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

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trunk/src/integrators/LDForceManager.cpp (file contents), Revision 945 by gezelter, Tue Apr 25 02:09:01 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"
47	<	namespace oopse {
46	>	#include "utils/PhysicalConstants.hpp"
47	>	#include "hydrodynamics/Sphere.hpp"
48	>	#include "hydrodynamics/Ellipsoid.hpp"
49	>	#include "utils/ElementsTable.hpp"
50
51	<	LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info){
52	<	Globals* simParams = info->getSimParams();
53	<
54	<	std::map<std::string, HydroProp> hydroPropMap;
55	<	if (simParams->haveHydroPropFile()) {
56	<	hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
53	<	} else {
54	<	sprintf( painCave.errMsg,
55	<	"HydroPropFile must be set if Langevin Dynamics is specified.\n");
56	<	painCave.severity = OOPSE_ERROR;
57	<	painCave.isFatal = 1;
58	<	simError();
59	<	}
60	<
51	>	namespace OpenMD {
52	>
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 67 | 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 78 | 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 87 | 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	<	SimInfo::MoleculeIterator i;
93	<	Molecule::IntegrableObjectIterator  j;
91	>
92	>	// Build the hydroProp map:
93	>	std::map<std::string, HydroProp*> hydroPropMap;
94	>
95		Molecule* mol;
96		StuntDouble* integrableObject;
97	<	for (mol = info->beginMolecule(i); mol != NULL; mol = info->nextMolecule(i)) {
98	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
97	>	SimInfo::MoleculeIterator i;
98	>	Molecule::IntegrableObjectIterator  j;
99	>	bool needHydroPropFile = false;
100	>
101	>	for (mol = info->beginMolecule(i); mol != NULL;
102	>	mol = info->nextMolecule(i)) {
103	>	for (integrableObject = mol->beginIntegrableObject(j);
104	>	integrableObject != NULL;
105		integrableObject = mol->nextIntegrableObject(j)) {
106	<	std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
107	<	if (iter != hydroPropMap.end()) {
108	<	hydroProps_.push_back(iter->second);
109	<	} else {
107	<	sprintf( painCave.errMsg,
108	<	"Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
109	<	painCave.severity = OOPSE_ERROR;
110	<	painCave.isFatal = 1;
111	<	simError();
106	>
107	>	if (integrableObject->isRigidBody()) {
108	>	RigidBody* rb = static_cast<RigidBody*>(integrableObject);
109	>	if (rb->getNumAtoms() > 1) needHydroPropFile = true;
110		}
111
112		}
113		}
114	<	variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
115	<	}
116	<	std::map<std::string, HydroProp> LDForceManager::parseFrictionFile(const std::string& filename) {
117	<	std::map<std::string, HydroProp> props;
114	>
115	>
116	>	if (needHydroPropFile) {
117	>	if (simParams->haveHydroPropFile()) {
118	>	hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
119	>	} else {
120	>	sprintf( painCave.errMsg,
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	>
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;
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	>
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);
162	>	GenericData* data = dAtomType->getPropertyByName("GayBerne");
163	>	if (data != NULL) {
164	>	GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
165	>
166	>	if (gayBerneData != NULL) {
167	>	GayBerneParam gayBerneParam = gayBerneData->getData();
168	>	currShape = new Ellipsoid(V3Zero,
