ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing:
trunk/src/integrators/LDForceManager.cpp (file contents), Revision 895 by tim, Mon Mar 13 22:42:40 2006 UTC vs.
branches/development/src/integrators/LDForceManager.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42		#include <fstream>
43	+	#include <iostream>
44		#include "integrators/LDForceManager.hpp"
45		#include "math/CholeskyDecomposition.hpp"
46	<	namespace oopse {
46	>	#include "utils/PhysicalConstants.hpp"
47	>	#include "hydrodynamics/Sphere.hpp"
48	>	#include "hydrodynamics/Ellipsoid.hpp"
49	>	#include "utils/ElementsTable.hpp"
50
51	<	LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info){
52	<	Globals* simParams = info->getSimParams();
53	<	std::map<std::string, HydroProp> hydroPropMap;
54	<	if (simParams->haveHydroPropFile()) {
55	<	hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
56	<	} else {
57	<	//error
51	>	namespace OpenMD {
52	>
53	>	LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info), forceTolerance_(1e-6), maxIterNum_(4) {
54	>	simParams = info->getSimParams();
55	>	veloMunge = new Velocitizer(info);
56	>
57	>	sphericalBoundaryConditions_ = false;
58	>	if (simParams->getUseSphericalBoundaryConditions()) {
59	>	sphericalBoundaryConditions_ = true;
60	>	if (simParams->haveLangevinBufferRadius()) {
61	>	langevinBufferRadius_ = simParams->getLangevinBufferRadius();
62	>	} else {
63	>	sprintf( painCave.errMsg,
64	>	"langevinBufferRadius must be specified "
65	>	"when useSphericalBoundaryConditions is turned on.\n");
66	>	painCave.severity = OPENMD_ERROR;
67	>	painCave.isFatal = 1;
68	>	simError();
69	>	}
70	>
71	>	if (simParams->haveFrozenBufferRadius()) {
72	>	frozenBufferRadius_ = simParams->getFrozenBufferRadius();
73	>	} else {
74	>	sprintf( painCave.errMsg,
75	>	"frozenBufferRadius must be specified "
76	>	"when useSphericalBoundaryConditions is turned on.\n");
77	>	painCave.severity = OPENMD_ERROR;
78	>	painCave.isFatal = 1;
79	>	simError();
80	>	}
81	>
82	>	if (frozenBufferRadius_ < langevinBufferRadius_) {
83	>	sprintf( painCave.errMsg,
84	>	"frozenBufferRadius has been set smaller than the "
85	>	"langevinBufferRadius.  This is probably an error.\n");
86	>	painCave.severity = OPENMD_WARNING;
87	>	painCave.isFatal = 0;
88	>	simError();
89	>	}
90		}
91
92	<	SimInfo::MoleculeIterator i;
93	<	Molecule::IntegrableObjectIterator  j;
92	>	// Build the hydroProp map:
93	>	std::map<std::string, HydroProp*> hydroPropMap;
94	>
95		Molecule* mol;
96		StuntDouble* integrableObject;
97	<	for (mol = info->beginMolecule(i); mol != NULL; mol = info->nextMolecule(i)) {
98	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
99	<	integrableObject = mol->nextIntegrableObject(j)) {
100	<	std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
101	<	if (iter != hydroPropMap.end()) {
102	<	hydroProps_.push_back(iter->second);
103	<	} else {
104	<	//error
105	<	}
106	<
107	<	}
97	>	SimInfo::MoleculeIterator i;
98	>	Molecule::IntegrableObjectIterator  j;
99	>	bool needHydroPropFile = false;
100	>
101	>	for (mol = info->beginMolecule(i); mol != NULL;
102	>	mol = info->nextMolecule(i)) {
