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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 1465 by chuckv, Fri Jul 9 23:08:25 2010 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]  Vardeman & Gezelter, in progress (2009).
40		*/
41		#include <fstream>
42	+	#include <iostream>
43		#include "integrators/LDForceManager.hpp"
44		#include "math/CholeskyDecomposition.hpp"
45	<	#include "utils/OOPSEConstant.hpp"
46	<	namespace oopse {
45	>	#include "utils/PhysicalConstants.hpp"
46	>	#include "hydrodynamics/Sphere.hpp"
47	>	#include "hydrodynamics/Ellipsoid.hpp"
48	>	#include "utils/ElementsTable.hpp"
49
50	<	LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info){
51	<	Globals* simParams = info->getSimParams();
52	<	std::map<std::string, HydroProp> hydroPropMap;
53	<	if (simParams->haveHydroPropFile()) {
54	<	hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
55	<	} else {
56	<	//error
50	>	namespace OpenMD {
51	>
52	>	LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info), forceTolerance_(1e-6), maxIterNum_(4) {
53	>	simParams = info->getSimParams();
54	>	veloMunge = new Velocitizer(info);
55	>
56	>	sphericalBoundaryConditions_ = false;
57	>	if (simParams->getUseSphericalBoundaryConditions()) {
58	>	sphericalBoundaryConditions_ = true;
59	>	if (simParams->haveLangevinBufferRadius()) {
60	>	langevinBufferRadius_ = simParams->getLangevinBufferRadius();
61	>	} else {
62	>	sprintf( painCave.errMsg,
63	>	"langevinBufferRadius must be specified "
64	>	"when useSphericalBoundaryConditions is turned on.\n");
65	>	painCave.severity = OPENMD_ERROR;
66	>	painCave.isFatal = 1;
67	>	simError();
68	>	}
69	>
70	>	if (simParams->haveFrozenBufferRadius()) {
71	>	frozenBufferRadius_ = simParams->getFrozenBufferRadius();
72	>	} else {
73	>	sprintf( painCave.errMsg,
74	>	"frozenBufferRadius must be specified "
75	>	"when useSphericalBoundaryConditions is turned on.\n");
76	>	painCave.severity = OPENMD_ERROR;
77	>	painCave.isFatal = 1;
78	>	simError();
79	>	}
80	>
81	>	if (frozenBufferRadius_ < langevinBufferRadius_) {
82	>	sprintf( painCave.errMsg,
83	>	"frozenBufferRadius has been set smaller than the "
84	>	"langevinBufferRadius.  This is probably an error.\n");
85	>	painCave.severity = OPENMD_WARNING;
86	>	painCave.isFatal = 0;
87	>	simError();
88	>	}
89		}
90
91	<	SimInfo::MoleculeIterator i;
92	<	Molecule::IntegrableObjectIterator  j;
91	>	// Build the hydroProp map:
92	>	std::map<std::string, HydroProp*> hydroPropMap;
93	>
94		Molecule* mol;
95		StuntDouble* integrableObject;
96	<	for (mol = info->beginMolecule(i); mol != NULL; mol = info->nextMolecule(i)) {
97	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
98	<	integrableObject = mol->nextIntegrableObject(j)) {
99	<	std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
100	<	if (iter != hydroPropMap.end()) {
101	<	hydroProps_.push_back(iter->second);
102	<	} else {
103	<	//error
104	<	}
105	<
106	<	}
96	>	SimInfo::MoleculeIterator i;
97	>	Molecule::IntegrableObjectIterator  j;
98	>	bool needHydroPropFile = false;
99	>
100	>	for (mol = info->beginMolecule(i); mol != NULL;
101	>	mol = info->nextMolecule(i)) {
102	>	for (integrableObject = mol->beginIntegrableObject(j);
103	>	integrableObject != NULL;
104	>	integrableObject = mol->nextIntegrableObject(j)) {
105	>
106	>	if (integrableObject->isRigidBody()) {
107	>	RigidBody* rb = static_cast<RigidBody*>(integrableObject);
108	>	if (rb->getNumAtoms() > 1) needHydroPropFile = true;
