
currProp.Xirtr(0,0) = tokenizer.nextTokenAsDouble(); |
| 275 |
< |
currProp.Xirtr(0,1) = tokenizer.nextTokenAsDouble(); |
| 276 |
< |
currProp.Xirtr(0,2) = tokenizer.nextTokenAsDouble(); |
| 277 |
< |
currProp.Xirtr(1,0) = tokenizer.nextTokenAsDouble(); |
| 278 |
< |
currProp.Xirtr(1,1) = tokenizer.nextTokenAsDouble(); |
| 279 |
< |
currProp.Xirtr(1,2) = tokenizer.nextTokenAsDouble(); |
| 280 |
< |
currProp.Xirtr(2,0) = tokenizer.nextTokenAsDouble(); |
| 281 |
< |
currProp.Xirtr(2,1) = tokenizer.nextTokenAsDouble(); |
| 282 |
< |
currProp.Xirtr(2,2) = tokenizer.nextTokenAsDouble(); |
| 283 |
< |
|
| 284 |
< |
currProp.Xirrr(0,0) = tokenizer.nextTokenAsDouble(); |
| 285 |
< |
currProp.Xirrr(0,1) = tokenizer.nextTokenAsDouble(); |
| 286 |
< |
currProp.Xirrr(0,2) = tokenizer.nextTokenAsDouble(); |
| 287 |
< |
currProp.Xirrr(1,0) = tokenizer.nextTokenAsDouble(); |
| 288 |
< |
currProp.Xirrr(1,1) = tokenizer.nextTokenAsDouble(); |
| 289 |
< |
currProp.Xirrr(1,2) = tokenizer.nextTokenAsDouble(); |
| 290 |
< |
currProp.Xirrr(2,0) = tokenizer.nextTokenAsDouble(); |
| 291 |
< |
currProp.Xirrr(2,1) = tokenizer.nextTokenAsDouble(); |
| 292 |
< |
currProp.Xirrr(2,2) = tokenizer.nextTokenAsDouble(); |
| 293 |
< |
|
| 294 |
< |
SquareMatrix<RealType, 6> Xir; |
| 295 |
< |
Xir.setSubMatrix(0, 0, currProp.Xirtt); |
| 296 |
< |
Xir.setSubMatrix(0, 3, currProp.Xirrt); |
| 297 |
< |
Xir.setSubMatrix(3, 0, currProp.Xirtr); |
| 298 |
< |
Xir.setSubMatrix(3, 3, currProp.Xirrr); |
| 299 |
< |
CholeskyDecomposition(Xir, currProp.S); |
| 300 |
< |
|
| 301 |
< |
props.insert(std::map<std::string, HydroProp>::value_type(atomName, currProp)); |
| 302 |
< |
} |
| 230 |
> |
HydroProp* currProp = new HydroProp(buffer); |
| 231 |
> |
props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp)); |
| 232 |
|
} |
| 233 |
< |
|
| 233 |
> |
|
| 234 |
|
return props; |
| 235 |
|
} |
| 236 |
< |
|
| 237 |
< |
void LDForceManager::postCalculation() { |
| 236 |
> |
|
| 237 |
> |
void LDForceManager::postCalculation(){ |
| 238 |
|
SimInfo::MoleculeIterator i; |
| 239 |
|
Molecule::IntegrableObjectIterator j; |
| 240 |
|
Molecule* mol; |
| 241 |
< |
StuntDouble* integrableObject; |
| 242 |
< |
Vector3d vel; |
| 241 |
> |
StuntDouble* sd; |
| 242 |
> |
RealType mass; |
| 243 |
|
Vector3d pos; |
| 244 |
|
Vector3d frc; |
| 245 |
|
Mat3x3d A; |
| 246 |
|
Mat3x3d Atrans; |
| 247 |
|
Vector3d Tb; |
| 248 |
|
Vector3d ji; |
| 320 |
– |
RealType mass; |
| 249 |
|
unsigned int index = 0; |
| 250 |
|
bool doLangevinForces; |
| 251 |
|
bool freezeMolecule; |
| 252 |
|
int fdf; |
| 253 |
< |
|
| 253 |
> |
|
| 254 |
|
fdf = 0; |
| 255 |
+ |
|
| 256 |
|
for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) { |
| 257 |
< |
|
| 257 |
> |
|
| 258 |
> |
doLangevinForces = true; |
| 259 |
> |
freezeMolecule = false; |
| 260 |
> |
|
| 261 |
|
if (sphericalBoundaryConditions_) { |
| 262 |
|
|
| 263 |
|
Vector3d molPos = mol->getCom(); |
| 264 |
|
RealType molRad = molPos.length(); |
| 265 |
< |
|
| 265 |
> |
|
| 266 |
|
doLangevinForces = false; |
| 335 |
– |
freezeMolecule = false; |
| 267 |
|
|
| 268 |
|
if (molRad > langevinBufferRadius_) { |
| 269 |
|
doLangevinForces = true; |
| 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 |
< |
if (integrableObject->isDirectional()){ |
| 287 |
< |
//calculate angular velocity in lab frame |
| 288 |
< |
Mat3x3d I = integrableObject->getI(); |
| 289 |
< |
