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

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trunk/src/brains/ForceManager.cpp (file contents), Revision 1215 by xsun, Wed Jan 23 21:22:37 2008 UTC vs.
branches/development/src/brains/ForceManager.cpp (file contents), Revision 1612 by gezelter, Fri Aug 12 19:59:56 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 __C
54	<	#include "UseTheForce/DarkSide/fInteractionMap.h"
53	>	#define __OPENMD_C
54		#include "utils/simError.h"
55		#include "primitives/Bond.hpp"
56		#include "primitives/Bend.hpp"
57	<	namespace oopse {
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	>	#include <cstdio>
63	>	#include <iostream>
64	>	#include <iomanip>
65	>
66	>	using namespace std;
67	>	namespace OpenMD {
68	>
69	>	ForceManager::ForceManager(SimInfo * info) : info_(info) {
70	>	forceField_ = info_->getForceField();
71	>	interactionMan_ = new InteractionManager();
72	>	fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
73	>	}
74	>
75	>	/**
76	>	* setupCutoffs
77	>	*
78	>	* Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
79	>	* and cutoffPolicy
80	>	*
81	>	* cutoffRadius : realType
82	>	*  If the cutoffRadius was explicitly set, use that value.
83	>	*  If the cutoffRadius was not explicitly set:
84	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
85	>	*      No electrostatic atoms?  Poll the atom types present in the
86	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
87	>	*      Use the maximum suggested value that was found.
88	>	*
89	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
90	>	*                        or SHIFTED_POTENTIAL)
91	>	*      If cutoffMethod was explicitly set, use that choice.
92	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
93	>	*
94	>	* cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
95	>	*      If cutoffPolicy was explicitly set, use that choice.
96	>	*      If cutoffPolicy was not explicitly set, use TRADITIONAL
97	>	*
98	>	* switchingRadius : realType
99	>	*  If the cutoffMethod was set to SWITCHED:
100	>	*      If the switchingRadius was explicitly set, use that value
101	>	*          (but do a sanity check first).
102	>	*      If the switchingRadius was not explicitly set: use 0.85 *
103	>	*      cutoffRadius_
104	>	*  If the cutoffMethod was not set to SWITCHED:
105	>	*      Set switchingRadius equal to cutoffRadius for safety.
106	>	*/
107	>	void ForceManager::setupCutoffs() {
108
109	<	if (!info_->isFortranInitialized()) {
110	<	info_->update();
64	<	}
109	>	Globals* simParams_ = info_->getSimParams();
110	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
111
112	<	preCalculation();
113	<
114	<	calcShortRangeInteraction();
112	>	if (simParams_->haveCutoffRadius()) {
113	>	rCut_ = simParams_->getCutoffRadius();
114	>	} else {
115	>	if (info_->usesElectrostaticAtoms()) {
116	>	sprintf(painCave.errMsg,
117	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
118	>	"\tOpenMD will use a default value of 12.0 angstroms"
119	>	"\tfor the cutoffRadius.\n");
120	>	painCave.isFatal = 0;
121	>	painCave.severity = OPENMD_INFO;
122	>	simError();
123	>	rCut_ = 12.0;
124	>	} else {
125	>	RealType thisCut;
126	>	set<AtomType*>::iterator i;
127	>	set<AtomType*> atomTypes;
128	>	atomTypes = info_->getSimulatedAtomTypes();
129	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
130	>	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
131	>	rCut_ = max(thisCut, rCut_);
132	>	}
133	>	sprintf(painCave.errMsg,
134	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
135	>	"\tOpenMD will use %lf angstroms.\n",
136	>	rCut_);
137	>	painCave.isFatal = 0;
138	>	painCave.severity = OPENMD_INFO;
139	>	simError();
140	>	}
141	>	}
142
143	<	calcLongRangeInteraction(needPotential, needStress);
143	>	fDecomp_->setUserCutoff(rCut_);
144	>	interactionMan_->setCutoffRadius(rCut_);
145
146	<	postCalculation(needStress);
146	>	map<string, CutoffMethod> stringToCutoffMethod;
147	>	stringToCutoffMethod["HARD"] = HARD;
148	>	stringToCutoffMethod["SWITCHED"] = SWITCHED;
149	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
150	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
151	>
152	>	if (simParams_->haveCutoffMethod()) {
153	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
154	>	map<string, CutoffMethod>::iterator i;
155	>	i = stringToCutoffMethod.find(cutMeth);
156	>	if (i == stringToCutoffMethod.end()) {
157	>	sprintf(painCave.errMsg,
158	>	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
159	>	"\tShould be one of: "
160	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
161	>	cutMeth.c_str());
162	>	painCave.isFatal = 1;
163	>	painCave.severity = OPENMD_ERROR;
164	>	simError();
165	>	} else {
166	>	cutoffMethod_ = i->second;
167	>	}
168	>	} else {
169	>	sprintf(painCave.errMsg,
170	>	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
171	>	"\tOpenMD will use SHIFTED_FORCE.\n");
172	>	painCave.isFatal = 0;
173	>	painCave.severity = OPENMD_INFO;
174	>	simError();
175	>	cutoffMethod_ = SHIFTED_FORCE;
176	>	}
177	>
178	>	map<string, CutoffPolicy> stringToCutoffPolicy;
179	>	stringToCutoffPolicy["MIX"] = MIX;
180	>	stringToCutoffPolicy["MAX"] = MAX;
181	>	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
182	>
183	>	std::string cutPolicy;
184	>	if (forceFieldOptions_.haveCutoffPolicy()){
185	>	cutPolicy = forceFieldOptions_.getCutoffPolicy();
186	>	}else if (simParams_->haveCutoffPolicy()) {
187	>	cutPolicy = simParams_->getCutoffPolicy();
188	>	}
189	>
190	>	if (!cutPolicy.empty()){
191	>	toUpper(cutPolicy);
192	>	map<string, CutoffPolicy>::iterator i;
193	>	i = stringToCutoffPolicy.find(cutPolicy);
194	>
195	>	if (i == stringToCutoffPolicy.end()) {
196	>	sprintf(painCave.errMsg,
197	>	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
198	>	"\tShould be one of: "
199	>	"MIX, MAX, or TRADITIONAL\n",
200	>	cutPolicy.c_str());
201	>	painCave.isFatal = 1;
202	>	painCave.severity = OPENMD_ERROR;
203	>	simError();
204	>	} else {
205	>	cutoffPolicy_ = i->second;
206	>	}
207	>	} else {
208	>	sprintf(painCave.errMsg,
209	>	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
210	>	"\tOpenMD will use TRADITIONAL.\n");
211	>	painCave.isFatal = 0;
212	>	painCave.severity = OPENMD_INFO;
213	>	simError();
214	>	cutoffPolicy_ = TRADITIONAL;
215	>	}
216	>
217	>	fDecomp_->setCutoffPolicy(cutoffPolicy_);
218	>
219	>	// create the switching function object:
220	>
221	>	switcher_ = new SwitchingFunction();
222	>
223	>	if (cutoffMethod_ == SWITCHED) {
224	>	if (simParams_->haveSwitchingRadius()) {
225	>	rSwitch_ = simParams_->getSwitchingRadius();
226	>	if (rSwitch_ > rCut_) {
227	>	sprintf(painCave.errMsg,
228	>	"ForceManager::setupCutoffs: switchingRadius (%f) is larger "
229	>	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
230	>	painCave.isFatal = 1;
231	>	painCave.severity = OPENMD_ERROR;
232	>	simError();
233	>	}
234	>	} else {
235	>	rSwitch_ = 0.85 * rCut_;
236	>	sprintf(painCave.errMsg,
237	>	"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
238	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
239	>	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
240	>	painCave.isFatal = 0;
241	>	painCave.severity = OPENMD_WARNING;
242	>	simError();
243	>	}
244	>	} else {
245	>	if (simParams_->haveSwitchingRadius()) {
246	>	map<string, CutoffMethod>::const_iterator it;
247	>	string theMeth;
248	>	for (it = stringToCutoffMethod.begin();
249	>	it != stringToCutoffMethod.end(); ++it) {
250	>	if (it->second == cutoffMethod_) {
251	>	theMeth = it->first;
252	>	break;
253	>	}
254	>	}
255	>	sprintf(painCave.errMsg,
256	>	"ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
257	>	"\tis not set to SWITCHED, so switchingRadius value\n"
258	>	"\twill be ignored for this simulation\n", theMeth.c_str());
259	>	painCave.isFatal = 0;
260	>	painCave.severity = OPENMD_WARNING;
261	>	simError();
262	>	}
263	>
264	>	rSwitch_ = rCut_;
265	>	}
266
267	+	// Default to cubic switching function.
268	+	sft_ = cubic;
269	+	if (simParams_->haveSwitchingFunctionType()) {
270	+	string funcType = simParams_->getSwitchingFunctionType();
271	+	toUpper(funcType);
272	+	if (funcType == "CUBIC") {
273	+	sft_ = cubic;
274	+	} else {
275	+	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
276	+	sft_ = fifth_order_poly;
277	+	} else {
278	+	// throw error
279	+	sprintf( painCave.errMsg,
280	+	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
281	+	"\tswitchingFunctionType must be one of: "
282	+	"\"cubic\" or \"fifth_order_polynomial\".",
283	+	funcType.c_str() );
284	+	painCave.isFatal = 1;
285	+	painCave.severity = OPENMD_ERROR;
286	+	simError();
287	+	}
288	+	}
289	+	}
290	+	switcher_->setSwitchType(sft_);
291	+	switcher_->setSwitch(rSwitch_, rCut_);
292	+	interactionMan_->setSwitchingRadius(rSwitch_);
293		}
294
295	+	void ForceManager::initialize() {
296	+
297	+	if (!info_->isTopologyDone()) {
298	+
299	+	info_->update();
300	+	interactionMan_->setSimInfo(info_);
301	+	interactionMan_->initialize();
302	+
303	+	// We want to delay the cutoffs until after the interaction
304	+	// manager has set up the atom-atom interactions so that we can
305	+	// query them for suggested cutoff values
306	+	setupCutoffs();
307	+
308	+	info_->prepareTopology();
309	+	}
310	+
311	+	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
312	+
313	+	// Force fields can set options on how to scale van der Waals and
314	+	// electrostatic interactions for atoms connected via bonds, bends
315	+	// and torsions in this case the topological distance between
316	+	// atoms is:
317	+	// 0 = topologically unconnected
318	+	// 1 = bonded together
319	+	// 2 = connected via a bend
320	+	// 3 = connected via a torsion
321	+
322	+	vdwScale_.reserve(4);
323	+	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
324	+
325	+	electrostaticScale_.reserve(4);
326	+	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
327	+
328	+	vdwScale_[0] = 1.0;
329	+	vdwScale_[1] = fopts.getvdw12scale();
330	+	vdwScale_[2] = fopts.getvdw13scale();
331	+	vdwScale_[3] = fopts.getvdw14scale();
332	+
333	+	electrostaticScale_[0] = 1.0;
334	+	electrostaticScale_[1] = fopts.getelectrostatic12scale();
335	+	electrostaticScale_[2] = fopts.getelectrostatic13scale();
336	+	electrostaticScale_[3] = fopts.getelectrostatic14scale();
337	+
338	+	fDecomp_->distributeInitialData();
339	+
340	+	initialized_ = true;
341	+
342	+	}
343	+
344	+	void ForceManager::calcForces() {
345	+
346	+	if (!initialized_) initialize();
347	+
348	+	preCalculation();
349	+	shortRangeInteractions();
350	+	longRangeInteractions();
351	+	postCalculation();
352	+	}
353	+
354		void ForceManager::preCalculation() {
355		SimInfo::MoleculeIterator mi;
356		Molecule* mol;
#	Line 80 | Line 358 | namespace oopse {
358		Atom* atom;
359		Molecule::RigidBodyIterator rbIter;
360		RigidBody* rb;
361	+	Molecule::CutoffGroupIterator ci;
362	+	CutoffGroup* cg;
363
364		// forces are zeroed here, before any are accumulated.
365	<	// NOTE: do not rezero the forces in Fortran.
86	<
365	>
366		for (mol = info_->beginMolecule(mi); mol != NULL;
367		mol = info_->nextMolecule(mi)) {
368	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
368	>	for(atom = mol->beginAtom(ai); atom != NULL;
369	>	atom = mol->nextAtom(ai)) {
370		atom->zeroForcesAndTorques();
371		}
372
#	Line 95 | Line 375 | namespace oopse {
375		rb = mol->nextRigidBody(rbIter)) {
376		rb->zeroForcesAndTorques();
377		}
378	+
379	+	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
380	+	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
381	+	cg = mol->nextCutoffGroup(ci)) {
382	+	//calculate the center of mass of cutoff group
383	+	cg->updateCOM();
384	+	}
385	+	}
386		}
387
388		// Zero out the stress tensor
#	Line 102 | Line 390 | namespace oopse {
390
391		}
392
393	<	void ForceManager::calcShortRangeInteraction() {
393	>	void ForceManager::shortRangeInteractions() {
394		Molecule* mol;
395		RigidBody* rb;
396		Bond* bond;
397		Bend* bend;
398		Torsion* torsion;
399	+	Inversion* inversion;
400		SimInfo::MoleculeIterator mi;
401		Molecule::RigidBodyIterator rbIter;
402		Molecule::BondIterator bondIter;;
403		Molecule::BendIterator  bendIter;
404		Molecule::TorsionIterator  torsionIter;
405	+	Molecule::InversionIterator  inversionIter;
406		RealType bondPotential = 0.0;
407		RealType bendPotential = 0.0;
408		RealType torsionPotential = 0.0;
409	+	RealType inversionPotential = 0.0;
410
411		//calculate short range interactions
412		for (mol = info_->beginMolecule(mi); mol != NULL;
#	Line 139 | Line 430 | namespace oopse {
430		RealType angle;
431		bend->calcForce(angle);
432		RealType currBendPot = bend->getPotential();
433	+
434		bendPotential += bend->getPotential();
435	<	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
435	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
436		if (i == bendDataSets.end()) {
437		BendDataSet dataSet;
438		dataSet.prev.angle = dataSet.curr.angle = angle;
439		dataSet.prev.potential = dataSet.curr.potential = currBendPot;
440		dataSet.deltaV = 0.0;
441	<	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
441	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
442	>	dataSet));
443		}else {
444		i->second.prev.angle = i->second.curr.angle;
445		i->second.prev.potential = i->second.curr.potential;
#	Line 163 | Line 456 | namespace oopse {
456		torsion->calcForce(angle);
457		RealType currTorsionPot = torsion->getPotential();
458		torsionPotential += torsion->getPotential();
459	<	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
459	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
460		if (i == torsionDataSets.end()) {
461		TorsionDataSet dataSet;
462		dataSet.prev.angle = dataSet.curr.angle = angle;
463		dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
464		dataSet.deltaV = 0.0;
465	<	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
465	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
466		}else {
467		i->second.prev.angle = i->second.curr.angle;
468		i->second.prev.potential = i->second.curr.potential;
#	Line 179 | Line 472 | namespace oopse {
472		i->second.prev.potential);
473		}
474		}
475	+
476	+	for (inversion = mol->beginInversion(inversionIter);
477	+	inversion != NULL;
478	+	inversion = mol->nextInversion(inversionIter)) {
479	+	RealType angle;
480	+	inversion->calcForce(angle);
481	+	RealType currInversionPot = inversion->getPotential();
482	+	inversionPotential += inversion->getPotential();
483	+	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
484	+	if (i == inversionDataSets.end()) {
485	+	InversionDataSet dataSet;
486	+	dataSet.prev.angle = dataSet.curr.angle = angle;
487	+	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
488	+	dataSet.deltaV = 0.0;
489	+	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
490	+	}else {
491	+	i->second.prev.angle = i->second.curr.angle;
492	+	i->second.prev.potential = i->second.curr.potential;
493	+	i->second.curr.angle = angle;
494	+	i->second.curr.potential = currInversionPot;
495	+	i->second.deltaV =  fabs(i->second.curr.potential -
496	+	i->second.prev.potential);
497	+	}
498	+	}
499		}
500
501		RealType  shortRangePotential = bondPotential + bendPotential +
502	<	torsionPotential;
502	>	torsionPotential +  inversionPotential;
503		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
504		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
505		curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
506		curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
507		curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
508	<
508	>	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
509		}
510
511	<	void ForceManager::calcLongRangeInteraction(bool needPotential,
195	<	bool needStress) {
196	<	Snapshot* curSnapshot;
197	<	DataStorage* config;
198	<	RealType* frc;
199	<	RealType* pos;
200	<	RealType* trq;
201	<	RealType* A;
202	<	RealType* electroFrame;
203	<	RealType* rc;
204	<
205	<	//get current snapshot from SimInfo
206	<	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
207	<
208	<	//get array pointers
209	<	config = &(curSnapshot->atomData);
210	<	frc = config->getArrayPointer(DataStorage::dslForce);
211	<	pos = config->getArrayPointer(DataStorage::dslPosition);
212	<	trq = config->getArrayPointer(DataStorage::dslTorque);
213	<	A   = config->getArrayPointer(DataStorage::dslAmat);
214	<	electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
511	>	void ForceManager::longRangeInteractions() {
512
513	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
514	+	DataStorage* config = &(curSnapshot->atomData);
515	+	DataStorage* cgConfig = &(curSnapshot->cgData);
516	+
517		//calculate the center of mass of cutoff group
518	+
519		SimInfo::MoleculeIterator mi;
520		Molecule* mol;
521		Molecule::CutoffGroupIterator ci;
522		CutoffGroup* cg;
523	<	Vector3d com;
524	<	std::vector<Vector3d> rcGroup;
223	<
224	<	if(info_->getNCutoffGroups() > 0){
225	<
523	>
524	>	if(info_->getNCutoffGroups() > 0){
525		for (mol = info_->beginMolecule(mi); mol != NULL;
526		mol = info_->nextMolecule(mi)) {
527		for(cg = mol->beginCutoffGroup(ci); cg != NULL;
528		cg = mol->nextCutoffGroup(ci)) {
529	<	cg->getCOM(com);
231	<	rcGroup.push_back(com);
529	>	cg->updateCOM();
530		}
531	<	}// end for (mol)
234	<
235	<	rc = rcGroup[0].getArrayPointer();
531	>	}
532		} else {
533		// center of mass of the group is the same as position of the atom
534		// if cutoff group does not exist
535	<	rc = pos;
535	>	cgConfig->position = config->position;
536		}
537	+
538	+	fDecomp_->zeroWorkArrays();
539	+	fDecomp_->distributeData();
540
541	<	//initialize data before passing to fortran
542	<	RealType longRangePotential[LR_POT_TYPES];
543	<	RealType lrPot = 0.0;
544	<	Vector3d totalDipole;
545	<	short int passedCalcPot = needPotential;
546	<	short int passedCalcStress = needStress;
547	<	int isError = 0;
541	>	int cg1, cg2, atom1, atom2, topoDist;
542	>	Vector3d d_grp, dag, d;
543	>	RealType rgrpsq, rgrp, r2, r;
544	>	RealType electroMult, vdwMult;
545	>	RealType vij;
546	>	Vector3d fij, fg, f1;
547	>	tuple3<RealType, RealType, RealType> cuts;
548	>	RealType rCutSq;
549	>	bool in_switching_region;
550	>	RealType sw, dswdr, swderiv;
551	>	vector<int> atomListColumn, atomListRow, atomListLocal;
552	>	InteractionData idat;
553	>	SelfData sdat;
554	>	RealType mf;
555	>	RealType lrPot;
556	>	RealType vpair;
557	>	potVec longRangePotential(0.0);
558	>	potVec workPot(0.0);
559
560	<	for (int i=0; i<LR_POT_TYPES;i++){
561	<	longRangePotential[i]=0.0; //Initialize array
562	<	}
560	>	int loopStart, loopEnd;
561	>
562	>	idat.vdwMult = &vdwMult;
563	>	idat.electroMult = &electroMult;
564	>	idat.pot = &workPot;
565	>	sdat.pot = fDecomp_->getEmbeddingPotential();
566	>	idat.vpair = &vpair;
567	>	idat.f1 = &f1;
568	>	idat.sw = &sw;
569	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
570	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
571
572	<	doForceLoop(pos,
573	<	rc,
574	<	A,
575	<	electroFrame,
576	<	frc,
259	<	trq,
260	<	tau.getArrayPointer(),
261	<	longRangePotential,
262	<	&passedCalcPot,
263	<	&passedCalcStress,
264	<	&isError );
265	<
266	<	if( isError ){
267	<	sprintf( painCave.errMsg,
268	<	"Error returned from the fortran force calculation.\n" );
269	<	painCave.isFatal = 1;
270	<	simError();
572	>	loopEnd = PAIR_LOOP;
573	>	if (info_->requiresPrepair() ) {
574	>	loopStart = PREPAIR_LOOP;
575	>	} else {
576	>	loopStart = PAIR_LOOP;
577		}
578	<	for (int i=0; i<LR_POT_TYPES;i++){
579	<	lrPot += longRangePotential[i]; //Quick hack
274	<	}
578	>
579	>	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
580
581	<	// grab the simulation box dipole moment if specified
582	<	if (info_->getCalcBoxDipole()){
583	<	getAccumulatedBoxDipole(totalDipole.getArrayPointer());
584	<
585	<	curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
586	<	curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
587	<	curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
581	>	if (iLoop == loopStart) {
582	>	bool update_nlist = fDecomp_->checkNeighborList();
583	>	if (update_nlist)
584	>	neighborList = fDecomp_->buildNeighborList();
585	>	}
586	>
587	>	for (vector<pair<int, int> >::iterator it = neighborList.begin();
588	>	it != neighborList.end(); ++it) {
589	>
590	>	cg1 = (*it).first;
591	>	cg2 = (*it).second;
592	>
593	>	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
594	>
595	>	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
596	>	curSnapshot->wrapVector(d_grp);
597	>	rgrpsq = d_grp.lengthSquare();
598	>
599	>	rCutSq = cuts.second;
600	>
601	>	if (rgrpsq < rCutSq) {
602	>	idat.rcut = &cuts.first;
603	>	if (iLoop == PAIR_LOOP) {
604	>	vij = 0.0;
605	>	fij = V3Zero;
606	>	}
607	>
608	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
609	>	rgrp);
610	>
611	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
612	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
613	>
614	>	for (vector<int>::iterator ia = atomListRow.begin();
615	>	ia != atomListRow.end(); ++ia) {
616	>	atom1 = (*ia);
617	>
618	>	for (vector<int>::iterator jb = atomListColumn.begin();
619	>	jb != atomListColumn.end(); ++jb) {
620	>	atom2 = (*jb);
621	>
622	>	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
623	>	vpair = 0.0;
624	>	workPot = 0.0;
625	>	f1 = V3Zero;
626	>
627	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
628	>
629	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
630	>	vdwMult = vdwScale_[topoDist];
631	>	electroMult = electrostaticScale_[topoDist];
632	>
633	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
634	>	idat.d = &d_grp;
635	>	idat.r2 = &rgrpsq;
636	>	} else {
637	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
638	>	curSnapshot->wrapVector( d );
639	>	r2 = d.lengthSquare();
640	>	idat.d = &d;
641	>	idat.r2 = &r2;
642	>	}
643	>
644	>	r = sqrt( *(idat.r2) );
645	>	idat.rij = &r;
646	>
647	>	if (iLoop == PREPAIR_LOOP) {
648	>	interactionMan_->doPrePair(idat);
649	>	} else {
650	>	interactionMan_->doPair(idat);
651	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
652	>
653	>	vij += vpair;
654	>	fij += f1;
655	>	tau -= outProduct( *(idat.d), f1);
656	>	}
657	>	}
658	>	}
659	>	}
660	>
661	>	if (iLoop == PAIR_LOOP) {
662	>	if (in_switching_region) {
663	>	swderiv = vij * dswdr / rgrp;
664	>	fg = swderiv * d_grp;
665	>	fij += fg;
666	>
667	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
668	>	tau -= outProduct( *(idat.d), fg);
669	>	}
670	>
671	>	for (vector<int>::iterator ia = atomListRow.begin();
672	>	ia != atomListRow.end(); ++ia) {
673	>	atom1 = (*ia);
674	>	mf = fDecomp_->getMassFactorRow(atom1);
675	>	// fg is the force on atom ia due to cutoff group's
676	>	// presence in switching region
677	>	fg = swderiv * d_grp * mf;
678	>	fDecomp_->addForceToAtomRow(atom1, fg);
679	>
680	>	if (atomListRow.size() > 1) {
681	>	if (info_->usesAtomicVirial()) {
682	>	// find the distance between the atom
683	>	// and the center of the cutoff group:
684	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
685	>	tau -= outProduct(dag, fg);
686	>	}
687	>	}
688	>	}
689	>	for (vector<int>::iterator jb = atomListColumn.begin();
690	>	jb != atomListColumn.end(); ++jb) {
691	>	atom2 = (*jb);
692	>	mf = fDecomp_->getMassFactorColumn(atom2);
693	>	// fg is the force on atom jb due to cutoff group's
694	>	// presence in switching region
695	>	fg = -swderiv * d_grp * mf;
696	>	fDecomp_->addForceToAtomColumn(atom2, fg);
697	>
698	>	if (atomListColumn.size() > 1) {
699	>	if (info_->usesAtomicVirial()) {
700	>	// find the distance between the atom
701	>	// and the center of the cutoff group:
702	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
703	>	tau -= outProduct(dag, fg);
704	>	}
705	>	}
706	>	}
707	>	}
708	>	//if (!SIM_uses_AtomicVirial) {
709	>	//  tau -= outProduct(d_grp, fij);
710	>	//}
711	>	}
712	>	}
713	>	}
714	>
715	>	if (iLoop == PREPAIR_LOOP) {
716	>	if (info_->requiresPrepair()) {
717	>
718	>	fDecomp_->collectIntermediateData();
719	>
720	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
721	>	fDecomp_->fillSelfData(sdat, atom1);
722	>	interactionMan_->doPreForce(sdat);
723	>	}
724	>
725	>	fDecomp_->distributeIntermediateData();
726	>
727	>	}
728	>	}
729	>
730		}
731
732	+	fDecomp_->collectData();
733	+
734	+	if (info_->requiresSelfCorrection()) {
735	+
736	+	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
737	+	fDecomp_->fillSelfData(sdat, atom1);
738	+	interactionMan_->doSelfCorrection(sdat);
739	+	}
740	+
741	+	}
742	+
743	+	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
744	+	*(fDecomp_->getPairwisePotential());
745	+
746	+	lrPot = longRangePotential.sum();
747	+
748		//store the tau and long range potential
749		curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
750	<	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
751	<	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
750	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
751	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
752		}
753
754
755	<	void ForceManager::postCalculation(bool needStress) {
755	>	void ForceManager::postCalculation() {
756		SimInfo::MoleculeIterator mi;
757		Molecule* mol;
758		Molecule::RigidBodyIterator rbIter;
#	Line 302 | Line 765 | namespace oopse {
765		mol = info_->nextMolecule(mi)) {
766		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
767		rb = mol->nextRigidBody(rbIter)) {
768	<	if (needStress) {
769	<	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
307	<	tau += rbTau;
308	<	} else{
309	<	rb->calcForcesAndTorques();
310	<	}
768	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
769	>	tau += rbTau;
770		}
771		}
772	<
314	<	if (needStress) {
772	>
773		#ifdef IS_MPI
774	<	Mat3x3d tmpTau(tau);
775	<	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
776	<	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
774	>	Mat3x3d tmpTau(tau);
775	>	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
776	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
777		#endif
778	<	curSnapshot->statData.setTau(tau);
321	<	}
778	>	curSnapshot->statData.setTau(tau);
779		}
780
781	<	} //end namespace oopse
781	>	} //end namespace OpenMD

Comparing:
trunk/src/brains/ForceManager.cpp (property svn:keywords), Revision 1215 by xsun, Wed Jan 23 21:22:37 2008 UTC vs.
branches/development/src/brains/ForceManager.cpp (property svn:keywords), Revision 1612 by gezelter, Fri Aug 12 19:59:56 2011 UTC

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