109	>	}
110	>
111	>	}
112		}
113	<	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()) {
113	>
114
115	<	}
115	>	if (needHydroPropFile) {
116	>	if (simParams->haveHydroPropFile()) {
117	>	hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
118	>	} else {
119	>	sprintf( painCave.errMsg,
120	>	"HydroPropFile must be set to a file name if Langevin Dynamics\n"
121	>	"\tis specified for rigidBodies which contain more than one atom\n"
122	>	"\tTo create a HydroPropFile, run the \"Hydro\" program.\n");
123	>	painCave.severity = OPENMD_ERROR;
124	>	painCave.isFatal = 1;
125	>	simError();
126	>	}
127
128	<	const unsigned int BufferSize = 65535;
129	<	char buffer[BufferSize];
130	<	while (ifs.getline(buffer, BufferSize)) {
131	<	StringTokenizer tokenizer(buffer);
132	<	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();
128	>	for (mol = info->beginMolecule(i); mol != NULL;
129	>	mol = info->nextMolecule(i)) {
130	>	for (integrableObject = mol->beginIntegrableObject(j);
131	>	integrableObject != NULL;
132	>	integrableObject = mol->nextIntegrableObject(j)) {
133
134	<	currProp.Ddtt(0,0) = tokenizer.nextTokenAsDouble();
135	<	currProp.Ddtt(0,1) = tokenizer.nextTokenAsDouble();
136	<	currProp.Ddtt(0,2) = tokenizer.nextTokenAsDouble();
137	<	currProp.Ddtt(1,0) = tokenizer.nextTokenAsDouble();
138	<	currProp.Ddtt(1,1) = tokenizer.nextTokenAsDouble();
139	<	currProp.Ddtt(1,2) = tokenizer.nextTokenAsDouble();
140	<	currProp.Ddtt(2,0) = tokenizer.nextTokenAsDouble();
141	<	currProp.Ddtt(2,1) = tokenizer.nextTokenAsDouble();
142	<	currProp.Ddtt(2,2) = tokenizer.nextTokenAsDouble();
134	>	std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
135	>	if (iter != hydroPropMap.end()) {
136	>	hydroProps_.push_back(iter->second);
137	>	} else {
138	>	sprintf( painCave.errMsg,
139	>	"Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
140	>	painCave.severity = OPENMD_ERROR;
141	>	painCave.isFatal = 1;
142	>	simError();
143	>	}
144	>	}
145	>	}
146	>	} else {
147	>
148	>	std::map<std::string, HydroProp*> hydroPropMap;
149	>	for (mol = info->beginMolecule(i); mol != NULL;
150	>	mol = info->nextMolecule(i)) {
151	>	for (integrableObject = mol->beginIntegrableObject(j);
152	>	integrableObject != NULL;
153	>	integrableObject = mol->nextIntegrableObject(j)) {
154	>	Shape* currShape = NULL;
155
156	<	currProp.Ddtr(0,0) = tokenizer.nextTokenAsDouble();
157	<	currProp.Ddtr(0,1) = tokenizer.nextTokenAsDouble();
158	<	currProp.Ddtr(0,2) = tokenizer.nextTokenAsDouble();
159	<	currProp.Ddtr(1,0) = tokenizer.nextTokenAsDouble();
160	<	currProp.Ddtr(1,1) = tokenizer.nextTokenAsDouble();
161	<	currProp.Ddtr(1,2) = tokenizer.nextTokenAsDouble();
162	<	currProp.Ddtr(2,0) = tokenizer.nextTokenAsDouble();
163	<	currProp.Ddtr(2,1) = tokenizer.nextTokenAsDouble();
164	<	currProp.Ddtr(2,2) = tokenizer.nextTokenAsDouble();
156	>	if (integrableObject->isAtom()){
157	>	Atom* atom = static_cast<Atom*>(integrableObject);
158	>	AtomType* atomType = atom->getAtomType();
159	>	if (atomType->isGayBerne()) {
160	>	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
161	>	GenericData* data = dAtomType->getPropertyByName("GayBerne");
162	>	if (data != NULL) {
163	>	GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
164	>
165	>	if (gayBerneData != NULL) {
166	>	GayBerneParam gayBerneParam = gayBerneData->getData();
167	>	currShape = new Ellipsoid(V3Zero,
168	>	gayBerneParam.GB_l / 2.0,
169	>	gayBerneParam.GB_d / 2.0,
170	>	Mat3x3d::identity());
