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root/OpenMD/branches/development/src/integrators/LDForceManager.cpp

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trunk/src/integrators/LDForceManager.cpp (file contents), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/integrators/LDForceManager.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 6 | Line 6
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.
#	Line 37 | Line 28
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, 24107 (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
51	<	using namespace OpenBabel;
50	<	namespace oopse {
51	>	namespace OpenMD {
52
53	<	LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info){
54	<	Globals* simParams = info->getSimParams();
55	<
53	>	LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info), forceTolerance_(1e-6), maxIterNum_(4) {
54	>	simParams = info->getSimParams();
55	>	veloMunge = new Velocitizer(info);
56	>
57		sphericalBoundaryConditions_ = false;
58		if (simParams->getUseSphericalBoundaryConditions()) {
59		sphericalBoundaryConditions_ = true;
#	Line 61 | Line 63 | namespace oopse {
63		sprintf( painCave.errMsg,
64		"langevinBufferRadius must be specified "
65		"when useSphericalBoundaryConditions is turned on.\n");
66	<	painCave.severity = OOPSE_ERROR;
66	>	painCave.severity = OPENMD_ERROR;
67		painCave.isFatal = 1;
68		simError();
69		}
#	Line 72 | Line 74 | namespace oopse {
74		sprintf( painCave.errMsg,
75		"frozenBufferRadius must be specified "
76		"when useSphericalBoundaryConditions is turned on.\n");
77	<	painCave.severity = OOPSE_ERROR;
77	>	painCave.severity = OPENMD_ERROR;
78		painCave.isFatal = 1;
79		simError();
80		}
#	Line 81 | Line 83 | namespace oopse {
83		sprintf( painCave.errMsg,
84		"frozenBufferRadius has been set smaller than the "
85		"langevinBufferRadius.  This is probably an error.\n");
86	<	painCave.severity = OOPSE_WARNING;
86	>	painCave.severity = OPENMD_WARNING;
87		painCave.isFatal = 0;
88		simError();
89		}
90		}
91
92		// Build the hydroProp map:
93	<	std::map<std::string, HydroProp> hydroPropMap;
93	>	std::map<std::string, HydroProp*> hydroPropMap;
94
95		Molecule* mol;
96		StuntDouble* integrableObject;
#	Line 116 | Line 118 | namespace oopse {
118		hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
119		} else {
120		sprintf( painCave.errMsg,
121	<	"HydroPropFile must be set to a file name if Langevin\n"
122	<	"\tDynamics is specified for rigidBodies which contain more\n"
123	<	"\tthan one atom.  To create a HydroPropFile, run \"Hydro\".\n");
124	<	painCave.severity = OOPSE_ERROR;
121	>	"HydroPropFile must be set to a file name if Langevin Dynamics\n"
122	>	"\tis specified for rigidBodies which contain more than one atom\n"
123	>	"\tTo create a HydroPropFile, run the \"Hydro\" program.\n");
124	>	painCave.severity = OPENMD_ERROR;
125		painCave.isFatal = 1;
126		simError();
127		}
128	<	std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
129	<	if (iter != hydroPropMap.end()) {
130	<	hydroProps_.push_back(iter->second);
131	<	} else {
132	<	sprintf( painCave.errMsg,
133	<	"Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
134	<	painCave.severity = OOPSE_ERROR;
135	<	painCave.isFatal = 1;
136	<	simError();
128	>
129	>	for (mol = info->beginMolecule(i); mol != NULL;
130	>	mol = info->nextMolecule(i)) {
131	>	for (integrableObject = mol->beginIntegrableObject(j);
132	>	integrableObject != NULL;
133	>	integrableObject = mol->nextIntegrableObject(j)) {
134	>
135	>	std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
136	>	if (iter != hydroPropMap.end()) {
137	>	hydroProps_.push_back(iter->second);
138	>	} else {
139	>	sprintf( painCave.errMsg,
140	>	"Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
141	>	painCave.severity = OPENMD_ERROR;
142	>	painCave.isFatal = 1;
143	>	simError();
144	>	}
145	>	}
146		}
147		} else {
148	<
149	<	std::map<std::string, HydroProp> hydroPropMap;
148	>
149	>	std::map<std::string, HydroProp*> hydroPropMap;
150		for (mol = info->beginMolecule(i); mol != NULL;
151		mol = info->nextMolecule(i)) {
152		for (integrableObject = mol->beginIntegrableObject(j);
153		integrableObject != NULL;
154		integrableObject = mol->nextIntegrableObject(j)) {
155		Shape* currShape = NULL;
156	<	if (integrableObject->isDirectionalAtom()) {
157	<	DirectionalAtom* dAtom = static_cast<DirectionalAtom*>(integrableObject);