169	>	gayBerneParam.GB_l / 2.0,
170	>	gayBerneParam.GB_d / 2.0,
171	>	Mat3x3d::identity());
172	>	} else {
173	>	sprintf( painCave.errMsg,
174	>	"Can not cast GenericData to GayBerneParam\n");
175	>	painCave.severity = 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 = OPENMD_ERROR;
182	>	painCave.isFatal = 1;
183	>	simError();
184	>	}
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	>	"Could not find atom type in default element.txt\n");
208	>	painCave.severity = OPENMD_ERROR;
209	>	painCave.isFatal = 1;
210	>	simError();
211	>	}
212	>	}
213	>	}
214	>	}
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	>	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 * PhysicalConstants::kb*simParams->getTargetTemp()/simParams->getDt();
244	>	}
245	>
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 125 | 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;
130	<	if (tokenizer.countTokens() >= 40) {
131	<	std::string atomName = tokenizer.nextToken();
132	<	currProp.cor[0] = tokenizer.nextTokenAsDouble();
133	<	currProp.cor[1] = tokenizer.nextTokenAsDouble();
134	<	currProp.cor[2] = tokenizer.nextTokenAsDouble();
135	<
136	<	currProp.Xirtt(0,0) = tokenizer.nextTokenAsDouble();
137	<	currProp.Xirtt(0,1) = tokenizer.nextTokenAsDouble();
138	<	currProp.Xirtt(0,2) = tokenizer.nextTokenAsDouble();
139	<	currProp.Xirtt(1,0) = tokenizer.nextTokenAsDouble();
140	<	currProp.Xirtt(1,1) = tokenizer.nextTokenAsDouble();
141	<	currProp.Xirtt(1,2) = tokenizer.nextTokenAsDouble();
142	<	currProp.Xirtt(2,0) = tokenizer.nextTokenAsDouble();
143	<	currProp.Xirtt(2,1) = tokenizer.nextTokenAsDouble();
144	<	currProp.Xirtt(2,2) = tokenizer.nextTokenAsDouble();
145	<
146	<	currProp.Xirrt(0,0) = tokenizer.nextTokenAsDouble();
147	<	currProp.Xirrt(0,1) = tokenizer.nextTokenAsDouble();
148	<	currProp.Xirrt(0,2) = tokenizer.nextTokenAsDouble();
149	<	currProp.Xirrt(1,0) = tokenizer.nextTokenAsDouble();
150	<	currProp.Xirrt(1,1) = tokenizer.nextTokenAsDouble();
151	<	currProp.Xirrt(1,2) = tokenizer.nextTokenAsDouble();
152	<	currProp.Xirrt(2,0) = tokenizer.nextTokenAsDouble();
153	<	currProp.Xirrt(2,1) = tokenizer.nextTokenAsDouble();
154	<	currProp.Xirrt(2,2) = tokenizer.nextTokenAsDouble();
155	<
156	<	currProp.Xirtr(0,0) = tokenizer.nextTokenAsDouble();
157	<	currProp.Xirtr(0,1) = tokenizer.nextTokenAsDouble();
158	<	currProp.Xirtr(0,2) = tokenizer.nextTokenAsDouble();
159	<	currProp.Xirtr(1,0) = tokenizer.nextTokenAsDouble();
160	<	currProp.Xirtr(1,1) = tokenizer.nextTokenAsDouble();
161	<	currProp.Xirtr(1,2) = tokenizer.nextTokenAsDouble();
162	<	currProp.Xirtr(2,0) = tokenizer.nextTokenAsDouble();
163	<	currProp.Xirtr(2,1) = tokenizer.nextTokenAsDouble();
164	<	currProp.Xirtr(2,2) = tokenizer.nextTokenAsDouble();
165	<
166	<	currProp.Xirrr(0,0) = tokenizer.nextTokenAsDouble();
167	<	currProp.Xirrr(0,1) = tokenizer.nextTokenAsDouble();
168	<	currProp.Xirrr(0,2) = tokenizer.nextTokenAsDouble();
169	<	currProp.Xirrr(1,0) = tokenizer.nextTokenAsDouble();
170	<	currProp.Xirrr(1,1) = tokenizer.nextTokenAsDouble();
171	<	currProp.Xirrr(1,2) = tokenizer.nextTokenAsDouble();
172	<	currProp.Xirrr(2,0) = tokenizer.nextTokenAsDouble();
173	<	currProp.Xirrr(2,1) = tokenizer.nextTokenAsDouble();
174	<	currProp.Xirrr(2,2) = tokenizer.nextTokenAsDouble();
175	<
176	<	SquareMatrix<double, 6> Xir;
177	<	Xir.setSubMatrix(0, 0, currProp.Xirtt);
