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root/OpenMD/trunk/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.
Revision 1610 by gezelter, Fri Aug 12 14:37:25 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]  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	>	namespace OpenMD {
61
62	<	/*
63	<	struct BendOrderStruct {
62	<	Bend* bend;
63	<	BendDataSet dataSet;
64	<	};
65	<	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;
72	<	}
73	<
74	<	bool  TorsionSortFunctor(const TorsionOrderStruct& t1, const TorsionOrderStruct& t2) {
75	<	return t1.dataSet.deltaV < t2.dataSet.deltaV;
76	<	}
77	<	*/
78	<	void ForceManager::calcForces(bool needPotential, bool needStress) {
79	<
62	>	void ForceManager::calcForces() {
63	>
64		if (!info_->isFortranInitialized()) {
65		info_->update();
66		}
67	<
67	>
68		preCalculation();
69
70		calcShortRangeInteraction();
71
72	<	calcLongRangeInteraction(needPotential, needStress);
72	>	calcLongRangeInteraction();
73
74		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	–	}
75
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	–	*/
76		}
77	<
77	>
78		void ForceManager::preCalculation() {
79		SimInfo::MoleculeIterator mi;
80		Molecule* mol;
#	Line 133 | Line 85 | namespace oopse {
85
86		// forces are zeroed here, before any are accumulated.
87		// NOTE: do not rezero the forces in Fortran.
88	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
88	>
89	>	for (mol = info_->beginMolecule(mi); mol != NULL;
90	>	mol = info_->nextMolecule(mi)) {
91		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
92		atom->zeroForcesAndTorques();
93		}
94	<
94	>
95		//change the positions of atoms which belong to the rigidbodies
96	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
96	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
97	>	rb = mol->nextRigidBody(rbIter)) {
98		rb->zeroForcesAndTorques();
99		}
100	+
101		}
102
103	+	// Zero out the stress tensor
104	+	tau *= 0.0;
105	+
106		}
107	<
107	>
108		void ForceManager::calcShortRangeInteraction() {
109		Molecule* mol;
110		RigidBody* rb;
111		Bond* bond;
112		Bend* bend;
113		Torsion* torsion;
114	+	Inversion* inversion;
115		SimInfo::MoleculeIterator mi;
116		Molecule::RigidBodyIterator rbIter;
117		Molecule::BondIterator bondIter;;
118		Molecule::BendIterator  bendIter;
119		Molecule::TorsionIterator  torsionIter;
120	<	double bondPotential = 0.0;
121	<	double bendPotential = 0.0;
122	<	double torsionPotential = 0.0;
120	>	Molecule::InversionIterator  inversionIter;
121	>	RealType bondPotential = 0.0;
122	>	RealType bendPotential = 0.0;
123	>	RealType torsionPotential = 0.0;
124	>	RealType inversionPotential = 0.0;
125
126		//calculate short range interactions
127	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
127	>	for (mol = info_->beginMolecule(mi); mol != NULL;
128	>	mol = info_->nextMolecule(mi)) {
129
130		//change the positions of atoms which belong to the rigidbodies
131	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
132	<	rb->updateAtoms();
131	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
132	>	rb = mol->nextRigidBody(rbIter)) {
133	>	rb->updateAtoms();
134		}
135
136	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
136	>	for (bond = mol->beginBond(bondIter); bond != NULL;
137	>	bond = mol->nextBond(bondIter)) {
138		bond->calcForce();
139		bondPotential += bond->getPotential();
140		}
141
142	<
143	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
144	<
145	<	double angle;
146	<	bend->calcForce(angle);
147	<	double currBendPot = bend->getPotential();
148	<	bendPotential += bend->getPotential();
149	<	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
150	<	if (i == bendDataSets.end()) {
151	<	BendDataSet dataSet;
152	<	dataSet.prev.angle = dataSet.curr.angle = angle;
153	<	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
154	<	dataSet.deltaV = 0.0;
155	<	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
156	<	}else {
157	<	i->second.prev.angle = i->second.curr.angle;
158	<	i->second.prev.potential = i->second.curr.potential;
159	<	i->second.curr.angle = angle;
160	<	i->second.curr.potential = currBendPot;
161	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
162	<	}
