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

Comparing:
trunk/src/integrators/LDForceManager.cpp (file contents), Revision 1216 by xsun, Wed Jan 23 21:22:50 2008 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	<	#include "utils/OOPSEConstant.hpp"
46	>	#include "utils/PhysicalConstants.hpp"
47		#include "hydrodynamics/Sphere.hpp"
48		#include "hydrodynamics/Ellipsoid.hpp"
49		#include "utils/ElementsTable.hpp"
50
51	<	namespace oopse {
51	>	namespace OpenMD {
52
53	<	LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info){
53	>	LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info), forceTolerance_(1e-6), maxIterNum_(4) {
54		simParams = info->getSimParams();
55		veloMunge = new Velocitizer(info);
56
#	Line 62 | Line 63 | namespace oopse {
63		sprintf( painCave.errMsg,
64		"langevinBufferRadius must be specified "
65		"when useSphericalBoundaryConditions is turned on.\n");
66	<	painCave.severity = OOPSE_ERROR;
66	>	painCave.severity = OPENMD_ERROR;
67		painCave.isFatal = 1;
68		simError();
69		}
#	Line 73 | Line 74 | namespace oopse {
74		sprintf( painCave.errMsg,
75		"frozenBufferRadius must be specified "
76		"when useSphericalBoundaryConditions is turned on.\n");
77	<	painCave.severity = OOPSE_ERROR;
77	>	painCave.severity = OPENMD_ERROR;
78		painCave.isFatal = 1;
79		simError();
80		}
#	Line 82 | Line 83 | namespace oopse {
83		sprintf( painCave.errMsg,
84		"frozenBufferRadius has been set smaller than the "
85		"langevinBufferRadius.  This is probably an error.\n");
86	<	painCave.severity = OOPSE_WARNING;
86	>	painCave.severity = OPENMD_WARNING;
87		painCave.isFatal = 0;
88		simError();
89		}
#	Line 117 | Line 118 | namespace oopse {
118		hydroPropMap = parseFrictionFile(simParams->getHydroPropFile());
119		} else {
120		sprintf( painCave.errMsg,
121	<	"HydroPropFile must be set to a file name if Langevin\n"
122	<	"\tDynamics is specified for rigidBodies which contain more\n"
123	<	"\tthan one atom.  To create a HydroPropFile, run \"Hydro\".\n");
124	<	painCave.severity = OOPSE_ERROR;
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		}
#	Line 137 | Line 138 | namespace oopse {
138		} else {
139		sprintf( painCave.errMsg,
140		"Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
141	<	painCave.severity = OOPSE_ERROR;
141	>	painCave.severity = OPENMD_ERROR;
142		painCave.isFatal = 1;
143		simError();
144		}
#	Line 171 | Line 172 | namespace oopse {
172		} else {
173		sprintf( painCave.errMsg,
174		"Can not cast GenericData to GayBerneParam\n");
175	<	painCave.severity = OOPSE_ERROR;
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 = OOPSE_ERROR;
181	>	painCave.severity = OPENMD_ERROR;
182		painCave.isFatal = 1;
183		simError();
184		}
#	Line 192 | Line 193 | namespace oopse {
193		} else {
194		sprintf( painCave.errMsg,
195		"Can not cast GenericData to LJParam\n");
196	<	painCave.severity = OOPSE_ERROR;
196	>	painCave.severity = OPENMD_ERROR;
197		painCave.isFatal = 1;
198		simError();
199		}
200		}
201		} else {
202	<	int obanum = etab.GetAtomicNum((atom->getType()).c_str());
203	<	if (obanum != 0) {
204	<	currShape = new Sphere(atom->getPos(), etab.GetVdwRad(obanum));
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 = OOPSE_ERROR;
208	>	painCave.severity = OPENMD_ERROR;
209		painCave.isFatal = 1;
210		simError();
211		}
212		}
213		}
214		}
215	+
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	+	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	+
230	+
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())
#	Line 223 | Line 240 | namespace oopse {
240		}
241		}
242		}
243	<	variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
243	>	variance_ = 2.0 * PhysicalConstants::kb*simParams->getTargetTemp()/simParams->getDt();
