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

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trunk/src/brains/ForceManager.cpp (file contents), Revision 664 by chuckv, Wed Oct 12 21:57:16 2005 UTC vs.
branches/development/src/brains/ForceManager.cpp (file contents), Revision 1868 by gezelter, Tue Apr 30 15:56:54 2013 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, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
44		* @file ForceManager.cpp
45		* @author tlin
46		* @date 11/09/2004
46	–	* @time 10:39am
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	<	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 "perturbations/ElectricField.hpp"
61	>	#include "parallel/ForceMatrixDecomposition.hpp"
62
63	<	void ForceManager::calcForces(bool needPotential, bool needStress) {
63	>	#include <cstdio>
64	>	#include <iostream>
65	>	#include <iomanip>
66
67	<	if (!info_->isFortranInitialized()) {
68	<	info_->update();
69	<	}
67	>	using namespace std;
68	>	namespace OpenMD {
69	>
70	>	ForceManager::ForceManager(SimInfo * info) : info_(info), switcher_(NULL) {
71	>	forceField_ = info_->getForceField();
72	>	interactionMan_ = new InteractionManager();
73	>	fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
74	>	thermo = new Thermo(info_);
75	>	}
76
77	<	preCalculation();
77	>	ForceManager::~ForceManager() {
78	>	perturbations_.clear();
79
80	<	calcShortRangeInteraction();
80	>	delete switcher_;
81	>	delete interactionMan_;
82	>	delete fDecomp_;
83	>	delete thermo;
84	>	}
85	>
86	>	/**
87	>	* setupCutoffs
88	>	*
89	>	* Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
90	>	* and cutoffPolicy
91	>	*
92	>	* cutoffRadius : realType
93	>	*  If the cutoffRadius was explicitly set, use that value.
94	>	*  If the cutoffRadius was not explicitly set:
95	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
96	>	*      No electrostatic atoms?  Poll the atom types present in the
97	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
98	>	*      Use the maximum suggested value that was found.
99	>	*
100	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
101	>	*                        or SHIFTED_POTENTIAL)
102	>	*      If cutoffMethod was explicitly set, use that choice.
103	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
104	>	*
105	>	* cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
106	>	*      If cutoffPolicy was explicitly set, use that choice.
107	>	*      If cutoffPolicy was not explicitly set, use TRADITIONAL
108	>	*
109	>	* switchingRadius : realType
110	>	*  If the cutoffMethod was set to SWITCHED:
111	>	*      If the switchingRadius was explicitly set, use that value
112	>	*          (but do a sanity check first).
113	>	*      If the switchingRadius was not explicitly set: use 0.85 *
114	>	*      cutoffRadius_
115	>	*  If the cutoffMethod was not set to SWITCHED:
116	>	*      Set switchingRadius equal to cutoffRadius for safety.
117	>	*/
118	>	void ForceManager::setupCutoffs() {
119	>
120	>	Globals* simParams_ = info_->getSimParams();
121	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
122	>	int mdFileVersion;
123	>	rCut_ = 0.0; //Needs a value for a later max() call;
124	>
125	>	if (simParams_->haveMDfileVersion())
126	>	mdFileVersion = simParams_->getMDfileVersion();
127	>	else
128	>	mdFileVersion = 0;
129	>
130	>	// We need the list of simulated atom types to figure out cutoffs
131	>	// as well as long range corrections.
132
133	<	calcLongRangeInteraction(needPotential, needStress);
133	>	set<AtomType*>::iterator i;
134	>	set<AtomType*> atomTypes_;
135	>	atomTypes_ = info_->getSimulatedAtomTypes();
136
137	<	postCalculation();
137	>	if (simParams_->haveCutoffRadius()) {
138	>	rCut_ = simParams_->getCutoffRadius();
139	>	} else {
140	>	if (info_->usesElectrostaticAtoms()) {
141	>	sprintf(painCave.errMsg,
142	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
143	>	"\tOpenMD will use a default value of 12.0 angstroms"
144	>	"\tfor the cutoffRadius.\n");
145	>	painCave.isFatal = 0;
146	>	painCave.severity = OPENMD_INFO;
147	>	simError();
148	>	rCut_ = 12.0;
149	>	} else {
150	>	RealType thisCut;
151	>	for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
152	>	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
153	>	rCut_ = max(thisCut, rCut_);
154	>	}
155	>	sprintf(painCave.errMsg,
156	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
157	>	"\tOpenMD will use %lf angstroms.\n",
158	>	rCut_);
159	>	painCave.isFatal = 0;
160	>	painCave.severity = OPENMD_INFO;
161	>	simError();
162	>	}
163	>	}
164	>
165	>	fDecomp_->setUserCutoff(rCut_);
166	>	interactionMan_->setCutoffRadius(rCut_);
167	>
168	>	map<string, CutoffMethod> stringToCutoffMethod;
169	>	stringToCutoffMethod["HARD"] = HARD;
170	>	stringToCutoffMethod["SWITCHED"] = SWITCHED;
171	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
172	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
173	>
174	>	if (simParams_->haveCutoffMethod()) {
175	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
176	>	map<string, CutoffMethod>::iterator i;
177	>	i = stringToCutoffMethod.find(cutMeth);
178	>	if (i == stringToCutoffMethod.end()) {
179	>	sprintf(painCave.errMsg,
180	>	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
181	>	"\tShould be one of: "
182	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
183	>	cutMeth.c_str());
184	>	painCave.isFatal = 1;
185	>	painCave.severity = OPENMD_ERROR;
186	>	simError();
187	>	} else {
188	>	cutoffMethod_ = i->second;
189	>	}
190	>	} else {
191	>	if (mdFileVersion > 1) {
192	>	sprintf(painCave.errMsg,
193	>	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
194	>	"\tOpenMD will use SHIFTED_FORCE.\n");
195	>	painCave.isFatal = 0;
196	>	painCave.severity = OPENMD_INFO;
197	>	simError();
198	>	cutoffMethod_ = SHIFTED_FORCE;
199	>	} else {
200	>	// handle the case where the old file version was in play
201	>	// (there should be no cutoffMethod, so we have to deduce it
202	>	// from other data).