158	<	AtomType* atomType = dAtom->getAtomType();
156	>
157	>	if (integrableObject->isAtom()){
158	>	Atom* atom = static_cast<Atom*>(integrableObject);
159	>	AtomType* atomType = atom->getAtomType();
160		if (atomType->isGayBerne()) {
161	<	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
150	<
161	>	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
162		GenericData* data = dAtomType->getPropertyByName("GayBerne");
163		if (data != NULL) {
164		GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
#	Line 155 | Line 166 | namespace oopse {
166		if (gayBerneData != NULL) {
167		GayBerneParam gayBerneParam = gayBerneData->getData();
168		currShape = new Ellipsoid(V3Zero,
169	<	gayBerneParam.GB_sigma/2.0,
170	<	gayBerneParam.GB_l2b_ratio*gayBerneParam.GB_sigma/2.0,
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;
175	>	painCave.severity = OPENMD_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;
181	>	painCave.severity = OPENMD_ERROR;
182		painCave.isFatal = 1;
183		simError();
184		}
185	<	}
186	<	} else {
187	<	Atom* atom = static_cast<Atom*>(integrableObject);
188	<	AtomType* atomType = atom->getAtomType();
189	<	if (atomType->isLennardJones()){
190	<	GenericData* data = atomType->getPropertyByName("LennardJones");
191	<	if (data != NULL) {
192	<	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
193	<
194	<	if (ljData != NULL) {
195	<	LJParam ljParam = ljData->getData();
196	<	currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0);
185	>	} else {
186	>	if (atomType->isLennardJones()){
187	>	GenericData* data = atomType->getPropertyByName("LennardJones");
188	>	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 = OPENMD_ERROR;
197	>	painCave.isFatal = 1;
198	>	simError();
199	>	}
200	>	}
201	>	} else {
202	>	int aNum = etab.GetAtomicNum((atom->getType()).c_str());
203	>	if (aNum != 0) {
204	>	currShape = new Sphere(atom->getPos(), etab.GetVdwRad(aNum));
205		} else {
206		sprintf( painCave.errMsg,
207	<	"Can not cast GenericData to LJParam\n");
208	<	painCave.severity = OOPSE_ERROR;
207	>	"Could not find atom type in default element.txt\n");
208	>	painCave.severity = OPENMD_ERROR;
209		painCave.isFatal = 1;
210		simError();
211	<	}
211	>	}
212		}
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	–	}
213		}
214		}
215	<	HydroProps currHydroProp = currShape->getHydroProps(simParams->getViscosity(),simParams->getTargetTemp());
216	<	std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
215	>
216	>	if (!simParams->haveTargetTemp()) {
217	>	sprintf(painCave.errMsg, "You can't use LangevinDynamics without a targetTemp!\n");
218	>	painCave.isFatal = 1;
219	>	painCave.severity = OPENMD_ERROR;
220	>	simError();
221	>	}
222	>
223	>	if (!simParams->haveViscosity()) {
224	>	sprintf(painCave.errMsg, "You can't use LangevinDynamics without a viscosity!\n");
225	>	painCave.isFatal = 1;
226	>	painCave.severity = OPENMD_ERROR;
227	>	simError();
228	>	}
229	>
230	>
231	>	HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp());
232	>	std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
233		if (iter != hydroPropMap.end())
234		hydroProps_.push_back(iter->second);
235		else {
236	<	HydroProp myProp;
237	<	myProp.cor = V3Zero;
238	<	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);
236	>	currHydroProp->complete();
237	>	hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(integrableObject->getType(), currHydroProp));
238	>	hydroProps_.push_back(currHydroProp);
239		}
240		}
241		}
242		}
243	<	variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
244	<	}
231	<
232	<
243	>	variance_ = 2.0 * PhysicalConstants::kb*simParams->getTargetTemp()/simParams->getDt();
244	>	}
245
246	<
247	<
236	<	std::map<std::string, HydroProp> LDForceManager::parseFrictionFile(const std::string& filename) {
237	<	std::map<std::string, HydroProp> props;
246	>	std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) {
247	>	std::map<std::string, HydroProp*> props;
248		std::ifstream ifs(filename.c_str());
249		if (ifs.is_open()) {
250
#	Line 243 | Line 253 | namespace oopse {
253		const unsigned int BufferSize = 65535;
254		char buffer[BufferSize];
255		while (ifs.getline(buffer, BufferSize)) {
256	<	StringTokenizer tokenizer(buffer);
257	<	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	<	}
256	>	HydroProp* currProp = new HydroProp(buffer);