244		}
245
246		std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) {
#	Line 243 | Line 260 | namespace oopse {
260		return props;
261		}
262
263	<	void LDForceManager::postCalculation(bool needStress){
263	>	void LDForceManager::postCalculation(){
264		SimInfo::MoleculeIterator i;
265		Molecule::IntegrableObjectIterator  j;
266		Molecule* mol;
267		StuntDouble* integrableObject;
268		RealType mass;
252	–	Vector3d vel;
269		Vector3d pos;
270		Vector3d frc;
271		Mat3x3d A;
#	Line 261 | Line 277 | namespace oopse {
277		bool freezeMolecule;
278		int fdf;
279
264	–
265	–
280		fdf = 0;
281
282		for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
#	Line 294 | Line 308 | namespace oopse {
308		fdf += integrableObject->freeze();
309
310		if (doLangevinForces) {
297	–	vel =integrableObject->getVel();
311		mass = integrableObject->getMass();
312		if (integrableObject->isDirectional()){
300	–	Mat3x3d I = integrableObject->getI();
301	–	Vector3d angMom = integrableObject->getJ();
302	–	A = integrableObject->getA();
303	–	Atrans = A.transpose();
313
314	<	Vector3d omegaBody;
306	<
307	<	if (integrableObject->isLinear()) {
308	<	int linearAxis = integrableObject->linearAxis();
309	<	int l = (linearAxis +1 )%3;
310	<	int m = (linearAxis +2 )%3;
311	<	omegaBody[l] = angMom[l] /I(l, l);
312	<	omegaBody[m] = angMom[m] /I(m, m);
313	<
314	<	} else {
315	<	omegaBody[0] = angMom[0] /I(0, 0);
316	<	omegaBody[1] = angMom[1] /I(1, 1);
317	<	omegaBody[2] = angMom[2] /I(2, 2);
318	<	}
314	>	// preliminaries for directional objects:
315
316	<	Vector3d omegaLab = Atrans * omegaBody;
317	<
322	<	// apply friction force and torque at center of resistance
323	<
316	>	A = integrableObject->getA();
317	>	Atrans = A.transpose();
318		Vector3d rcrLab = Atrans * hydroProps_[index]->getCOR();
325	–	Vector3d vcdLab = vel + cross(omegaLab, rcrLab);
326	–
327	–	Vector3d vcdBody = A * vcdLab;
328	–	Vector3d frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omegaBody);
319
330	–	Vector3d frictionForceLab = Atrans * frictionForceBody;
331	–	integrableObject->addFrc(frictionForceLab);
332	–	Vector3d frictionTorqueBody = -(hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omegaBody);
333	–	Vector3d frictionTorqueLab = Atrans * frictionTorqueBody;
334	–	integrableObject->addTrq(frictionTorqueLab + cross(rcrLab, frictionForceLab));
335	–
320		//apply random force and torque at center of resistance
321	+
322		Vector3d randomForceBody;
323		Vector3d randomTorqueBody;
324		genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
#	Line 341 | Line 326 | namespace oopse {
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	+	omegaBody[l] = angMomStep[l] /I(l, l);
372	+	omegaBody[m] = angMomStep[m] /I(m, m);
373	+
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	+	// 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		//spherical atom
413	<	Vector3d frictionForce = -(hydroProps_[index]->getXitt() * vel);
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	<	integrableObject->addFrc(frictionForce+randomForce);
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
#	Line 364 | Line 469 | namespace oopse {
469		if(!simParams->getUsePeriodicBoundaryConditions())
470		veloMunge->removeAngularDrift();
471
472	<	ForceManager::postCalculation(needStress);
472	>	ForceManager::postCalculation();
473		}
474
475		void LDForceManager::genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance) {

Comparing:
trunk/src/integrators/LDForceManager.cpp (property svn:keywords), Revision 1216 by xsun, Wed Jan 23 21:22:50 2008 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
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