Vector3d angMom = integrableObject->getJ(); |
| 290 |
< |
Vector3d omega; |
| 360 |
< |
|
| 361 |
< |
if (integrableObject->isLinear()) { |
| 362 |
< |
int linearAxis = integrableObject->linearAxis(); |
| 363 |
< |
int l = (linearAxis +1 )%3; |
| 364 |
< |
int m = (linearAxis +2 )%3; |
| 365 |
< |
omega[l] = angMom[l] /I(l, l); |
| 366 |
< |
omega[m] = angMom[m] /I(m, m); |
| 367 |
< |
|
| 368 |
< |
} else { |
| 369 |
< |
omega[0] = angMom[0] /I(0, 0); |
| 370 |
< |
omega[1] = angMom[1] /I(1, 1); |
| 371 |
< |
omega[2] = angMom[2] /I(2, 2); |
| 372 |
< |
} |
| 373 |
< |
|
| 374 |
< |
//apply friction force and torque at center of resistance |
| 375 |
< |
A = integrableObject->getA(); |
| 284 |
> |
if (doLangevinForces) { |
| 285 |
> |
mass = sd->getMass(); |
| 286 |
> |
if (sd->isDirectional()){ |
| 287 |
> |
|
| 288 |
> |
// preliminaries for directional objects: |
| 289 |
> |
|
| 290 |
> |
A = sd->getA(); |
| 291 |
|
Atrans = A.transpose(); |
| 292 |
< |
Vector3d rcr = Atrans * hydroProps_[index].cor; |
| 293 |
< |
Vector3d vcdLab = vel + cross(omega, rcr); |
| 379 |
< |
Vector3d vcdBody = A* vcdLab; |
| 380 |
< |
Vector3d frictionForceBody = -(hydroProps_[index].Xirtt * vcdBody + hydroProps_[index].Xirrt * omega); |
| 381 |
< |
Vector3d frictionForceLab = Atrans*frictionForceBody; |
| 382 |
< |
integrableObject->addFrc(frictionForceLab); |
| 383 |
< |
Vector3d frictionTorqueBody = - (hydroProps_[index].Xirtr * vcdBody + hydroProps_[index].Xirrr * omega); |
| 384 |
< |
Vector3d frictionTorqueLab = Atrans*frictionTorqueBody; |
| 385 |
< |
integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab)); |
| 386 |
< |
|
| 292 |
> |
Vector3d rcrLab = Atrans * hydroProps_[index]->getCOR(); |
| 293 |
> |
|
| 294 |
|
//apply random force and torque at center of resistance |
| 295 |
+ |
|
| 296 |
|
Vector3d randomForceBody; |
| 297 |
|
Vector3d randomTorqueBody; |
| 298 |
|
genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_); |
| 299 |
< |
Vector3d randomForceLab = Atrans*randomForceBody; |
| 300 |
< |
Vector3d randomTorqueLab = Atrans* randomTorqueBody; |
| 301 |
< |
integrableObject->addFrc(randomForceLab); |
| 302 |
< |
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].Xirtt *vel); |
| 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 |
|
|
| 436 |
|
|
| 437 |
|
} |
| 438 |
|
} |
| 439 |
+ |
|
| 440 |
|
info_->setFdf(fdf); |
| 441 |
< |
|
| 441 |
> |
veloMunge->removeComDrift(); |
| 442 |
> |
// Remove angular drift if we are not using periodic boundary conditions. |
| 443 |
> |
if(!simParams->getUsePeriodicBoundaryConditions()) |
| 444 |
> |
veloMunge->removeAngularDrift(); |
| 445 |
> |
|
| 446 |
|
ForceManager::postCalculation(); |
| 447 |
|
} |
| 448 |
|
|
| 451 |
|
|
| 452 |
|
Vector<RealType, 6> Z; |
| 453 |
|
Vector<RealType, 6> generalForce; |
| 421 |
– |
|
| 454 |
|
|
| 455 |
|
Z[0] = randNumGen_.randNorm(0, variance); |
| 456 |
|
Z[1] = randNumGen_.randNorm(0, variance); |
| 459 |
|
Z[4] = randNumGen_.randNorm(0, variance); |
| 460 |
|
Z[5] = randNumGen_.randNorm(0, variance); |
| 461 |
|
|
| 462 |
< |
|
| 431 |
< |
generalForce = hydroProps_[index].S*Z; |
| 462 |
> |
generalForce = hydroProps_[index]->getS()*Z; |
| 463 |
|
|
| 464 |
|
force[0] = generalForce[0]; |
| 465 |
|
force[1] = generalForce[1]; |
| 468 |
|
torque[1] = generalForce[4]; |
| 469 |
|
torque[2] = generalForce[5]; |
| 470 |
|
|
| 471 |
< |
} |
| 471 |
> |
} |
| 472 |
|
|
| 473 |
|
} |
