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

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trunk/src/brains/ForceManager.cpp (file contents), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/brains/ForceManager.cpp (file contents), Revision 1577 by gezelter, Wed Jun 8 20:26:56 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]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 47 | Line 47
47		* @version 1.0
48		*/
49
50	+
51		#include "brains/ForceManager.hpp"
52		#include "primitives/Molecule.hpp"
53	<	#include "UseTheForce/doForces_interface.h"
53	>	#define __OPENMD_C
54		#include "utils/simError.h"
55	<	namespace oopse {
55	>	#include "primitives/Bond.hpp"
56	>	#include "primitives/Bend.hpp"
57	>	#include "primitives/Torsion.hpp"
58	>	#include "primitives/Inversion.hpp"
59	>	#include "nonbonded/NonBondedInteraction.hpp"
60	>	#include "parallel/ForceMatrixDecomposition.hpp"
61
62	<	void ForceManager::calcForces(bool needPotential, bool needStress) {
62	>	using namespace std;
63	>	namespace OpenMD {
64	>
65	>	ForceManager::ForceManager(SimInfo * info) : info_(info) {
66	>	forceField_ = info_->getForceField();
67	>	fDecomp_ = new ForceMatrixDecomposition(info_);
68	>	interactionMan_ = new InteractionManager();
69	>	}
70
71	<	if (!info_->isFortranInitialized()) {
72	<	info_->update();
71	>	/**
72	>	* setupCutoffs
73	>	*
74	>	* Sets the values of cutoffRadius, cutoffMethod, and cutoffPolicy
75	>	*
76	>	* cutoffRadius : realType
77	>	*  If the cutoffRadius was explicitly set, use that value.
78	>	*  If the cutoffRadius was not explicitly set:
79	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
80	>	*      No electrostatic atoms?  Poll the atom types present in the
81	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
82	>	*      Use the maximum suggested value that was found.
83	>	*
84	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
85	>	*      If cutoffMethod was explicitly set, use that choice.
86	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
87	>	*
88	>	* cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
89	>	*      If cutoffPolicy was explicitly set, use that choice.
90	>	*      If cutoffPolicy was not explicitly set, use TRADITIONAL
91	>	*/
92	>	void ForceManager::setupCutoffs() {
93	>
94	>	Globals* simParams_ = info_->getSimParams();
95	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
96	>
97	>	if (simParams_->haveCutoffRadius()) {
98	>	rCut_ = simParams_->getCutoffRadius();
99	>	} else {
100	>	if (info_->usesElectrostaticAtoms()) {
101	>	sprintf(painCave.errMsg,
102	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
103	>	"\tOpenMD will use a default value of 12.0 angstroms"
104	>	"\tfor the cutoffRadius.\n");
105	>	painCave.isFatal = 0;
106	>	painCave.severity = OPENMD_INFO;
107	>	simError();
108	>	rCut_ = 12.0;
109	>	} else {
110	>	RealType thisCut;
111	>	set<AtomType*>::iterator i;
112	>	set<AtomType*> atomTypes;
113	>	atomTypes = info_->getSimulatedAtomTypes();
114	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
115	>	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
116	>	rCut_ = max(thisCut, rCut_);
117	>	}
118	>	sprintf(painCave.errMsg,
119	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
120	>	"\tOpenMD will use %lf angstroms.\n",
121	>	rCut_);
122	>	painCave.isFatal = 0;
123	>	painCave.severity = OPENMD_INFO;
124	>	simError();
125	>	}
126		}
127
128	<	preCalculation();
129	<
130	<	calcShortRangeInteraction();
128	>	map<string, CutoffMethod> stringToCutoffMethod;
129	>	stringToCutoffMethod["HARD"] = HARD;
130	>	stringToCutoffMethod["SWITCHED"] = SWITCHED;