103	>	for (integrableObject = mol->beginIntegrableObject(j);
104	>	integrableObject != NULL;
105	>	integrableObject = mol->nextIntegrableObject(j)) {
106	>
107	>	if (integrableObject->isRigidBody()) {
108	>	RigidBody* rb = static_cast<RigidBody*>(integrableObject);
109	>	if (rb->getNumAtoms() > 1) needHydroPropFile = true;
110	>	}
111	>
112	>	}
113		}
114	<	variance_ = 2.0*simParams->getDt();
72	<	}
73	<	std::map<std::string, HydroProp> LDForceManager::parseFrictionFile(const std::string& filename) {
74	<	std::map<std::string, HydroProp> props;
75	<	std::ifstream ifs(filename.c_str());
76	<	if (ifs.is_open()) {
114	>
115
116	<	}
116	>	if (needHydroPropFile) {
117	>	if (simParams->haveHydroPropFile()) {
118	>	hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
119	>	} else {
120	>	sprintf( painCave.errMsg,
121	>	"HydroPropFile must be set to a file name if Langevin Dynamics\n"
122	>	"\tis specified for rigidBodies which contain more than one atom\n"
123	>	"\tTo create a HydroPropFile, run the \"Hydro\" program.\n");
124	>	painCave.severity = OPENMD_ERROR;
125	>	painCave.isFatal = 1;
126	>	simError();
127	>	}
128
129	<	const unsigned int BufferSize = 65535;
130	<	char buffer[BufferSize];
131	<	while (ifs.getline(buffer, BufferSize)) {
132	<	StringTokenizer tokenizer(buffer);
133	<	HydroProp currProp;
85	<	if (tokenizer.countTokens() >= 67) {
86	<	std::string atomName = tokenizer.nextToken();
87	<	currProp.cod[0] = tokenizer.nextTokenAsDouble();
88	<	currProp.cod[1] = tokenizer.nextTokenAsDouble();
89	<	currProp.cod[2] = tokenizer.nextTokenAsDouble();
129	>	for (mol = info->beginMolecule(i); mol != NULL;
130	>	mol = info->nextMolecule(i)) {
131	>	for (integrableObject = mol->beginIntegrableObject(j);
132	>	integrableObject != NULL;
133	>	integrableObject = mol->nextIntegrableObject(j)) {
134
135	<	currProp.Ddtt(0,0) = tokenizer.nextTokenAsDouble();
136	<	currProp.Ddtt(0,1) = tokenizer.nextTokenAsDouble();
137	<	currProp.Ddtt(0,2) = tokenizer.nextTokenAsDouble();
138	<	currProp.Ddtt(1,0) = tokenizer.nextTokenAsDouble();
139	<	currProp.Ddtt(1,1) = tokenizer.nextTokenAsDouble();
140	<	currProp.Ddtt(1,2) = tokenizer.nextTokenAsDouble();
141	<	currProp.Ddtt(2,0) = tokenizer.nextTokenAsDouble();
142	<	currProp.Ddtt(2,1) = tokenizer.nextTokenAsDouble();
143	<	currProp.Ddtt(2,2) = tokenizer.nextTokenAsDouble();
135	>	std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
136	>	if (iter != hydroPropMap.end()) {
137	>	hydroProps_.push_back(iter->second);
138	>	} else {
139	>	sprintf( painCave.errMsg,
140	>	"Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
141	>	painCave.severity = OPENMD_ERROR;
142	>	painCave.isFatal = 1;
143	>	simError();
144	>	}
145	>	}
146	>	}
147	>	} else {
148	>
149	>	std::map<std::string, HydroProp*> hydroPropMap;
150	>	for (mol = info->beginMolecule(i); mol != NULL;
151	>	mol = info->nextMolecule(i)) {
152	>	for (integrableObject = mol->beginIntegrableObject(j);
153	>	integrableObject != NULL;
154	>	integrableObject = mol->nextIntegrableObject(j)) {
155	>	Shape* currShape = NULL;
156
157	<	currProp.Ddtr(0,0) = tokenizer.nextTokenAsDouble();