163	<	}
164	<
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	<	}
142	>	for (bend = mol->beginBend(bendIter); bend != NULL;
143	>	bend = mol->nextBend(bendIter)) {
144	>
145	>	RealType angle;
146	>	bend->calcForce(angle);
147	>	RealType currBendPot = bend->getPotential();
148	>
149	>	bendPotential += bend->getPotential();
150	>	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
151	>	if (i == bendDataSets.end()) {
152	>	BendDataSet dataSet;
153	>	dataSet.prev.angle = dataSet.curr.angle = angle;
154	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
155	>	dataSet.deltaV = 0.0;
156	>	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
157	>	}else {
158	>	i->second.prev.angle = i->second.curr.angle;
159	>	i->second.prev.potential = i->second.curr.potential;
160	>	i->second.curr.angle = angle;
161	>	i->second.curr.potential = currBendPot;
162	>	i->second.deltaV =  fabs(i->second.curr.potential -
163	>	i->second.prev.potential);
164	>	}
165		}
166	+
167	+	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
168	+	torsion = mol->nextTorsion(torsionIter)) {
169	+	RealType angle;
170	+	torsion->calcForce(angle);
171	+	RealType currTorsionPot = torsion->getPotential();
172	+	torsionPotential += torsion->getPotential();
173	+	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
174	+	if (i == torsionDataSets.end()) {
175	+	TorsionDataSet dataSet;
176	+	dataSet.prev.angle = dataSet.curr.angle = angle;
177	+	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
178	+	dataSet.deltaV = 0.0;
179	+	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
180	+	}else {
181	+	i->second.prev.angle = i->second.curr.angle;
182	+	i->second.prev.potential = i->second.curr.potential;
183	+	i->second.curr.angle = angle;
184	+	i->second.curr.potential = currTorsionPot;
185	+	i->second.deltaV =  fabs(i->second.curr.potential -
186	+	i->second.prev.potential);
187	+	}
188	+	}
189
190	+	for (inversion = mol->beginInversion(inversionIter);
191	+	inversion != NULL;
192	+	inversion = mol->nextInversion(inversionIter)) {
193	+	RealType angle;
194	+	inversion->calcForce(angle);
195	+	RealType currInversionPot = inversion->getPotential();
196	+	inversionPotential += inversion->getPotential();
197	+	std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
198	+	if (i == inversionDataSets.end()) {
199	+	InversionDataSet dataSet;
200	+	dataSet.prev.angle = dataSet.curr.angle = angle;
201	+	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
202	+	dataSet.deltaV = 0.0;
203	+	inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
204	+	}else {
205	+	i->second.prev.angle = i->second.curr.angle;
206	+	i->second.prev.potential = i->second.curr.potential;
207	+	i->second.curr.angle = angle;
208	+	i->second.curr.potential = currInversionPot;
209	+	i->second.deltaV =  fabs(i->second.curr.potential -
210	+	i->second.prev.potential);
211	+	}
212	+	}
213		}
214
215	<	double  shortRangePotential = bondPotential + bendPotential + torsionPotential;
215	>	RealType  shortRangePotential = bondPotential + bendPotential +
216	>	torsionPotential +  inversionPotential;
217		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
218		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
219		curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
220		curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
221		curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
222	+	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
223
224		}
225	<
226	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
225	>
226	>	void ForceManager::calcLongRangeInteraction() {
227		Snapshot* curSnapshot;
228		DataStorage* config;
229	<	double* frc;
230	<	double* pos;
231	<	double* trq;
232	<	double* A;
233	<	double* electroFrame;
234	<	double* rc;
229	>	RealType* frc;
230	>	RealType* pos;
231	>	RealType* trq;
232	>	RealType* A;
233	>	RealType* electroFrame;
234	>	RealType* rc;
235	>	RealType* particlePot;
236
237		//get current snapshot from SimInfo
238		curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
239	<
239	>
240		//get array pointers
241		config = &(curSnapshot->atomData);
242		frc = config->getArrayPointer(DataStorage::dslForce);
#	Line 249 | Line 244 | namespace oopse {
244		trq = config->getArrayPointer(DataStorage::dslTorque);