203	>
204	>	sprintf(painCave.errMsg,
205	>	"ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
206	>	"\tOpenMD found a file which does not set a cutoffMethod.\n"
207	>	"\tOpenMD will attempt to deduce a cutoffMethod using the\n"
208	>	"\tbehavior of the older (version 1) code.  To remove this\n"
209	>	"\twarning, add an explicit cutoffMethod and change the top\n"
210	>	"\tof the file so that it begins with <OpenMD version=2>\n");
211	>	painCave.isFatal = 0;
212	>	painCave.severity = OPENMD_WARNING;
213	>	simError();
214	>
215	>	// The old file version tethered the shifting behavior to the
216	>	// electrostaticSummationMethod keyword.
217
218	+	if (simParams_->haveElectrostaticSummationMethod()) {
219	+	string myMethod = simParams_->getElectrostaticSummationMethod();
220	+	toUpper(myMethod);
221	+
222	+	if (myMethod == "SHIFTED_POTENTIAL") {
223	+	cutoffMethod_ = SHIFTED_POTENTIAL;
224	+	} else if (myMethod == "SHIFTED_FORCE") {
225	+	cutoffMethod_ = SHIFTED_FORCE;
226	+	}
227	+
228	+	if (simParams_->haveSwitchingRadius())
229	+	rSwitch_ = simParams_->getSwitchingRadius();
230	+
231	+	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
232	+	if (simParams_->haveSwitchingRadius()){
233	+	sprintf(painCave.errMsg,
234	+	"ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
235	+	"\tA value was set for the switchingRadius\n"
236	+	"\teven though the electrostaticSummationMethod was\n"
237	+	"\tset to %s\n", myMethod.c_str());
238	+	painCave.severity = OPENMD_WARNING;
239	+	painCave.isFatal = 1;
240	+	simError();
241	+	}
242	+	}
243	+	if (abs(rCut_ - rSwitch_) < 0.0001) {
244	+	if (cutoffMethod_ == SHIFTED_FORCE) {
245	+	sprintf(painCave.errMsg,
246	+	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
247	+	"\tcutoffRadius and switchingRadius are set to the\n"
248	+	"\tsame value.  OpenMD will use shifted force\n"
249	+	"\tpotentials instead of switching functions.\n");
250	+	painCave.isFatal = 0;
251	+	painCave.severity = OPENMD_WARNING;
252	+	simError();
253	+	} else {
254	+	cutoffMethod_ = SHIFTED_POTENTIAL;
255	+	sprintf(painCave.errMsg,
256	+	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
257	+	"\tcutoffRadius and switchingRadius are set to the\n"
258	+	"\tsame value.  OpenMD will use shifted potentials\n"
259	+	"\tinstead of switching functions.\n");
260	+	painCave.isFatal = 0;
261	+	painCave.severity = OPENMD_WARNING;
262	+	simError();
263	+	}
264	+	}
265	+	}
266	+	}
267	+	}
268	+
269	+	map<string, CutoffPolicy> stringToCutoffPolicy;
270	+	stringToCutoffPolicy["MIX"] = MIX;
271	+	stringToCutoffPolicy["MAX"] = MAX;
272	+	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
273	+
274	+	string cutPolicy;
275	+	if (forceFieldOptions_.haveCutoffPolicy()){
276	+	cutPolicy = forceFieldOptions_.getCutoffPolicy();
277	+	}else if (simParams_->haveCutoffPolicy()) {
278	+	cutPolicy = simParams_->getCutoffPolicy();
279	+	}
280	+
281	+	if (!cutPolicy.empty()){
282	+	toUpper(cutPolicy);
283	+	map<string, CutoffPolicy>::iterator i;
284	+	i = stringToCutoffPolicy.find(cutPolicy);
285	+
286	+	if (i == stringToCutoffPolicy.end()) {
287	+	sprintf(painCave.errMsg,
288	+	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
289	+	"\tShould be one of: "
290	+	"MIX, MAX, or TRADITIONAL\n",
291	+	cutPolicy.c_str());
292	+	painCave.isFatal = 1;
293	+	painCave.severity = OPENMD_ERROR;
294	+	simError();
295	+	} else {
296	+	cutoffPolicy_ = i->second;
297	+	}
298	+	} else {
299	+	sprintf(painCave.errMsg,
300	+	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
301	+	"\tOpenMD will use TRADITIONAL.\n");
302	+	painCave.isFatal = 0;
303	+	painCave.severity = OPENMD_INFO;
304	+	simError();
305	+	cutoffPolicy_ = TRADITIONAL;
306	+	}
307	+
308	+	fDecomp_->setCutoffPolicy(cutoffPolicy_);
309	+
310	+	// create the switching function object:
311	+
312	+	switcher_ = new SwitchingFunction();
