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

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trunk/src/integrators/LDForceManager.cpp (file contents), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/integrators/LDForceManager.cpp (file contents), Revision 1769 by gezelter, Mon Jul 9 14:15:52 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"
46	>	#include "utils/PhysicalConstants.hpp"
47		#include "hydrodynamics/Sphere.hpp"
48		#include "hydrodynamics/Ellipsoid.hpp"
49	<	#include "openbabel/mol.hpp"
49	>	#include "utils/ElementsTable.hpp"
50	>	#include "types/LennardJonesAdapter.hpp"
51	>	#include "types/GayBerneAdapter.hpp"
52
53	<	using namespace OpenBabel;
50	<	namespace oopse {
53	>	namespace OpenMD {
54
55	<	LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info){
56	<	Globals* simParams = info->getSimParams();
57	<
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;
#	Line 61 | Line 65 | namespace oopse {
65		sprintf( painCave.errMsg,
66		"langevinBufferRadius must be specified "
67		"when useSphericalBoundaryConditions is turned on.\n");
68	<	painCave.severity = OOPSE_ERROR;
68	>	painCave.severity = OPENMD_ERROR;
69		painCave.isFatal = 1;
70		simError();
71		}
#	Line 72 | Line 76 | namespace oopse {
76		sprintf( painCave.errMsg,
77		"frozenBufferRadius must be specified "
78		"when useSphericalBoundaryConditions is turned on.\n");
79	<	painCave.severity = OOPSE_ERROR;
79	>	painCave.severity = OPENMD_ERROR;
80		painCave.isFatal = 1;
81		simError();
82		}
#	Line 81 | Line 85 | namespace oopse {
85		sprintf( painCave.errMsg,
86		"frozenBufferRadius has been set smaller than the "
87		"langevinBufferRadius.  This is probably an error.\n");
88	<	painCave.severity = OOPSE_WARNING;
88	>	painCave.severity = OPENMD_WARNING;
89		painCave.isFatal = 0;
90		simError();
91		}
92		}
93
94		// Build the hydroProp map:
95	<	std::map<std::string, HydroProp> hydroPropMap;
95	>	std::map<std::string, HydroProp*> hydroPropMap;
96
97		Molecule* mol;
98	<	StuntDouble* integrableObject;
98	>	StuntDouble* sd;
99		SimInfo::MoleculeIterator i;
100		Molecule::IntegrableObjectIterator  j;
101		bool needHydroPropFile = false;
102
103		for (mol = info->beginMolecule(i); mol != NULL;
104		mol = info->nextMolecule(i)) {
105	<	for (integrableObject = mol->beginIntegrableObject(j);
106	<	integrableObject != NULL;
107	<	integrableObject = mol->nextIntegrableObject(j)) {
105	>
106	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
107	>	sd = mol->nextIntegrableObject(j)) {
108
109	<	if (integrableObject->isRigidBody()) {
110	<	RigidBody* rb = static_cast<RigidBody*>(integrableObject);
109	>	if (sd->isRigidBody()) {
110	>	RigidBody* rb = static_cast<RigidBody*>(sd);
111		if (rb->getNumAtoms() > 1) needHydroPropFile = true;
112		}
113
#	Line 116 | Line 120 | namespace oopse {
120		hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
121		} else {
122		sprintf( painCave.errMsg,
123	<	"HydroPropFile must be set to a file name if Langevin\n"
124	<	"\tDynamics is specified for rigidBodies which contain more\n"
125	<	"\tthan one atom.  To create a HydroPropFile, run \"Hydro\".\n");
126	<	painCave.severity = OOPSE_ERROR;
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	<	std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
131	<	if (iter != hydroPropMap.end()) {
132	<	hydroProps_.push_back(iter->second);
