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

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trunk/src/integrators/LDForceManager.cpp (file contents), Revision 908 by tim, Mon Mar 20 19:12:14 2006 UTC vs.
branches/development/src/integrators/LDForceManager.cpp (file contents), Revision 1769 by gezelter, Mon Jul 9 14:15:52 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"
47	<	namespace oopse {
46	>	#include "utils/PhysicalConstants.hpp"
47	>	#include "hydrodynamics/Sphere.hpp"
48	>	#include "hydrodynamics/Ellipsoid.hpp"
49	>	#include "utils/ElementsTable.hpp"
50	>	#include "types/LennardJonesAdapter.hpp"
51	>	#include "types/GayBerneAdapter.hpp"
52
53	<	LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info){
54	<	Globals* simParams = info->getSimParams();
55	<	std::map<std::string, HydroProp> hydroPropMap;
56	<	if (simParams->haveHydroPropFile()) {
57	<	hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
58	<	} else {
59	<	//error
53	>	namespace OpenMD {
54	>
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;
62	>	if (simParams->haveLangevinBufferRadius()) {
63	>	langevinBufferRadius_ = simParams->getLangevinBufferRadius();
64	>	} else {
65	>	sprintf( painCave.errMsg,
66	>	"langevinBufferRadius must be specified "
67	>	"when useSphericalBoundaryConditions is turned on.\n");
68	>	painCave.severity = OPENMD_ERROR;
69	>	painCave.isFatal = 1;
70	>	simError();
71	>	}
72	>
73	>	if (simParams->haveFrozenBufferRadius()) {
74	>	frozenBufferRadius_ = simParams->getFrozenBufferRadius();
75	>	} else {
76	>	sprintf( painCave.errMsg,
77	>	"frozenBufferRadius must be specified "
78	>	"when useSphericalBoundaryConditions is turned on.\n");
79	>	painCave.severity = OPENMD_ERROR;
80	>	painCave.isFatal = 1;
81	>	simError();
82	>	}
83	>
84	>	if (frozenBufferRadius_ < langevinBufferRadius_) {
85	>	sprintf( painCave.errMsg,
86	>	"frozenBufferRadius has been set smaller than the "
87	>	"langevinBufferRadius.  This is probably an error.\n");
88	>	painCave.severity = OPENMD_WARNING;
89	>	painCave.isFatal = 0;
90	>	simError();
91	>	}
92		}
93
94	<	SimInfo::MoleculeIterator i;
95	<	Molecule::IntegrableObjectIterator  j;
94	>	// Build the hydroProp map:
95	>	std::map<std::string, HydroProp*> hydroPropMap;
96	>
97		Molecule* mol;
98	<	StuntDouble* integrableObject;
99	<	for (mol = info->beginMolecule(i); mol != NULL; mol = info->nextMolecule(i)) {
100	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
101	<	integrableObject = mol->nextIntegrableObject(j)) {
102	<	std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
103	<	if (iter != hydroPropMap.end()) {
104	<	hydroProps_.push_back(iter->second);
98	>	StuntDouble* sd;
99	>	SimInfo::MoleculeIterator i;
100	>	Molecule::IntegrableObjectIterator  j;
101	>	bool needHydroPropFile = false;
102	>
103	>	for (mol = info->beginMolecule(i); mol != NULL;
104	>	mol = info->nextMolecule(i)) {
105	>
106	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
107	>	sd = mol->nextIntegrableObject(j)) {
108	>
109	>	if (sd->isRigidBody()) {
110	>	RigidBody* rb = static_cast<RigidBody*>(sd);
