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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 1710 by gezelter, Fri May 18 21:44:02 2012 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	>	#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), forceTolerance_(1e-6), maxIterNum_(4) {
56	>	simParams = info->getSimParams();
57	>	veloMunge = new Velocitizer(info);
58	>
59		sphericalBoundaryConditions_ = false;
60		if (simParams->getUseSphericalBoundaryConditions()) {
61		sphericalBoundaryConditions_ = true;
#	Line 61 | Line 65 | namespace oopse {
65		sprintf( painCave.errMsg,
66		"langevinBufferRadius must be specified "
67		"when useSphericalBoundaryConditions is turned on.\n");
68	<	painCave.severity = OOPSE_ERROR;
68	>	painCave.severity = OPENMD_ERROR;
69		painCave.isFatal = 1;
70		simError();
71		}
#	Line 72 | Line 76 | namespace oopse {
76		sprintf( painCave.errMsg,
77		"frozenBufferRadius must be specified "
78		"when useSphericalBoundaryConditions is turned on.\n");
79	<	painCave.severity = OOPSE_ERROR;
79	>	painCave.severity = OPENMD_ERROR;
80		painCave.isFatal = 1;
81		simError();
82		}
#	Line 81 | Line 85 | namespace oopse {
85		sprintf( painCave.errMsg,
86		"frozenBufferRadius has been set smaller than the "
87		"langevinBufferRadius.  This is probably an error.\n");
88	<	painCave.severity = OOPSE_WARNING;
88	>	painCave.severity = OPENMD_WARNING;
89		painCave.isFatal = 0;
90		simError();
91		}
92		}
93
94		// Build the hydroProp map:
95	<	std::map<std::string, HydroProp> hydroPropMap;
95	>	std::map<std::string, HydroProp*> hydroPropMap;
96
97		Molecule* mol;
98		StuntDouble* integrableObject;
#	Line 116 | Line 120 | namespace oopse {
120		hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
121		} else {
122		sprintf( painCave.errMsg,
123	<	"HydroPropFile must be set to a file name if Langevin\n"
124	<	"\tDynamics is specified for rigidBodies which contain more\n"
125	<	"\tthan one atom.  To create a HydroPropFile, run \"Hydro\".\n");
126	<	painCave.severity = OOPSE_ERROR;
123	>	"HydroPropFile must be set to a file name if Langevin Dynamics\n"
124	>	"\tis specified for rigidBodies which contain more than one atom\n"
125	>	"\tTo create a HydroPropFile, run the \"Hydro\" program.\n");
126	>	painCave.severity = OPENMD_ERROR;
127		painCave.isFatal = 1;
128		simError();
129		}
130	<	std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
131	<	if (iter != hydroPropMap.end()) {
132	<	hydroProps_.push_back(iter->second);
133	<	} else {
134	<	sprintf( painCave.errMsg,
135	<	"Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
136	<	painCave.severity = OOPSE_ERROR;
137	<	painCave.isFatal = 1;
138	<	simError();
130	>
131	>	for (mol = info->beginMolecule(i); mol != NULL;
132	>	mol = info->nextMolecule(i)) {
133	>	for (integrableObject = mol->beginIntegrableObject(j);
134	>	integrableObject != NULL;
135	>	integrableObject = mol->nextIntegrableObject(j)) {
136	>
137	>	std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
138	>	if (iter != hydroPropMap.end()) {
139	>	hydroProps_.push_back(iter->second);
140	>	} else {
141	>	sprintf( painCave.errMsg,
142	>	"Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
143	>	painCave.severity = OPENMD_ERROR;
144	>	painCave.isFatal = 1;
145	>	simError();
146	>	}
147	>	}
148		}
149		} else {
150	<
151	<	std::map<std::string, HydroProp> hydroPropMap;
150	>
151	>	std::map<std::string, HydroProp*> hydroPropMap;
152		for (mol = info->beginMolecule(i); mol != NULL;
153		mol = info->nextMolecule(i)) {
154		for (integrableObject = mol->beginIntegrableObject(j);
155		integrableObject != NULL;
156		integrableObject = mol->nextIntegrableObject(j)) {
157		Shape* currShape = NULL;
158	<	if (integrableObject->isDirectionalAtom()) {
159	<	DirectionalAtom* dAtom = static_cast<DirectionalAtom*>(integrableObject);
147	<	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 {
158	>
159	>	if (integrableObject->isAtom()){
160		Atom* atom = static_cast<Atom*>(integrableObject);