133	<	} else {
134	<	sprintf( painCave.errMsg,
135	<	"Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
136	<	painCave.severity = OOPSE_ERROR;
137	<	painCave.isFatal = 1;
138	<	simError();
130	>
131	>	for (mol = info->beginMolecule(i); mol != NULL;
132	>	mol = info->nextMolecule(i)) {
133	>
134	>	for (sd = mol->beginIntegrableObject(j);  sd != NULL;
135	>	sd = mol->nextIntegrableObject(j)) {
136	>
137	>	std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(sd->getType());
138	>	if (iter != hydroPropMap.end()) {
139	>	hydroProps_.push_back(iter->second);
140	>	} else {
141	>	sprintf( painCave.errMsg,
142	>	"Can not find resistance tensor for atom [%s]\n", sd->getType().c_str());
143	>	painCave.severity = OPENMD_ERROR;
144	>	painCave.isFatal = 1;
145	>	simError();
146	>	}
147	>	}
148		}
149		} else {
150	<
151	<	std::map<std::string, HydroProp> hydroPropMap;
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)) {
154	>
155	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
156	>	sd = mol->nextIntegrableObject(j)) {
157	>
158		Shape* currShape = NULL;
159	<	if (integrableObject->isDirectionalAtom()) {
160	<	DirectionalAtom* dAtom = static_cast<DirectionalAtom*>(integrableObject);
161	<	AtomType* atomType = dAtom->getAtomType();
148	<	if (atomType->isGayBerne()) {
149	<	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
150	<
151	<	GenericData* data = dAtomType->getPropertyByName("GayBerne");
152	<	if (data != NULL) {
153	<	GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
154	<
155	<	if (gayBerneData != NULL) {
156	<	GayBerneParam gayBerneParam = gayBerneData->getData();
157	<	currShape = new Ellipsoid(V3Zero,
158	<	gayBerneParam.GB_sigma/2.0,
159	<	gayBerneParam.GB_l2b_ratio*gayBerneParam.GB_sigma/2.0,
160	<	Mat3x3d::identity());
161	<	} else {
162	<	sprintf( painCave.errMsg,
163	<	"Can not cast GenericData to GayBerneParam\n");
164	<	painCave.severity = OOPSE_ERROR;
165	<	painCave.isFatal = 1;
166	<	simError();
167	<	}
168	<	} else {
169	<	sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n");
170	<	painCave.severity = OOPSE_ERROR;
171	<	painCave.isFatal = 1;
172	<	simError();
173	<	}
174	<	}
175	<	} else {
176	<	Atom* atom = static_cast<Atom*>(integrableObject);
159	>
160	>	if (sd->isAtom()){
161	>	Atom* atom = static_cast<Atom*>(sd);
162		AtomType* atomType = atom->getAtomType();
163	<	if (atomType->isLennardJones()){
164	<	GenericData* data = atomType->getPropertyByName("LennardJones");
165	<	if (data != NULL) {
166	<	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
167	<
168	<	if (ljData != NULL) {
169	<	LJParam ljParam = ljData->getData();
170	<	currShape = new Sphere(atom->getPos(), ljParam.sigma/2.0);
163	>	GayBerneAdapter gba = GayBerneAdapter(atomType);
164	>	if (gba.isGayBerne()) {
165	>	currShape = new Ellipsoid(V3Zero, gba.getL() / 2.0,
166	>	gba.getD() / 2.0,
167	>	Mat3x3d::identity());
168	>	} else {
169	>	LennardJonesAdapter lja = LennardJonesAdapter(atomType);
170	>	if (lja.isLennardJones()){
171	>	currShape = new Sphere(atom->getPos(), lja.getSigma()/2.0);
172	>	} else {
173	>	int aNum = etab.GetAtomicNum((atom->getType()).c_str());
174	>	if (aNum != 0) {
175	>	currShape = new Sphere(atom->getPos(), etab.GetVdwRad(aNum));
176		} else {
177		sprintf( painCave.errMsg,
178	<	"Can not cast GenericData to LJParam\n");