111	>	if (rb->getNumAtoms() > 1) needHydroPropFile = true;
112	>	}
113	>
114	>	}
115	>	}
116	>
117	>
118	>	if (needHydroPropFile) {
119	>	if (simParams->haveHydroPropFile()) {
120	>	hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
121	>	} else {
122	>	sprintf( painCave.errMsg,
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	>
131	>	for (mol = info->beginMolecule(i); mol != NULL;
132	>	mol = info->nextMolecule(i)) {
133	>
134	>	for (sd = mol->beginIntegrableObject(j);  sd != NULL;
135	>	sd = mol->nextIntegrableObject(j)) {
136	>
137	>	std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(sd->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", sd->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;
152	>	for (mol = info->beginMolecule(i); mol != NULL;
153	>	mol = info->nextMolecule(i)) {
154	>
155	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
156	>	sd = mol->nextIntegrableObject(j)) {
157	>
158	>	Shape* currShape = NULL;
159	>
160	>	if (sd->isAtom()){
161	>	Atom* atom = static_cast<Atom*>(sd);
162	>	AtomType* atomType = atom->getAtomType();
163	>	GayBerneAdapter gba = GayBerneAdapter(atomType);
164	>	if (gba.isGayBerne()) {
165	>	currShape = new Ellipsoid(V3Zero, gba.getL() / 2.0,
166	>	gba.getD() / 2.0,
167	>	Mat3x3d::identity());
168		} else {
169	<	//error
169	>	LennardJonesAdapter lja = LennardJonesAdapter(atomType);
170	>	if (lja.isLennardJones()){
171	>	currShape = new Sphere(atom->getPos(), lja.getSigma()/2.0);
172	>	} else {
173	>	int aNum = etab.GetAtomicNum((atom->getType()).c_str());
174	>	if (aNum != 0) {
175	>	currShape = new Sphere(atom->getPos(), etab.GetVdwRad(aNum));
176	>	} else {
177	>	sprintf( painCave.errMsg,
178	>	"Could not find atom type in default element.txt\n");
179	>	painCave.severity = OPENMD_ERROR;
180	>	painCave.isFatal = 1;
181	>	simError();
182	>	}
183	>	}
184		}
185	<
186	<	}
185	>	}
186	>
187	>	if (!simParams->haveTargetTemp()) {
188	>	sprintf(painCave.errMsg, "You can't use LangevinDynamics without a targetTemp!\n");
189	>	painCave.isFatal = 1;
190	>	painCave.severity = OPENMD_ERROR;
191	>	simError();
192	>	}
193	>
194	>	if (!simParams->haveViscosity()) {
195	>	sprintf(painCave.errMsg, "You can't use LangevinDynamics without a viscosity!\n");
196	>	painCave.isFatal = 1;
197	>	painCave.severity = OPENMD_ERROR;
198	>	simError();
199	>	}
200	>
201	>
202	>	HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp());
203	>	std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(sd->getType());
204	>	if (iter != hydroPropMap.end())
205	>	hydroProps_.push_back(iter->second);
206	>	else {
207	>	currHydroProp->complete();
208	>	hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(sd->getType(), currHydroProp));
209	>	hydroProps_.push_back(currHydroProp);
210	>	}
211	>	}
212	>	}
213		}
214	<	variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
215	<	}
216	<	std::map<std::string, HydroProp> LDForceManager::parseFrictionFile(const std::string& filename) {
217	<	std::map<std::string, HydroProp> props;
214	>	variance_ = 2.0 * PhysicalConstants::kb*simParams->getTargetTemp()/simParams->getDt();