161		AtomType* atomType = atom->getAtomType();
162	<	if (atomType->isLennardJones()){
163	<	GenericData* data = atomType->getPropertyByName("LennardJones");
164	<	if (data != NULL) {
165	<	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
166	<
167	<	if (ljData != NULL) {
168	<	LJParam ljParam = ljData->getData();
169	<	currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0);
162	>	GayBerneAdapter gba = GayBerneAdapter(atomType);
163	>	if (gba.isGayBerne()) {
164	>	currShape = new Ellipsoid(V3Zero, gba.getL() / 2.0,
165	>	gba.getD() / 2.0,
166	>	Mat3x3d::identity());
167	>	} else {
168	>	LennardJonesAdapter lja = LennardJonesAdapter(atomType);
169	>	if (lja.isLennardJones()){
170	>	currShape = new Sphere(atom->getPos(), lja.getSigma()/2.0);
171	>	} else {
172	>	int aNum = etab.GetAtomicNum((atom->getType()).c_str());
173	>	if (aNum != 0) {
174	>	currShape = new Sphere(atom->getPos(), etab.GetVdwRad(aNum));
175		} else {
176		sprintf( painCave.errMsg,
177	<	"Can not cast GenericData to LJParam\n");
178	<	painCave.severity = OOPSE_ERROR;
177	>	"Could not find atom type in default element.txt\n");
178	>	painCave.severity = OPENMD_ERROR;
179		painCave.isFatal = 1;
180		simError();
181	<	}
181	>	}
182		}
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	–	}
183		}
184		}
185	<	HydroProps currHydroProp = currShape->getHydroProps(simParams->getViscosity(),simParams->getTargetTemp());
186	<	std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
185	>
186	>	if (!simParams->haveTargetTemp()) {
187	>	sprintf(painCave.errMsg, "You can't use LangevinDynamics without a targetTemp!\n");
188	>	painCave.isFatal = 1;
189	>	painCave.severity = OPENMD_ERROR;
190	>	simError();
191	>	}
192	>
193	>	if (!simParams->haveViscosity()) {
194	>	sprintf(painCave.errMsg, "You can't use LangevinDynamics without a viscosity!\n");
195	>	painCave.isFatal = 1;
196	>	painCave.severity = OPENMD_ERROR;
197	>	simError();
198	>	}
199	>
200	>
201	>	HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp());
202	>	std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
203		if (iter != hydroPropMap.end())
204		hydroProps_.push_back(iter->second);
205		else {
206	<	HydroProp myProp;
207	<	myProp.cor = V3Zero;
208	<	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);
206	>	currHydroProp->complete();
207	>	hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(integrableObject->getType(), currHydroProp));
208	>	hydroProps_.push_back(currHydroProp);
209		}
210		}
211		}
212		}
213	<	variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
214	<	}
231	<
232	<
213	>	variance_ = 2.0 * PhysicalConstants::kb*simParams->getTargetTemp()/simParams->getDt();
214	>	}
215
216	<
217	<
236	<	std::map<std::string, HydroProp> LDForceManager::parseFrictionFile(const std::string& filename) {
237	<	std::map<std::string, HydroProp> props;
216	>	std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) {
217	>	std::map<std::string, HydroProp*> props;
218		std::ifstream ifs(filename.c_str());
219		if (ifs.is_open()) {
220
#	Line 243 | Line 223 | namespace oopse {
223		const unsigned int BufferSize = 65535;
224		char buffer[BufferSize];
225		while (ifs.getline(buffer, BufferSize)) {
226	<	StringTokenizer tokenizer(buffer);
227	<	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	<	}
226	>	HydroProp* currProp = new HydroProp(buffer);
227	>	props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
228		}
229	<
229	>
230		return props;
231		}
232	<
233	<	void LDForceManager::postCalculation() {
232	>
233	>	void LDForceManager::postCalculation(){
234		SimInfo::MoleculeIterator i;
235		Molecule::IntegrableObjectIterator  j;
236		Molecule* mol;
237		StuntDouble* integrableObject;
238	<	Vector3d vel;
238	>	RealType mass;
239		Vector3d pos;
240		Vector3d frc;
241		Mat3x3d A;
242		Mat3x3d Atrans;
243		Vector3d Tb;
244		Vector3d ji;
320	–	RealType mass;
245		unsigned int index = 0;
246		bool doLangevinForces;
247		bool freezeMolecule;
248		int fdf;
