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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 1710 by gezelter, Fri May 18 21:44:02 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 "utils/ElementsTable.hpp"
50	+	#include "types/LennardJonesAdapter.hpp"
51	+	#include "types/GayBerneAdapter.hpp"
52
53	<	namespace oopse {
53	>	namespace OpenMD {
54
55	<	LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info){
55	>	LDForceManager::LDForceManager(SimInfo* info) : ForceManager(info), forceTolerance_(1e-6), maxIterNum_(4) {
56		simParams = info->getSimParams();
57		veloMunge = new Velocitizer(info);
58
#	Line 62 | 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 73 | 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 82 | 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		}
#	Line 117 | 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		}
#	Line 137 | Line 140 | namespace oopse {
140		} else {
141		sprintf( painCave.errMsg,
142		"Can not find resistance tensor for atom [%s]\n", integrableObject->getType().c_str());
143	<	painCave.severity = OOPSE_ERROR;
143	>	painCave.severity = OPENMD_ERROR;
144		painCave.isFatal = 1;
145		simError();
146		}
#	Line 156 | Line 159 | namespace oopse {
159		if (integrableObject->isAtom()){
160		Atom* atom = static_cast<Atom*>(integrableObject);
161		AtomType* atomType = atom->getAtomType();
162	<	if (atomType->isGayBerne()) {
163	<	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
164	<	GenericData* data = dAtomType->getPropertyByName("GayBerne");
165	<	if (data != NULL) {
166	<	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 = OOPSE_ERROR;
175	<	painCave.isFatal = 1;
176	<	simError();
177	<	}
178	<	} else {
179	<	sprintf( painCave.errMsg, "Can not find Parameters for GayBerne\n");
180	<	painCave.severity = OOPSE_ERROR;
181	<	painCave.isFatal = 1;
182	<	simError();
183	<	}
162	>	GayBerneAdapter gba = GayBerneAdapter(atomType);
163	>	if (gba.isGayBerne()) {
164	>	currShape = new Ellipsoid(V3Zero, gba.getL() / 2.0,
165	>	gba.getD() / 2.0,
166	>	Mat3x3d::identity());
167		} else {
168	<	if (atomType->isLennardJones()){
169	<	GenericData* data = atomType->getPropertyByName("LennardJones");
170	<	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 = OOPSE_ERROR;
196	<	painCave.isFatal = 1;
197	<	simError();
198	<	}
199	<	}
168	>	LennardJonesAdapter lja = LennardJonesAdapter(atomType);
169	>	if (lja.isLennardJones()){
170	>	currShape = new Sphere(atom->getPos(), lja.getSigma()/2.0);
171		} else {
172	<	int obanum = etab.GetAtomicNum((atom->getType()).c_str());
173	<	if (obanum != 0) {
174	<	currShape = new Sphere(atom->getPos(), etab.GetVdwRad(obanum));
172	>	int aNum = etab.GetAtomicNum((atom->getType()).c_str());
173	>	if (aNum != 0) {
174	>	currShape = new Sphere(atom->getPos(), etab.GetVdwRad(aNum));
175		} else {
176		sprintf( painCave.errMsg,
177		"Could not find atom type in default element.txt\n");
178	<	painCave.severity = OOPSE_ERROR;
178	>	painCave.severity = OPENMD_ERROR;
179		painCave.isFatal = 1;
180		simError();
181		}
182		}
183		}
184		}
185	+
186	+	if (!simParams->haveTargetTemp()) {
187	+	sprintf(painCave.errMsg, "You can't use LangevinDynamics without a targetTemp!\n");
188	+	painCave.isFatal = 1;
189	+	painCave.severity = OPENMD_ERROR;
190	+	simError();
191	+	}
192	+
193	+	if (!simParams->haveViscosity()) {
194	+	sprintf(painCave.errMsg, "You can't use LangevinDynamics without a viscosity!\n");
195	+	painCave.isFatal = 1;
196	+	painCave.severity = OPENMD_ERROR;
197	+	simError();
198	+	}
199	+
200	+
201		HydroProp* currHydroProp = currShape->getHydroProp(simParams->getViscosity(),simParams->getTargetTemp());
202		std::map<std::string, HydroProp*>::iterator iter = hydroPropMap.find(integrableObject->getType());
203		if (iter != hydroPropMap.end())
