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root/OpenMD/branches/development/src/brains/ForceManager.cpp

Comparing:
trunk/src/brains/ForceManager.cpp (file contents), Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
branches/development/src/brains/ForceManager.cpp (file contents), Revision 1469 by gezelter, Mon Jul 19 14:07:59 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
42		/**
#	Line 50 | Line 50
50		#include "brains/ForceManager.hpp"
51		#include "primitives/Molecule.hpp"
52		#include "UseTheForce/doForces_interface.h"
53	<	#define __C
53	>	#define __OPENMD_C
54		#include "UseTheForce/DarkSide/fInteractionMap.h"
55		#include "utils/simError.h"
56	+	#include "primitives/Bond.hpp"
57		#include "primitives/Bend.hpp"
58	<	#include "primitives/Bend.hpp"
59	<	namespace oopse {
58	>	#include "primitives/Torsion.hpp"
59	>	#include "primitives/Inversion.hpp"
60
61	<	/*
62	<	struct BendOrderStruct {
63	<	Bend* bend;
64	<	BendDataSet dataSet;
65	<	};
66	<	struct TorsionOrderStruct {
66	<	Torsion* torsion;
67	<	TorsionDataSet dataSet;
68	<	};
69	<
70	<	bool  BendSortFunctor(const BendOrderStruct& b1, const BendOrderStruct& b2) {
71	<	return b1.dataSet.deltaV < b2.dataSet.deltaV;
61	>	namespace OpenMD {
62	>
63	>	ForceManager::ForceManager(SimInfo * info) : info_(info),
64	>	NBforcesInitialized_(false) {
65	>	std::cerr << __PRETTY_FUNCTION__ << "\n";
66	>	lj_ = new LJ(info_->getForceField());
67		}
68	<
69	<	bool  TorsionSortFunctor(const TorsionOrderStruct& t1, const TorsionOrderStruct& t2) {
70	<	return t1.dataSet.deltaV < t2.dataSet.deltaV;
71	<	}
77	<	*/
78	<	void ForceManager::calcForces(bool needPotential, bool needStress) {
79	<
68	>
69	>	void ForceManager::calcForces() {
70	>
71	>	std::cerr << __PRETTY_FUNCTION__ << "\n";
72		if (!info_->isFortranInitialized()) {
73		info_->update();
74		}
75	+
76	+	if (!NBforcesInitialized_) {
77	+	lj_->initialize();
78	+	}
79
80		preCalculation();
81
82		calcShortRangeInteraction();
83
84	<	calcLongRangeInteraction(needPotential, needStress);
84	>	calcLongRangeInteraction();
85
86		postCalculation();
91	–
92	–	/*
93	–	std::vector<BendOrderStruct> bendOrderStruct;
94	–	for(std::map<Bend*, BendDataSet>::iterator i = bendDataSets.begin(); i != bendDataSets.end(); ++i) {
95	–	BendOrderStruct tmp;
96	–	tmp.bend= const_cast<Bend*>(i->first);
97	–	tmp.dataSet = i->second;
98	–	bendOrderStruct.push_back(tmp);
99	–	}
100	–
101	–	std::vector<TorsionOrderStruct> torsionOrderStruct;
102	–	for(std::map<Torsion*, TorsionDataSet>::iterator j = torsionDataSets.begin(); j != torsionDataSets.end(); ++j) {
103	–	TorsionOrderStruct tmp;
104	–	tmp.torsion = const_cast<Torsion*>(j->first);
105	–	tmp.dataSet = j->second;
106	–	torsionOrderStruct.push_back(tmp);
107	–	}
87
109	–	std::sort(bendOrderStruct.begin(), bendOrderStruct.end(), std::ptr_fun(BendSortFunctor));
110	–	std::sort(torsionOrderStruct.begin(), torsionOrderStruct.end(), std::ptr_fun(TorsionSortFunctor));
111	–	std::cout << "bend" << std::endl;
112	–	for (std::vector<BendOrderStruct>::iterator k = bendOrderStruct.begin(); k != bendOrderStruct.end(); ++k) {
113	–	Bend* bend = k->bend;
114	–	std::cout << "atom1=" <<bend->getAtomA()->getGlobalIndex() << ",atom2 = "<< bend->getAtomB()->getGlobalIndex() << ",atom3="<<bend->getAtomC()->getGlobalIndex() << " ";
115	–	std::cout << "deltaV=" << k->dataSet.deltaV << ",p_theta=" << k->dataSet.prev.angle <<",p_pot=" << k->dataSet.prev.potential<< ",c_theta=" << k->dataSet.curr.angle << ", c_pot = " << k->dataSet.curr.potential <<std::endl;
116	–	}
117	–	std::cout << "torsio" << std::endl;
118	–	for (std::vector<TorsionOrderStruct>::iterator l = torsionOrderStruct.begin(); l != torsionOrderStruct.end(); ++l) {
119	–	Torsion* torsion = l->torsion;
120	–	std::cout << "atom1=" <<torsion->getAtomA()->getGlobalIndex() << ",atom2 = "<< torsion->getAtomB()->getGlobalIndex() << ",atom3="<<torsion->getAtomC()->getGlobalIndex() << ",atom4="<<torsion->getAtomD()->getGlobalIndex()<< " ";
121	–	std::cout << "deltaV=" << l->dataSet.deltaV << ",p_theta=" << l->dataSet.prev.angle <<",p_pot=" << l->dataSet.prev.potential<< ",c_theta=" << l->dataSet.curr.angle << ", c_pot = " << l->dataSet.curr.potential <<std::endl;