158	<	currProp.Ddtr(0,1) = tokenizer.nextTokenAsDouble();
159	<	currProp.Ddtr(0,2) = tokenizer.nextTokenAsDouble();
160	<	currProp.Ddtr(1,0) = tokenizer.nextTokenAsDouble();
161	<	currProp.Ddtr(1,1) = tokenizer.nextTokenAsDouble();
162	<	currProp.Ddtr(1,2) = tokenizer.nextTokenAsDouble();
163	<	currProp.Ddtr(2,0) = tokenizer.nextTokenAsDouble();
164	<	currProp.Ddtr(2,1) = tokenizer.nextTokenAsDouble();
165	<	currProp.Ddtr(2,2) = tokenizer.nextTokenAsDouble();
157	>	if (integrableObject->isAtom()){
158	>	Atom* atom = static_cast<Atom*>(integrableObject);
159	>	AtomType* atomType = atom->getAtomType();
160	>	if (atomType->isGayBerne()) {
161	>	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
162	>	GenericData* data = dAtomType->getPropertyByName("GayBerne");
163	>	if (data != NULL) {
164	>	GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
165	>
166	>	if (gayBerneData != NULL) {
167	>	GayBerneParam gayBerneParam = gayBerneData->getData();
168	>	currShape = new Ellipsoid(V3Zero,
169	>	gayBerneParam.GB_l / 2.0,
170	>	gayBerneParam.GB_d / 2.0,
171	>	Mat3x3d::identity());
172	>	} else {
173	>	sprintf( painCave.errMsg,
174	>	"Can not cast GenericData to GayBerneParam\n");
175	>	painCave.severity = OPENMD_ERROR;
176	>	painCave.isFatal = 1;
177	>	simError();
178	>	}
179	>	} else {
180	>	sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n");
181	>	painCave.severity = OPENMD_ERROR;
182	>	painCave.isFatal = 1;
183	>	simError();
184	>	}
185	>	} else {
186	>	if (atomType->isLennardJones()){
187	>	GenericData* data = atomType->getPropertyByName("LennardJones");
188	>	if (data != NULL) {
189	>	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
190	>	if (ljData != NULL) {
191	>	LJParam ljParam = ljData->getData();
192	>	currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0);
193	>	} else {
194	>	sprintf( painCave.errMsg,
195	>	"Can not cast GenericData to LJParam\n");
196	>	painCave.severity = OPENMD_ERROR;
197	>	painCave.isFatal = 1;
198	>	simError();
199	>	}
200	>	}
201	>	} else {
202	>	int aNum = etab.GetAtomicNum((atom->getType()).c_str());
203	>	if (aNum != 0) {
204	>	currShape = new Sphere(atom->getPos(), etab.GetVdwRad(aNum));
205	>	} else {
206	>	sprintf( painCave.errMsg,
207	>	"Could not find atom type in default element.txt\n");
208	>	painCave.severity = OPENMD_ERROR;
209	>	painCave.isFatal = 1;
210	>	simError();
211	>	}
212	>	}
213	>	}
214	>	}
215
216	<	currProp.Ddrr(0,0) = tokenizer.nextTokenAsDouble();
217	<	currProp.Ddrr(0,1) = tokenizer.nextTokenAsDouble();
218	<	currProp.Ddrr(0,2) = tokenizer.nextTokenAsDouble();
219	<	currProp.Ddrr(1,0) = tokenizer.nextTokenAsDouble();
220	<	currProp.Ddrr(1,1) = tokenizer.nextTokenAsDouble();
221	<	currProp.Ddrr(1,2) = tokenizer.nextTokenAsDouble();
117	<	currProp.Ddrr(2,0) = tokenizer.nextTokenAsDouble();
118	<	currProp.Ddrr(2,1) = tokenizer.nextTokenAsDouble();
119	<	currProp.Ddrr(2,2) = tokenizer.nextTokenAsDouble();
216	>	if (!simParams->haveTargetTemp()) {
217	>	sprintf(painCave.errMsg, "You can't use LangevinDynamics without a targetTemp!\n");
218	>	painCave.isFatal = 1;
219	>	painCave.severity = OPENMD_ERROR;