245		A   = config->getArrayPointer(DataStorage::dslAmat);
246		electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
247	+	particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
248
249		//calculate the center of mass of cutoff group
250		SimInfo::MoleculeIterator mi;
#	Line 257 | Line 253 | namespace oopse {
253		CutoffGroup* cg;
254		Vector3d com;
255		std::vector<Vector3d> rcGroup;
256	<
256	>
257		if(info_->getNCutoffGroups() > 0){
258	<
259	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
260	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
258	>
259	>	for (mol = info_->beginMolecule(mi); mol != NULL;
260	>	mol = info_->nextMolecule(mi)) {
261	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
262	>	cg = mol->nextCutoffGroup(ci)) {
263		cg->getCOM(com);
264		rcGroup.push_back(com);
265		}
#	Line 269 | Line 267 | namespace oopse {
267
268		rc = rcGroup[0].getArrayPointer();
269		} else {
270	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
270	>	// center of mass of the group is the same as position of the atom
271	>	// if cutoff group does not exist
272		rc = pos;
273		}
275	–
276	–	//initialize data before passing to fortran
277	–	double longRangePotential[LR_POT_TYPES];
278	–	double lrPot = 0.0;
274
275	<	Mat3x3d tau;
276	<	short int passedCalcPot = needPotential;
277	<	short int passedCalcStress = needStress;
275	>	//initialize data before passing to fortran
276	>	RealType longRangePotential[LR_POT_TYPES];
277	>	RealType lrPot = 0.0;
278	>	Vector3d totalDipole;
279		int isError = 0;
280
281		for (int i=0; i<LR_POT_TYPES;i++){
282		longRangePotential[i]=0.0; //Initialize array
283		}
284	<
285	<	doForceLoop( pos,
286	<	rc,
287	<	A,
288	<	electroFrame,
289	<	frc,
290	<	trq,
291	<	tau.getArrayPointer(),
292	<	longRangePotential,
293	<	&passedCalcPot,
294	<	&passedCalcStress,
295	<	&isError );
300	<
284	>
285	>	doForceLoop(pos,
286	>	rc,
287	>	A,
288	>	electroFrame,
289	>	frc,
290	>	trq,
291	>	tau.getArrayPointer(),
292	>	longRangePotential,
293	>	particlePot,
294	>	&isError );
295	>
296		if( isError ){
297		sprintf( painCave.errMsg,
298		"Error returned from the fortran force calculation.\n" );
#	Line 307 | Line 302 | namespace oopse {
302		for (int i=0; i<LR_POT_TYPES;i++){
303		lrPot += longRangePotential[i]; //Quick hack
304		}
305	<
305	>
306	>	// grab the simulation box dipole moment if specified
307	>	if (info_->getCalcBoxDipole()){
308	>	getAccumulatedBoxDipole(totalDipole.getArrayPointer());
309	>
310	>	curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
311	>	curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
312	>	curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
313	>	}
314	>
315		//store the tau and long range potential
316		curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
317		curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
318		curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
315	–
316	–	curSnapshot->statData.setTau(tau);
319		}
320
321	<
321	>
322		void ForceManager::postCalculation() {
323		SimInfo::MoleculeIterator mi;
324		Molecule* mol;
325		Molecule::RigidBodyIterator rbIter;
326		RigidBody* rb;
327	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
328
329		// collect the atomic forces onto rigid bodies
330	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
331	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
332	<	rb->calcForcesAndTorques();
330	>
331	>	for (mol = info_->beginMolecule(mi); mol != NULL;
332	>	mol = info_->nextMolecule(mi)) {
333	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
334	>	rb = mol->nextRigidBody(rbIter)) {
335	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
336	>	tau += rbTau;
337		}
338		}
339	<
339	>
340	>	#ifdef IS_MPI
341	>	Mat3x3d tmpTau(tau);
342	>	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
343	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
344	>	#endif
345	>	curSnapshot->statData.setTau(tau);
346		}
347
348	<	} //end namespace oopse
348	>	} //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.
Revision 1610 by gezelter, Fri Aug 12 14:37:25 2011 UTC

#	Line 0 | Line 1
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