313	+
314	+	if (cutoffMethod_ == SWITCHED) {
315	+	if (simParams_->haveSwitchingRadius()) {
316	+	rSwitch_ = simParams_->getSwitchingRadius();
317	+	if (rSwitch_ > rCut_) {
318	+	sprintf(painCave.errMsg,
319	+	"ForceManager::setupCutoffs: switchingRadius (%f) is larger "
320	+	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
321	+	painCave.isFatal = 1;
322	+	painCave.severity = OPENMD_ERROR;
323	+	simError();
324	+	}
325	+	} else {
326	+	rSwitch_ = 0.85 * rCut_;
327	+	sprintf(painCave.errMsg,
328	+	"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
329	+	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
330	+	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
331	+	painCave.isFatal = 0;
332	+	painCave.severity = OPENMD_WARNING;
333	+	simError();
334	+	}
335	+	} else {
336	+	if (mdFileVersion > 1) {
337	+	// throw an error if we define a switching radius and don't need one.
338	+	// older file versions should not do this.
339	+	if (simParams_->haveSwitchingRadius()) {
340	+	map<string, CutoffMethod>::const_iterator it;
341	+	string theMeth;
342	+	for (it = stringToCutoffMethod.begin();
343	+	it != stringToCutoffMethod.end(); ++it) {
344	+	if (it->second == cutoffMethod_) {
345	+	theMeth = it->first;
346	+	break;
347	+	}
348	+	}
349	+	sprintf(painCave.errMsg,
350	+	"ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
351	+	"\tis not set to SWITCHED, so switchingRadius value\n"
352	+	"\twill be ignored for this simulation\n", theMeth.c_str());
353	+	painCave.isFatal = 0;
354	+	painCave.severity = OPENMD_WARNING;
355	+	simError();
356	+	}
357	+	}
358	+	rSwitch_ = rCut_;
359	+	}
360	+
361	+	// Default to cubic switching function.
362	+	sft_ = cubic;
363	+	if (simParams_->haveSwitchingFunctionType()) {
364	+	string funcType = simParams_->getSwitchingFunctionType();
365	+	toUpper(funcType);
366	+	if (funcType == "CUBIC") {
367	+	sft_ = cubic;
368	+	} else {
369	+	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
370	+	sft_ = fifth_order_poly;
371	+	} else {
372	+	// throw error
373	+	sprintf( painCave.errMsg,
374	+	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
375	+	"\tswitchingFunctionType must be one of: "
376	+	"\"cubic\" or \"fifth_order_polynomial\".",
377	+	funcType.c_str() );
378	+	painCave.isFatal = 1;
379	+	painCave.severity = OPENMD_ERROR;
380	+	simError();
381	+	}
382	+	}
383	+	}
384	+	switcher_->setSwitchType(sft_);
385	+	switcher_->setSwitch(rSwitch_, rCut_);
386		}
387
388	+
389	+
390	+
391	+	void ForceManager::initialize() {
392	+
393	+	if (!info_->isTopologyDone()) {
394	+
395	+	info_->update();
396	+	interactionMan_->setSimInfo(info_);
397	+	interactionMan_->initialize();
398	+
399	+	// We want to delay the cutoffs until after the interaction
400	+	// manager has set up the atom-atom interactions so that we can
401	+	// query them for suggested cutoff values
402	+	setupCutoffs();
403	+
404	+	info_->prepareTopology();
405	+
406	+	doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
407	+	doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
408	+	if (doHeatFlux_) doParticlePot_ = true;
409	+
410	+	doElectricField_ = info_->getSimParams()->getOutputElectricField();
411	+
412	+	}
413	+
414	+	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
415	+
416	+	// Force fields can set options on how to scale van der Waals and
417	+	// electrostatic interactions for atoms connected via bonds, bends
418	+	// and torsions in this case the topological distance between
419	+	// atoms is:
420	+	// 0 = topologically unconnected
421	+	// 1 = bonded together
422	+	// 2 = connected via a bend
423	+	// 3 = connected via a torsion
424	+
425	+	vdwScale_.reserve(4);
426	+	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
427	+
428	+	electrostaticScale_.reserve(4);
429	+	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
430	+
