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

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trunk/src/integrators/LDForceManager.cpp (file contents), Revision 904 by tim, Thu Mar 16 22:50:48 2006 UTC vs.
branches/development/src/integrators/LDForceManager.cpp (file contents), Revision 1874 by gezelter, Wed May 15 15:09:35 2013 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, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42		#include <fstream>
43	+	#include <iostream>
44		#include "integrators/LDForceManager.hpp"
45		#include "math/CholeskyDecomposition.hpp"
46	<	#include "utils/OOPSEConstant.hpp"
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);
66	<	} else {
67	<	//error
68	<	}
69	<
70	<	}
71	<	}
72	<	variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
73	<	}
74	<	std::map<std::string, HydroProp> LDForceManager::parseFrictionFile(const std::string& filename) {
75	<	std::map<std::string, HydroProp> props;
76	<	std::ifstream ifs(filename.c_str());
77	<	if (ifs.is_open()) {
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	<	const unsigned int BufferSize = 65535;
119	<	char buffer[BufferSize];
120	<	while (ifs.getline(buffer, BufferSize)) {
121	<	StringTokenizer tokenizer(buffer);
122	<	HydroProp currProp;
123	<	if (tokenizer.countTokens() >= 67) {
124	<	std::string atomName = tokenizer.nextToken();
125	<	currProp.cod[0] = tokenizer.nextTokenAsDouble();
126	<	currProp.cod[1] = tokenizer.nextTokenAsDouble();
127	<	currProp.cod[2] = tokenizer.nextTokenAsDouble();
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	<	currProp.Ddtt(0,0) = tokenizer.nextTokenAsDouble();
132	<	currProp.Ddtt(0,1) = tokenizer.nextTokenAsDouble();
94	<	currProp.Ddtt(0,2) = tokenizer.nextTokenAsDouble();
95	<	currProp.Ddtt(1,0) = tokenizer.nextTokenAsDouble();
96	<	currProp.Ddtt(1,1) = tokenizer.nextTokenAsDouble();
97	<	currProp.Ddtt(1,2) = tokenizer.nextTokenAsDouble();
98	<	currProp.Ddtt(2,0) = tokenizer.nextTokenAsDouble();
99	<	currProp.Ddtt(2,1) = tokenizer.nextTokenAsDouble();
100	<	currProp.Ddtt(2,2) = tokenizer.nextTokenAsDouble();
131	>	for (mol = info->beginMolecule(i); mol != NULL;
132	>	mol = info->nextMolecule(i)) {
133
134	<	currProp.Ddtr(0,0) = tokenizer.nextTokenAsDouble();
135	<	currProp.Ddtr(0,1) = tokenizer.nextTokenAsDouble();
104	<	currProp.Ddtr(0,2) = tokenizer.nextTokenAsDouble();
105	<	currProp.Ddtr(1,0) = tokenizer.nextTokenAsDouble();
106	<	currProp.Ddtr(1,1) = tokenizer.nextTokenAsDouble();
107	<	currProp.Ddtr(1,2) = tokenizer.nextTokenAsDouble();
108	<	currProp.Ddtr(2,0) = tokenizer.nextTokenAsDouble();
109	<	currProp.Ddtr(2,1) = tokenizer.nextTokenAsDouble();
110	<	currProp.Ddtr(2,2) = tokenizer.nextTokenAsDouble();
134	>	for (sd = mol->beginIntegrableObject(j);  sd != NULL;
135	>	sd = mol->nextIntegrableObject(j)) {
136
137	<	currProp.Ddrr(0,0) = tokenizer.nextTokenAsDouble();
138	<	currProp.Ddrr(0,1) = tokenizer.nextTokenAsDouble();
139	<	currProp.Ddrr(0,2) = tokenizer.nextTokenAsDouble();
140	<	currProp.Ddrr(1,0) = tokenizer.nextTokenAsDouble();
141	<	currProp.Ddrr(1,1) = tokenizer.nextTokenAsDouble();
142	<	currProp.Ddrr(1,2) = tokenizer.nextTokenAsDouble();
143	<	currProp.Ddrr(2,0) = tokenizer.nextTokenAsDouble();
144	<	currProp.Ddrr(2,1) = tokenizer.nextTokenAsDouble();
145	<	currProp.Ddrr(2,2) = tokenizer.nextTokenAsDouble();
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	<	currProp.Xidtt(0,0) = tokenizer.nextTokenAsDouble();
156	<	currProp.Xidtt(0,1) = tokenizer.nextTokenAsDouble();