220	>	simError();
221	>	}
222
223	<	currProp.Xidtt(0,0) = tokenizer.nextTokenAsDouble();
224	<	currProp.Xidtt(0,1) = tokenizer.nextTokenAsDouble();
225	<	currProp.Xidtt(0,2) = tokenizer.nextTokenAsDouble();
226	<	currProp.Xidtt(1,0) = tokenizer.nextTokenAsDouble();
227	<	currProp.Xidtt(1,1) = tokenizer.nextTokenAsDouble();
228	<	currProp.Xidtt(1,2) = tokenizer.nextTokenAsDouble();
127	<	currProp.Xidtt(2,0) = tokenizer.nextTokenAsDouble();
128	<	currProp.Xidtt(2,1) = tokenizer.nextTokenAsDouble();
129	<	currProp.Xidtt(2,2) = tokenizer.nextTokenAsDouble();
223	>	if (!simParams->haveViscosity()) {
224	>	sprintf(painCave.errMsg, "You can't use LangevinDynamics without a viscosity!\n");
225	>	painCave.isFatal = 1;
226	>	painCave.severity = OPENMD_ERROR;
227	>	simError();
228	>	}
229
131	–	currProp.Xidrt(0,0) = tokenizer.nextTokenAsDouble();
132	–	currProp.Xidrt(0,1) = tokenizer.nextTokenAsDouble();
133	–	currProp.Xidrt(0,2) = tokenizer.nextTokenAsDouble();
134	–	currProp.Xidrt(1,0) = tokenizer.nextTokenAsDouble();
135	–	currProp.Xidrt(1,1) = tokenizer.nextTokenAsDouble();
136	–	currProp.Xidrt(1,2) = tokenizer.nextTokenAsDouble();
137	–	currProp.Xidrt(2,0) = tokenizer.nextTokenAsDouble();
138	–	currProp.Xidrt(2,1) = tokenizer.nextTokenAsDouble();
139	–	currProp.Xidrt(2,2) = tokenizer.nextTokenAsDouble();
140	–
141	–	currProp.Xidtr(0,0) = tokenizer.nextTokenAsDouble();
142	–	currProp.Xidtr(0,1) = tokenizer.nextTokenAsDouble();
143	–	currProp.Xidtr(0,2) = tokenizer.nextTokenAsDouble();
144	–	currProp.Xidtr(1,0) = tokenizer.nextTokenAsDouble();
145	–	currProp.Xidtr(1,1) = tokenizer.nextTokenAsDouble();
146	–	currProp.Xidtr(1,2) = tokenizer.nextTokenAsDouble();
147	–	currProp.Xidtr(2,0) = tokenizer.nextTokenAsDouble();
148	–	currProp.Xidtr(2,1) = tokenizer.nextTokenAsDouble();
149	–	currProp.Xidtr(2,2) = tokenizer.nextTokenAsDouble();
230
231	<	currProp.Xidrr(0,0) = tokenizer.nextTokenAsDouble();
232	<	currProp.Xidrr(0,1) = tokenizer.nextTokenAsDouble();
233	<	currProp.Xidrr(0,2) = tokenizer.nextTokenAsDouble();
234	<	currProp.Xidrr(1,0) = tokenizer.nextTokenAsDouble();
235	<	currProp.Xidrr(1,1) = tokenizer.nextTokenAsDouble();
236	<	currProp.Xidrr(1,2) = tokenizer.nextTokenAsDouble();
237	<	currProp.Xidrr(2,0) = tokenizer.nextTokenAsDouble();
238	<	currProp.Xidrr(2,1) = tokenizer.nextTokenAsDouble();
239	<	currProp.Xidrr(2,2) = tokenizer.nextTokenAsDouble();
160	<	props.insert(std::map<std::string, HydroProp>::value_type(atomName, currProp));
231	>	HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp());
232	>	std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
233	>	if (iter != hydroPropMap.end())
234	>	hydroProps_.push_back(iter->second);
235	>	else {
236	>	currHydroProp->complete();
237	>	hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(integrableObject->getType(), currHydroProp));
238	>	hydroProps_.push_back(currHydroProp);
239	>	}
240		}
241	+	}
242		}
243	+	variance_ = 2.0 * PhysicalConstants::kb*simParams->getTargetTemp()/simParams->getDt();
244	+	}
245
246	+	std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) {
247	+	std::map<std::string, HydroProp*> props;