171	>	} else {
172	>	sprintf( painCave.errMsg,
173	>	"Can not cast GenericData to GayBerneParam\n");
174	>	painCave.severity = OPENMD_ERROR;
175	>	painCave.isFatal = 1;
176	>	simError();
177	>	}
178	>	} else {
179	>	sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n");
180	>	painCave.severity = OPENMD_ERROR;
181	>	painCave.isFatal = 1;
182	>	simError();
183	>	}
184	>	} else {
185	>	if (atomType->isLennardJones()){
186	>	GenericData* data = atomType->getPropertyByName("LennardJones");
187	>	if (data != NULL) {
188	>	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
189	>	if (ljData != NULL) {
190	>	LJParam ljParam = ljData->getData();
191	>	currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0);
192	>	} else {
193	>	sprintf( painCave.errMsg,
194	>	"Can not cast GenericData to LJParam\n");
195	>	painCave.severity = OPENMD_ERROR;
196	>	painCave.isFatal = 1;
197	>	simError();
198	>	}
199	>	}
200	>	} else {
201	>	int aNum = etab.GetAtomicNum((atom->getType()).c_str());
202	>	if (aNum != 0) {
203	>	currShape = new Sphere(atom->getPos(), etab.GetVdwRad(aNum));
204	>	} else {
205	>	sprintf( painCave.errMsg,
206	>	"Could not find atom type in default element.txt\n");
207	>	painCave.severity = OPENMD_ERROR;
208	>	painCave.isFatal = 1;
209	>	simError();
210	>	}
211	>	}
212	>	}
213	>	}
214
215	<	currProp.Ddrr(0,0) = tokenizer.nextTokenAsDouble();
216	<	currProp.Ddrr(0,1) = tokenizer.nextTokenAsDouble();
217	<	currProp.Ddrr(0,2) = tokenizer.nextTokenAsDouble();
218	<	currProp.Ddrr(1,0) = tokenizer.nextTokenAsDouble();
219	<	currProp.Ddrr(1,1) = tokenizer.nextTokenAsDouble();
220	<	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();
215	>	if (!simParams->haveTargetTemp()) {
216	>	sprintf(painCave.errMsg, "You can't use LangevinDynamics without a targetTemp!\n");
217	>	painCave.isFatal = 1;
218	>	painCave.severity = OPENMD_ERROR;
219	>	simError();
220	>	}
221
222	<	currProp.Xidtt(0,0) = tokenizer.nextTokenAsDouble();
223	<	currProp.Xidtt(0,1) = tokenizer.nextTokenAsDouble();
224	<	currProp.Xidtt(0,2) = tokenizer.nextTokenAsDouble();
225	<	currProp.Xidtt(1,0) = tokenizer.nextTokenAsDouble();
226	<	currProp.Xidtt(1,1) = tokenizer.nextTokenAsDouble();
227	<	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();
222	>	if (!simParams->haveViscosity()) {
223	>	sprintf(painCave.errMsg, "You can't use LangevinDynamics without a viscosity!\n");
224	>	painCave.isFatal = 1;
225	>	painCave.severity = OPENMD_ERROR;
226	>	simError();
227	>	}
228
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();
229
230	<	currProp.Xidrr(0,0) = tokenizer.nextTokenAsDouble();
231	<	currProp.Xidrr(0,1) = tokenizer.nextTokenAsDouble();
232	<	currProp.Xidrr(0,2) = tokenizer.nextTokenAsDouble();
233	<	currProp.Xidrr(1,0) = tokenizer.nextTokenAsDouble();
234	<	currProp.Xidrr(1,1) = tokenizer.nextTokenAsDouble();
235	<	currProp.Xidrr(1,2) = tokenizer.nextTokenAsDouble();
236	<	currProp.Xidrr(2,0) = tokenizer.nextTokenAsDouble();
237	<	currProp.Xidrr(2,1) = tokenizer.nextTokenAsDouble();
238	<	currProp.Xidrr(2,2) = tokenizer.nextTokenAsDouble();
161	<	props.insert(std::map<std::string, HydroProp>::value_type(atomName, currProp));
230	>	HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp());
231	>	std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
232	>	if (iter != hydroPropMap.end())
233	>	hydroProps_.push_back(iter->second);
234	>	else {
235	>	currHydroProp->complete();
236	>	hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(integrableObject->getType(), currHydroProp));