179	<	painCave.severity = OOPSE_ERROR;
178	>	"Could not find atom type in default element.txt\n");
179	>	painCave.severity = OPENMD_ERROR;
180		painCave.isFatal = 1;
181		simError();
182	<	}
182	>	}
183		}
194	–	} else {
195	–	int obanum = etab.GetAtomicNum((atom->getType()).c_str());
196	–	if (obanum != 0) {
197	–	currShape = new Sphere(atom->getPos(), etab.GetVdwRad(obanum));
198	–	} else {
199	–	sprintf( painCave.errMsg,
200	–	"Could not find atom type in default element.txt\n");
201	–	painCave.severity = OOPSE_ERROR;
202	–	painCave.isFatal = 1;
203	–	simError();
204	–	}
184		}
185		}
186	<	HydroProps currHydroProp = currShape->getHydroProps(simParams->getViscosity(),simParams->getTargetTemp());
187	<	std::map<std::string, HydroProp>::iterator iter = hydroPropMap.find(integrableObject->getType());
186	>
187	>	if (!simParams->haveTargetTemp()) {
188	>	sprintf(painCave.errMsg, "You can't use LangevinDynamics without a targetTemp!\n");
189	>	painCave.isFatal = 1;
190	>	painCave.severity = OPENMD_ERROR;
191	>	simError();
192	>	}
193	>
194	>	if (!simParams->haveViscosity()) {
195	>	sprintf(painCave.errMsg, "You can't use LangevinDynamics without a viscosity!\n");
196	>	painCave.isFatal = 1;
197	>	painCave.severity = OPENMD_ERROR;
198	>	simError();
199	>	}
200	>
201	>
202	>	HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp());
203	>	std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(sd->getType());
204		if (iter != hydroPropMap.end())
205		hydroProps_.push_back(iter->second);
206		else {
207	<	HydroProp myProp;
208	<	myProp.cor = V3Zero;
209	<	for (int i1 = 0; i1 < 3; i1++) {
215	<	for (int j1 = 0; j1 < 3; j1++) {
216	<	myProp.Xirtt(i1,j1) = currHydroProp.Xi(i1,j1);
217	<	myProp.Xirrt(i1,j1) = currHydroProp.Xi(i1,j1+3);
218	<	myProp.Xirtr(i1,j1) = currHydroProp.Xi(i1+3,j1);
219	<	myProp.Xirrr(i1,j1) = currHydroProp.Xi(i1+3,j1+3);
220	<	}
221	<	}
222	<	CholeskyDecomposition(currHydroProp.Xi, myProp.S);
223	<	hydroPropMap.insert(std::map<std::string, HydroProp>::value_type(integrableObject->getType(), myProp));
224	<	hydroProps_.push_back(myProp);
207	>	currHydroProp->complete();
208	>	hydroPropMap.insert(std::map<std::string, HydroProp*>::value_type(sd->getType(), currHydroProp));
209	>	hydroProps_.push_back(currHydroProp);
210		}
211		}
212		}
213		}
214	<	variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
215	<	}
231	<
232	<
214	>	variance_ = 2.0 * PhysicalConstants::kb*simParams->getTargetTemp()/simParams->getDt();
215	>	}
216
217	<
218	<
236	<	std::map<std::string, HydroProp> LDForceManager::parseFrictionFile(const std::string& filename) {
237	<	std::map<std::string, HydroProp> props;
217	>	std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) {
218	>	std::map<std::string, HydroProp*> props;
219		std::ifstream ifs(filename.c_str());
220		if (ifs.is_open()) {
221
#	Line 243 | Line 224 | namespace oopse {
224		const unsigned int BufferSize = 65535;
225		char buffer[BufferSize];
226		while (ifs.getline(buffer, BufferSize)) {
227	<	StringTokenizer tokenizer(buffer);
228	<	HydroProp currProp;
248	<	if (tokenizer.countTokens() >= 40) {
249	<	std::string atomName = tokenizer.nextToken();
250	<	currProp.cor[0] = tokenizer.nextTokenAsDouble();
251	<	currProp.cor[1] = tokenizer.nextTokenAsDouble();
252	<	currProp.cor[2] = tokenizer.nextTokenAsDouble();
253	<
254	<	currProp.Xirtt(0,0) = tokenizer.nextTokenAsDouble();