248	+	std::ifstream ifs(filename.c_str());
249	+	if (ifs.is_open()) {
250	+
251	+	}
252	+
253	+	const unsigned int BufferSize = 65535;
254	+	char buffer[BufferSize];
255	+	while (ifs.getline(buffer, BufferSize)) {
256	+	HydroProp* currProp = new HydroProp(buffer);
257	+	props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
258	+	}
259	+
260		return props;
261		}
262	<
263	<	void LDForceManager::postCalculation() {
262	>
263	>	void LDForceManager::postCalculation(){
264		SimInfo::MoleculeIterator i;
265		Molecule::IntegrableObjectIterator  j;
266		Molecule* mol;
267		StuntDouble* integrableObject;
268	<	Vector3d vel;
268	>	RealType mass;
269		Vector3d pos;
270		Vector3d frc;
271		Mat3x3d A;
272	+	Mat3x3d Atrans;
273		Vector3d Tb;
274		Vector3d ji;
178	–	double mass;
275		unsigned int index = 0;
276	+	bool doLangevinForces;
277	+	bool freezeMolecule;
278	+	int fdf;
279	+
280	+	fdf = 0;
281	+
282		for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
181	–	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
182	–	integrableObject = mol->nextIntegrableObject(j)) {
283
284	<	vel =integrableObject->getVel();
284	>	doLangevinForces = true;
285	>	freezeMolecule = false;
286	>
287	>	if (sphericalBoundaryConditions_) {
288	>
289	>	Vector3d molPos = mol->getCom();
290	>	RealType molRad = molPos.length();
291	>
292	>	doLangevinForces = false;
293	>
294	>	if (molRad > langevinBufferRadius_) {
295	>	doLangevinForces = true;
296	>	freezeMolecule = false;
297	>	}
298	>	if (molRad > frozenBufferRadius_) {
299	>	doLangevinForces = false;
300	>	freezeMolecule = true;
301	>	}
302	>	}
303	>
304	>	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
305	>	integrableObject = mol->nextIntegrableObject(j)) {
306	>
307	>	if (freezeMolecule)
308	>	fdf += integrableObject->freeze();
309	>
310	>	if (doLangevinForces) {
311	>	mass = integrableObject->getMass();
312		if (integrableObject->isDirectional()){
186	–	//calculate angular velocity in lab frame
187	–	Mat3x3d I = integrableObject->getI();
188	–	Vector3d angMom = integrableObject->getJ();
189	–	Vector3d omega;
313
314	<	if (integrableObject->isLinear()) {
314	>	// preliminaries for directional objects:
315	>
316	>	A = integrableObject->getA();
317	>	Atrans = A.transpose();
318	>	Vector3d rcrLab = Atrans * hydroProps_[index]->getCOR();
319	>
320	>	//apply random force and torque at center of resistance
321	>
322	>	Vector3d randomForceBody;
323	>	Vector3d randomTorqueBody;
324	>	genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
325	>	Vector3d randomForceLab = Atrans * randomForceBody;
326	>	Vector3d randomTorqueLab = Atrans * randomTorqueBody;
327	>	integrableObject->addFrc(randomForceLab);
328	>	integrableObject->addTrq(randomTorqueLab + cross(rcrLab, randomForceLab ));
329	>
330	>	Mat3x3d I = integrableObject->getI();
331	>	Vector3d omegaBody;
332	>
333	>	// What remains contains velocity explicitly, but the velocity required
334	>	// is at the full step: v(t + h), while we have initially the velocity
335	>	// at the half step: v(t + h/2).  We need to iterate to converge the
336	>	// friction force and friction torque vectors.