215	>	}
216	>
217	>	std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) {
218	>	std::map<std::string, HydroProp*> props;
219		std::ifstream ifs(filename.c_str());
220		if (ifs.is_open()) {
221	<
221	>
222		}
223	<
223	>
224		const unsigned int BufferSize = 65535;
225		char buffer[BufferSize];
226		while (ifs.getline(buffer, BufferSize)) {
227	<	StringTokenizer tokenizer(buffer);
228	<	HydroProp currProp;
86	<	if (tokenizer.countTokens() >= 40) {
87	<	std::string atomName = tokenizer.nextToken();
88	<	currProp.cor[0] = tokenizer.nextTokenAsDouble();
89	<	currProp.cor[1] = tokenizer.nextTokenAsDouble();
90	<	currProp.cor[2] = tokenizer.nextTokenAsDouble();
91	<
92	<	currProp.Xirtt(0,0) = tokenizer.nextTokenAsDouble();
93	<	currProp.Xirtt(0,1) = tokenizer.nextTokenAsDouble();
94	<	currProp.Xirtt(0,2) = tokenizer.nextTokenAsDouble();
95	<	currProp.Xirtt(1,0) = tokenizer.nextTokenAsDouble();
96	<	currProp.Xirtt(1,1) = tokenizer.nextTokenAsDouble();
97	<	currProp.Xirtt(1,2) = tokenizer.nextTokenAsDouble();
98	<	currProp.Xirtt(2,0) = tokenizer.nextTokenAsDouble();
99	<	currProp.Xirtt(2,1) = tokenizer.nextTokenAsDouble();
100	<	currProp.Xirtt(2,2) = tokenizer.nextTokenAsDouble();
101	<
102	<	currProp.Xirrt(0,0) = tokenizer.nextTokenAsDouble();
103	<	currProp.Xirrt(0,1) = tokenizer.nextTokenAsDouble();
104	<	currProp.Xirrt(0,2) = tokenizer.nextTokenAsDouble();
105	<	currProp.Xirrt(1,0) = tokenizer.nextTokenAsDouble();
106	<	currProp.Xirrt(1,1) = tokenizer.nextTokenAsDouble();
107	<	currProp.Xirrt(1,2) = tokenizer.nextTokenAsDouble();
108	<	currProp.Xirrt(2,0) = tokenizer.nextTokenAsDouble();
109	<	currProp.Xirrt(2,1) = tokenizer.nextTokenAsDouble();
110	<	currProp.Xirrt(2,2) = tokenizer.nextTokenAsDouble();
111	<
112	<	currProp.Xirtr(0,0) = tokenizer.nextTokenAsDouble();
113	<	currProp.Xirtr(0,1) = tokenizer.nextTokenAsDouble();
114	<	currProp.Xirtr(0,2) = tokenizer.nextTokenAsDouble();
115	<	currProp.Xirtr(1,0) = tokenizer.nextTokenAsDouble();
116	<	currProp.Xirtr(1,1) = tokenizer.nextTokenAsDouble();
117	<	currProp.Xirtr(1,2) = tokenizer.nextTokenAsDouble();
118	<	currProp.Xirtr(2,0) = tokenizer.nextTokenAsDouble();
119	<	currProp.Xirtr(2,1) = tokenizer.nextTokenAsDouble();
120	<	currProp.Xirtr(2,2) = tokenizer.nextTokenAsDouble();
121	<
122	<	currProp.Xirrr(0,0) = tokenizer.nextTokenAsDouble();
123	<	currProp.Xirrr(0,1) = tokenizer.nextTokenAsDouble();
124	<	currProp.Xirrr(0,2) = tokenizer.nextTokenAsDouble();
125	<	currProp.Xirrr(1,0) = tokenizer.nextTokenAsDouble();
126	<	currProp.Xirrr(1,1) = tokenizer.nextTokenAsDouble();
127	<	currProp.Xirrr(1,2) = tokenizer.nextTokenAsDouble();
128	<	currProp.Xirrr(2,0) = tokenizer.nextTokenAsDouble();
129	<	currProp.Xirrr(2,1) = tokenizer.nextTokenAsDouble();
130	<	currProp.Xirrr(2,2) = tokenizer.nextTokenAsDouble();
131	<
132	<	SquareMatrix<double, 6> Xir;
133	<	Xir.setSubMatrix(0, 0, currProp.Xirtt);
134	<	Xir.setSubMatrix(0, 3, currProp.Xirrt);
135	<	Xir.setSubMatrix(3, 0, currProp.Xirtr);
136	<	Xir.setSubMatrix(3, 3, currProp.Xirrr);