131	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
132	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
133	>
134	>	if (simParams_->haveCutoffMethod()) {
135	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
136	>	map<string, CutoffMethod>::iterator i;
137	>	i = stringToCutoffMethod.find(cutMeth);
138	>	if (i == stringToCutoffMethod.end()) {
139	>	sprintf(painCave.errMsg,
140	>	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
141	>	"\tShould be one of: "
142	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
143	>	cutMeth.c_str());
144	>	painCave.isFatal = 1;
145	>	painCave.severity = OPENMD_ERROR;
146	>	simError();
147	>	} else {
148	>	cutoffMethod_ = i->second;
149	>	}
150	>	} else {
151	>	sprintf(painCave.errMsg,
152	>	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
153	>	"\tOpenMD will use SHIFTED_FORCE.\n");
154	>	painCave.isFatal = 0;
155	>	painCave.severity = OPENMD_INFO;
156	>	simError();
157	>	cutoffMethod_ = SHIFTED_FORCE;
158	>	}
159
160	<	calcLongRangeInteraction(needPotential, needStress);
160	>	map<string, CutoffPolicy> stringToCutoffPolicy;
161	>	stringToCutoffPolicy["MIX"] = MIX;
162	>	stringToCutoffPolicy["MAX"] = MAX;
163	>	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
164
165	<	postCalculation();
166	<
165	>	std::string cutPolicy;
166	>	if (forceFieldOptions_.haveCutoffPolicy()){
167	>	cutPolicy = forceFieldOptions_.getCutoffPolicy();
168	>	}else if (simParams_->haveCutoffPolicy()) {
169	>	cutPolicy = simParams_->getCutoffPolicy();
170	>	}
171	>
172	>	if (!cutPolicy.empty()){
173	>	toUpper(cutPolicy);
174	>	map<string, CutoffPolicy>::iterator i;
175	>	i = stringToCutoffPolicy.find(cutPolicy);
176	>
177	>	if (i == stringToCutoffPolicy.end()) {
178	>	sprintf(painCave.errMsg,
179	>	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
180	>	"\tShould be one of: "
181	>	"MIX, MAX, or TRADITIONAL\n",
182	>	cutPolicy.c_str());
183	>	painCave.isFatal = 1;
184	>	painCave.severity = OPENMD_ERROR;
185	>	simError();
186	>	} else {
187	>	cutoffPolicy_ = i->second;
188	>	}
189	>	} else {
190	>	sprintf(painCave.errMsg,
191	>	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
192	>	"\tOpenMD will use TRADITIONAL.\n");
193	>	painCave.isFatal = 0;
194	>	painCave.severity = OPENMD_INFO;
195	>	simError();
196	>	cutoffPolicy_ = TRADITIONAL;
197	>	}
198		}
199
200	+	/**
201	+	* setupSwitching
202	+	*
203	+	* Sets the values of switchingRadius and
204	+	*  If the switchingRadius was explicitly set, use that value (but check it)
205	+	*  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
206	+	*/
207	+	void ForceManager::setupSwitching() {
208	+	Globals* simParams_ = info_->getSimParams();
209	+
210	+	// create the switching function object:
211	+	switcher_ = new SwitchingFunction();
212	+
213	+	if (simParams_->haveSwitchingRadius()) {
214	+	rSwitch_ = simParams_->getSwitchingRadius();
215	+	if (rSwitch_ > rCut_) {
216	+	sprintf(painCave.errMsg,
217	+	"ForceManager::setupSwitching: switchingRadius (%f) is larger "
218	+	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
219	+	painCave.isFatal = 1;
220	+	painCave.severity = OPENMD_ERROR;
221	+	simError();
222	+	}
223	+	} else {
224	+	rSwitch_ = 0.85 * rCut_;
225	+	sprintf(painCave.errMsg,
226	+	"ForceManager::setupSwitching: No value was set for the switchingRadius.\n"
227	+	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
228	+	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
229	+	painCave.isFatal = 0;
230	+	painCave.severity = OPENMD_WARNING;
231	+	simError();
232	+	}
233	+
234	+	// Default to cubic switching function.
235	+	sft_ = cubic;
236	+	if (simParams_->haveSwitchingFunctionType()) {
237	+	string funcType = simParams_->getSwitchingFunctionType();
238	+	toUpper(funcType);
239	+	if (funcType == "CUBIC") {
240	+	sft_ = cubic;
241	+	} else {
242	+	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
243	+	sft_ = fifth_order_poly;
244	+	} else {
245	+	// throw error
246	+	sprintf( painCave.errMsg,
247	+	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
248	+	"\tswitchingFunctionType must be one of: "
249	+	"\"cubic\" or \"fifth_order_polynomial\".",
250	+	funcType.c_str() );
251	+	painCave.isFatal = 1;
252	+	painCave.severity = OPENMD_ERROR;
253	+	simError();
254	+	}
255	+	}
256	+	}
257	+	switcher_->setSwitchType(sft_);
258	+	switcher_->setSwitch(rSwitch_, rCut_);
259	+	}
260	+
261	+	void ForceManager::initialize() {
262	+
263	+	if (!info_->isTopologyDone()) {
264	+	info_->update();
265	+	interactionMan_->setSimInfo(info_);
266	+	interactionMan_->initialize();
267	+
268	+	// We want to delay the cutoffs until after the interaction
269	+	// manager has set up the atom-atom interactions so that we can
270	+	// query them for suggested cutoff values
271	+
272	+	setupCutoffs();
273	+	setupSwitching();
274	+
275	+	info_->prepareTopology();
276	+	}
277	+
278	+	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
279	+
280	+	// Force fields can set options on how to scale van der Waals and electrostatic
281	+	// interactions for atoms connected via bonds, bends and torsions
282	+	// in this case the topological distance between atoms is:
283	+	// 0 = topologically unconnected
284	+	// 1 = bonded together
285	+	// 2 = connected via a bend
286	+	// 3 = connected via a torsion
287	+
288	+	vdwScale_.reserve(4);
289	+	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
290	+
291	+	electrostaticScale_.reserve(4);
292	+	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
293	+
294	+	vdwScale_[0] = 1.0;
295	+	vdwScale_[1] = fopts.getvdw12scale();
296	+	vdwScale_[2] = fopts.getvdw13scale();
297	+	vdwScale_[3] = fopts.getvdw14scale();
298	+
299	+	electrostaticScale_[0] = 1.0;
300	+	electrostaticScale_[1] = fopts.getelectrostatic12scale();
301	+	electrostaticScale_[2] = fopts.getelectrostatic13scale();
302	+	electrostaticScale_[3] = fopts.getelectrostatic14scale();
303	+
304	+	fDecomp_->distributeInitialData();
305	+
306	+	initialized_ = true;
307	+
308	+	}
309	+
310	+	void ForceManager::calcForces() {
311	+
312	+	if (!initialized_) initialize();
313	+
314	+	preCalculation();
315	+	shortRangeInteractions();
316	+	longRangeInteractions();
317	+	postCalculation();
318	+	}
319	+
320		void ForceManager::preCalculation() {
321		SimInfo::MoleculeIterator mi;
322		Molecule* mol;
#	Line 76 | Line 324 | namespace oopse {
324		Atom* atom;
325		Molecule::RigidBodyIterator rbIter;
326		RigidBody* rb;
327	+	Molecule::CutoffGroupIterator ci;
328	+	CutoffGroup* cg;
329
330		// forces are zeroed here, before any are accumulated.
331	<	// NOTE: do not rezero the forces in Fortran.
332	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
331	>
332	>	for (mol = info_->beginMolecule(mi); mol != NULL;
333	>	mol = info_->nextMolecule(mi)) {
334		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
335		atom->zeroForcesAndTorques();
336		}
337	<
337	>
338		//change the positions of atoms which belong to the rigidbodies
339	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
339	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
340	>	rb = mol->nextRigidBody(rbIter)) {
341		rb->zeroForcesAndTorques();
342		}
343	+
344	+	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
345	+	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
346	+	cg = mol->nextCutoffGroup(ci)) {
347	+	//calculate the center of mass of cutoff group
348	+	cg->updateCOM();
349	+	}
350	+	}
351		}
352	+
353	+	// Zero out the stress tensor
354	+	tau *= 0.0;
355
356		}
357	<
358	<	void ForceManager::calcShortRangeInteraction() {
357	>
358	>	void ForceManager::shortRangeInteractions() {
359		Molecule* mol;
360		RigidBody* rb;
361		Bond* bond;
362		Bend* bend;
363		Torsion* torsion;
364	+	Inversion* inversion;
365		SimInfo::MoleculeIterator mi;
366		Molecule::RigidBodyIterator rbIter;
367		Molecule::BondIterator bondIter;;
368		Molecule::BendIterator  bendIter;
369		Molecule::TorsionIterator  torsionIter;
370	+	Molecule::InversionIterator  inversionIter;
371	+	RealType bondPotential = 0.0;
372	+	RealType bendPotential = 0.0;
373	+	RealType torsionPotential = 0.0;
374	+	RealType inversionPotential = 0.0;
375
376		//calculate short range interactions
377	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
377	>	for (mol = info_->beginMolecule(mi); mol != NULL;
378	>	mol = info_->nextMolecule(mi)) {
379
380		//change the positions of atoms which belong to the rigidbodies
381	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
382	<	rb->updateAtoms();
381	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
382	>	rb = mol->nextRigidBody(rbIter)) {
383	>	rb->updateAtoms();
384		}
385
386	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
387	<	bond->calcForce();
386	>	for (bond = mol->beginBond(bondIter); bond != NULL;
387	>	bond = mol->nextBond(bondIter)) {
388	>	bond->calcForce();
389	>	bondPotential += bond->getPotential();
390		}
391
392	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
393	<	bend->calcForce();
392	>	for (bend = mol->beginBend(bendIter); bend != NULL;
393	>	bend = mol->nextBend(bendIter)) {
394	>
395	>	RealType angle;
396	>	bend->calcForce(angle);
397	>	RealType currBendPot = bend->getPotential();
398	>
399	>	bendPotential += bend->getPotential();
400	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
401	>	if (i == bendDataSets.end()) {
402	>	BendDataSet dataSet;
403	>	dataSet.prev.angle = dataSet.curr.angle = angle;
404	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
405	>	dataSet.deltaV = 0.0;
406	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
407	>	}else {
408	>	i->second.prev.angle = i->second.curr.angle;
409	>	i->second.prev.potential = i->second.curr.potential;
410	>	i->second.curr.angle = angle;
411	>	i->second.curr.potential = currBendPot;
412	>	i->second.deltaV =  fabs(i->second.curr.potential -
413	>	i->second.prev.potential);
414	>	}
415		}
416	<
417	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
418	<	torsion->calcForce();
419	<	}
420	<
416	>
417	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
418	>	torsion = mol->nextTorsion(torsionIter)) {
419	>	RealType angle;
420	>	torsion->calcForce(angle);
421	>	RealType currTorsionPot = torsion->getPotential();
422	>	torsionPotential += torsion->getPotential();
423	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
424	>	if (i == torsionDataSets.end()) {
425	>	TorsionDataSet dataSet;
426	>	dataSet.prev.angle = dataSet.curr.angle = angle;
427	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
428	>	dataSet.deltaV = 0.0;
429	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
430	>	}else {
431	>	i->second.prev.angle = i->second.curr.angle;
432	>	i->second.prev.potential = i->second.curr.potential;
433	>	i->second.curr.angle = angle;
434	>	i->second.curr.potential = currTorsionPot;
435	>	i->second.deltaV =  fabs(i->second.curr.potential -
436	>	i->second.prev.potential);
437	>	}
438	>	}
439	>
440	>	for (inversion = mol->beginInversion(inversionIter);
441	>	inversion != NULL;
442	>	inversion = mol->nextInversion(inversionIter)) {
443	>	RealType angle;
444	>	inversion->calcForce(angle);
445	>	RealType currInversionPot = inversion->getPotential();
446	>	inversionPotential += inversion->getPotential();
447	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
448	>	if (i == inversionDataSets.end()) {
449	>	InversionDataSet dataSet;
450	>	dataSet.prev.angle = dataSet.curr.angle = angle;
451	>	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
452	>	dataSet.deltaV = 0.0;
453	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
454	>	}else {
455	>	i->second.prev.angle = i->second.curr.angle;
456	>	i->second.prev.potential = i->second.curr.potential;
457	>	i->second.curr.angle = angle;
458	>	i->second.curr.potential = currInversionPot;
459	>	i->second.deltaV =  fabs(i->second.curr.potential -
460	>	i->second.prev.potential);
461	>	}
462	>	}
463		}
464
465	<	double  shortRangePotential = 0.0;
466	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
131	<	shortRangePotential += mol->getPotential();
132	<	}
133	<
465	>	RealType  shortRangePotential = bondPotential + bendPotential +
466	>	torsionPotential +  inversionPotential;
467		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
468		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
469	+	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
470	+	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
471	+	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
472	+	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
473		}
474	+
475	+	void ForceManager::longRangeInteractions() {
476
477	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
478	<	Snapshot* curSnapshot;
479	<	DataStorage* config;
480	<	double* frc;
481	<	double* pos;
482	<	double* trq;
483	<	double* A;
484	<	double* electroFrame;
485	<	double* rc;
477	>	// some of this initial stuff will go away:
478	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
479	>	DataStorage* config = &(curSnapshot->atomData);
480	>	DataStorage* cgConfig = &(curSnapshot->cgData);
481	>	RealType* frc = config->getArrayPointer(DataStorage::dslForce);
482	>	RealType* pos = config->getArrayPointer(DataStorage::dslPosition);
483	>	RealType* trq = config->getArrayPointer(DataStorage::dslTorque);
484	>	RealType* A = config->getArrayPointer(DataStorage::dslAmat);
485	>	RealType* electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
486	>	RealType* particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
487	>	RealType* rc;
488	>
489	>	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
490	>	rc = cgConfig->getArrayPointer(DataStorage::dslPosition);
491	>	} else {
492	>	// center of mass of the group is the same as position of the atom
493	>	// if cutoff group does not exist
494	>	rc = pos;
495	>	}
496
497	<	//get current snapshot from SimInfo
498	<	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
497	>	// new stuff starts here:
498	>	fDecomp_->zeroWorkArrays();
499	>	fDecomp_->distributeData();
500	>
501	>	int cg1, cg2, atom1, atom2;
502	>	Vector3d d_grp, dag;
503	>	RealType rgrpsq, rgrp;
504	>	RealType vij;
505	>	Vector3d fij, fg;
506	>	tuple3<RealType, RealType, RealType> cuts;
507	>	RealType rCutSq;
508	>	bool in_switching_region;
509	>	RealType sw, dswdr, swderiv;
510	>	vector<int> atomListColumn, atomListRow, atomListLocal;
511	>	InteractionData idat;
512	>	SelfData sdat;
513	>	RealType mf;
514	>	potVec pot(0.0);
515	>	potVec longRangePotential(0.0);
516	>	RealType lrPot;
517
518	<	//get array pointers
152	<	config = &(curSnapshot->atomData);
153	<	frc = config->getArrayPointer(DataStorage::dslForce);
154	<	pos = config->getArrayPointer(DataStorage::dslPosition);
155	<	trq = config->getArrayPointer(DataStorage::dslTorque);
156	<	A   = config->getArrayPointer(DataStorage::dslAmat);
157	<	electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
518	>	int loopStart, loopEnd;
519
520	<	//calculate the center of mass of cutoff group
521	<	SimInfo::MoleculeIterator mi;
522	<	Molecule* mol;
523	<	Molecule::CutoffGroupIterator ci;
524	<	CutoffGroup* cg;
525	<	Vector3d com;
526	<	std::vector<Vector3d> rcGroup;
520	>	loopEnd = PAIR_LOOP;
521	>	if (info_->requiresPrepair() ) {
522	>	loopStart = PREPAIR_LOOP;
523	>	} else {
524	>	loopStart = PAIR_LOOP;
525	>	}
526	>
527	>	for (int iLoop = loopStart; iLoop < loopEnd; iLoop++) {
528	>
529	>	if (iLoop == loopStart) {
530	>	bool update_nlist = fDecomp_->checkNeighborList();
531	>	if (update_nlist)
532	>	neighborList = fDecomp_->buildNeighborList();
533	>	}
534	>
535	>	for (vector<pair<int, int> >::iterator it = neighborList.begin();
536	>	it != neighborList.end(); ++it) {
537	>
538	>	cg1 = (*it).first;
539	>	cg2 = (*it).second;
540	>
541	>	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
542	>
543	>	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
544	>	curSnapshot->wrapVector(d_grp);
545	>	rgrpsq = d_grp.lengthSquare();
546	>
547	>	rCutSq = cuts.second;
548	>
549	>	if (rgrpsq < rCutSq) {
550	>	*(idat.rcut) = cuts.first;
551	>	if (iLoop == PAIR_LOOP) {
552	>	vij *= 0.0;
553	>	fij = V3Zero;
554	>	}
555	>
556	>	in_switching_region = switcher_->getSwitch(rgrpsq, *(idat.sw), dswdr,
557	>	rgrp);
558	>
559	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
560	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
561	>
562	>	for (vector<int>::iterator ia = atomListRow.begin();
563	>	ia != atomListRow.end(); ++ia) {
564	>	atom1 = (*ia);
565	>
566	>	for (vector<int>::iterator jb = atomListColumn.begin();
567	>	jb != atomListColumn.end(); ++jb) {
568	>	atom2 = (*jb);
569	>
570	>	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
571	>
572	>	pot *= 0.0;
573	>
574	>	idat = fDecomp_->fillInteractionData(atom1, atom2);
575	>	*(idat.pot) = pot;
576	>
577	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
578	>	*(idat.d) = d_grp;
579	>	*(idat.r2) = rgrpsq;
580	>	} else {
581	>	*(idat.d) = fDecomp_->getInteratomicVector(atom1, atom2);
582	>	curSnapshot->wrapVector( *(idat.d) );
583	>	*(idat.r2) = idat.d->lengthSquare();
584	>	}
585	>
586	>	*(idat.rij) = sqrt( *(idat.r2) );
587	>
588	>	if (iLoop == PREPAIR_LOOP) {
589	>	interactionMan_->doPrePair(idat);
590	>	} else {
591	>	interactionMan_->doPair(idat);
592	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
593	>	vij += *(idat.vpair);
594	>	fij += *(idat.f1);
595	>	tau -= outProduct( *(idat.d), *(idat.f1));
596	>	}
597	>	}
598	>	}
599	>	}
600	>
601	>	if (iLoop == PAIR_LOOP) {
602	>	if (in_switching_region) {
603	>	swderiv = vij * dswdr / rgrp;
604	>	fg = swderiv * d_grp;
605	>
606	>	fij += fg;
607	>
608	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
609	>	tau -= outProduct( *(idat.d), fg);
610	>	}
611	>
612	>	for (vector<int>::iterator ia = atomListRow.begin();
613	>	ia != atomListRow.end(); ++ia) {
614	>	atom1 = (*ia);
615	>	mf = fDecomp_->getMassFactorRow(atom1);
616	>	// fg is the force on atom ia due to cutoff group's
617	>	// presence in switching region
618	>	fg = swderiv * d_grp * mf;
619	>	fDecomp_->addForceToAtomRow(atom1, fg);
620	>
621	>	if (atomListRow.size() > 1) {
622	>	if (info_->usesAtomicVirial()) {
623	>	// find the distance between the atom
624	>	// and the center of the cutoff group:
625	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
626	>	tau -= outProduct(dag, fg);
627	>	}
628	>	}
629	>	}
630	>	for (vector<int>::iterator jb = atomListColumn.begin();
631	>	jb != atomListColumn.end(); ++jb) {
632	>	atom2 = (*jb);
633	>	mf = fDecomp_->getMassFactorColumn(atom2);
634	>	// fg is the force on atom jb due to cutoff group's
635	>	// presence in switching region
636	>	fg = -swderiv * d_grp * mf;
637	>	fDecomp_->addForceToAtomColumn(atom2, fg);
638	>
639	>	if (atomListColumn.size() > 1) {
640	>	if (info_->usesAtomicVirial()) {
641	>	// find the distance between the atom
642	>	// and the center of the cutoff group:
643	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
644	>	tau -= outProduct(dag, fg);
645	>	}
646	>	}
647	>	}
648	>	}
649	>	//if (!SIM_uses_AtomicVirial) {
650	>	//  tau -= outProduct(d_grp, fij);
651	>	//}
652	>	}
653	>	}
654	>	}
655	>
656	>	if (iLoop == PREPAIR_LOOP) {
657	>	if (info_->requiresPrepair()) {
658	>	fDecomp_->collectIntermediateData();
659	>
660	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
661	>	sdat = fDecomp_->fillSelfData(atom1);
662	>	interactionMan_->doPreForce(sdat);
663	>	}
664	>
665	>	fDecomp_->distributeIntermediateData();
666	>	}
667	>	}
668	>
669	>	}
670
671	<	if(info_->getNCutoffGroups() > 0){
671	>	fDecomp_->collectData();
672	>
673	>	if ( info_->requiresSkipCorrection() ) {
674	>
675	>	for (int atom1 = 0; atom1 < fDecomp_->getNAtomsInRow(); atom1++) {
676
677	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
678	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
679	<	cg->getCOM(com);
680	<	rcGroup.push_back(com);
677	>	vector<int> skipList = fDecomp_->getSkipsForRowAtom( atom1 );
678	>
679	>	for (vector<int>::iterator jb = skipList.begin();
680	>	jb != skipList.end(); ++jb) {
681	>
682	>	atom2 = (*jb);
683	>	idat = fDecomp_->fillSkipData(atom1, atom2);
684	>	interactionMan_->doSkipCorrection(idat);
685	>
686		}
687	<	}// end for (mol)
175	<
176	<	rc = rcGroup[0].getArrayPointer();
177	<	} else {
178	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
179	<	rc = pos;
687	>	}
688		}
689	<
690	<	//initialize data before passing to fortran
183	<	double longRangePotential = 0.0;
184	<	Mat3x3d tau;
185	<	short int passedCalcPot = needPotential;
186	<	short int passedCalcStress = needStress;
187	<	int isError = 0;
689	>
690	>	if (info_->requiresSelfCorrection()) {
691
692	<	doForceLoop( pos,
693	<	rc,
694	<	A,
695	<	electroFrame,
193	<	frc,
194	<	trq,
195	<	tau.getArrayPointer(),
196	<	&longRangePotential,
197	<	&passedCalcPot,
198	<	&passedCalcStress,
199	<	&isError );
692	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
693	>	sdat = fDecomp_->fillSelfData(atom1);
694	>	interactionMan_->doSelfCorrection(sdat);
695	>	}
696
201	–	if( isError ){
202	–	sprintf( painCave.errMsg,
203	–	"Error returned from the fortran force calculation.\n" );
204	–	painCave.isFatal = 1;
205	–	simError();
697		}
698
699	+	longRangePotential = fDecomp_->getLongRangePotential();
700	+	lrPot = longRangePotential.sum();
701	+
702		//store the tau and long range potential
703	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential;
704	<	curSnapshot->statData.setTau(tau);
703	>	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
704	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
705	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
706		}
707
708	<
708	>
709		void ForceManager::postCalculation() {
710		SimInfo::MoleculeIterator mi;
711		Molecule* mol;
712		Molecule::RigidBodyIterator rbIter;
713		RigidBody* rb;
714	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
715
716		// collect the atomic forces onto rigid bodies
717	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
718	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
719	<	rb->calcForcesAndTorques();
717	>
718	>	for (mol = info_->beginMolecule(mi); mol != NULL;
719	>	mol = info_->nextMolecule(mi)) {
720	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
721	>	rb = mol->nextRigidBody(rbIter)) {
722	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
723	>	tau += rbTau;
724		}
725		}
726	<
726	>
727	>	#ifdef IS_MPI
728	>	Mat3x3d tmpTau(tau);
729	>	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
730	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
731	>	#endif
732	>	curSnapshot->statData.setTau(tau);
733		}
734
735	<	} //end namespace oopse
735	>	} //end namespace OpenMD

Comparing:
trunk/src/brains/ForceManager.cpp (property svn:keywords), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/brains/ForceManager.cpp (property svn:keywords), Revision 1577 by gezelter, Wed Jun 8 20:26:56 2011 UTC

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