122	–	}
123	–	*/
88		}
89	<
89	>
90		void ForceManager::preCalculation() {
91		SimInfo::MoleculeIterator mi;
92		Molecule* mol;
#	Line 133 | Line 97 | namespace oopse {
97
98		// forces are zeroed here, before any are accumulated.
99		// NOTE: do not rezero the forces in Fortran.
100	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
100	>
101	>	for (mol = info_->beginMolecule(mi); mol != NULL;
102	>	mol = info_->nextMolecule(mi)) {
103		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
104		atom->zeroForcesAndTorques();
105		}
106	<
106	>
107		//change the positions of atoms which belong to the rigidbodies
108	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
108	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
109	>	rb = mol->nextRigidBody(rbIter)) {
110		rb->zeroForcesAndTorques();
111		}
112	+
113		}
114
115	+	// Zero out the stress tensor
116	+	tau *= 0.0;
117	+
118		}
119	<
119	>
120		void ForceManager::calcShortRangeInteraction() {
121		Molecule* mol;
122		RigidBody* rb;
123		Bond* bond;
124		Bend* bend;
125		Torsion* torsion;
126	+	Inversion* inversion;
127		SimInfo::MoleculeIterator mi;
128		Molecule::RigidBodyIterator rbIter;
129		Molecule::BondIterator bondIter;;
130		Molecule::BendIterator  bendIter;
131		Molecule::TorsionIterator  torsionIter;
132	<	double bondPotential = 0.0;
133	<	double bendPotential = 0.0;
134	<	double torsionPotential = 0.0;
132	>	Molecule::InversionIterator  inversionIter;
133	>	RealType bondPotential = 0.0;
134	>	RealType bendPotential = 0.0;
135	>	RealType torsionPotential = 0.0;
136	>	RealType inversionPotential = 0.0;
137
138		//calculate short range interactions
139	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
139	>	for (mol = info_->beginMolecule(mi); mol != NULL;
140	>	mol = info_->nextMolecule(mi)) {
141
142		//change the positions of atoms which belong to the rigidbodies
143	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
144	<	rb->updateAtoms();
143	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
144	>	rb = mol->nextRigidBody(rbIter)) {
145	>	rb->updateAtoms();
146		}
147
148	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
148	>	for (bond = mol->beginBond(bondIter); bond != NULL;
149	>	bond = mol->nextBond(bondIter)) {
150		bond->calcForce();
151		bondPotential += bond->getPotential();
152		}
153
154	<
155	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
156	<
157	<	double angle;
158	<	bend->calcForce(angle);
159	<	double currBendPot = bend->getPotential();
160	<	bendPotential += bend->getPotential();
161	<	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
162	<	if (i == bendDataSets.end()) {
163	<	BendDataSet dataSet;
164	<	dataSet.prev.angle = dataSet.curr.angle = angle;
165	<	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
166	<	dataSet.deltaV = 0.0;
167	<	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
168	<	}else {
169	<	i->second.prev.angle = i->second.curr.angle;
170	<	i->second.prev.potential = i->second.curr.potential;
171	<	i->second.curr.angle = angle;
172	<	i->second.curr.potential = currBendPot;
173	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
174	<	}
175	<	}
176	<
200	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
201	<	double angle;
202	<	torsion->calcForce(angle);
203	<	double currTorsionPot = torsion->getPotential();
204	<	torsionPotential += torsion->getPotential();
205	<	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
206	<	if (i == torsionDataSets.end()) {
207	<	TorsionDataSet dataSet;
208	<	dataSet.prev.angle = dataSet.curr.angle = angle;
209	<	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
210	<	dataSet.deltaV = 0.0;
211	<	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
212	<	}else {
213	<	i->second.prev.angle = i->second.curr.angle;
214	<	i->second.prev.potential = i->second.curr.potential;
215	<	i->second.curr.angle = angle;
216	<	i->second.curr.potential = currTorsionPot;
217	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
218	<	}
154	>	for (bend = mol->beginBend(bendIter); bend != NULL;
155	>	bend = mol->nextBend(bendIter)) {
156	>
157	>	RealType angle;
158	>	bend->calcForce(angle);
