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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 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"
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);
105	<	} else {
106	<	//error
107	<	}
108	<
109	<	}
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	>	for (integrableObject = mol->beginIntegrableObject(j);
106	>	integrableObject != NULL;
107	>	integrableObject = mol->nextIntegrableObject(j)) {
108	>
109	>	if (integrableObject->isRigidBody()) {
110	>	RigidBody* rb = static_cast<RigidBody*>(integrableObject);
111	>	if (rb->getNumAtoms() > 1) needHydroPropFile = true;
112	>	}
113	>
114	>	}
115		}
116	<	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()) {
116	>
117
118	<	}
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	<	const unsigned int BufferSize = 65535;
132	<	char buffer[BufferSize];
133	<	while (ifs.getline(buffer, BufferSize)) {
134	<	StringTokenizer tokenizer(buffer);
135	<	HydroProp currProp;
86	<	if (tokenizer.countTokens() >= 67) {
87	<	std::string atomName = tokenizer.nextToken();
88	<	currProp.cod[0] = tokenizer.nextTokenAsDouble();
89	<	currProp.cod[1] = tokenizer.nextTokenAsDouble();
90	<	currProp.cod[2] = tokenizer.nextTokenAsDouble();
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	<	currProp.Ddtt(0,0) = tokenizer.nextTokenAsDouble();
138	<	currProp.Ddtt(0,1) = tokenizer.nextTokenAsDouble();
139	<	currProp.Ddtt(0,2) = tokenizer.nextTokenAsDouble();
140	<	currProp.Ddtt(1,0) = tokenizer.nextTokenAsDouble();
141	<	currProp.Ddtt(1,1) = tokenizer.nextTokenAsDouble();
142	<	currProp.Ddtt(1,2) = tokenizer.nextTokenAsDouble();
143	<	currProp.Ddtt(2,0) = tokenizer.nextTokenAsDouble();
144	<	currProp.Ddtt(2,1) = tokenizer.nextTokenAsDouble();
145	<	currProp.Ddtt(2,2) = tokenizer.nextTokenAsDouble();
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;
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
159	<	currProp.Ddtr(0,0) = tokenizer.nextTokenAsDouble();
160	<	currProp.Ddtr(0,1) = tokenizer.nextTokenAsDouble();
161	<	currProp.Ddtr(0,2) = tokenizer.nextTokenAsDouble();
162	<	currProp.Ddtr(1,0) = tokenizer.nextTokenAsDouble();
163	<	currProp.Ddtr(1,1) = tokenizer.nextTokenAsDouble();
164	<	currProp.Ddtr(1,2) = tokenizer.nextTokenAsDouble();
165	<	currProp.Ddtr(2,0) = tokenizer.nextTokenAsDouble();
166	<	currProp.Ddtr(2,1) = tokenizer.nextTokenAsDouble();
167	<	currProp.Ddtr(2,2) = tokenizer.nextTokenAsDouble();
159	>	if (integrableObject->isAtom()){
160	>	Atom* atom = static_cast<Atom*>(integrableObject);
161	>	AtomType* atomType = atom->getAtomType();
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	>	"Could not find atom type in default element.txt\n");
178	>	painCave.severity = OPENMD_ERROR;
179	>	painCave.isFatal = 1;
180	>	simError();
181	>	}
182	>	}
183	>	}
184	>	}
185
186	<	currProp.Ddrr(0,0) = tokenizer.nextTokenAsDouble();
187	<	currProp.Ddrr(0,1) = tokenizer.nextTokenAsDouble();
188	<	currProp.Ddrr(0,2) = tokenizer.nextTokenAsDouble();
189	<	currProp.Ddrr(1,0) = tokenizer.nextTokenAsDouble();
190	<	currProp.Ddrr(1,1) = tokenizer.nextTokenAsDouble();
191	<	currProp.Ddrr(1,2) = tokenizer.nextTokenAsDouble();
118	<	currProp.Ddrr(2,0) = tokenizer.nextTokenAsDouble();
119	<	currProp.Ddrr(2,1) = tokenizer.nextTokenAsDouble();
120	<	currProp.Ddrr(2,2) = tokenizer.nextTokenAsDouble();
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	<	currProp.Xidtt(0,0) = tokenizer.nextTokenAsDouble();
194	<	currProp.Xidtt(0,1) = tokenizer.nextTokenAsDouble();
195	<	currProp.Xidtt(0,2) = tokenizer.nextTokenAsDouble();
196	<	currProp.Xidtt(1,0) = tokenizer.nextTokenAsDouble();
197	<	currProp.Xidtt(1,1) = tokenizer.nextTokenAsDouble();
198	<	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();
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
132	–	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();
200
201	<	currProp.Xidrr(0,0) = tokenizer.nextTokenAsDouble();
202	<	currProp.Xidrr(0,1) = tokenizer.nextTokenAsDouble();
203	<	currProp.Xidrr(0,2) = tokenizer.nextTokenAsDouble();
204	<	currProp.Xidrr(1,0) = tokenizer.nextTokenAsDouble();
205	<	currProp.Xidrr(1,1) = tokenizer.nextTokenAsDouble();
206	<	currProp.Xidrr(1,2) = tokenizer.nextTokenAsDouble();
207	<	currProp.Xidrr(2,0) = tokenizer.nextTokenAsDouble();
208	<	currProp.Xidrr(2,1) = tokenizer.nextTokenAsDouble();
209	<	currProp.Xidrr(2,2) = tokenizer.nextTokenAsDouble();
161	<	props.insert(std::map<std::string, HydroProp>::value_type(atomName, currProp));
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	>	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 * PhysicalConstants::kb*simParams->getTargetTemp()/simParams->getDt();
214	+	}
215	+
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	+
221	+	}
222	+
223	+	const unsigned int BufferSize = 65535;
224	+	char buffer[BufferSize];