255	<	currProp.Xirtt(0,1) = tokenizer.nextTokenAsDouble();
256	<	currProp.Xirtt(0,2) = tokenizer.nextTokenAsDouble();
257	<	currProp.Xirtt(1,0) = tokenizer.nextTokenAsDouble();
258	<	currProp.Xirtt(1,1) = tokenizer.nextTokenAsDouble();
259	<	currProp.Xirtt(1,2) = tokenizer.nextTokenAsDouble();
260	<	currProp.Xirtt(2,0) = tokenizer.nextTokenAsDouble();
261	<	currProp.Xirtt(2,1) = tokenizer.nextTokenAsDouble();
262	<	currProp.Xirtt(2,2) = tokenizer.nextTokenAsDouble();
263	<
264	<	currProp.Xirrt(0,0) = tokenizer.nextTokenAsDouble();
265	<	currProp.Xirrt(0,1) = tokenizer.nextTokenAsDouble();
266	<	currProp.Xirrt(0,2) = tokenizer.nextTokenAsDouble();
267	<	currProp.Xirrt(1,0) = tokenizer.nextTokenAsDouble();
268	<	currProp.Xirrt(1,1) = tokenizer.nextTokenAsDouble();
269	<	currProp.Xirrt(1,2) = tokenizer.nextTokenAsDouble();
270	<	currProp.Xirrt(2,0) = tokenizer.nextTokenAsDouble();
271	<	currProp.Xirrt(2,1) = tokenizer.nextTokenAsDouble();
272	<	currProp.Xirrt(2,2) = tokenizer.nextTokenAsDouble();
273	<
274	<	currProp.Xirtr(0,0) = tokenizer.nextTokenAsDouble();
275	<	currProp.Xirtr(0,1) = tokenizer.nextTokenAsDouble();
276	<	currProp.Xirtr(0,2) = tokenizer.nextTokenAsDouble();
277	<	currProp.Xirtr(1,0) = tokenizer.nextTokenAsDouble();
278	<	currProp.Xirtr(1,1) = tokenizer.nextTokenAsDouble();
279	<	currProp.Xirtr(1,2) = tokenizer.nextTokenAsDouble();
280	<	currProp.Xirtr(2,0) = tokenizer.nextTokenAsDouble();
281	<	currProp.Xirtr(2,1) = tokenizer.nextTokenAsDouble();
282	<	currProp.Xirtr(2,2) = tokenizer.nextTokenAsDouble();
283	<
284	<	currProp.Xirrr(0,0) = tokenizer.nextTokenAsDouble();
285	<	currProp.Xirrr(0,1) = tokenizer.nextTokenAsDouble();
286	<	currProp.Xirrr(0,2) = tokenizer.nextTokenAsDouble();
287	<	currProp.Xirrr(1,0) = tokenizer.nextTokenAsDouble();
288	<	currProp.Xirrr(1,1) = tokenizer.nextTokenAsDouble();
289	<	currProp.Xirrr(1,2) = tokenizer.nextTokenAsDouble();
290	<	currProp.Xirrr(2,0) = tokenizer.nextTokenAsDouble();
291	<	currProp.Xirrr(2,1) = tokenizer.nextTokenAsDouble();
292	<	currProp.Xirrr(2,2) = tokenizer.nextTokenAsDouble();
293	<
294	<	SquareMatrix<RealType, 6> Xir;
295	<	Xir.setSubMatrix(0, 0, currProp.Xirtt);
296	<	Xir.setSubMatrix(0, 3, currProp.Xirrt);
297	<	Xir.setSubMatrix(3, 0, currProp.Xirtr);
298	<	Xir.setSubMatrix(3, 3, currProp.Xirrr);
299	<	CholeskyDecomposition(Xir, currProp.S);
300	<
301	<	props.insert(std::map<std::string, HydroProp>::value_type(atomName, currProp));
302	<	}
227	>	HydroProp* currProp = new HydroProp(buffer);
228	>	props.insert(std::map<std::string, HydroProp*>::value_type(currProp->getName(), currProp));
229		}
230	<
230	>
231		return props;
232		}
233	<
234	<	void LDForceManager::postCalculation() {
233	>
234	>	void LDForceManager::postCalculation(){
235		SimInfo::MoleculeIterator i;
236		Molecule::IntegrableObjectIterator  j;
237		Molecule* mol;
238	<	StuntDouble* integrableObject;
239	<	Vector3d vel;
238	>	StuntDouble* sd;
239	>	RealType mass;
240		Vector3d pos;
241		Vector3d frc;
242		Mat3x3d A;
243		Mat3x3d Atrans;
244		Vector3d Tb;
245		Vector3d ji;
320	–	RealType mass;
246		unsigned int index = 0;
247		bool doLangevinForces;
248		bool freezeMolecule;
249		int fdf;
250	<
250	>
251		fdf = 0;
252	+
253		for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
254	<
254	>
255	>	doLangevinForces = true;
256	>	freezeMolecule = false;
257	>
258		if (sphericalBoundaryConditions_) {
259
260		Vector3d molPos = mol->getCom();
261		RealType molRad = molPos.length();
262	<
262	>
263		doLangevinForces = false;
335	–	freezeMolecule = false;
264
265		if (molRad > langevinBufferRadius_) {
266		doLangevinForces = true;
#	Line 344 | Line 272 | namespace oopse {
272		}
273		}
274
275	<	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
276	<	integrableObject = mol->nextIntegrableObject(j)) {
275	>	for (sd = mol->beginIntegrableObject(j); sd != NULL;
276	>	sd = mol->nextIntegrableObject(j)) {
277
278		if (freezeMolecule)
279	<	fdf += integrableObject->freeze();
279	>	fdf += sd->freeze();
280
281	<	if (doLangevinForces) {
282	<	vel =integrableObject->getVel();
283	<	if (integrableObject->isDirectional()){
284	<	//calculate angular velocity in lab frame
285	<	Mat3x3d I = integrableObject->getI();
286	<	Vector3d angMom = integrableObject->getJ();
287	<	Vector3d omega;
360	<
361	<	if (integrableObject->isLinear()) {
362	<	int linearAxis = integrableObject->linearAxis();
363	<	int l = (linearAxis +1 )%3;
364	<	int m = (linearAxis +2 )%3;
365	<	omega[l] = angMom[l] /I(l, l);
366	<	omega[m] = angMom[m] /I(m, m);
367	<
368	<	} else {
369	<	omega[0] = angMom[0] /I(0, 0);
370	<	omega[1] = angMom[1] /I(1, 1);
371	<	omega[2] = angMom[2] /I(2, 2);
372	<	}
373	<
374	<	//apply friction force and torque at center of resistance
375	<	A = integrableObject->getA();
281	>	if (doLangevinForces) {
282	>	mass = sd->getMass();
283	>	if (sd->isDirectional()){
284	>
285	>	// preliminaries for directional objects:
286	>
287	>	A = sd->getA();
288		Atrans = A.transpose();
289	<	Vector3d rcr = Atrans * hydroProps_[index].cor;
290	<	Vector3d vcdLab = vel + cross(omega, rcr);
379	<	Vector3d vcdBody = A* vcdLab;
380	<	Vector3d frictionForceBody = -(hydroProps_[index].Xirtt * vcdBody + hydroProps_[index].Xirrt * omega);
381	<	Vector3d frictionForceLab = Atrans*frictionForceBody;
382	<	integrableObject->addFrc(frictionForceLab);
383	<	Vector3d frictionTorqueBody = - (hydroProps_[index].Xirtr * vcdBody + hydroProps_[index].Xirrr * omega);
384	<	Vector3d frictionTorqueLab = Atrans*frictionTorqueBody;
385	<	integrableObject->addTrq(frictionTorqueLab+ cross(rcr, frictionForceLab));
386	<
289	>	Vector3d rcrLab = Atrans * hydroProps_[index]->getCOR();
290	>
291		//apply random force and torque at center of resistance
292	+
293		Vector3d randomForceBody;
294		Vector3d randomTorqueBody;
295		genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
296	<	Vector3d randomForceLab = Atrans*randomForceBody;
297	<	Vector3d randomTorqueLab = Atrans* randomTorqueBody;
298	<	integrableObject->addFrc(randomForceLab);
299	<	integrableObject->addTrq(randomTorqueLab + cross(rcr, randomForceLab ));
296	>	Vector3d randomForceLab = Atrans * randomForceBody;
297	>	Vector3d randomTorqueLab = Atrans * randomTorqueBody;
298	>	sd->addFrc(randomForceLab);
299	>	sd->addTrq(randomTorqueLab + cross(rcrLab, randomForceLab ));
300	>
301	>	Mat3x3d I = sd->getI();
302	>	Vector3d omegaBody;
303	>
304	>	// What remains contains velocity explicitly, but the velocity required
305	>	// is at the full step: v(t + h), while we have initially the velocity
306	>	// at the half step: v(t + h/2).  We need to iterate to converge the
307	>	// friction force and friction torque vectors.
308	>
309	>	// this is the velocity at the half-step:
310
311	+	Vector3d vel =sd->getVel();
312	+	Vector3d angMom = sd->getJ();
313	+
314	+	//estimate velocity at full-step using everything but friction forces:
315	+
316	+	frc = sd->getFrc();
317	+	Vector3d velStep = vel + (dt2_ /mass * PhysicalConstants::energyConvert) * frc;
318	+
319	+	Tb = sd->lab2Body(sd->getTrq());
320	+	Vector3d angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * Tb;
321	+
322	+	Vector3d omegaLab;
323	+	Vector3d vcdLab;
324	+	Vector3d vcdBody;
325	+	Vector3d frictionForceBody;
326	+	Vector3d frictionForceLab(0.0);
327	+	Vector3d oldFFL;  // used to test for convergence
328	+	Vector3d frictionTorqueBody(0.0);
329	+	Vector3d oldFTB;  // used to test for convergence
330	+	Vector3d frictionTorqueLab;
331	+	RealType fdot;
332	+	RealType tdot;
333	+
334	+	//iteration starts here:
335	+
336	+	for (int k = 0; k < maxIterNum_; k++) {
337	+
338	+	if (sd->isLinear()) {
339	+	int linearAxis = sd->linearAxis();
340	+	int l = (linearAxis +1 )%3;
341	+	int m = (linearAxis +2 )%3;
342	+	omegaBody[l] = angMomStep[l] /I(l, l);
343	+	omegaBody[m] = angMomStep[m] /I(m, m);
344	+
345	+	} else {
346	+	omegaBody[0] = angMomStep[0] /I(0, 0);
347	+	omegaBody[1] = angMomStep[1] /I(1, 1);
348	+	omegaBody[2] = angMomStep[2] /I(2, 2);
349	+	}
350	+
351	+	omegaLab = Atrans * omegaBody;
352	+
353	+	// apply friction force and torque at center of resistance
354	+
355	+	vcdLab = velStep + cross(omegaLab, rcrLab);
356	+	vcdBody = A * vcdLab;
357	+	frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omegaBody);
358	+	oldFFL = frictionForceLab;
359	+	frictionForceLab = Atrans * frictionForceBody;
360	+	oldFTB = frictionTorqueBody;
361	+	frictionTorqueBody = -(hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omegaBody);
362	+	frictionTorqueLab = Atrans * frictionTorqueBody;
363	+
364	+	// re-estimate velocities at full-step using friction forces:
365	+
366	+	velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForceLab);
367	+	angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * (Tb + frictionTorqueBody);
368	+
369	+	// check for convergence (if the vectors have converged, fdot and tdot will both be 1.0):
370	+
371	+	fdot = dot(frictionForceLab, oldFFL) / frictionForceLab.lengthSquare();
372	+	tdot = dot(frictionTorqueBody, oldFTB) / frictionTorqueBody.lengthSquare();
373	+
374	+	if (fabs(1.0 - fdot) <= forceTolerance_ && fabs(1.0 - tdot) <= forceTolerance_)
375	+	break; // iteration ends here
376	+	}
377	+
378	+	sd->addFrc(frictionForceLab);
379	+	sd->addTrq(frictionTorqueLab + cross(rcrLab, frictionForceLab));
380	+
381	+
382		} else {
383		//spherical atom
384	<	Vector3d frictionForce = -(hydroProps_[index].Xirtt *vel);
384	>
385		Vector3d randomForce;
386		Vector3d randomTorque;
387		genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
388	+	sd->addFrc(randomForce);
389	+
390	+	// What remains contains velocity explicitly, but the velocity required
391	+	// is at the full step: v(t + h), while we have initially the velocity
392	+	// at the half step: v(t + h/2).  We need to iterate to converge the
393	+	// friction force vector.
394	+
395	+	// this is the velocity at the half-step:
396
397	<	integrableObject->addFrc(frictionForce+randomForce);
397	>	Vector3d vel =sd->getVel();
398	>
399	>	//estimate velocity at full-step using everything but friction forces:
400	>
401	>	frc = sd->getFrc();
402	>	Vector3d velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * frc;
403	>
404	>	Vector3d frictionForce(0.0);
405	>	Vector3d oldFF;  // used to test for convergence
406	>	RealType fdot;
407	>
408	>	//iteration starts here:
409	>
410	>	for (int k = 0; k < maxIterNum_; k++) {
411	>
412	>	oldFF = frictionForce;
413	>	frictionForce = -hydroProps_[index]->getXitt() * velStep;
414	>
415	>	// re-estimate velocities at full-step using friction forces:
416	>
417	>	velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForce);
418	>
419	>	// check for convergence (if the vector has converged, fdot will be 1.0):
420	>
421	>	fdot = dot(frictionForce, oldFF) / frictionForce.lengthSquare();
422	>
423	>	if (fabs(1.0 - fdot) <= forceTolerance_)
424	>	break; // iteration ends here
425	>	}
426	>
427	>	sd->addFrc(frictionForce);
428	>
429		}
430		}
431
#	Line 408 | Line 433 | namespace oopse {
433
434		}
435		}
436	+
437		info_->setFdf(fdf);
438	<
438	>	veloMunge->removeComDrift();
439	>	// Remove angular drift if we are not using periodic boundary conditions.
440	>	if(!simParams->getUsePeriodicBoundaryConditions())
441	>	veloMunge->removeAngularDrift();
442	>
443		ForceManager::postCalculation();
444		}
445
#	Line 418 | Line 448 | void LDForceManager::genRandomForceAndTorque(Vector3d&
448
449		Vector<RealType, 6> Z;
450		Vector<RealType, 6> generalForce;
421	–
451
452		Z[0] = randNumGen_.randNorm(0, variance);
453		Z[1] = randNumGen_.randNorm(0, variance);
#	Line 427 | Line 456 | void LDForceManager::genRandomForceAndTorque(Vector3d&
456		Z[4] = randNumGen_.randNorm(0, variance);
457		Z[5] = randNumGen_.randNorm(0, variance);
458
459	<
431	<	generalForce = hydroProps_[index].S*Z;
459	>	generalForce = hydroProps_[index]->getS()*Z;
460
461		force[0] = generalForce[0];
462		force[1] = generalForce[1];
#	Line 437 | Line 465 | void LDForceManager::genRandomForceAndTorque(Vector3d&
465		torque[1] = generalForce[4];
466		torque[2] = generalForce[5];
467
468	<	}
468	>	}
469
470		}

Comparing:
trunk/src/integrators/LDForceManager.cpp (property svn:keywords), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/integrators/LDForceManager.cpp (property svn:keywords), Revision 1769 by gezelter, Mon Jul 9 14:15:52 2012 UTC

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