431	+	vdwScale_[0] = 1.0;
432	+	vdwScale_[1] = fopts.getvdw12scale();
433	+	vdwScale_[2] = fopts.getvdw13scale();
434	+	vdwScale_[3] = fopts.getvdw14scale();
435	+
436	+	electrostaticScale_[0] = 1.0;
437	+	electrostaticScale_[1] = fopts.getelectrostatic12scale();
438	+	electrostaticScale_[2] = fopts.getelectrostatic13scale();
439	+	electrostaticScale_[3] = fopts.getelectrostatic14scale();
440	+
441	+	if (info_->getSimParams()->haveElectricField()) {
442	+	ElectricField* eField = new ElectricField(info_);
443	+	perturbations_.push_back(eField);
444	+	}
445	+
446	+	usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
447	+
448	+	fDecomp_->distributeInitialData();
449	+
450	+	initialized_ = true;
451	+
452	+	}
453	+
454	+	void ForceManager::calcForces() {
455	+
456	+	if (!initialized_) initialize();
457	+
458	+	preCalculation();
459	+	shortRangeInteractions();
460	+	longRangeInteractions();
461	+	postCalculation();
462	+	}
463	+
464		void ForceManager::preCalculation() {
465		SimInfo::MoleculeIterator mi;
466		Molecule* mol;
#	Line 78 | Line 468 | namespace oopse {
468		Atom* atom;
469		Molecule::RigidBodyIterator rbIter;
470		RigidBody* rb;
471	+	Molecule::CutoffGroupIterator ci;
472	+	CutoffGroup* cg;
473
474	<	// forces are zeroed here, before any are accumulated.
475	<	// NOTE: do not rezero the forces in Fortran.
476	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
477	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
474	>	// forces and potentials are zeroed here, before any are
475	>	// accumulated.
476	>
477	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
478	>
479	>	snap->setBondPotential(0.0);
480	>	snap->setBendPotential(0.0);
481	>	snap->setTorsionPotential(0.0);
482	>	snap->setInversionPotential(0.0);
483	>
484	>	potVec zeroPot(0.0);
485	>	snap->setLongRangePotential(zeroPot);
486	>	snap->setExcludedPotentials(zeroPot);
487	>
488	>	snap->setRestraintPotential(0.0);
489	>	snap->setRawPotential(0.0);
490	>
491	>	for (mol = info_->beginMolecule(mi); mol != NULL;
492	>	mol = info_->nextMolecule(mi)) {
493	>	for(atom = mol->beginAtom(ai); atom != NULL;
494	>	atom = mol->nextAtom(ai)) {
495		atom->zeroForcesAndTorques();
496		}
497	<
497	>
498		//change the positions of atoms which belong to the rigidbodies
499	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
499	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
500	>	rb = mol->nextRigidBody(rbIter)) {
501		rb->zeroForcesAndTorques();
502		}
503	+
504	+	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
505	+	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
506	+	cg = mol->nextCutoffGroup(ci)) {
507	+	//calculate the center of mass of cutoff group
508	+	cg->updateCOM();
509	+	}
510	+	}
511		}
512
513	+	// Zero out the stress tensor
514	+	stressTensor *= 0.0;
515	+	// Zero out the heatFlux
516	+	fDecomp_->setHeatFlux( Vector3d(0.0) );
517		}
518	<
519	<	void ForceManager::calcShortRangeInteraction() {
518	>
519	>	void ForceManager::shortRangeInteractions() {
520		Molecule* mol;
521		RigidBody* rb;
522		Bond* bond;
523		Bend* bend;
524		Torsion* torsion;
525	+	Inversion* inversion;
526		SimInfo::MoleculeIterator mi;
527		Molecule::RigidBodyIterator rbIter;
528		Molecule::BondIterator bondIter;;
529		Molecule::BendIterator  bendIter;
530		Molecule::TorsionIterator  torsionIter;
531	+	Molecule::InversionIterator  inversionIter;
532	+	RealType bondPotential = 0.0;
533	+	RealType bendPotential = 0.0;
534	+	RealType torsionPotential = 0.0;
535	+	RealType inversionPotential = 0.0;
536
537		//calculate short range interactions
538	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
538	>	for (mol = info_->beginMolecule(mi); mol != NULL;
539	>	mol = info_->nextMolecule(mi)) {
540
541		//change the positions of atoms which belong to the rigidbodies
542	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