137	<	CholeskyDecomposition(Xir, currProp.S);
138	<
139	<	props.insert(std::map<std::string, HydroProp>::value_type(atomName, currProp));
140	<	}
227	>	HydroProp* currProp = new HydroProp(buffer);
228	>	props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
229		}
230
231		return props;
232		}
233	<
234	<	void LDForceManager::postCalculation() {
233	>
234	>	void LDForceManager::postCalculation(){
235		SimInfo::MoleculeIterator i;
236		Molecule::IntegrableObjectIterator  j;
237		Molecule* mol;
238	<	StuntDouble* integrableObject;
239	<	Vector3d vel;
238	>	StuntDouble* sd;
239	>	RealType mass;
240		Vector3d pos;
241		Vector3d frc;
242		Mat3x3d A;
243		Mat3x3d Atrans;
244		Vector3d Tb;
245		Vector3d ji;
158	–	double mass;
246		unsigned int index = 0;
247	+	bool doLangevinForces;
248	+	bool freezeMolecule;
249	+	int fdf;
250	+
251	+	fdf = 0;
252	+
253		for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
161	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
162	–	integrableObject = mol->nextIntegrableObject(j)) {
254
255	<	vel =integrableObject->getVel();
256	<	if (integrableObject->isDirectional()){
166	<	//calculate angular velocity in lab frame
167	<	Mat3x3d I = integrableObject->getI();
168	<	Vector3d angMom = integrableObject->getJ();
169	<	Vector3d omega;
255	>	doLangevinForces = true;
256	>	freezeMolecule = false;
257
258	<	if (integrableObject->isLinear()) {
259	<	int linearAxis = integrableObject->linearAxis();
258	>	if (sphericalBoundaryConditions_) {
259	>
260	>	Vector3d molPos = mol->getCom();
261	>	RealType molRad = molPos.length();
262	>
263	>	doLangevinForces = false;
264	>
265	>	if (molRad > langevinBufferRadius_) {
266	>	doLangevinForces = true;
267	>	freezeMolecule = false;
268	>	}
269	>	if (molRad > frozenBufferRadius_) {
270	>	doLangevinForces = false;
271	>	freezeMolecule = true;
272	>	}
273	>	}
274	>
275	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
276	>	sd = mol->nextIntegrableObject(j)) {
277	>
278	>	if (freezeMolecule)
279	>	fdf += sd->freeze();
280	>
281	>	if (doLangevinForces) {
282	>	mass = sd->getMass();
283	>	if (sd->isDirectional()){
284	>
285	>	// preliminaries for directional objects:
286	>
287	>	A = sd->getA();
288	>	Atrans = A.transpose();
289	>	Vector3d rcrLab = Atrans * hydroProps_[index]->getCOR();
290	>
291	>	//apply random force and torque at center of resistance
292	>
293	>	Vector3d randomForceBody;
294	>	Vector3d randomTorqueBody;
295	>	genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
296	>	Vector3d randomForceLab = Atrans * randomForceBody;
297	>	Vector3d randomTorqueLab = Atrans * randomTorqueBody;
298	>	sd->addFrc(randomForceLab);
299	>	sd->addTrq(randomTorqueLab + cross(rcrLab, randomForceLab ));
300	>
301	>	Mat3x3d I = sd->getI();
302	>	Vector3d omegaBody;
303	>
304	>	// What remains contains velocity explicitly, but the velocity required
305	>	// is at the full step: v(t + h), while we have initially the velocity
306	>	// at the half step: v(t + h/2).  We need to iterate to converge the
307	>	// friction force and friction torque vectors.