249	<
249	>
250		fdf = 0;
251	+
252		for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
253	<
253	>
254	>	doLangevinForces = true;
255	>	freezeMolecule = false;
256	>
257		if (sphericalBoundaryConditions_) {
258
259		Vector3d molPos = mol->getCom();
260		RealType molRad = molPos.length();
261	<
261	>
262		doLangevinForces = false;
335	–	freezeMolecule = false;
263
264		if (molRad > langevinBufferRadius_) {
265		doLangevinForces = true;
#	Line 350 | Line 277 | namespace oopse {
277		if (freezeMolecule)
278		fdf += integrableObject->freeze();
279
280	<	if (doLangevinForces) {
281	<	vel =integrableObject->getVel();
280	>	if (doLangevinForces) {
281	>	mass = integrableObject->getMass();
282		if (integrableObject->isDirectional()){
283	<	//calculate angular velocity in lab frame
284	<	Mat3x3d I = integrableObject->getI();
285	<	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
283	>
284	>	// preliminaries for directional objects:
285	>
286		A = integrableObject->getA();
287		Atrans = A.transpose();
288	<	Vector3d rcr = Atrans * hydroProps_[index].cor;
289	<	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	<
288	>	Vector3d rcrLab = Atrans * hydroProps_[index]->getCOR();
289	>
290		//apply random force and torque at center of resistance
291	+
292		Vector3d randomForceBody;
293		Vector3d randomTorqueBody;
294		genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
295	<	Vector3d randomForceLab = Atrans*randomForceBody;
296	<	Vector3d randomTorqueLab = Atrans* randomTorqueBody;
295	>	Vector3d randomForceLab = Atrans * randomForceBody;
296	>	Vector3d randomTorqueLab = Atrans * randomTorqueBody;
297		integrableObject->addFrc(randomForceLab);
298	<	integrableObject->addTrq(randomTorqueLab + cross(rcr, randomForceLab ));
298	>	integrableObject->addTrq(randomTorqueLab + cross(rcrLab, randomForceLab ));
299	>
300	>	Mat3x3d I = integrableObject->getI();
301	>	Vector3d omegaBody;
302	>
303	>	// What remains contains velocity explicitly, but the velocity required
304	>	// is at the full step: v(t + h), while we have initially the velocity
305	>	// at the half step: v(t + h/2).  We need to iterate to converge the
306	>	// friction force and friction torque vectors.
307	>
308	>	// this is the velocity at the half-step:
309
310	+	Vector3d vel =integrableObject->getVel();
311	+	Vector3d angMom = integrableObject->getJ();
312	+
313	+	//estimate velocity at full-step using everything but friction forces:
314	+
315	+	frc = integrableObject->getFrc();
316	+	Vector3d velStep = vel + (dt2_ /mass * PhysicalConstants::energyConvert) * frc;
317	+
318	+	Tb = integrableObject->lab2Body(integrableObject->getTrq());
319	+	Vector3d angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * Tb;
320	+
321	+	Vector3d omegaLab;
322	+	Vector3d vcdLab;
323	+	Vector3d vcdBody;
324	+	Vector3d frictionForceBody;
325	+	Vector3d frictionForceLab(0.0);
326	+	Vector3d oldFFL;  // used to test for convergence
327	+	Vector3d frictionTorqueBody(0.0);
328	+	Vector3d oldFTB;  // used to test for convergence
329	+	Vector3d frictionTorqueLab;
330	+	RealType fdot;
331	+	RealType tdot;
332	+
333	+	//iteration starts here:
334	+
335	+	for (int k = 0; k < maxIterNum_; k++) {
336	+
337	+	if (integrableObject->isLinear()) {
338	+	int linearAxis = integrableObject->linearAxis();
339	+	int l = (linearAxis +1 )%3;
340	+	int m = (linearAxis +2 )%3;
341	+	omegaBody[l] = angMomStep[l] /I(l, l);
342	+	omegaBody[m] = angMomStep[m] /I(m, m);
343	+
344	+	} else {
345	+	omegaBody[0] = angMomStep[0] /I(0, 0);
346	+	omegaBody[1] = angMomStep[1] /I(1, 1);
347	+	omegaBody[2] = angMomStep[2] /I(2, 2);
348	+	}
349	+
350	+	omegaLab = Atrans * omegaBody;
351	+
352	+	// apply friction force and torque at center of resistance
353	+
354	+	vcdLab = velStep + cross(omegaLab, rcrLab);
355	+	vcdBody = A * vcdLab;
356	+	frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omegaBody);
357	+	oldFFL = frictionForceLab;
358	+	frictionForceLab = Atrans * frictionForceBody;