257	>	props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
258		}
259	<
259	>
260		return props;
261		}
262	<
263	<	void LDForceManager::postCalculation() {
262	>
263	>	void LDForceManager::postCalculation(){
264		SimInfo::MoleculeIterator i;
265		Molecule::IntegrableObjectIterator  j;
266		Molecule* mol;
267		StuntDouble* integrableObject;
268	<	Vector3d vel;
268	>	RealType mass;
269		Vector3d pos;
270		Vector3d frc;
271		Mat3x3d A;
272		Mat3x3d Atrans;
273		Vector3d Tb;
274		Vector3d ji;
320	–	RealType mass;
275		unsigned int index = 0;
276		bool doLangevinForces;
277		bool freezeMolecule;
278		int fdf;
279	<
279	>
280		fdf = 0;
281	+
282		for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
283	<
283	>
284	>	doLangevinForces = true;
285	>	freezeMolecule = false;
286	>
287		if (sphericalBoundaryConditions_) {
288
289		Vector3d molPos = mol->getCom();
290		RealType molRad = molPos.length();
291	<
291	>
292		doLangevinForces = false;
335	–	freezeMolecule = false;
293
294		if (molRad > langevinBufferRadius_) {
295		doLangevinForces = true;
#	Line 350 | Line 307 | namespace oopse {
307		if (freezeMolecule)
308		fdf += integrableObject->freeze();
309
310	<	if (doLangevinForces) {
311	<	vel =integrableObject->getVel();
310	>	if (doLangevinForces) {
311	>	mass = integrableObject->getMass();
312		if (integrableObject->isDirectional()){
313	<	//calculate angular velocity in lab frame
314	<	Mat3x3d I = integrableObject->getI();
315	<	Vector3d angMom = integrableObject->getJ();
359	<	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
313	>
314	>	// preliminaries for directional objects:
315	>
316		A = integrableObject->getA();
317		Atrans = A.transpose();
318	<	Vector3d rcr = Atrans * hydroProps_[index].cor;
319	<	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	<
318	>	Vector3d rcrLab = Atrans * hydroProps_[index]->getCOR();
319	>
320		//apply random force and torque at center of resistance
321	+
322		Vector3d randomForceBody;
323		Vector3d randomTorqueBody;
324		genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
325	<	Vector3d randomForceLab = Atrans*randomForceBody;
326	<	Vector3d randomTorqueLab = Atrans* randomTorqueBody;
325	>	Vector3d randomForceLab = Atrans * randomForceBody;
326	>	Vector3d randomTorqueLab = Atrans * randomTorqueBody;
327		integrableObject->addFrc(randomForceLab);
328	<	integrableObject->addTrq(randomTorqueLab + cross(rcr, randomForceLab ));
328	>	integrableObject->addTrq(randomTorqueLab + cross(rcrLab, randomForceLab ));
329	>
330	>	Mat3x3d I = integrableObject->getI();
331	>	Vector3d omegaBody;
332	>
333	>	// What remains contains velocity explicitly, but the velocity required
334	>	// is at the full step: v(t + h), while we have initially the velocity
335	>	// at the half step: v(t + h/2).  We need to iterate to converge the
336	>	// friction force and friction torque vectors.
337	>
338	>	// this is the velocity at the half-step:
339
340	+	Vector3d vel =integrableObject->getVel();
341	+	Vector3d angMom = integrableObject->getJ();
342	+
343	+	//estimate velocity at full-step using everything but friction forces:
344	+
345	+	frc = integrableObject->getFrc();
346	+	Vector3d velStep = vel + (dt2_ /mass * PhysicalConstants::energyConvert) * frc;
347	+
348	+	Tb = integrableObject->lab2Body(integrableObject->getTrq());
349	+	Vector3d angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * Tb;
350	+
351	+	Vector3d omegaLab;
352	+	Vector3d vcdLab;
353	+	Vector3d vcdBody;
354	+	Vector3d frictionForceBody;
355	+	Vector3d frictionForceLab(0.0);
356	+	Vector3d oldFFL;  // used to test for convergence
357	+	Vector3d frictionTorqueBody(0.0);
358	+	Vector3d oldFTB;  // used to test for convergence
359	+	Vector3d frictionTorqueLab;
360	+	RealType fdot;
361	+	RealType tdot;
362	+
363	+	//iteration starts here:
364	+
365	+	for (int k = 0; k < maxIterNum_; k++) {
366	+
367	+	if (integrableObject->isLinear()) {
368	+	int linearAxis = integrableObject->linearAxis();
369	+	int l = (linearAxis +1 )%3;
370	+	int m = (linearAxis +2 )%3;
371	+	omegaBody[l] = angMomStep[l] /I(l, l);
372	+	omegaBody[m] = angMomStep[m] /I(m, m);
373	+
374	+	} else {
375	+	omegaBody[0] = angMomStep[0] /I(0, 0);
376	+	omegaBody[1] = angMomStep[1] /I(1, 1);
377	+	omegaBody[2] = angMomStep[2] /I(2, 2);
378	+	}
379	+
380	+	omegaLab = Atrans * omegaBody;
381	+
382	+	// apply friction force and torque at center of resistance