308	>
309	>	// this is the velocity at the half-step:
310	>
311	>	Vector3d vel =sd->getVel();
312	>	Vector3d angMom = sd->getJ();
313	>
314	>	//estimate velocity at full-step using everything but friction forces:
315	>
316	>	frc = sd->getFrc();
317	>	Vector3d velStep = vel + (dt2_ /mass * PhysicalConstants::energyConvert) * frc;
318	>
319	>	Tb = sd->lab2Body(sd->getTrq());
320	>	Vector3d angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * Tb;
321	>
322	>	Vector3d omegaLab;
323	>	Vector3d vcdLab;
324	>	Vector3d vcdBody;
325	>	Vector3d frictionForceBody;
326	>	Vector3d frictionForceLab(0.0);
327	>	Vector3d oldFFL;  // used to test for convergence
328	>	Vector3d frictionTorqueBody(0.0);
329	>	Vector3d oldFTB;  // used to test for convergence
330	>	Vector3d frictionTorqueLab;
331	>	RealType fdot;
332	>	RealType tdot;
333	>
334	>	//iteration starts here:
335	>
336	>	for (int k = 0; k < maxIterNum_; k++) {
337	>
338	>	if (sd->isLinear()) {
339	>	int linearAxis = sd->linearAxis();
340		int l = (linearAxis +1 )%3;
341		int m = (linearAxis +2 )%3;
342	<	omega[l] = angMom[l] /I(l, l);
343	<	omega[m] = angMom[m] /I(m, m);
342	>	omegaBody[l] = angMomStep[l] /I(l, l);
343	>	omegaBody[m] = angMomStep[m] /I(m, m);
344
345	<	} else {
346	<	omega[0] = angMom[0] /I(0, 0);
347	<	omega[1] = angMom[1] /I(1, 1);
348	<	omega[2] = angMom[2] /I(2, 2);
349	<	}
345	>	} else {
346	>	omegaBody[0] = angMomStep[0] /I(0, 0);
347	>	omegaBody[1] = angMomStep[1] /I(1, 1);
348	>	omegaBody[2] = angMomStep[2] /I(2, 2);
349	>	}
350	>
351	>	omegaLab = Atrans * omegaBody;
352	>
353	>	// apply friction force and torque at center of resistance
354	>
355	>	vcdLab = velStep + cross(omegaLab, rcrLab);
356	>	vcdBody = A * vcdLab;
357	>	frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omegaBody);
358	>	oldFFL = frictionForceLab;
359	>	frictionForceLab = Atrans * frictionForceBody;
360	>	oldFTB = frictionTorqueBody;
361	>	frictionTorqueBody = -(hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omegaBody);
362	>	frictionTorqueLab = Atrans * frictionTorqueBody;
363	>
364	>	// re-estimate velocities at full-step using friction forces:
365	>
366	>	velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForceLab);
367	>	angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * (Tb + frictionTorqueBody);
368
369	<	//apply friction force and torque at center of resistance
370	<	A = integrableObject->getA();
371	<	Atrans = A.transpose();
372	<	Vector3d rcr = Atrans * hydroProps_[index].cor;
373	<	Vector3d vcdLab = vel + cross(omega, rcr);
374	<	Vector3d vcdBody = A* vcdLab;
375	<	Vector3d frictionForceBody = -(hydroProps_[index].Xirtt * vcdBody + hydroProps_[index].Xirrt * omega);
376	<	Vector3d frictionForceLab = Atrans*frictionForceBody;
192	<	integrableObject->addFrc(frictionForceLab);
193	<	Vector3d frictionTorqueBody = - (hydroProps_[index].Xirtr * vcdBody + hydroProps_[index].Xirrr * omega);
194	<	Vector3d frictionTorqueLab = Atrans*frictionTorqueBody;
195	<	integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab));
369	>	// check for convergence (if the vectors have converged, fdot and tdot will both be 1.0):
370	>
371	>	fdot = dot(frictionForceLab, oldFFL) / frictionForceLab.lengthSquare();
372	>	tdot = dot(frictionTorqueBody, oldFTB) / frictionTorqueBody.lengthSquare();
373	>
374	>	if (fabs(1.0 - fdot) <= forceTolerance_ && fabs(1.0 - tdot) <= forceTolerance_)
375	>	break; // iteration ends here
376	>	}
377
378	<	//apply random force and torque at center of resistance
379	<	Vector3d randomForceBody;
199	<	Vector3d randomTorqueBody;
200	<	genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
201	<	Vector3d randomForceLab = Atrans*randomForceBody;
202	<	Vector3d randomTorqueLab = Atrans* randomTorqueBody;
203	<	integrableObject->addFrc(randomForceLab);
204	<	integrableObject->addTrq(randomTorqueLab + cross(rcr, randomForceLab ));
378	>	sd->addFrc(frictionForceLab);
379	>	sd->addTrq(frictionTorqueLab + cross(rcrLab, frictionForceLab));
380
381	+
382		} else {
383	<	//spheric atom
208	<	Vector3d frictionForce = -(hydroProps_[index].Xirtt *vel);
209	<	Vector3d randomForce;
210	<	Vector3d randomTorque;
211	<	genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
383	>	//spherical atom
384
385	<	integrableObject->addFrc(frictionForce+randomForce);
386	<	}
385	>	Vector3d randomForce;
386	>	Vector3d randomTorque;
387	>	genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
388	>	sd->addFrc(randomForce);
389
390	+	// What remains contains velocity explicitly, but the velocity required
391	+	// is at the full step: v(t + h), while we have initially the velocity
392	+	// at the half step: v(t + h/2).  We need to iterate to converge the
393	+	// friction force vector.
394	+
395	+	// this is the velocity at the half-step:
396	+
397	+	Vector3d vel =sd->getVel();
398	+
399	+	//estimate velocity at full-step using everything but friction forces:
400	+
401	+	frc = sd->getFrc();
402	+	Vector3d velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * frc;
403	+
404	+	Vector3d frictionForce(0.0);
405	+	Vector3d oldFF;  // used to test for convergence
406	+	RealType fdot;
407	+
408	+	//iteration starts here:
409	+
410	+	for (int k = 0; k < maxIterNum_; k++) {
411	+
412	+	oldFF = frictionForce;
413	+	frictionForce = -hydroProps_[index]->getXitt() * velStep;
414	+
415	+	// re-estimate velocities at full-step using friction forces:
416	+
417	+	velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForce);
418	+
419	+	// check for convergence (if the vector has converged, fdot will be 1.0):
420	+
421	+	fdot = dot(frictionForce, oldFF) / frictionForce.lengthSquare();
422	+
423	+	if (fabs(1.0 - fdot) <= forceTolerance_)
424	+	break; // iteration ends here
425	+	}
426	+
427	+	sd->addFrc(frictionForce);
428	+
429	+	}
430	+	}
431	+
432		++index;
433
434		}
435		}
436
437	<	ForceManager::postCalculation();
437	>	info_->setFdf(fdf);
438	>	veloMunge->removeComDrift();
439	>	// Remove angular drift if we are not using periodic boundary conditions.
440	>	if(!simParams->getUsePeriodicBoundaryConditions())
441	>	veloMunge->removeAngularDrift();
442
443	<
224	<
443	>	ForceManager::postCalculation();
444		}
445
446	<	void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, double variance) {
446	>	void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
447
448
449	<	Vector<double, 6> Z;
450	<	Vector<double, 6> generalForce;
232	<
449	>	Vector<RealType, 6> Z;
450	>	Vector<RealType, 6> generalForce;
451
452		Z[0] = randNumGen_.randNorm(0, variance);
453		Z[1] = randNumGen_.randNorm(0, variance);
#	Line 238 | Line 456 | void LDForceManager::genRandomForceAndTorque(Vector3d&
456		Z[4] = randNumGen_.randNorm(0, variance);
457		Z[5] = randNumGen_.randNorm(0, variance);
458
459	<
242	<	generalForce = hydroProps_[index].S*Z;
459	>	generalForce = hydroProps_[index]->getS()*Z;
460
461		force[0] = generalForce[0];
462		force[1] = generalForce[1];
#	Line 248 | Line 465 | void LDForceManager::genRandomForceAndTorque(Vector3d&
465		torque[1] = generalForce[4];
466		torque[2] = generalForce[5];
467
468	<	}
468	>	}
469
470		}

Comparing:
trunk/src/integrators/LDForceManager.cpp (property svn:keywords), Revision 908 by tim, Mon Mar 20 19:12:14 2006 UTC vs.
branches/development/src/integrators/LDForceManager.cpp (property svn:keywords), Revision 1769 by gezelter, Mon Jul 9 14:15:52 2012 UTC

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