543	<	rb->updateAtoms();
542	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
543	>	rb = mol->nextRigidBody(rbIter)) {
544	>	rb->updateAtoms();
545		}
546
547	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
548	<	bond->calcForce();
547	>	for (bond = mol->beginBond(bondIter); bond != NULL;
548	>	bond = mol->nextBond(bondIter)) {
549	>	bond->calcForce(doParticlePot_);
550	>	bondPotential += bond->getPotential();
551		}
552
553	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
554	<	bend->calcForce();
555	<	}
556	<
557	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
558	<	torsion->calcForce();
553	>	for (bend = mol->beginBend(bendIter); bend != NULL;
554	>	bend = mol->nextBend(bendIter)) {
555	>
556	>	RealType angle;
557	>	bend->calcForce(angle, doParticlePot_);
558	>	RealType currBendPot = bend->getPotential();
559	>
560	>	bendPotential += bend->getPotential();
561	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
562	>	if (i == bendDataSets.end()) {
563	>	BendDataSet dataSet;
564	>	dataSet.prev.angle = dataSet.curr.angle = angle;
565	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
566	>	dataSet.deltaV = 0.0;
567	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
568	>	dataSet));
569	>	}else {
570	>	i->second.prev.angle = i->second.curr.angle;
571	>	i->second.prev.potential = i->second.curr.potential;
572	>	i->second.curr.angle = angle;
573	>	i->second.curr.potential = currBendPot;
574	>	i->second.deltaV =  fabs(i->second.curr.potential -
575	>	i->second.prev.potential);
576	>	}
577		}
578	<
578	>
579	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
580	>	torsion = mol->nextTorsion(torsionIter)) {
581	>	RealType angle;
582	>	torsion->calcForce(angle, doParticlePot_);
583	>	RealType currTorsionPot = torsion->getPotential();
584	>	torsionPotential += torsion->getPotential();
585	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
586	>	if (i == torsionDataSets.end()) {
587	>	TorsionDataSet dataSet;
588	>	dataSet.prev.angle = dataSet.curr.angle = angle;
589	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
590	>	dataSet.deltaV = 0.0;
591	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
592	>	}else {
593	>	i->second.prev.angle = i->second.curr.angle;
594	>	i->second.prev.potential = i->second.curr.potential;
595	>	i->second.curr.angle = angle;
596	>	i->second.curr.potential = currTorsionPot;
597	>	i->second.deltaV =  fabs(i->second.curr.potential -
598	>	i->second.prev.potential);
599	>	}
600	>	}
601	>
602	>	for (inversion = mol->beginInversion(inversionIter);
603	>	inversion != NULL;
604	>	inversion = mol->nextInversion(inversionIter)) {
605	>	RealType angle;
606	>	inversion->calcForce(angle, doParticlePot_);
607	>	RealType currInversionPot = inversion->getPotential();
608	>	inversionPotential += inversion->getPotential();
609	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
610	>	if (i == inversionDataSets.end()) {
611	>	InversionDataSet dataSet;
612	>	dataSet.prev.angle = dataSet.curr.angle = angle;
613	>	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
614	>	dataSet.deltaV = 0.0;
615	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
616	>	}else {
617	>	i->second.prev.angle = i->second.curr.angle;
618	>	i->second.prev.potential = i->second.curr.potential;
619	>	i->second.curr.angle = angle;
620	>	i->second.curr.potential = currInversionPot;
621	>	i->second.deltaV =  fabs(i->second.curr.potential -
622	>	i->second.prev.potential);
623	>	}
624	>	}
625		}
130	–
131	–	double  shortRangePotential = 0.0;
132	–	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
133	–	shortRangePotential += mol->getPotential();
134	–	}
626
627	+	#ifdef IS_MPI
628	+	// Collect from all nodes.  This should eventually be moved into a
629	+	// SystemDecomposition, but this is a better place than in
630	+	// Thermo to do the collection.
631	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
632	+	MPI::SUM);
633	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
634	+	MPI::SUM);
635	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
636	+	MPI::REALTYPE, MPI::SUM);
637	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
638	+	MPI::REALTYPE, MPI::SUM);
639	+	#endif
640	+
641		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
137	–	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
138	–	}
642
643	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
644	<	Snapshot* curSnapshot;
645	<	DataStorage* config;
646	<	double* frc;
144	<	double* pos;
145	<	double* trq;
146	<	double* A;
147	<	double* electroFrame;
148	<	double* rc;
643	>	curSnapshot->setBondPotential(bondPotential);
644	>	curSnapshot->setBendPotential(bendPotential);
645	>	curSnapshot->setTorsionPotential(torsionPotential);
646	>	curSnapshot->setInversionPotential(inversionPotential);
647
648	<	//get current snapshot from SimInfo
649	<	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
648	>	// RealType shortRangePotential = bondPotential + bendPotential +
649	>	//   torsionPotential +  inversionPotential;
650
651	<	//get array pointers
652	<	config = &(curSnapshot->atomData);
653	<	frc = config->getArrayPointer(DataStorage::dslForce);
654	<	pos = config->getArrayPointer(DataStorage::dslPosition);
157	<	trq = config->getArrayPointer(DataStorage::dslTorque);
158	<	A   = config->getArrayPointer(DataStorage::dslAmat);
159	<	electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
651	>	// curSnapshot->setShortRangePotential(shortRangePotential);
652	>	}
653	>
654	>	void ForceManager::longRangeInteractions() {
655
656	+
657	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
658	+	DataStorage* config = &(curSnapshot->atomData);
659	+	DataStorage* cgConfig = &(curSnapshot->cgData);
660	+
661		//calculate the center of mass of cutoff group
662	+
663		SimInfo::MoleculeIterator mi;
664		Molecule* mol;
665		Molecule::CutoffGroupIterator ci;
666		CutoffGroup* cg;
166	–	Vector3d com;
167	–	std::vector<Vector3d> rcGroup;
667
668	<	if(info_->getNCutoffGroups() > 0){
669	<
670	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
671	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
672	<	cg->getCOM(com);
673	<	rcGroup.push_back(com);
668	>	if(info_->getNCutoffGroups() > 0){
669	>	for (mol = info_->beginMolecule(mi); mol != NULL;
670	>	mol = info_->nextMolecule(mi)) {
671	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
672	>	cg = mol->nextCutoffGroup(ci)) {
673	>	cg->updateCOM();
674		}
675	<	}// end for (mol)
177	<
178	<	rc = rcGroup[0].getArrayPointer();
675	>	}
676		} else {
677	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
678	<	rc = pos;
677	>	// center of mass of the group is the same as position of the atom
678	>	// if cutoff group does not exist
679	>	cgConfig->position = config->position;
680	>	cgConfig->velocity = config->velocity;
681		}
682	<
683	<	//initialize data before passing to fortran
684	<	double longRangePotential[LR_POT_TYPES];
186	<	double lrPot = 0.0;
682	>
683	>	fDecomp_->zeroWorkArrays();
684	>	fDecomp_->distributeData();
685
686	<	Mat3x3d tau;
687	<	short int passedCalcPot = needPotential;
688	<	short int passedCalcStress = needStress;
689	<	int isError = 0;
686	>	int cg1, cg2, atom1, atom2, topoDist;
687	>	Vector3d d_grp, dag, d, gvel2, vel2;
688	>	RealType rgrpsq, rgrp, r2, r;
689	>	RealType electroMult, vdwMult;
690	>	RealType vij;
691	>	Vector3d fij, fg, f1;
692	>	tuple3<RealType, RealType, RealType> cuts;
693	>	RealType rCutSq;
694	>	bool in_switching_region;
695	>	RealType sw, dswdr, swderiv;
696	>	vector<int> atomListColumn, atomListRow, atomListLocal;
697	>	InteractionData idat;
698	>	SelfData sdat;
699	>	RealType mf;
700	>	RealType vpair;
701	>	RealType dVdFQ1(0.0);
702	>	RealType dVdFQ2(0.0);
703	>	potVec longRangePotential(0.0);
704	>	potVec workPot(0.0);
705	>	potVec exPot(0.0);
706	>	Vector3d eField1(0.0);
707	>	Vector3d eField2(0.0);
708	>	vector<int>::iterator ia, jb;
709
710	<	for (int i=0; i<LR_POT_TYPES;i++){
711	<	longRangePotential[i]=0.0; //Initialize array
710	>	int loopStart, loopEnd;
711	>
712	>	idat.vdwMult = &vdwMult;
713	>	idat.electroMult = &electroMult;
714	>	idat.pot = &workPot;
715	>	idat.excludedPot = &exPot;
716	>	sdat.pot = fDecomp_->getEmbeddingPotential();
717	>	sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
718	>	idat.vpair = &vpair;
719	>	idat.dVdFQ1 = &dVdFQ1;
720	>	idat.dVdFQ2 = &dVdFQ2;
721	>	idat.eField1 = &eField1;
722	>	idat.eField2 = &eField2;
723	>	idat.f1 = &f1;
724	>	idat.sw = &sw;
725	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
726	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
727	>	idat.doParticlePot = doParticlePot_;
728	>	idat.doElectricField = doElectricField_;
729	>	sdat.doParticlePot = doParticlePot_;
730	>
731	>	loopEnd = PAIR_LOOP;
732	>	if (info_->requiresPrepair() ) {
733	>	loopStart = PREPAIR_LOOP;
734	>	} else {
735	>	loopStart = PAIR_LOOP;
736		}
737	+	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
738	+
739	+	if (iLoop == loopStart) {
740	+	bool update_nlist = fDecomp_->checkNeighborList();
741	+	if (update_nlist) {
742	+	if (!usePeriodicBoundaryConditions_)
743	+	Mat3x3d bbox = thermo->getBoundingBox();
744	+	neighborList = fDecomp_->buildNeighborList();
745	+	}
746	+	}
747
748	+	for (vector<pair<int, int> >::iterator it = neighborList.begin();
749	+	it != neighborList.end(); ++it) {
750	+
751	+	cg1 = (*it).first;
752	+	cg2 = (*it).second;
753	+
754	+	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
755
756	+	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
757
758	<	doForceLoop( pos,
759	<	rc,
760	<	A,
202	<	electroFrame,
203	<	frc,
204	<	trq,
205	<	tau.getArrayPointer(),
206	<	longRangePotential,
207	<	&passedCalcPot,
208	<	&passedCalcStress,
209	<	&isError );
758	>	curSnapshot->wrapVector(d_grp);
759	>	rgrpsq = d_grp.lengthSquare();
760	>	rCutSq = cuts.second;
761
762	<	if( isError ){
763	<	sprintf( painCave.errMsg,
764	<	"Error returned from the fortran force calculation.\n" );
765	<	painCave.isFatal = 1;
766	<	simError();
767	<	}
768	<	for (int i=0; i<LR_POT_TYPES;i++){
769	<	lrPot += longRangePotential[i]; //Quick hack
762	>	if (rgrpsq < rCutSq) {
763	>	idat.rcut = &cuts.first;
764	>	if (iLoop == PAIR_LOOP) {
765	>	vij = 0.0;
766	>	fij = V3Zero;
767	>	eField1 = V3Zero;
768	>	eField2 = V3Zero;
769	>	}
770	>
771	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
772	>	rgrp);
773	>
774	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
775	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
776	>
777	>	if (doHeatFlux_)
778	>	gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
779	>
780	>	for (ia = atomListRow.begin();
781	>	ia != atomListRow.end(); ++ia) {
782	>	atom1 = (*ia);
783	>
784	>	for (jb = atomListColumn.begin();
785	>	jb != atomListColumn.end(); ++jb) {
786	>	atom2 = (*jb);
787	>
788	>	if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
789	>
790	>	vpair = 0.0;
791	>	workPot = 0.0;
792	>	exPot = 0.0;
793	>	f1 = V3Zero;
794	>	dVdFQ1 = 0.0;
795	>	dVdFQ2 = 0.0;
796	>
797	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
798	>
799	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
800	>	vdwMult = vdwScale_[topoDist];
801	>	electroMult = electrostaticScale_[topoDist];
802	>
803	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
804	>	idat.d = &d_grp;
805	>	idat.r2 = &rgrpsq;
806	>	if (doHeatFlux_)
807	>	vel2 = gvel2;
808	>	} else {
809	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
810	>	curSnapshot->wrapVector( d );
811	>	r2 = d.lengthSquare();
812	>	idat.d = &d;
813	>	idat.r2 = &r2;
814	>	if (doHeatFlux_)
815	>	vel2 = fDecomp_->getAtomVelocityColumn(atom2);
816	>	}
817	>
818	>	r = sqrt( *(idat.r2) );
819	>	idat.rij = &r;
820	>
821	>	if (iLoop == PREPAIR_LOOP) {
822	>	interactionMan_->doPrePair(idat);
823	>	} else {
824	>	interactionMan_->doPair(idat);
825	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
826	>	vij += vpair;
827	>	fij += f1;
828	>	stressTensor -= outProduct( *(idat.d), f1);
829	>	if (doHeatFlux_)
830	>	fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
831	>	}
832	>	}
833	>	}
834	>	}
835	>
836	>	if (iLoop == PAIR_LOOP) {
837	>	if (in_switching_region) {
838	>	swderiv = vij * dswdr / rgrp;
839	>	fg = swderiv * d_grp;
840	>	fij += fg;
841	>
842	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
843	>	if (!fDecomp_->skipAtomPair(atomListRow[0],
844	>	atomListColumn[0],
845	>	cg1, cg2)) {
846	>	stressTensor -= outProduct( *(idat.d), fg);
847	>	if (doHeatFlux_)
848	>	fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
849	>	}
850	>	}
851	>
852	>	for (ia = atomListRow.begin();
853	>	ia != atomListRow.end(); ++ia) {
854	>	atom1 = (*ia);
855	>	mf = fDecomp_->getMassFactorRow(atom1);
856	>	// fg is the force on atom ia due to cutoff group's
857	>	// presence in switching region
858	>	fg = swderiv * d_grp * mf;
859	>	fDecomp_->addForceToAtomRow(atom1, fg);
860	>	if (atomListRow.size() > 1) {
861	>	if (info_->usesAtomicVirial()) {
862	>	// find the distance between the atom
863	>	// and the center of the cutoff group:
864	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
865	>	stressTensor -= outProduct(dag, fg);
866	>	if (doHeatFlux_)
867	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
868	>	}
869	>	}
870	>	}
871	>	for (jb = atomListColumn.begin();
872	>	jb != atomListColumn.end(); ++jb) {
873	>	atom2 = (*jb);
874	>	mf = fDecomp_->getMassFactorColumn(atom2);
875	>	// fg is the force on atom jb due to cutoff group's
876	>	// presence in switching region
877	>	fg = -swderiv * d_grp * mf;
878	>	fDecomp_->addForceToAtomColumn(atom2, fg);
879	>
880	>	if (atomListColumn.size() > 1) {
881	>	if (info_->usesAtomicVirial()) {
882	>	// find the distance between the atom
883	>	// and the center of the cutoff group:
884	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
885	>	stressTensor -= outProduct(dag, fg);
886	>	if (doHeatFlux_)
887	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
888	>	}
889	>	}
890	>	}
891	>	}
892	>	//if (!info_->usesAtomicVirial()) {
893	>	//  stressTensor -= outProduct(d_grp, fij);
894	>	//  if (doHeatFlux_)
895	>	//     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
896	>	//}
897	>	}
898	>	}
899	>	}
900	>
901	>	if (iLoop == PREPAIR_LOOP) {
902	>	if (info_->requiresPrepair()) {
903	>
904	>	fDecomp_->collectIntermediateData();
905	>
906	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
907	>	fDecomp_->fillSelfData(sdat, atom1);
908	>	interactionMan_->doPreForce(sdat);
909	>	}
910	>
911	>	fDecomp_->distributeIntermediateData();
912	>
913	>	}
914	>	}
915		}
916	+
917	+	// collects pairwise information
918	+	fDecomp_->collectData();
919	+
920	+	if (info_->requiresSelfCorrection()) {
921	+	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
922	+	fDecomp_->fillSelfData(sdat, atom1);
923	+	interactionMan_->doSelfCorrection(sdat);
924	+	}
925	+	}
926
927	<	//store the tau and long range potential
928	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
223	<	//  curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential;
224	<	curSnapshot->statData.setTau(tau);
225	<	}
927	>	// collects single-atom information
928	>	fDecomp_->collectSelfData();
929
930	+	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
931	+	*(fDecomp_->getPairwisePotential());
932
933	+	curSnapshot->setLongRangePotential(longRangePotential);
934	+
935	+	curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
936	+	*(fDecomp_->getExcludedPotential()));
937	+
938	+	}
939	+
940	+
941		void ForceManager::postCalculation() {
942	+
943	+	vector<Perturbation*>::iterator pi;
944	+	for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
945	+	(*pi)->applyPerturbation();
946	+	}
947	+
948		SimInfo::MoleculeIterator mi;
949		Molecule* mol;
950		Molecule::RigidBodyIterator rbIter;
951		RigidBody* rb;
952	<
952	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
953	>
954		// collect the atomic forces onto rigid bodies
955	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
956	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
957	<	rb->calcForcesAndTorques();
955	>
956	>	for (mol = info_->beginMolecule(mi); mol != NULL;
957	>	mol = info_->nextMolecule(mi)) {
958	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
959	>	rb = mol->nextRigidBody(rbIter)) {
960	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
961	>	stressTensor += rbTau;
962		}
963		}
964	+
965	+	#ifdef IS_MPI
966	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
967	+	MPI::REALTYPE, MPI::SUM);
968	+	#endif
969	+	curSnapshot->setStressTensor(stressTensor);
970	+
971	+	if (info_->getSimParams()->getUseLongRangeCorrections()) {
972	+	/*
973	+	RealType vol = curSnapshot->getVolume();
974	+	RealType Elrc(0.0);
975	+	RealType Wlrc(0.0);
976
977	<	}
977	>	set<AtomType*>::iterator i;
978	>	set<AtomType*>::iterator j;
979	>
980	>	RealType n_i, n_j;
981	>	RealType rho_i, rho_j;
982	>	pair<RealType, RealType> LRI;
983	>
984	>	for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
985	>	n_i = RealType(info_->getGlobalCountOfType(*i));
986	>	rho_i = n_i /  vol;
987	>	for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) {
988	>	n_j = RealType(info_->getGlobalCountOfType(*j));
989	>	rho_j = n_j / vol;
990	>
991	>	LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) );
992
993	<	} //end namespace oopse
993	>	Elrc += n_i   * rho_j * LRI.first;
994	>	Wlrc -= rho_i * rho_j * LRI.second;
995	>	}
996	>	}
997	>	Elrc *= 2.0 * NumericConstant::PI;
998	>	Wlrc *= 2.0 * NumericConstant::PI;
999	>
1000	>	RealType lrp = curSnapshot->getLongRangePotential();
1001	>	curSnapshot->setLongRangePotential(lrp + Elrc);
1002	>	stressTensor += Wlrc * SquareMatrix3<RealType>::identity();
1003	>	curSnapshot->setStressTensor(stressTensor);
1004	>	*/
1005	>
1006	>	}
1007	>	}
1008	>	}

Comparing:
trunk/src/brains/ForceManager.cpp (property svn:keywords), Revision 664 by chuckv, Wed Oct 12 21:57:16 2005 UTC vs.
branches/development/src/brains/ForceManager.cpp (property svn:keywords), Revision 1868 by gezelter, Tue Apr 30 15:56:54 2013 UTC

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