159	>	RealType currBendPot = bend->getPotential();
160	>
161	>	bendPotential += bend->getPotential();
162	>	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
163	>	if (i == bendDataSets.end()) {
164	>	BendDataSet dataSet;
165	>	dataSet.prev.angle = dataSet.curr.angle = angle;
166	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
167	>	dataSet.deltaV = 0.0;
168	>	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
169	>	}else {
170	>	i->second.prev.angle = i->second.curr.angle;
171	>	i->second.prev.potential = i->second.curr.potential;
172	>	i->second.curr.angle = angle;
173	>	i->second.curr.potential = currBendPot;
174	>	i->second.deltaV =  fabs(i->second.curr.potential -
175	>	i->second.prev.potential);
176	>	}
177		}
178	+
179	+	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
180	+	torsion = mol->nextTorsion(torsionIter)) {
181	+	RealType angle;
182	+	torsion->calcForce(angle);
183	+	RealType currTorsionPot = torsion->getPotential();
184	+	torsionPotential += torsion->getPotential();
185	+	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
186	+	if (i == torsionDataSets.end()) {
187	+	TorsionDataSet dataSet;
188	+	dataSet.prev.angle = dataSet.curr.angle = angle;
189	+	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
190	+	dataSet.deltaV = 0.0;
191	+	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
192	+	}else {
193	+	i->second.prev.angle = i->second.curr.angle;
194	+	i->second.prev.potential = i->second.curr.potential;
195	+	i->second.curr.angle = angle;
196	+	i->second.curr.potential = currTorsionPot;
197	+	i->second.deltaV =  fabs(i->second.curr.potential -
198	+	i->second.prev.potential);
199	+	}
200	+	}
201
202	+	for (inversion = mol->beginInversion(inversionIter);
203	+	inversion != NULL;
204	+	inversion = mol->nextInversion(inversionIter)) {
205	+	RealType angle;
206	+	inversion->calcForce(angle);
207	+	RealType currInversionPot = inversion->getPotential();
208	+	inversionPotential += inversion->getPotential();
209	+	std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
210	+	if (i == inversionDataSets.end()) {
211	+	InversionDataSet dataSet;
212	+	dataSet.prev.angle = dataSet.curr.angle = angle;
213	+	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
214	+	dataSet.deltaV = 0.0;
215	+	inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
216	+	}else {
217	+	i->second.prev.angle = i->second.curr.angle;
218	+	i->second.prev.potential = i->second.curr.potential;
219	+	i->second.curr.angle = angle;
220	+	i->second.curr.potential = currInversionPot;
221	+	i->second.deltaV =  fabs(i->second.curr.potential -
222	+	i->second.prev.potential);
223	+	}
224	+	}
225		}
226
227	<	double  shortRangePotential = bondPotential + bendPotential + torsionPotential;
227	>	RealType  shortRangePotential = bondPotential + bendPotential +
228	>	torsionPotential +  inversionPotential;
229		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
230		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
231		curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
232		curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
233		curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
234	+	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
235
236		}
237	<
238	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
237	>
238	>	void ForceManager::calcLongRangeInteraction() {
239		Snapshot* curSnapshot;
240		DataStorage* config;
241	<	double* frc;
242	<	double* pos;
243	<	double* trq;
244	<	double* A;
245	<	double* electroFrame;
246	<	double* rc;
241	>	RealType* frc;
242	>	RealType* pos;
243	>	RealType* trq;
244	>	RealType* A;
245	>	RealType* electroFrame;
246	>	RealType* rc;
247	>	RealType* particlePot;
248
249		//get current snapshot from SimInfo
250		curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
251	<
251	>
252		//get array pointers
253		config = &(curSnapshot->atomData);
254		frc = config->getArrayPointer(DataStorage::dslForce);
#	Line 249 | Line 256 | namespace oopse {
256		trq = config->getArrayPointer(DataStorage::dslTorque);
257		A   = config->getArrayPointer(DataStorage::dslAmat);
258		electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
259	+	particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
260
261		//calculate the center of mass of cutoff group
262		SimInfo::MoleculeIterator mi;
#	Line 257 | Line 265 | namespace oopse {
265		CutoffGroup* cg;
266		Vector3d com;
267		std::vector<Vector3d> rcGroup;
268	<
268	>
269		if(info_->getNCutoffGroups() > 0){
270	<
271	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
272	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
270	>
271	>	for (mol = info_->beginMolecule(mi); mol != NULL;
272	>	mol = info_->nextMolecule(mi)) {
273	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
274	>	cg = mol->nextCutoffGroup(ci)) {
275		cg->getCOM(com);
276		rcGroup.push_back(com);
277		}
#	Line 269 | Line 279 | namespace oopse {
279
280		rc = rcGroup[0].getArrayPointer();
281		} else {
282	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
282	>	// center of mass of the group is the same as position of the atom
283	>	// if cutoff group does not exist
284		rc = pos;
285		}
275	–
276	–	//initialize data before passing to fortran
277	–	double longRangePotential[LR_POT_TYPES];
278	–	double lrPot = 0.0;
286
287	<	Mat3x3d tau;
288	<	short int passedCalcPot = needPotential;
289	<	short int passedCalcStress = needStress;
287	>	//initialize data before passing to fortran
288	>	RealType longRangePotential[LR_POT_TYPES];
289	>	RealType lrPot = 0.0;
290	>	Vector3d totalDipole;
291		int isError = 0;
292
293		for (int i=0; i<LR_POT_TYPES;i++){
294		longRangePotential[i]=0.0; //Initialize array
295		}
296	<
297	<	doForceLoop( pos,
298	<	rc,
299	<	A,
300	<	electroFrame,
301	<	frc,
302	<	trq,
303	<	tau.getArrayPointer(),
304	<	longRangePotential,
305	<	&passedCalcPot,
306	<	&passedCalcStress,
307	<	&isError );
300	<
296	>
297	>	doForceLoop(pos,
298	>	rc,
299	>	A,
300	>	electroFrame,
301	>	frc,
302	>	trq,
303	>	tau.getArrayPointer(),
304	>	longRangePotential,
305	>	particlePot,
306	>	&isError );
307	>
308		if( isError ){
309		sprintf( painCave.errMsg,
310		"Error returned from the fortran force calculation.\n" );
#	Line 307 | Line 314 | namespace oopse {
314		for (int i=0; i<LR_POT_TYPES;i++){
315		lrPot += longRangePotential[i]; //Quick hack
316		}
317	<
317	>
318	>	// grab the simulation box dipole moment if specified
319	>	if (info_->getCalcBoxDipole()){
320	>	getAccumulatedBoxDipole(totalDipole.getArrayPointer());
321	>
322	>	curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
323	>	curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
324	>	curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
325	>	}
326	>
327		//store the tau and long range potential
328		curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
329		curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
330		curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
315	–
316	–	curSnapshot->statData.setTau(tau);
331		}
332
333	<
333	>
334		void ForceManager::postCalculation() {
335		SimInfo::MoleculeIterator mi;
336		Molecule* mol;
337		Molecule::RigidBodyIterator rbIter;
338		RigidBody* rb;
339	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
340
341		// collect the atomic forces onto rigid bodies
342	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
343	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
344	<	rb->calcForcesAndTorques();
342	>
343	>	for (mol = info_->beginMolecule(mi); mol != NULL;
344	>	mol = info_->nextMolecule(mi)) {
345	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
346	>	rb = mol->nextRigidBody(rbIter)) {
347	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
348	>	tau += rbTau;
349		}
350		}
351	<
351	>
352	>	#ifdef IS_MPI
353	>	Mat3x3d tmpTau(tau);
354	>	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
355	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
356	>	#endif
357	>	curSnapshot->statData.setTau(tau);
358		}
359
360	<	} //end namespace oopse
360	>	} //end namespace OpenMD

Comparing:
trunk/src/brains/ForceManager.cpp (property svn:keywords), Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
branches/development/src/brains/ForceManager.cpp (property svn:keywords), Revision 1469 by gezelter, Mon Jul 19 14:07:59 2010 UTC

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