237	>	hydroProps_.push_back(currHydroProp);
238	>	}
239		}
240	+	}
241		}
242	+	variance_ = 2.0 * PhysicalConstants::kb*simParams->getTargetTemp()/simParams->getDt();
243	+	}
244
245	+	std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) {
246	+	std::map<std::string, HydroProp*> props;
247	+	std::ifstream ifs(filename.c_str());
248	+	if (ifs.is_open()) {
249	+
250	+	}
251	+
252	+	const unsigned int BufferSize = 65535;
253	+	char buffer[BufferSize];
254	+	while (ifs.getline(buffer, BufferSize)) {
255	+	HydroProp* currProp = new HydroProp(buffer);
256	+	props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
257	+	}
258	+
259		return props;
260		}
261	<
262	<	void LDForceManager::postCalculation() {
261	>
262	>	void LDForceManager::postCalculation(){
263		SimInfo::MoleculeIterator i;
264		Molecule::IntegrableObjectIterator  j;
265		Molecule* mol;
266		StuntDouble* integrableObject;
267	<	Vector3d vel;
267	>	RealType mass;
268		Vector3d pos;
269		Vector3d frc;
270		Mat3x3d A;
271		Mat3x3d Atrans;
272		Vector3d Tb;
273		Vector3d ji;
180	–	double mass;
274		unsigned int index = 0;
275	+	bool doLangevinForces;
276	+	bool freezeMolecule;
277	+	int fdf;
278	+
279	+	fdf = 0;
280	+
281		for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
183	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
184	–	integrableObject = mol->nextIntegrableObject(j)) {
282
283	<	vel =integrableObject->getVel();
283	>	doLangevinForces = true;
284	>	freezeMolecule = false;
285	>
286	>	if (sphericalBoundaryConditions_) {
287	>
288	>	Vector3d molPos = mol->getCom();
289	>	RealType molRad = molPos.length();
290	>
291	>	doLangevinForces = false;
292	>
293	>	if (molRad > langevinBufferRadius_) {
294	>	doLangevinForces = true;
295	>	freezeMolecule = false;
296	>	}
297	>	if (molRad > frozenBufferRadius_) {
298	>	doLangevinForces = false;
299	>	freezeMolecule = true;
300	>	}
301	>	}
302	>
303	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
304	>	integrableObject = mol->nextIntegrableObject(j)) {
305	>
306	>	if (freezeMolecule)
307	>	fdf += integrableObject->freeze();
308	>
309	>	if (doLangevinForces) {
310	>	mass = integrableObject->getMass();
311		if (integrableObject->isDirectional()){
188	–	//calculate angular velocity in lab frame
189	–	Mat3x3d I = integrableObject->getI();
190	–	Vector3d angMom = integrableObject->getJ();
191	–	Vector3d omega;
312
313	<	if (integrableObject->isLinear()) {
313	>	// preliminaries for directional objects:
314	>
315	>	A = integrableObject->getA();
316	>	Atrans = A.transpose();
317	>	Vector3d rcrLab = Atrans * hydroProps_[index]->getCOR();
318	>
319	>	//apply random force and torque at center of resistance
320	>
321	>	Vector3d randomForceBody;
322	>	Vector3d randomTorqueBody;
323	>	genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
324	>	Vector3d randomForceLab = Atrans * randomForceBody;
325	>	Vector3d randomTorqueLab = Atrans * randomTorqueBody;
326	>	integrableObject->addFrc(randomForceLab);
327	>	integrableObject->addTrq(randomTorqueLab + cross(rcrLab, randomForceLab ));
328	>
329	>	Mat3x3d I = integrableObject->getI();
330	>	Vector3d omegaBody;
331	>
332	>	// What remains contains velocity explicitly, but the velocity required
333	>	// is at the full step: v(t + h), while we have initially the velocity
334	>	// at the half step: v(t + h/2).  We need to iterate to converge the
335	>	// friction force and friction torque vectors.