383	+
384	+	vcdLab = velStep + cross(omegaLab, rcrLab);
385	+	vcdBody = A * vcdLab;
386	+	frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omegaBody);
387	+	oldFFL = frictionForceLab;
388	+	frictionForceLab = Atrans * frictionForceBody;
389	+	oldFTB = frictionTorqueBody;
390	+	frictionTorqueBody = -(hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omegaBody);
391	+	frictionTorqueLab = Atrans * frictionTorqueBody;
392	+
393	+	// re-estimate velocities at full-step using friction forces:
394	+
395	+	velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForceLab);
396	+	angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * (Tb + frictionTorqueBody);
397	+
398	+	// check for convergence (if the vectors have converged, fdot and tdot will both be 1.0):
399	+
400	+	fdot = dot(frictionForceLab, oldFFL) / frictionForceLab.lengthSquare();
401	+	tdot = dot(frictionTorqueBody, oldFTB) / frictionTorqueBody.lengthSquare();
402	+
403	+	if (fabs(1.0 - fdot) <= forceTolerance_ && fabs(1.0 - tdot) <= forceTolerance_)
404	+	break; // iteration ends here
405	+	}
406	+
407	+	integrableObject->addFrc(frictionForceLab);
408	+	integrableObject->addTrq(frictionTorqueLab + cross(rcrLab, frictionForceLab));
409	+
410	+
411		} else {
412		//spherical atom
413	<	Vector3d frictionForce = -(hydroProps_[index].Xirtt *vel);
413	>
414		Vector3d randomForce;
415		Vector3d randomTorque;
416		genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
417	+	integrableObject->addFrc(randomForce);
418	+
419	+	// What remains contains velocity explicitly, but the velocity required
420	+	// is at the full step: v(t + h), while we have initially the velocity
421	+	// at the half step: v(t + h/2).  We need to iterate to converge the
422	+	// friction force vector.
423	+
424	+	// this is the velocity at the half-step:
425
426	<	integrableObject->addFrc(frictionForce+randomForce);
426	>	Vector3d vel =integrableObject->getVel();
427	>
428	>	//estimate velocity at full-step using everything but friction forces:
429	>
430	>	frc = integrableObject->getFrc();
431	>	Vector3d velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * frc;
432	>
433	>	Vector3d frictionForce(0.0);
434	>	Vector3d oldFF;  // used to test for convergence
435	>	RealType fdot;
436	>
437	>	//iteration starts here:
438	>
439	>	for (int k = 0; k < maxIterNum_; k++) {
440	>
441	>	oldFF = frictionForce;
442	>	frictionForce = -hydroProps_[index]->getXitt() * velStep;
443	>
444	>	// re-estimate velocities at full-step using friction forces:
445	>
446	>	velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForce);
447	>
448	>	// check for convergence (if the vector has converged, fdot will be 1.0):
449	>
450	>	fdot = dot(frictionForce, oldFF) / frictionForce.lengthSquare();
451	>
452	>	if (fabs(1.0 - fdot) <= forceTolerance_)
453	>	break; // iteration ends here
454	>	}
455	>
456	>	integrableObject->addFrc(frictionForce);
457	>
458		}
459		}
460
#	Line 408 | Line 462 | namespace oopse {
462
463		}
464		}
465	+
466		info_->setFdf(fdf);
467	<
467	>	veloMunge->removeComDrift();
468	>	// Remove angular drift if we are not using periodic boundary conditions.
469	>	if(!simParams->getUsePeriodicBoundaryConditions())
470	>	veloMunge->removeAngularDrift();
471	>
472		ForceManager::postCalculation();
473		}
474
#	Line 418 | Line 477 | void LDForceManager::genRandomForceAndTorque(Vector3d&
477
478		Vector<RealType, 6> Z;
479		Vector<RealType, 6> generalForce;
421	–
480
481		Z[0] = randNumGen_.randNorm(0, variance);
482		Z[1] = randNumGen_.randNorm(0, variance);
#	Line 427 | Line 485 | void LDForceManager::genRandomForceAndTorque(Vector3d&
485		Z[4] = randNumGen_.randNorm(0, variance);
486		Z[5] = randNumGen_.randNorm(0, variance);
487
488	<
431	<	generalForce = hydroProps_[index].S*Z;
488	>	generalForce = hydroProps_[index]->getS()*Z;
489
490		force[0] = generalForce[0];
491		force[1] = generalForce[1];
#	Line 437 | Line 494 | void LDForceManager::genRandomForceAndTorque(Vector3d&
494		torque[1] = generalForce[4];
495		torque[2] = generalForce[5];
496
497	<	}
497	>	}
498
499		}

Comparing:
trunk/src/integrators/LDForceManager.cpp (property svn:keywords), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/integrators/LDForceManager.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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