178	<	Xir.setSubMatrix(0, 3, currProp.Xirrt);
179	<	Xir.setSubMatrix(3, 0, currProp.Xirtr);
180	<	Xir.setSubMatrix(3, 3, currProp.Xirrr);
181	<	CholeskyDecomposition(Xir, currProp.S);
182	<
183	<	props.insert(std::map<std::string, HydroProp>::value_type(atomName, currProp));
184	<	}
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;
202	–	double 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	<	double molRad = molPos.length();
291	<
290	>	RealType molRad = molPos.length();
291	>
292		doLangevinForces = false;
217	–	freezeMolecule = false;
293
294		if (molRad > langevinBufferRadius_) {
295		doLangevinForces = true;
#	Line 226 | Line 301 | namespace oopse {
301		}
302		}
303
304	<	if (doLangevinForces) {
305	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
231	<	integrableObject = mol->nextIntegrableObject(j)) {
304	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
305	>	integrableObject = mol->nextIntegrableObject(j)) {
306
307	<	vel =integrableObject->getVel();
307	>	if (freezeMolecule)
308	>	fdf += integrableObject->freeze();
309	>
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();
238	<	Vector3d omega;
239	<
240	<	if (integrableObject->isLinear()) {
241	<	int linearAxis = integrableObject->linearAxis();
242	<	int l = (linearAxis +1 )%3;
243	<	int m = (linearAxis +2 )%3;
244	<	omega[l] = angMom[l] /I(l, l);
245	<	omega[m] = angMom[m] /I(m, m);
246	<
247	<	} else {
248	<	omega[0] = angMom[0] /I(0, 0);
249	<	omega[1] = angMom[1] /I(1, 1);
250	<	omega[2] = angMom[2] /I(2, 2);
251	<	}
252	<
253	<	//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);
258	<	Vector3d vcdBody = A* vcdLab;
259	<	Vector3d frictionForceBody = -(hydroProps_[index].Xirtt * vcdBody + hydroProps_[index].Xirrt * omega);
260	<	Vector3d frictionForceLab = Atrans*frictionForceBody;
261	<	integrableObject->addFrc(frictionForceLab);
262	<	Vector3d frictionTorqueBody = - (hydroProps_[index].Xirtr * vcdBody + hydroProps_[index].Xirrr * omega);
263	<	Vector3d frictionTorqueLab = Atrans*frictionTorqueBody;
264	<	integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab));
265	<
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
461	<	++index;
461	>	++index;
462
287	–	}
463		}
464	<	if (freezeMolecule)
465	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
291	<	integrableObject = mol->nextIntegrableObject(j)) {
292	<	fdf += integrableObject->freeze();
293	<	}
294	<	}
295	<
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
475	<	void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, double variance) {
475	>	void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
476
477
478	<	Vector<double, 6> Z;
479	<	Vector<double, 6> generalForce;
306	<
478	>	Vector<RealType, 6> Z;
479	>	Vector<RealType, 6> generalForce;
480
481		Z[0] = randNumGen_.randNorm(0, variance);
482		Z[1] = randNumGen_.randNorm(0, variance);
#	Line 312 | Line 485 | void LDForceManager::genRandomForceAndTorque(Vector3d&
485		Z[4] = randNumGen_.randNorm(0, variance);
486		Z[5] = randNumGen_.randNorm(0, variance);
487
488	<
316	<	generalForce = hydroProps_[index].S*Z;
488	>	generalForce = hydroProps_[index]->getS()*Z;
489
490		force[0] = generalForce[0];
491		force[1] = generalForce[1];
#	Line 322 | 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 945 by gezelter, Tue Apr 25 02:09:01 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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