124	<	currProp.Xidtt(0,2) = tokenizer.nextTokenAsDouble();
125	<	currProp.Xidtt(1,0) = tokenizer.nextTokenAsDouble();
126	<	currProp.Xidtt(1,1) = tokenizer.nextTokenAsDouble();
127	<	currProp.Xidtt(1,2) = tokenizer.nextTokenAsDouble();
128	<	currProp.Xidtt(2,0) = tokenizer.nextTokenAsDouble();
129	<	currProp.Xidtt(2,1) = tokenizer.nextTokenAsDouble();
130	<	currProp.Xidtt(2,2) = tokenizer.nextTokenAsDouble();
155	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
156	>	sd = mol->nextIntegrableObject(j)) {
157
158	<	currProp.Xidrt(0,0) = tokenizer.nextTokenAsDouble();
133	<	currProp.Xidrt(0,1) = tokenizer.nextTokenAsDouble();
134	<	currProp.Xidrt(0,2) = tokenizer.nextTokenAsDouble();
135	<	currProp.Xidrt(1,0) = tokenizer.nextTokenAsDouble();
136	<	currProp.Xidrt(1,1) = tokenizer.nextTokenAsDouble();
137	<	currProp.Xidrt(1,2) = tokenizer.nextTokenAsDouble();
138	<	currProp.Xidrt(2,0) = tokenizer.nextTokenAsDouble();
139	<	currProp.Xidrt(2,1) = tokenizer.nextTokenAsDouble();
140	<	currProp.Xidrt(2,2) = tokenizer.nextTokenAsDouble();
141	<
142	<	currProp.Xidtr(0,0) = tokenizer.nextTokenAsDouble();
143	<	currProp.Xidtr(0,1) = tokenizer.nextTokenAsDouble();
144	<	currProp.Xidtr(0,2) = tokenizer.nextTokenAsDouble();
145	<	currProp.Xidtr(1,0) = tokenizer.nextTokenAsDouble();
146	<	currProp.Xidtr(1,1) = tokenizer.nextTokenAsDouble();
147	<	currProp.Xidtr(1,2) = tokenizer.nextTokenAsDouble();
148	<	currProp.Xidtr(2,0) = tokenizer.nextTokenAsDouble();
149	<	currProp.Xidtr(2,1) = tokenizer.nextTokenAsDouble();
150	<	currProp.Xidtr(2,2) = tokenizer.nextTokenAsDouble();
158	>	Shape* currShape = NULL;
159
160	<	currProp.Xidrr(0,0) = tokenizer.nextTokenAsDouble();
161	<	currProp.Xidrr(0,1) = tokenizer.nextTokenAsDouble();
162	<	currProp.Xidrr(0,2) = tokenizer.nextTokenAsDouble();
163	<	currProp.Xidrr(1,0) = tokenizer.nextTokenAsDouble();
164	<	currProp.Xidrr(1,1) = tokenizer.nextTokenAsDouble();
165	<	currProp.Xidrr(1,2) = tokenizer.nextTokenAsDouble();
166	<	currProp.Xidrr(2,0) = tokenizer.nextTokenAsDouble();
167	<	currProp.Xidrr(2,1) = tokenizer.nextTokenAsDouble();
168	<	currProp.Xidrr(2,2) = tokenizer.nextTokenAsDouble();
169	<	props.insert(std::map<std::string, HydroProp>::value_type(atomName, currProp));
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	>	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	>
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	>	delete currShape;
212		}
213	+	}
214		}
215	+	variance_ = 2.0 * PhysicalConstants::kb*simParams->getTargetTemp()/simParams->getDt();
216	+	}
217
218	+	std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) {
219	+	std::map<std::string, HydroProp*> props;
220	+	std::ifstream ifs(filename.c_str());
221	+	if (ifs.is_open()) {
222	+
223	+	}
224	+
225	+	const unsigned int BufferSize = 65535;
226	+	char buffer[BufferSize];
227	+	while (ifs.getline(buffer, BufferSize)) {
228	+	HydroProp* currProp = new HydroProp(buffer);
229	+	props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
230	+	}
231	+
232		return props;
233		}
234	<
235	<	void LDForceManager::postCalculation() {
234	>
235	>	void LDForceManager::postCalculation(){
236		SimInfo::MoleculeIterator i;
237		Molecule::IntegrableObjectIterator  j;
238		Molecule* mol;
239	<	StuntDouble* integrableObject;
240	<	Vector3d vel;
239	>	StuntDouble* sd;
240	>	RealType mass;
241		Vector3d pos;
242		Vector3d frc;
243		Mat3x3d A;
244		Mat3x3d Atrans;
245		Vector3d Tb;
246		Vector3d ji;
180	–	double mass;
247		unsigned int index = 0;
248	+	bool doLangevinForces;
249	+	bool freezeMolecule;
250	+	int fdf;
251	+
252	+	fdf = 0;
253	+
254		for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
183	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
184	–	integrableObject = mol->nextIntegrableObject(j)) {
255
256	<	vel =integrableObject->getVel();
257	<	if (integrableObject->isDirectional()){
188	<	//calculate angular velocity in lab frame
189	<	Mat3x3d I = integrableObject->getI();
190	<	Vector3d angMom = integrableObject->getJ();
191	<	Vector3d omega;
256	>	doLangevinForces = true;
257	>	freezeMolecule = false;
258
259	<	if (integrableObject->isLinear()) {
260	<	int linearAxis = integrableObject->linearAxis();
259	>	if (sphericalBoundaryConditions_) {
260	>
261	>	Vector3d molPos = mol->getCom();
262	>	RealType molRad = molPos.length();
263	>
264	>	doLangevinForces = false;
265	>
266	>	if (molRad > langevinBufferRadius_) {
267	>	doLangevinForces = true;
268	>	freezeMolecule = false;
269	>	}
270	>	if (molRad > frozenBufferRadius_) {
271	>	doLangevinForces = false;
272	>	freezeMolecule = true;
273	>	}
274	>	}
275	>
276	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
277	>	sd = mol->nextIntegrableObject(j)) {
278	>
279	>	if (freezeMolecule)
280	>	fdf += sd->freeze();
281	>
282	>	if (doLangevinForces) {
283	>	mass = sd->getMass();
284	>	if (sd->isDirectional()){
285	>
286	>	// preliminaries for directional objects:
287	>
288	>	A = sd->getA();
289	>	Atrans = A.transpose();
290	>	Vector3d rcrLab = Atrans * hydroProps_[index]->getCOR();
291	>
292	>	//apply random force and torque at center of resistance
293	>
294	>	Vector3d randomForceBody;
295	>	Vector3d randomTorqueBody;
296	>	genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
297	>	Vector3d randomForceLab = Atrans * randomForceBody;
298	>	Vector3d randomTorqueLab = Atrans * randomTorqueBody;
299	>	sd->addFrc(randomForceLab);
300	>	sd->addTrq(randomTorqueLab + cross(rcrLab, randomForceLab ));
301	>
302	>	Mat3x3d I = sd->getI();
303	>	Vector3d omegaBody;
304	>
305	>	// What remains contains velocity explicitly, but the velocity required
306	>	// is at the full step: v(t + h), while we have initially the velocity
307	>	// at the half step: v(t + h/2).  We need to iterate to converge the
308	>	// friction force and friction torque vectors.
309	>
310	>	// this is the velocity at the half-step:
311	>
312	>	Vector3d vel =sd->getVel();
313	>	Vector3d angMom = sd->getJ();
314	>
315	>	//estimate velocity at full-step using everything but friction forces:
316	>
317	>	frc = sd->getFrc();
318	>	Vector3d velStep = vel + (dt2_ /mass * PhysicalConstants::energyConvert) * frc;
319	>
320	>	Tb = sd->lab2Body(sd->getTrq());
321	>	Vector3d angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * Tb;
322	>
323	>	Vector3d omegaLab;
324	>	Vector3d vcdLab;
325	>	Vector3d vcdBody;
326	>	Vector3d frictionForceBody;
327	>	Vector3d frictionForceLab(0.0);
328	>	Vector3d oldFFL;  // used to test for convergence
329	>	Vector3d frictionTorqueBody(0.0);
330	>	Vector3d oldFTB;  // used to test for convergence
331	>	Vector3d frictionTorqueLab;
332	>	RealType fdot;
333	>	RealType tdot;
334	>
335	>	//iteration starts here:
336	>
337	>	for (int k = 0; k < maxIterNum_; k++) {
338	>
339	>	if (sd->isLinear()) {
340	>	int linearAxis = sd->linearAxis();
341		int l = (linearAxis +1 )%3;
342		int m = (linearAxis +2 )%3;
343	<	omega[l] = angMom[l] /I(l, l);
344	<	omega[m] = angMom[m] /I(m, m);
343	>	omegaBody[l] = angMomStep[l] /I(l, l);
344	>	omegaBody[m] = angMomStep[m] /I(m, m);
345
346	<	} else {
347	<	omega[0] = angMom[0] /I(0, 0);
348	<	omega[1] = angMom[1] /I(1, 1);
349	<	omega[2] = angMom[2] /I(2, 2);
350	<	}
346	>	} else {
347	>	omegaBody[0] = angMomStep[0] /I(0, 0);
348	>	omegaBody[1] = angMomStep[1] /I(1, 1);
349	>	omegaBody[2] = angMomStep[2] /I(2, 2);
350	>	}
351	>
352	>	omegaLab = Atrans * omegaBody;
353	>
354	>	// apply friction force and torque at center of resistance
355	>
356	>	vcdLab = velStep + cross(omegaLab, rcrLab);
357	>	vcdBody = A * vcdLab;
358	>	frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omegaBody);
359	>	oldFFL = frictionForceLab;
360	>	frictionForceLab = Atrans * frictionForceBody;
361	>	oldFTB = frictionTorqueBody;
362	>	frictionTorqueBody = -(hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omegaBody);
363	>	frictionTorqueLab = Atrans * frictionTorqueBody;
364	>
365	>	// re-estimate velocities at full-step using friction forces:
366	>
367	>	velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForceLab);
368	>	angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * (Tb + frictionTorqueBody);
369
370	<	//apply friction force and torque at center of diffusion
371	<	A = integrableObject->getA();
372	<	Atrans = A.transpose();
373	<	Vector3d rcd = Atrans * hydroProps_[index].cod;
374	<	Vector3d vcd = vel + cross(omega, rcd);
375	<	vcd = A* vcd;
376	<	Vector3d frictionForce = -(hydroProps_[index].Xidtt * vcd + hydroProps_[index].Xidrt * omega);
377	<	frictionForce = Atrans*frictionForce;
378	<	integrableObject->addFrc(frictionForce);
379	<	Vector3d frictionTorque = - (hydroProps_[index].Xidtr * vcd + hydroProps_[index].Xidrr * omega);
380	<	frictionTorque = Atrans*frictionTorque;
381	<	integrableObject->addTrq(frictionTorque+ cross(rcd, frictionForce));
382	<
219	<	//apply random force and torque at center of diffustion
220	<	Vector3d randomForce;
221	<	Vector3d randomTorque;
222	<	genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
223	<	randomForce = Atrans*randomForce;
224	<	randomTorque = Atrans* randomTorque;
225	<	integrableObject->addFrc(randomForce);
226	<	integrableObject->addTrq(randomTorque + cross(rcd, randomForce ));
227	<
370	>	// check for convergence (if the vectors have converged, fdot and tdot will both be 1.0):
371	>
372	>	fdot = dot(frictionForceLab, oldFFL) / frictionForceLab.lengthSquare();
373	>	tdot = dot(frictionTorqueBody, oldFTB) / frictionTorqueBody.lengthSquare();
374	>
375	>	if (fabs(1.0 - fdot) <= forceTolerance_ && fabs(1.0 - tdot) <= forceTolerance_)
376	>	break; // iteration ends here
377	>	}
378	>
379	>	sd->addFrc(frictionForceLab);
380	>	sd->addTrq(frictionTorqueLab + cross(rcrLab, frictionForceLab));
381	>
382	>
383		} else {
384	<	//spheric atom
230	<	Vector3d frictionForce = -(hydroProps_[index].Xidtt *vel);
231	<	Vector3d randomForce;
232	<	Vector3d randomTorque;
233	<	genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
384	>	//spherical atom
385
386	<	//randomForce /= OOPSEConstant::energyConvert;
387	<	//randomTorque /= OOPSEConstant::energyConvert;
388	<	integrableObject->addFrc(frictionForce+randomForce);
389	<	}
386	>	Vector3d randomForce;
387	>	Vector3d randomTorque;
388	>	genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
389	>	sd->addFrc(randomForce);
390
391	+	// What remains contains velocity explicitly, but the velocity required
392	+	// is at the full step: v(t + h), while we have initially the velocity
393	+	// at the half step: v(t + h/2).  We need to iterate to converge the
394	+	// friction force vector.
395	+
396	+	// this is the velocity at the half-step:
397	+
398	+	Vector3d vel =sd->getVel();
399	+
400	+	//estimate velocity at full-step using everything but friction forces:
401	+
402	+	frc = sd->getFrc();
403	+	Vector3d velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * frc;
404	+
405	+	Vector3d frictionForce(0.0);
406	+	Vector3d oldFF;  // used to test for convergence
407	+	RealType fdot;
408	+
409	+	//iteration starts here:
410	+
411	+	for (int k = 0; k < maxIterNum_; k++) {
412	+
413	+	oldFF = frictionForce;
414	+	frictionForce = -hydroProps_[index]->getXitt() * velStep;
415	+
416	+	// re-estimate velocities at full-step using friction forces:
417	+
418	+	velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForce);
419	+
420	+	// check for convergence (if the vector has converged, fdot will be 1.0):
421	+
422	+	fdot = dot(frictionForce, oldFF) / frictionForce.lengthSquare();
423	+
424	+	if (fabs(1.0 - fdot) <= forceTolerance_)
425	+	break; // iteration ends here
426	+	}
427	+
428	+	sd->addFrc(frictionForce);
429	+
430	+	}
431	+	}
432	+
433		++index;
434
435		}
436		}
437
438	<	ForceManager::postCalculation();
438	>	info_->setFdf(fdf);
439	>	veloMunge->removeComDrift();
440	>	// Remove angular drift if we are not using periodic boundary conditions.
441	>	if(!simParams->getUsePeriodicBoundaryConditions())
442	>	veloMunge->removeAngularDrift();
443
444	<
248	<
444	>	ForceManager::postCalculation();
445		}
446
447	<	void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, double variance) {
252	<	/*
253	<	SquareMatrix<double, 6> Dd;
254	<	SquareMatrix<double, 6> S;
255	<	Vector<double, 6> Z;
256	<	Vector<double, 6> generalForce;
257	<	Dd.setSubMatrix(0, 0, hydroProps_[index].Ddtt);
258	<	Dd.setSubMatrix(0, 3, hydroProps_[index].Ddtr.transpose());
259	<	Dd.setSubMatrix(3, 0, hydroProps_[index].Ddtr);
260	<	Dd.setSubMatrix(3, 3, hydroProps_[index].Ddrr);
261	<	CholeskyDecomposition(Dd, S);
262	<	*/
447	>	void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
448
264	–	SquareMatrix<double, 6> Xid;
265	–	SquareMatrix<double, 6> S;
266	–	Vector<double, 6> Z;
267	–	Vector<double, 6> generalForce;
268	–	Xid.setSubMatrix(0, 0, hydroProps_[index].Xidtt);
269	–	Xid.setSubMatrix(0, 3, hydroProps_[index].Xidrt);
270	–	Xid.setSubMatrix(3, 0, hydroProps_[index].Xidtr);
271	–	Xid.setSubMatrix(3, 3, hydroProps_[index].Xidrr);
272	–	CholeskyDecomposition(Xid, S);
449
450	<	/*
451	<	Xid *= variance;
276	<	Z[0] = randNumGen_.randNorm(0, 1.0);
277	<	Z[1] = randNumGen_.randNorm(0, 1.0);
278	<	Z[2] = randNumGen_.randNorm(0, 1.0);
279	<	Z[3] = randNumGen_.randNorm(0, 1.0);
280	<	Z[4] = randNumGen_.randNorm(0, 1.0);
281	<	Z[5] = randNumGen_.randNorm(0, 1.0);
282	<	*/
450	>	Vector<RealType, 6> Z;
451	>	Vector<RealType, 6> generalForce;
452
453		Z[0] = randNumGen_.randNorm(0, variance);
454		Z[1] = randNumGen_.randNorm(0, variance);
#	Line 288 | Line 457 | void LDForceManager::genRandomForceAndTorque(Vector3d&
457		Z[4] = randNumGen_.randNorm(0, variance);
458		Z[5] = randNumGen_.randNorm(0, variance);
459
460	<
292	<	generalForce = S*Z;
460	>	generalForce = hydroProps_[index]->getS()*Z;
461
462		force[0] = generalForce[0];
463		force[1] = generalForce[1];
#	Line 298 | Line 466 | void LDForceManager::genRandomForceAndTorque(Vector3d&
466		torque[1] = generalForce[4];
467		torque[2] = generalForce[5];
468
469	<	}
469	>	}
470
471		}

Comparing:
trunk/src/integrators/LDForceManager.cpp (property svn:keywords), Revision 904 by tim, Thu Mar 16 22:50:48 2006 UTC vs.
branches/development/src/integrators/LDForceManager.cpp (property svn:keywords), Revision 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

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