225	+	while (ifs.getline(buffer, BufferSize)) {
226	+	HydroProp* currProp = new HydroProp(buffer);
227	+	props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
228		}
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;
180	–	double mass;
245		unsigned int index = 0;
246	+	bool doLangevinForces;
247	+	bool freezeMolecule;
248	+	int fdf;
249	+
250	+	fdf = 0;
251	+
252		for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
183	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
184	–	integrableObject = mol->nextIntegrableObject(j)) {
253
254	<	vel =integrableObject->getVel();
254	>	doLangevinForces = true;
255	>	freezeMolecule = false;
256	>
257	>	if (sphericalBoundaryConditions_) {
258	>
259	>	Vector3d molPos = mol->getCom();
260	>	RealType molRad = molPos.length();
261	>
262	>	doLangevinForces = false;
263	>
264	>	if (molRad > langevinBufferRadius_) {
265	>	doLangevinForces = true;
266	>	freezeMolecule = false;
267	>	}
268	>	if (molRad > frozenBufferRadius_) {
269	>	doLangevinForces = false;
270	>	freezeMolecule = true;
271	>	}
272	>	}
273	>
274	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
275	>	integrableObject = mol->nextIntegrableObject(j)) {
276	>
277	>	if (freezeMolecule)
278	>	fdf += integrableObject->freeze();
279	>
280	>	if (doLangevinForces) {
281	>	mass = integrableObject->getMass();
282		if (integrableObject->isDirectional()){
188	–	//calculate angular velocity in lab frame
189	–	Mat3x3d I = integrableObject->getI();
190	–	Vector3d angMom = integrableObject->getJ();
191	–	Vector3d omega;
283
284	<	if (integrableObject->isLinear()) {
284	>	// preliminaries for directional objects:
285	>
286	>	A = integrableObject->getA();
287	>	Atrans = A.transpose();
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;
297	>	integrableObject->addFrc(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	<	omega[l] = angMom[l] /I(l, l);
342	<	omega[m] = angMom[m] /I(m, m);
341	>	omegaBody[l] = angMomStep[l] /I(l, l);
342	>	omegaBody[m] = angMomStep[m] /I(m, m);
343
344	<	} else {
345	<	omega[0] = angMom[0] /I(0, 0);
346	<	omega[1] = angMom[1] /I(1, 1);
347	<	omega[2] = angMom[2] /I(2, 2);
348	<	}
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	<	//apply friction force and torque at center of diffusion
369	<	A = integrableObject->getA();
370	<	Atrans = A.transpose();
371	<	Vector3d rcd = Atrans * hydroProps_[index].cod;
372	<	Vector3d vcd = vel + cross(omega, rcd);
373	<	vcd = A* vcd;
374	<	Vector3d frictionForce = -(hydroProps_[index].Xidtt * vcd + hydroProps_[index].Xidrt * omega);
375	<	frictionForce = Atrans*frictionForce;
376	<	integrableObject->addFrc(frictionForce);
377	<	Vector3d frictionTorque = - (hydroProps_[index].Xidtr * vcd + hydroProps_[index].Xidrr * omega);
378	<	frictionTorque = Atrans*frictionTorque;
379	<	integrableObject->addTrq(frictionTorque+ cross(rcd, frictionForce));
380	<
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	<
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	<	//spheric atom
230	<	Vector3d frictionForce = -(hydroProps_[index].Xidtt *vel);
231	<	Vector3d randomForce;
232	<	Vector3d randomTorque;
233	<	genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
382	>	//spherical atom
383
384	<	//randomForce /= OOPSEConstant::energyConvert;
385	<	//randomTorque /= OOPSEConstant::energyConvert;
386	<	integrableObject->addFrc(frictionForce+randomForce);
387	<	}
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	+	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	+
431		++index;
432
433		}
434		}
435
436	<	ForceManager::postCalculation();
436	>	info_->setFdf(fdf);
437	>	veloMunge->removeComDrift();
438	>	// Remove angular drift if we are not using periodic boundary conditions.
439	>	if(!simParams->getUsePeriodicBoundaryConditions())
440	>	veloMunge->removeAngularDrift();
441
442	<
248	<
442	>	ForceManager::postCalculation();
443		}
444
445	<	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	<	*/
445	>	void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
446
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);
447
448	<	/*
449	<	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	<	*/
448	>	Vector<RealType, 6> Z;
449	>	Vector<RealType, 6> generalForce;
450
451		Z[0] = randNumGen_.randNorm(0, variance);
452		Z[1] = randNumGen_.randNorm(0, variance);
#	Line 288 | Line 455 | void LDForceManager::genRandomForceAndTorque(Vector3d&
455		Z[4] = randNumGen_.randNorm(0, variance);
456		Z[5] = randNumGen_.randNorm(0, variance);
457
458	<
292	<	generalForce = S*Z;
458	>	generalForce = hydroProps_[index]->getS()*Z;
459
460		force[0] = generalForce[0];
461		force[1] = generalForce[1];
#	Line 298 | 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 904 by tim, Thu Mar 16 22:50:48 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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