337	>
338	>	// this is the velocity at the half-step:
339	>
340	>	Vector3d vel =integrableObject->getVel();
341	>	Vector3d angMom = integrableObject->getJ();
342	>
343	>	//estimate velocity at full-step using everything but friction forces:
344	>
345	>	frc = integrableObject->getFrc();
346	>	Vector3d velStep = vel + (dt2_ /mass * PhysicalConstants::energyConvert) * frc;
347	>
348	>	Tb = integrableObject->lab2Body(integrableObject->getTrq());
349	>	Vector3d angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * Tb;
350	>
351	>	Vector3d omegaLab;
352	>	Vector3d vcdLab;
353	>	Vector3d vcdBody;
354	>	Vector3d frictionForceBody;
355	>	Vector3d frictionForceLab(0.0);
356	>	Vector3d oldFFL;  // used to test for convergence
357	>	Vector3d frictionTorqueBody(0.0);
358	>	Vector3d oldFTB;  // used to test for convergence
359	>	Vector3d frictionTorqueLab;
360	>	RealType fdot;
361	>	RealType tdot;
362	>
363	>	//iteration starts here:
364	>
365	>	for (int k = 0; k < maxIterNum_; k++) {
366	>
367	>	if (integrableObject->isLinear()) {
368		int linearAxis = integrableObject->linearAxis();
369		int l = (linearAxis +1 )%3;
370		int m = (linearAxis +2 )%3;
371	<	omega[l] = angMom[l] /I(l, l);
372	<	omega[m] = angMom[m] /I(m, m);
371	>	omegaBody[l] = angMomStep[l] /I(l, l);
372	>	omegaBody[m] = angMomStep[m] /I(m, m);
373
374	<	} else {
375	<	omega[0] = angMom[0] /I(0, 0);
376	<	omega[1] = angMom[1] /I(1, 1);
377	<	omega[2] = angMom[2] /I(2, 2);
378	<	}
374	>	} else {
375	>	omegaBody[0] = angMomStep[0] /I(0, 0);
376	>	omegaBody[1] = angMomStep[1] /I(1, 1);
377	>	omegaBody[2] = angMomStep[2] /I(2, 2);
378	>	}
379	>
380	>	omegaLab = Atrans * omegaBody;
381	>
382	>	// apply friction force and torque at center of resistance
383	>
384	>	vcdLab = velStep + cross(omegaLab, rcrLab);
385	>	vcdBody = A * vcdLab;
386	>	frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omegaBody);
387	>	oldFFL = frictionForceLab;
388	>	frictionForceLab = Atrans * frictionForceBody;
389	>	oldFTB = frictionTorqueBody;
390	>	frictionTorqueBody = -(hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omegaBody);
391	>	frictionTorqueLab = Atrans * frictionTorqueBody;
392	>
393	>	// re-estimate velocities at full-step using friction forces:
394	>
395	>	velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForceLab);
396	>	angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * (Tb + frictionTorqueBody);
397
398	<	//apply friction force and torque at center of diffusion
399	<	A = integrableObject->getA();
400	<	Vector3d rcd = A.transpose() * hydroProps_[index].cod;
401	<	Vector3d vcd = vel + cross(omega, rcd);
402	<	Vector3d frictionForce = -(hydroProps_[index].Xidtt * vcd + hydroProps_[index].Xidrt * omega);
403	<	integrableObject->addFrc(frictionForce);
404	<	Vector3d frictionTorque = - (hydroProps_[index].Xidtr * vcd + hydroProps_[index].Xidrr * omega);
405	<	integrableObject->addTrq(frictionTorque);
406	<
407	<	//apply random force and torque at center of diffustion
408	<	Vector3d randomForce;
409	<	Vector3d randomTorque;
410	<	genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
217	<	integrableObject->addFrc(randomForce);
218	<	integrableObject->addTrq(randomTorque + cross(rcd, randomForce ));
219	<
398	>	// check for convergence (if the vectors have converged, fdot and tdot will both be 1.0):
399	>
400	>	fdot = dot(frictionForceLab, oldFFL) / frictionForceLab.lengthSquare();
401	>	tdot = dot(frictionTorqueBody, oldFTB) / frictionTorqueBody.lengthSquare();
402	>
403	>	if (fabs(1.0 - fdot) <= forceTolerance_ && fabs(1.0 - tdot) <= forceTolerance_)
404	>	break; // iteration ends here
405	>	}
406	>
407	>	integrableObject->addFrc(frictionForceLab);
408	>	integrableObject->addTrq(frictionTorqueLab + cross(rcrLab, frictionForceLab));
409	>
410	>
411		} else {
412	<	//spheric atom
222	<	Vector3d frictionForce = -(hydroProps_[index].Xidtt *vel);
223	<	Vector3d randomForce;
224	<	Vector3d randomTorque;
225	<	genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
226	<	integrableObject->addFrc(frictionForce+randomForce);
227	<	}
412	>	//spherical atom
413
414	+	Vector3d randomForce;
415	+	Vector3d randomTorque;
416	+	genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
417	+	integrableObject->addFrc(randomForce);
418	+
419	+	// What remains contains velocity explicitly, but the velocity required
420	+	// is at the full step: v(t + h), while we have initially the velocity
421	+	// at the half step: v(t + h/2).  We need to iterate to converge the
422	+	// friction force vector.