#	Line 223 | Line 210 | namespace oopse {
210		}
211		}
212		}
213	<	variance_ = 2.0 * OOPSEConstant::kb*simParams->getTargetTemp()/simParams->getDt();
213	>	variance_ = 2.0 * PhysicalConstants::kb*simParams->getTargetTemp()/simParams->getDt();
214		}
215
216		std::map<std::string, HydroProp*> LDForceManager::parseFrictionFile(const std::string& filename) {
#	Line 243 | Line 230 | namespace oopse {
230		return props;
231		}
232
233	<	void LDForceManager::postCalculation(bool needStress){
233	>	void LDForceManager::postCalculation(){
234		SimInfo::MoleculeIterator i;
235		Molecule::IntegrableObjectIterator  j;
236		Molecule* mol;
237		StuntDouble* integrableObject;
238		RealType mass;
252	–	Vector3d vel;
239		Vector3d pos;
240		Vector3d frc;
241		Mat3x3d A;
#	Line 261 | Line 247 | namespace oopse {
247		bool freezeMolecule;
248		int fdf;
249
264	–
265	–
250		fdf = 0;
251
252		for (mol = info_->beginMolecule(i); mol != NULL; mol = info_->nextMolecule(i)) {
#	Line 294 | Line 278 | namespace oopse {
278		fdf += integrableObject->freeze();
279
280		if (doLangevinForces) {
297	–	vel =integrableObject->getVel();
281		mass = integrableObject->getMass();
282		if (integrableObject->isDirectional()){
283	<	Mat3x3d I = integrableObject->getI();
284	<	Vector3d angMom = integrableObject->getJ();
283	>
284	>	// preliminaries for directional objects:
285	>
286		A = integrableObject->getA();
287		Atrans = A.transpose();
288	+	Vector3d rcrLab = Atrans * hydroProps_[index]->getCOR();
289
305	–	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	–	}
319	–
320	–	Vector3d omegaLab = Atrans * omegaBody;
321	–
322	–	// apply friction force and torque at center of resistance
323	–
324	–	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);
329	–
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	–
290		//apply random force and torque at center of resistance
291	+
292		Vector3d randomForceBody;
293		Vector3d randomTorqueBody;
294		genRandomForceAndTorque(randomForceBody, randomTorqueBody, index, variance_);
#	Line 341 | Line 296 | namespace oopse {
296		Vector3d randomTorqueLab = Atrans * randomTorqueBody;
297		integrableObject->addFrc(randomForceLab);
298		integrableObject->addTrq(randomTorqueLab + cross(rcrLab, randomForceLab ));
299	+
300	+	Mat3x3d I = integrableObject->getI();
301	+	Vector3d omegaBody;
302	+
303	+	// What remains contains velocity explicitly, but the velocity required
304	+	// is at the full step: v(t + h), while we have initially the velocity
305	+	// at the half step: v(t + h/2).  We need to iterate to converge the
306	+	// friction force and friction torque vectors.
307	+
308	+	// this is the velocity at the half-step:
309
310	+	Vector3d vel =integrableObject->getVel();
311	+	Vector3d angMom = integrableObject->getJ();
312	+
313	+	//estimate velocity at full-step using everything but friction forces:
314	+
315	+	frc = integrableObject->getFrc();
316	+	Vector3d velStep = vel + (dt2_ /mass * PhysicalConstants::energyConvert) * frc;
317	+
318	+	Tb = integrableObject->lab2Body(integrableObject->getTrq());
319	+	Vector3d angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * Tb;
320	+
321	+	Vector3d omegaLab;
322	+	Vector3d vcdLab;
323	+	Vector3d vcdBody;
324	+	Vector3d frictionForceBody;
325	+	Vector3d frictionForceLab(0.0);
326	+	Vector3d oldFFL;  // used to test for convergence
327	+	Vector3d frictionTorqueBody(0.0);
328	+	Vector3d oldFTB;  // used to test for convergence
329	+	Vector3d frictionTorqueLab;
330	+	RealType fdot;
331	+	RealType tdot;
332	+
333	+	//iteration starts here:
334	+
335	+	for (int k = 0; k < maxIterNum_; k++) {
336	+
337	+	if (integrableObject->isLinear()) {
338	+	int linearAxis = integrableObject->linearAxis();
339	+	int l = (linearAxis +1 )%3;
340	+	int m = (linearAxis +2 )%3;
341	+	omegaBody[l] = angMomStep[l] /I(l, l);