359	+	oldFTB = frictionTorqueBody;
360	+	frictionTorqueBody = -(hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omegaBody);
361	+	frictionTorqueLab = Atrans * frictionTorqueBody;
362	+
363	+	// re-estimate velocities at full-step using friction forces:
364	+
365	+	velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForceLab);
366	+	angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * (Tb + frictionTorqueBody);
367	+
368	+	// check for convergence (if the vectors have converged, fdot and tdot will both be 1.0):
369	+
370	+	fdot = dot(frictionForceLab, oldFFL) / frictionForceLab.lengthSquare();
371	+	tdot = dot(frictionTorqueBody, oldFTB) / frictionTorqueBody.lengthSquare();
372	+
373	+	if (fabs(1.0 - fdot) <= forceTolerance_ && fabs(1.0 - tdot) <= forceTolerance_)
374	+	break; // iteration ends here
375	+	}
376	+
377	+	integrableObject->addFrc(frictionForceLab);
378	+	integrableObject->addTrq(frictionTorqueLab + cross(rcrLab, frictionForceLab));
379	+
380	+
381		} else {
382		//spherical atom
383	<	Vector3d frictionForce = -(hydroProps_[index].Xirtt *vel);
383	>
384		Vector3d randomForce;
385		Vector3d randomTorque;
386		genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
387	+	integrableObject->addFrc(randomForce);
388	+
389	+	// What remains contains velocity explicitly, but the velocity required
390	+	// is at the full step: v(t + h), while we have initially the velocity
391	+	// at the half step: v(t + h/2).  We need to iterate to converge the
392	+	// friction force vector.
393	+
394	+	// this is the velocity at the half-step:
395
396	<	integrableObject->addFrc(frictionForce+randomForce);
396	>	Vector3d vel =integrableObject->getVel();
397	>
398	>	//estimate velocity at full-step using everything but friction forces:
399	>
400	>	frc = integrableObject->getFrc();
401	>	Vector3d velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * frc;
402	>
403	>	Vector3d frictionForce(0.0);
404	>	Vector3d oldFF;  // used to test for convergence
405	>	RealType fdot;
406	>
407	>	//iteration starts here:
408	>
409	>	for (int k = 0; k < maxIterNum_; k++) {
410	>
411	>	oldFF = frictionForce;
412	>	frictionForce = -hydroProps_[index]->getXitt() * velStep;
413	>
414	>	// re-estimate velocities at full-step using friction forces:
415	>
416	>	velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForce);
417	>
418	>	// check for convergence (if the vector has converged, fdot will be 1.0):
419	>
420	>	fdot = dot(frictionForce, oldFF) / frictionForce.lengthSquare();
421	>
422	>	if (fabs(1.0 - fdot) <= forceTolerance_)
423	>	break; // iteration ends here
424	>	}
425	>
426	>	integrableObject->addFrc(frictionForce);
427	>
428		}
429		}
430
#	Line 408 | Line 432 | namespace oopse {
432
433		}
434		}
435	+
436		info_->setFdf(fdf);
437	<
437	>	veloMunge->removeComDrift();
438	>	// Remove angular drift if we are not using periodic boundary conditions.
439	>	if(!simParams->getUsePeriodicBoundaryConditions())
440	>	veloMunge->removeAngularDrift();
441	>
442		ForceManager::postCalculation();
443		}
444
#	Line 418 | Line 447 | void LDForceManager::genRandomForceAndTorque(Vector3d&
447
448		Vector<RealType, 6> Z;
449		Vector<RealType, 6> generalForce;
421	–
450
451		Z[0] = randNumGen_.randNorm(0, variance);
452		Z[1] = randNumGen_.randNorm(0, variance);
#	Line 427 | Line 455 | void LDForceManager::genRandomForceAndTorque(Vector3d&
455		Z[4] = randNumGen_.randNorm(0, variance);
456		Z[5] = randNumGen_.randNorm(0, variance);
457
458	<
431	<	generalForce = hydroProps_[index].S*Z;
458	>	generalForce = hydroProps_[index]->getS()*Z;
459
460		force[0] = generalForce[0];
461		force[1] = generalForce[1];
#	Line 437 | Line 464 | void LDForceManager::genRandomForceAndTorque(Vector3d&
464		torque[1] = generalForce[4];
465		torque[2] = generalForce[5];
466
467	<	}
467	>	}
468
469		}

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 1710 by gezelter, Fri May 18 21:44:02 2012 UTC

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