423	+
424	+	// this is the velocity at the half-step:
425	+
426	+	Vector3d vel =integrableObject->getVel();
427	+
428	+	//estimate velocity at full-step using everything but friction forces:
429	+
430	+	frc = integrableObject->getFrc();
431	+	Vector3d velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * frc;
432	+
433	+	Vector3d frictionForce(0.0);
434	+	Vector3d oldFF;  // used to test for convergence
435	+	RealType fdot;
436	+
437	+	//iteration starts here:
438	+
439	+	for (int k = 0; k < maxIterNum_; k++) {
440	+
441	+	oldFF = frictionForce;
442	+	frictionForce = -hydroProps_[index]->getXitt() * velStep;
443	+
444	+	// re-estimate velocities at full-step using friction forces:
445	+
446	+	velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForce);
447	+
448	+	// check for convergence (if the vector has converged, fdot will be 1.0):
449	+
450	+	fdot = dot(frictionForce, oldFF) / frictionForce.lengthSquare();
451	+
452	+	if (fabs(1.0 - fdot) <= forceTolerance_)
453	+	break; // iteration ends here
454	+	}
455	+
456	+	integrableObject->addFrc(frictionForce);
457	+
458	+	}
459	+	}
460	+
461		++index;
462
463		}
464		}
465
466	<	ForceManager::postCalculation();
466	>	info_->setFdf(fdf);
467	>	veloMunge->removeComDrift();
468	>	// Remove angular drift if we are not using periodic boundary conditions.
469	>	if(!simParams->getUsePeriodicBoundaryConditions())
470	>	veloMunge->removeAngularDrift();
471
472	+	ForceManager::postCalculation();
473	+	}
474
475	+	void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {
476
238	–	}
477
478	<	void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, double variance) {
479	<	SquareMatrix<double, 6> Dd;
480	<	SquareMatrix<double, 6> S;
243	<	Vector<double, 6> Z;
244	<	Vector<double, 6> generalForce;
245	<	Dd.setSubMatrix(0, 0, hydroProps_[index].Ddtt);
246	<	Dd.setSubMatrix(0, 3, hydroProps_[index].Ddtr.transpose());
247	<	Dd.setSubMatrix(3, 0, hydroProps_[index].Ddtr);
248	<	Dd.setSubMatrix(3, 3, hydroProps_[index].Ddrr);
249	<	CholeskyDecomposition(Dd, S);
250	<
478	>	Vector<RealType, 6> Z;
479	>	Vector<RealType, 6> generalForce;
480	>
481		Z[0] = randNumGen_.randNorm(0, variance);
482		Z[1] = randNumGen_.randNorm(0, variance);
483		Z[2] = randNumGen_.randNorm(0, variance);
484		Z[3] = randNumGen_.randNorm(0, variance);
485		Z[4] = randNumGen_.randNorm(0, variance);
486		Z[5] = randNumGen_.randNorm(0, variance);
487	<
488	<	generalForce = S*Z;
487	>
488	>	generalForce = hydroProps_[index]->getS()*Z;
489	>
490		force[0] = generalForce[0];
491		force[1] = generalForce[1];
492		force[2] = generalForce[2];
#	Line 263 | Line 494 | void LDForceManager::genRandomForceAndTorque(Vector3d&
494		torque[1] = generalForce[4];
495		torque[2] = generalForce[5];
496
497	<	}
497	>	}
498
499		}

Comparing:
trunk/src/integrators/LDForceManager.cpp (property svn:keywords), Revision 895 by tim, Mon Mar 13 22:42:40 2006 UTC vs.
branches/development/src/integrators/LDForceManager.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines