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root/OpenMD/trunk/src/integrators/LDForceManager.cpp

Comparing trunk/src/integrators/LDForceManager.cpp (file contents):
Revision 904 by tim, Thu Mar 16 22:50:48 2006 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 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),
56	>	maxIterNum_(4),
57	>	forceTolerance_(1e-6) {
58	>	simParams = info->getSimParams();
59	>	veloMunge = new Velocitizer(info);
60	>
61	>	sphericalBoundaryConditions_ = false;
62	>	if (simParams->getUseSphericalBoundaryConditions()) {
63	>	sphericalBoundaryConditions_ = true;
64	>	if (simParams->haveLangevinBufferRadius()) {
65	>	langevinBufferRadius_ = simParams->getLangevinBufferRadius();
66	>	} else {
67	>	sprintf( painCave.errMsg,
68	>	"langevinBufferRadius must be specified "
69	>	"when useSphericalBoundaryConditions is turned on.\n");
70	>	painCave.severity = OPENMD_ERROR;
71	>	painCave.isFatal = 1;
72	>	simError();
73	>	}
74	>
75	>	if (simParams->haveFrozenBufferRadius()) {
76	>	frozenBufferRadius_ = simParams->getFrozenBufferRadius();
77	>	} else {
78	>	sprintf( painCave.errMsg,
79	>	"frozenBufferRadius must be specified "
80	>	"when useSphericalBoundaryConditions is turned on.\n");
81	>	painCave.severity = OPENMD_ERROR;
82	>	painCave.isFatal = 1;
83	>	simError();
84	>	}
85	>
86	>	if (frozenBufferRadius_ < langevinBufferRadius_) {
87	>	sprintf( painCave.errMsg,
88	>	"frozenBufferRadius has been set smaller than the "
89	>	"langevinBufferRadius.  This is probably an error.\n");
90	>	painCave.severity = OPENMD_WARNING;
91	>	painCave.isFatal = 0;
92	>	simError();
93	>	}
94		}
95
96	<	SimInfo::MoleculeIterator i;
97	<	Molecule::IntegrableObjectIterator  j;
96	>	// Build the hydroProp map:
97	>	std::map<std::string, HydroProp*> hydroPropMap;
98	>
99		Molecule* mol;
100	<	StuntDouble* integrableObject;
101	<	for (mol = info->beginMolecule(i); mol != NULL; mol = info->nextMolecule(i)) {
102	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
103	<	integrableObject = mol->nextIntegrableObject(j)) {
104	<	std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
105	<	if (iter != hydroPropMap.end()) {
106	<	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()) {
100	>	StuntDouble* sd;
101	>	SimInfo::MoleculeIterator i;
102	>	Molecule::IntegrableObjectIterator  j;
103	>	bool needHydroPropFile = false;
104	>
105	>	for (mol = info->beginMolecule(i); mol != NULL;
106	>	mol = info->nextMolecule(i)) {
107
108	+	for (sd = mol->beginIntegrableObject(j); sd != NULL;
109	+	sd = mol->nextIntegrableObject(j)) {
110	+
111	+	if (sd->isRigidBody()) {
112	+	RigidBody* rb = static_cast<RigidBody*>(sd);
113	+	if (rb->getNumAtoms() > 1) needHydroPropFile = true;
114	+	}
115	+
116	+	}
117		}
118	+
119
120	<	const unsigned int BufferSize = 65535;
121	<	char buffer[BufferSize];
122	<	while (ifs.getline(buffer, BufferSize)) {
123	<	StringTokenizer tokenizer(buffer);
124	<	HydroProp currProp;
125	<	if (tokenizer.countTokens() >= 67) {
126	<	std::string atomName = tokenizer.nextToken();
127	<	currProp.cod[0] = tokenizer.nextTokenAsDouble();
128	<	currProp.cod[1] = tokenizer.nextTokenAsDouble();
129	<	currProp.cod[2] = tokenizer.nextTokenAsDouble();
120	>	if (needHydroPropFile) {
121	>	if (simParams->haveHydroPropFile()) {
122	>	hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
123	>	} else {
124	>	sprintf( painCave.errMsg,
125	>	"HydroPropFile must be set to a file name if Langevin Dynamics\n"
126	>	"\tis specified for rigidBodies which contain more than one atom\n"
127	>	"\tTo create a HydroPropFile, run the \"Hydro\" program.\n");
128	>	painCave.severity = OPENMD_ERROR;
129	>	painCave.isFatal = 1;
130	>	simError();
131	>	}
132
133	<	currProp.Ddtt(0,0) = tokenizer.nextTokenAsDouble();
134	<	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();
133	>	for (mol = info->beginMolecule(i); mol != NULL;
134	>	mol = info->nextMolecule(i)) {
135
136	<	currProp.Ddtr(0,0) = tokenizer.nextTokenAsDouble();
137	<	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();
136	>	for (sd = mol->beginIntegrableObject(j);  sd != NULL;
137	>	sd = mol->nextIntegrableObject(j)) {
138
139	<	currProp.Ddrr(0,0) = tokenizer.nextTokenAsDouble();
140	<	currProp.Ddrr(0,1) = tokenizer.nextTokenAsDouble();
141	<	currProp.Ddrr(0,2) = tokenizer.nextTokenAsDouble();
142	<	currProp.Ddrr(1,0) = tokenizer.nextTokenAsDouble();
143	<	currProp.Ddrr(1,1) = tokenizer.nextTokenAsDouble();
144	<	currProp.Ddrr(1,2) = tokenizer.nextTokenAsDouble();
145	<	currProp.Ddrr(2,0) = tokenizer.nextTokenAsDouble();
146	<	currProp.Ddrr(2,1) = tokenizer.nextTokenAsDouble();
147	<	currProp.Ddrr(2,2) = tokenizer.nextTokenAsDouble();
139	>	std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(sd->getType());
140	>	if (iter != hydroPropMap.end()) {
141	>	hydroProps_.push_back(iter->second);
142	>	} else {
143	>	sprintf( painCave.errMsg,
144	>	"Can not find resistance tensor for atom [%s]\n", sd->getType().c_str());
145	>	painCave.severity = OPENMD_ERROR;
146	>	painCave.isFatal = 1;
147	>	simError();
148	>	}
149	>	}
150	>	}
151	>	} else {
152	>
153	>	std::map<std::string, HydroProp*> hydroPropMap;
154	>	for (mol = info->beginMolecule(i); mol != NULL;
155	>	mol = info->nextMolecule(i)) {
156
157	<	currProp.Xidtt(0,0) = tokenizer.nextTokenAsDouble();
158	<	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();
157	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
158	>	sd = mol->nextIntegrableObject(j)) {
159
160	<	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();
160	>	Shape* currShape = NULL;
161
162	<	currProp.Xidrr(0,0) = tokenizer.nextTokenAsDouble();
163	<	currProp.Xidrr(0,1) = tokenizer.nextTokenAsDouble();
164	<	currProp.Xidrr(0,2) = tokenizer.nextTokenAsDouble();
165	<	currProp.Xidrr(1,0) = tokenizer.nextTokenAsDouble();
166	<	currProp.Xidrr(1,1) = tokenizer.nextTokenAsDouble();
167	<	currProp.Xidrr(1,2) = tokenizer.nextTokenAsDouble();
168	<	currProp.Xidrr(2,0) = tokenizer.nextTokenAsDouble();
169	<	currProp.Xidrr(2,1) = tokenizer.nextTokenAsDouble();
170	<	currProp.Xidrr(2,2) = tokenizer.nextTokenAsDouble();
171	<	props.insert(std::map<std::string, HydroProp>::value_type(atomName, currProp));
162	>	if (sd->isAtom()){
163	>	Atom* atom = static_cast<Atom*>(sd);
164	>	AtomType* atomType = atom->getAtomType();
165	>	GayBerneAdapter gba = GayBerneAdapter(atomType);
166	>	if (gba.isGayBerne()) {
167	>	currShape = new Ellipsoid(V3Zero, gba.getL() / 2.0,
168	>	gba.getD() / 2.0,
169	>	Mat3x3d::identity());
170	>	} else {
171	>	LennardJonesAdapter lja = LennardJonesAdapter(atomType);
172	>	if (lja.isLennardJones()){
173	>	currShape = new Sphere(atom->getPos(), lja.getSigma()/2.0);
174	>	} else {
175	>	int aNum = etab.GetAtomicNum((atom->getType()).c_str());
176	>	if (aNum != 0) {
177	>	currShape = new Sphere(atom->getPos(), etab.GetVdwRad(aNum));
178	>	} else {
179	>	sprintf( painCave.errMsg,
180	>	"Could not find atom type in default element.txt\n");
181	>	painCave.severity = OPENMD_ERROR;
182	>	painCave.isFatal = 1;
183	>	simError();
184	>	}
185	>	}
186	>	}
187	>	}
188	>
189	>	if (!simParams->haveTargetTemp()) {
190	>	sprintf(painCave.errMsg, "You can't use LangevinDynamics without a targetTemp!\n");
191	>	painCave.isFatal = 1;
192	>	painCave.severity = OPENMD_ERROR;
193	>	simError();
194	>	}
195	>
196	>	if (!simParams->haveViscosity()) {
197	>	sprintf(painCave.errMsg, "You can't use LangevinDynamics without a viscosity!\n");
198	>	painCave.isFatal = 1;
199	>	painCave.severity = OPENMD_ERROR;
200	>	simError();
201	>	}
202	>
203	>
204	>	HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp());
205	>	std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(sd->getType());
206	>	if (iter != hydroPropMap.end())
207	>	hydroProps_.push_back(iter->second);
208	>	else {
209	>	currHydroProp->complete();
210	>	hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(sd->getType(), currHydroProp));
211	>	hydroProps_.push_back(currHydroProp);
212	>	}
213	>	delete currShape;
214		}
215	+	}
216		}
217	+	variance_ = 2.0 * PhysicalConstants::kb*simParams->getTargetTemp()/simParams->getDt();
218	+	}
219
220	+	std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) {
221	+	std::map<std::string, HydroProp*> props;
222	+	std::ifstream ifs(filename.c_str());
223	+	if (ifs.is_open()) {
224	+
225	+	}
226	+
227	+	const unsigned int BufferSize = 65535;
228	+	char buffer[BufferSize];
229	+	while (ifs.getline(buffer, BufferSize)) {
230	+	HydroProp* currProp = new HydroProp(buffer);
231	+	props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
232	+	}
233	+
234		return props;
235		}
236	<
237	<	void LDForceManager::postCalculation() {
236	>
237	>	void LDForceManager::postCalculation(){
238		SimInfo::MoleculeIterator i;
239		Molecule::IntegrableObjectIterator  j;
240		Molecule* mol;
241	<	StuntDouble* integrableObject;
242	<	Vector3d vel;
241	>	StuntDouble* sd;
242	>	RealType mass;
243		Vector3d pos;
244		Vector3d frc;
245		Mat3x3d A;
246		Mat3x3d Atrans;
247		Vector3d Tb;
248		Vector3d ji;
180	–	double mass;
249		unsigned int index = 0;
250	+	bool doLangevinForces;
251	+	bool freezeMolecule;
252	+	int fdf;
253	+
254	+	fdf = 0;
255	+
256		for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
183	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
184	–	integrableObject = mol->nextIntegrableObject(j)) {
257
258	<	vel =integrableObject->getVel();
259	<	if (integrableObject->isDirectional()){
188	<	//calculate angular velocity in lab frame
189	<	Mat3x3d I = integrableObject->getI();
190	<	Vector3d angMom = integrableObject->getJ();
191	<	Vector3d omega;
258	>	doLangevinForces = true;
259	>	freezeMolecule = false;
260
261	<	if (integrableObject->isLinear()) {
262	<	int linearAxis = integrableObject->linearAxis();
261	>	if (sphericalBoundaryConditions_) {
262	>
263	>	Vector3d molPos = mol->getCom();
264	>	RealType molRad = molPos.length();
265	>
266	>	doLangevinForces = false;
267	>
268	>	if (molRad > langevinBufferRadius_) {
269	>	doLangevinForces = true;
270	>	freezeMolecule = false;
271	>	}
272	>	if (molRad > frozenBufferRadius_) {
273	>	doLangevinForces = false;
274	>	freezeMolecule = true;
275	>	}
276	>	}
277	>
278	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
279	>	sd = mol->nextIntegrableObject(j)) {
280	>
281	>	if (freezeMolecule)
282	>	fdf += sd->freeze();
283	>
284	>	if (doLangevinForces) {
285	>	mass = sd->getMass();
286	>	if (sd->isDirectional()){
287	>
288	>	// preliminaries for directional objects:
289	>
290	>	A = sd->getA();
291	>	Atrans = A.transpose();
292	>	Vector3d rcrLab = Atrans * hydroProps_[index]->getCOR();
293	>
294	>	//apply random force and torque at center of resistance
295	>
296	>	Vector3d randomForceBody;
297	>	Vector3d randomTorqueBody;
298	>	genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
299	>	Vector3d randomForceLab = Atrans * randomForceBody;
300	>	Vector3d randomTorqueLab = Atrans * randomTorqueBody;
301	>	sd->addFrc(randomForceLab);
302	>	sd->addTrq(randomTorqueLab + cross(rcrLab, randomForceLab ));
303	>
304	>	Mat3x3d I = sd->getI();
305	>	Vector3d omegaBody;
306	>
307	>	// What remains contains velocity explicitly, but the velocity required
308	>	// is at the full step: v(t + h), while we have initially the velocity
309	>	// at the half step: v(t + h/2).  We need to iterate to converge the
310	>	// friction force and friction torque vectors.
311	>
312	>	// this is the velocity at the half-step:
313	>
314	>	Vector3d vel =sd->getVel();
315	>	Vector3d angMom = sd->getJ();
316	>
317	>	//estimate velocity at full-step using everything but friction forces:
318	>
319	>	frc = sd->getFrc();
320	>	Vector3d velStep = vel + (dt2_ /mass * PhysicalConstants::energyConvert) * frc;
321	>
322	>	Tb = sd->lab2Body(sd->getTrq());
323	>	Vector3d angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * Tb;
324	>
325	>	Vector3d omegaLab;
326	>	Vector3d vcdLab;
327	>	Vector3d vcdBody;
328	>	Vector3d frictionForceBody;
329	>	Vector3d frictionForceLab(0.0);
330	>	Vector3d oldFFL;  // used to test for convergence
331	>	Vector3d frictionTorqueBody(0.0);
332	>	Vector3d oldFTB;  // used to test for convergence
333	>	Vector3d frictionTorqueLab;
334	>	RealType fdot;
335	>	RealType tdot;
336	>
337	>	//iteration starts here:
338	>
339	>	for (int k = 0; k < maxIterNum_; k++) {
340	>
341	>	if (sd->isLinear()) {
342	>	int linearAxis = sd->linearAxis();
343		int l = (linearAxis +1 )%3;
344		int m = (linearAxis +2 )%3;
345	<	omega[l] = angMom[l] /I(l, l);
346	<	omega[m] = angMom[m] /I(m, m);
345	>	omegaBody[l] = angMomStep[l] /I(l, l);
346	>	omegaBody[m] = angMomStep[m] /I(m, m);
347
348	<	} else {
349	<	omega[0] = angMom[0] /I(0, 0);
350	<	omega[1] = angMom[1] /I(1, 1);
351	<	omega[2] = angMom[2] /I(2, 2);
352	<	}
348	>	} else {
349	>	omegaBody[0] = angMomStep[0] /I(0, 0);
350	>	omegaBody[1] = angMomStep[1] /I(1, 1);
351	>	omegaBody[2] = angMomStep[2] /I(2, 2);
352	>	}
353	>
354	>	omegaLab = Atrans * omegaBody;
355	>
356	>	// apply friction force and torque at center of resistance
357	>
358	>	vcdLab = velStep + cross(omegaLab, rcrLab);
359	>	vcdBody = A * vcdLab;
360	>	frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omegaBody);
361	>	oldFFL = frictionForceLab;
362	>	frictionForceLab = Atrans * frictionForceBody;
363	>	oldFTB = frictionTorqueBody;
364	>	frictionTorqueBody = -(hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omegaBody);
365	>	frictionTorqueLab = Atrans * frictionTorqueBody;
366	>
367	>	// re-estimate velocities at full-step using friction forces:
368	>
369	>	velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForceLab);
370	>	angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * (Tb + frictionTorqueBody);
371
372	<	//apply friction force and torque at center of diffusion
373	<	A = integrableObject->getA();
374	<	Atrans = A.transpose();
375	<	Vector3d rcd = Atrans * hydroProps_[index].cod;
376	<	Vector3d vcd = vel + cross(omega, rcd);
377	<	vcd = A* vcd;
378	<	Vector3d frictionForce = -(hydroProps_[index].Xidtt * vcd + hydroProps_[index].Xidrt * omega);
379	<	frictionForce = Atrans*frictionForce;
380	<	integrableObject->addFrc(frictionForce);
381	<	Vector3d frictionTorque = - (hydroProps_[index].Xidtr * vcd + hydroProps_[index].Xidrr * omega);
382	<	frictionTorque = Atrans*frictionTorque;
383	<	integrableObject->addTrq(frictionTorque+ cross(rcd, frictionForce));
384	<
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	<
372	>	// check for convergence (if the vectors have converged, fdot and tdot will both be 1.0):
373	>
374	>	fdot = dot(frictionForceLab, oldFFL) / frictionForceLab.lengthSquare();
375	>	tdot = dot(frictionTorqueBody, oldFTB) / frictionTorqueBody.lengthSquare();
376	>
377	>	if (fabs(1.0 - fdot) <= forceTolerance_ && fabs(1.0 - tdot) <= forceTolerance_)
378	>	break; // iteration ends here
379	>	}
380	>
381	>	sd->addFrc(frictionForceLab);
382	>	sd->addTrq(frictionTorqueLab + cross(rcrLab, frictionForceLab));
383	>
384	>
385		} else {
386	<	//spheric atom
230	<	Vector3d frictionForce = -(hydroProps_[index].Xidtt *vel);
231	<	Vector3d randomForce;
232	<	Vector3d randomTorque;
233	<	genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
386	>	//spherical atom
387
388	<	//randomForce /= OOPSEConstant::energyConvert;
389	<	//randomTorque /= OOPSEConstant::energyConvert;
390	<	integrableObject->addFrc(frictionForce+randomForce);
391	<	}
388	>	Vector3d randomForce;
389	>	Vector3d randomTorque;
390	>	genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
391	>	sd->addFrc(randomForce);
392
393	+	// What remains contains velocity explicitly, but the velocity required
394	+	// is at the full step: v(t + h), while we have initially the velocity
395	+	// at the half step: v(t + h/2).  We need to iterate to converge the
396	+	// friction force vector.
397	+
398	+	// this is the velocity at the half-step:
399	+
400	+	Vector3d vel =sd->getVel();
401	+
402	+	//estimate velocity at full-step using everything but friction forces:
403	+
404	+	frc = sd->getFrc();
405	+	Vector3d velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * frc;
406	+
407	+	Vector3d frictionForce(0.0);
408	+	Vector3d oldFF;  // used to test for convergence
409	+	RealType fdot;
410	+
411	+	//iteration starts here:
412	+
413	+	for (int k = 0; k < maxIterNum_; k++) {
414	+
415	+	oldFF = frictionForce;
416	+	frictionForce = -hydroProps_[index]->getXitt() * velStep;
417	+
418	+	// re-estimate velocities at full-step using friction forces:
419	+
420	+	velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForce);
421	+
422	+	// check for convergence (if the vector has converged, fdot will be 1.0):
423	+
424	+	fdot = dot(frictionForce, oldFF) / frictionForce.lengthSquare();
425	+
426	+	if (fabs(1.0 - fdot) <= forceTolerance_)
427	+	break; // iteration ends here
428	+	}
429	+
430	+	sd->addFrc(frictionForce);
431	+
432	+	}
433	+	}
434	+
435		++index;
436
437		}
438		}
439
440	<	ForceManager::postCalculation();
440	>	info_->setFdf(fdf);
441	>	veloMunge->removeComDrift();
442	>	// Remove angular drift if we are not using periodic boundary conditions.
443	>	if(!simParams->getUsePeriodicBoundaryConditions())
444	>	veloMunge->removeAngularDrift();
445
446	<
248	<
446	>	ForceManager::postCalculation();
447		}
448
449	<	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	<	*/
449	>	void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
450
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);
451
452	<	/*
453	<	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	<	*/
452	>	Vector<RealType, 6> Z;
453	>	Vector<RealType, 6> generalForce;
454
455		Z[0] = randNumGen_.randNorm(0, variance);
456		Z[1] = randNumGen_.randNorm(0, variance);
#	Line 288 | Line 459 | void LDForceManager::genRandomForceAndTorque(Vector3d&
459		Z[4] = randNumGen_.randNorm(0, variance);
460		Z[5] = randNumGen_.randNorm(0, variance);
461
462	<
292	<	generalForce = S*Z;
462	>	generalForce = hydroProps_[index]->getS()*Z;
463
464		force[0] = generalForce[0];
465		force[1] = generalForce[1];
#	Line 298 | Line 468 | void LDForceManager::genRandomForceAndTorque(Vector3d&
468		torque[1] = generalForce[4];
469		torque[2] = generalForce[5];
470
471	<	}
471	>	}
472
473		}

Comparing trunk/src/integrators/LDForceManager.cpp (property svn:keywords):
Revision 904 by tim, Thu Mar 16 22:50:48 2006 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

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