342	+	omegaBody[m] = angMomStep[m] /I(m, m);
343	+
344	+	} else {
345	+	omegaBody[0] = angMomStep[0] /I(0, 0);
346	+	omegaBody[1] = angMomStep[1] /I(1, 1);
347	+	omegaBody[2] = angMomStep[2] /I(2, 2);
348	+	}
349	+
350	+	omegaLab = Atrans * omegaBody;
351	+
352	+	// apply friction force and torque at center of resistance
353	+
354	+	vcdLab = velStep + cross(omegaLab, rcrLab);
355	+	vcdBody = A * vcdLab;
356	+	frictionForceBody = -(hydroProps_[index]->getXitt() * vcdBody + hydroProps_[index]->getXirt() * omegaBody);
357	+	oldFFL = frictionForceLab;
358	+	frictionForceLab = Atrans * frictionForceBody;
359	+	oldFTB = frictionTorqueBody;
360	+	frictionTorqueBody = -(hydroProps_[index]->getXitr() * vcdBody + hydroProps_[index]->getXirr() * omegaBody);
361	+	frictionTorqueLab = Atrans * frictionTorqueBody;
362	+
363	+	// re-estimate velocities at full-step using friction forces:
364	+
365	+	velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForceLab);
366	+	angMomStep = angMom + (dt2_ * PhysicalConstants::energyConvert) * (Tb + frictionTorqueBody);
367	+
368	+	// check for convergence (if the vectors have converged, fdot and tdot will both be 1.0):
369	+
370	+	fdot = dot(frictionForceLab, oldFFL) / frictionForceLab.lengthSquare();
371	+	tdot = dot(frictionTorqueBody, oldFTB) / frictionTorqueBody.lengthSquare();
372	+
373	+	if (fabs(1.0 - fdot) <= forceTolerance_ && fabs(1.0 - tdot) <= forceTolerance_)
374	+	break; // iteration ends here
375	+	}
376	+
377	+	integrableObject->addFrc(frictionForceLab);
378	+	integrableObject->addTrq(frictionTorqueLab + cross(rcrLab, frictionForceLab));
379	+
380	+
381		} else {
382		//spherical atom
383	<	Vector3d frictionForce = -(hydroProps_[index]->getXitt() * vel);
383	>
384		Vector3d randomForce;
385		Vector3d randomTorque;
386		genRandomForceAndTorque(randomForce, randomTorque, index, variance_);
387	+	integrableObject->addFrc(randomForce);
388	+
389	+	// What remains contains velocity explicitly, but the velocity required
390	+	// is at the full step: v(t + h), while we have initially the velocity
391	+	// at the half step: v(t + h/2).  We need to iterate to converge the
392	+	// friction force vector.
393	+
394	+	// this is the velocity at the half-step:
395
396	<	integrableObject->addFrc(frictionForce+randomForce);
396	>	Vector3d vel =integrableObject->getVel();
397	>
398	>	//estimate velocity at full-step using everything but friction forces:
399	>
400	>	frc = integrableObject->getFrc();
401	>	Vector3d velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * frc;
402	>
403	>	Vector3d frictionForce(0.0);
404	>	Vector3d oldFF;  // used to test for convergence
405	>	RealType fdot;
406	>
407	>	//iteration starts here:
408	>
409	>	for (int k = 0; k < maxIterNum_; k++) {
410	>
411	>	oldFF = frictionForce;
412	>	frictionForce = -hydroProps_[index]->getXitt() * velStep;
413	>
414	>	// re-estimate velocities at full-step using friction forces:
415	>
416	>	velStep = vel + (dt2_ / mass * PhysicalConstants::energyConvert) * (frc + frictionForce);
417	>
418	>	// check for convergence (if the vector has converged, fdot will be 1.0):
419	>
420	>	fdot = dot(frictionForce, oldFF) / frictionForce.lengthSquare();
421	>
422	>	if (fabs(1.0 - fdot) <= forceTolerance_)
423	>	break; // iteration ends here
424	>	}
425	>
426	>	integrableObject->addFrc(frictionForce);
427	>
428		}
429		}
430
#	Line 364 | Line 439 | namespace oopse {
439		if(!simParams->getUsePeriodicBoundaryConditions())
440		veloMunge->removeAngularDrift();
441
442	<	ForceManager::postCalculation(needStress);
442	>	ForceManager::postCalculation();
443		}
444
445		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 1710 by gezelter, Fri May 18 21:44:02 2012 UTC

#	Line 0 | Line 1
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