336	>
337	>	// this is the velocity at the half-step:
338	>
339	>	Vector3d vel =integrableObject->getVel();
340	>	Vector3d angMom = integrableObject->getJ();
341	>
342	>	//estimate velocity at full-step using everything but friction forces:
343	>
344	>	frc = integrableObject->getFrc();
345	>	Vector3d velStep = vel + (dt2_ /mass * PhysicalConstants::energyConvert) * frc;
346	>
347	>	Tb = integrableObject->lab2Body(integrableObject->getTrq());
348	>	Vector3d angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * Tb;
349	>
350	>	Vector3d omegaLab;
351	>	Vector3d vcdLab;
352	>	Vector3d vcdBody;
353	>	Vector3d frictionForceBody;
354	>	Vector3d frictionForceLab(0.0);
355	>	Vector3d oldFFL;  // used to test for convergence
356	>	Vector3d frictionTorqueBody(0.0);
357	>	Vector3d oldFTB;  // used to test for convergence
358	>	Vector3d frictionTorqueLab;
359	>	RealType fdot;
360	>	RealType tdot;
361	>
362	>	//iteration starts here:
363	>
364	>	for (int k = 0; k < maxIterNum_; k++) {
365	>
366	>	if (integrableObject->isLinear()) {
367		int linearAxis = integrableObject->linearAxis();
368		int l = (linearAxis +1 )%3;
369		int m = (linearAxis +2 )%3;
370	<	omega[l] = angMom[l] /I(l, l);
371	<	omega[m] = angMom[m] /I(m, m);
370	>	omegaBody[l] = angMomStep[l] /I(l, l);
371	>	omegaBody[m] = angMomStep[m] /I(m, m);
372
373	<	} else {
374	<	omega[0] = angMom[0] /I(0, 0);
375	<	omega[1] = angMom[1] /I(1, 1);
376	<	omega[2] = angMom[2] /I(2, 2);
377	<	}
373	>	} else {
374	>	omegaBody[0] = angMomStep[0] /I(0, 0);
375	>	omegaBody[1] = angMomStep[1] /I(1, 1);
376	>	omegaBody[2] = angMomStep[2] /I(2, 2);
377	>	}
378	>
379	>	omegaLab = Atrans * omegaBody;
380	>
381	>	// apply friction force and torque at center of resistance
382	>
383	>	vcdLab = velStep + cross(omegaLab, rcrLab);
384	>	vcdBody = A * vcdLab;
385	>	frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omegaBody);
386	>	oldFFL = frictionForceLab;
387	>	frictionForceLab = Atrans * frictionForceBody;
388	>	oldFTB = frictionTorqueBody;
389	>	frictionTorqueBody = -(hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omegaBody);
390	>	frictionTorqueLab = Atrans * frictionTorqueBody;
391	>
392	>	// re-estimate velocities at full-step using friction forces:
393	>
394	>	velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForceLab);
395	>	angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * (Tb + frictionTorqueBody);
396
397	<	//apply friction force and torque at center of diffusion
398	<	A = integrableObject->getA();
399	<	Atrans = A.transpose();
400	<	Vector3d rcd = Atrans * hydroProps_[index].cod;
401	<	Vector3d vcd = vel + cross(omega, rcd);
402	<	vcd = A* vcd;
403	<	Vector3d frictionForce = -(hydroProps_[index].Xidtt * vcd + hydroProps_[index].Xidrt * omega);
404	<	frictionForce = Atrans*frictionForce;
405	<	integrableObject->addFrc(frictionForce);
406	<	Vector3d frictionTorque = - (hydroProps_[index].Xidtr * vcd + hydroProps_[index].Xidrr * omega);
407	<	frictionTorque = Atrans*frictionTorque;
408	<	integrableObject->addTrq(frictionTorque+ cross(rcd, frictionForce));
409	<
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	<
397	>	// check for convergence (if the vectors have converged, fdot and tdot will both be 1.0):
398	>
399	>	fdot = dot(frictionForceLab, oldFFL) / frictionForceLab.lengthSquare();
400	>	tdot = dot(frictionTorqueBody, oldFTB) / frictionTorqueBody.lengthSquare();
401	>
402	>	if (fabs(1.0 - fdot) <= forceTolerance_ && fabs(1.0 - tdot) <= forceTolerance_)
403	>	break; // iteration ends here
404	>	}
405	>
406	>	integrableObject->addFrc(frictionForceLab);
407	>	integrableObject->addTrq(frictionTorqueLab + cross(rcrLab, frictionForceLab));
408	>
409	>
410		} else {
411	<	//spheric atom
230	<	Vector3d frictionForce = -(hydroProps_[index].Xidtt *vel);
231	<	Vector3d randomForce;
232	<	Vector3d randomTorque;
233	<	genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
411	>	//spherical atom
412
413	<	//randomForce /= OOPSEConstant::energyConvert;
414	<	//randomTorque /= OOPSEConstant::energyConvert;
415	<	integrableObject->addFrc(frictionForce+randomForce);
416	<	}
413	>	Vector3d randomForce;
414	>	Vector3d randomTorque;
415	>	genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
416	>	integrableObject->addFrc(randomForce);
417
418	+	// What remains contains velocity explicitly, but the velocity required
419	+	// is at the full step: v(t + h), while we have initially the velocity
420	+	// at the half step: v(t + h/2).  We need to iterate to converge the
421	+	// friction force vector.
422	+
423	+	// this is the velocity at the half-step:
424	+
425	+	Vector3d vel =integrableObject->getVel();
426	+
427	+	//estimate velocity at full-step using everything but friction forces:
428	+
429	+	frc = integrableObject->getFrc();
430	+	Vector3d velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * frc;
431	+
432	+	Vector3d frictionForce(0.0);
433	+	Vector3d oldFF;  // used to test for convergence
434	+	RealType fdot;
435	+
436	+	//iteration starts here:
437	+
438	+	for (int k = 0; k < maxIterNum_; k++) {
439	+
440	+	oldFF = frictionForce;
441	+	frictionForce = -hydroProps_[index]->getXitt() * velStep;
442	+
443	+	// re-estimate velocities at full-step using friction forces:
444	+
445	+	velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForce);
446	+
447	+	// check for convergence (if the vector has converged, fdot will be 1.0):
448	+
449	+	fdot = dot(frictionForce, oldFF) / frictionForce.lengthSquare();
450	+
451	+	if (fabs(1.0 - fdot) <= forceTolerance_)
452	+	break; // iteration ends here
453	+	}
454	+
455	+	integrableObject->addFrc(frictionForce);
456	+
457	+	}
458	+	}
459	+
460		++index;
461
462		}
463		}
464
465	<	ForceManager::postCalculation();
465	>	info_->setFdf(fdf);
466	>	veloMunge->removeComDrift();
467	>	// Remove angular drift if we are not using periodic boundary conditions.
468	>	if(!simParams->getUsePeriodicBoundaryConditions())
469	>	veloMunge->removeAngularDrift();
470
471	<
248	<
471	>	ForceManager::postCalculation();
472		}
473
474	<	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	<	*/
474	>	void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
475
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);
476
477	<	/*
478	<	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	<	*/
477	>	Vector<RealType, 6> Z;
478	>	Vector<RealType, 6> generalForce;
479
480		Z[0] = randNumGen_.randNorm(0, variance);
481		Z[1] = randNumGen_.randNorm(0, variance);
#	Line 288 | Line 484 | void LDForceManager::genRandomForceAndTorque(Vector3d&
484		Z[4] = randNumGen_.randNorm(0, variance);
485		Z[5] = randNumGen_.randNorm(0, variance);
486
487	<
292	<	generalForce = S*Z;
487	>	generalForce = hydroProps_[index]->getS()*Z;
488
489		force[0] = generalForce[0];
490		force[1] = generalForce[1];
#	Line 298 | Line 493 | void LDForceManager::genRandomForceAndTorque(Vector3d&
493		torque[1] = generalForce[4];
494		torque[2] = generalForce[5];
495
496	<	}
496	>	}
497
498		}

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 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

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