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

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trunk/src/brains/ForceManager.cpp (file contents), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/devel_omp/src/brains/ForceManager.cpp (file contents), Revision 1595 by chuckv, Tue Jul 19 18:50:04 2011 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	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	<	/**
43	<	* @file ForceManager.cpp
44	<	* @author tlin
45	<	* @date 11/09/2004
46	<	* @time 10:39am
47	<	* @version 1.0
48	<	*/
42	>	/**
43	>	* @file ForceManager.cpp
44	>	* @author tlin
45	>	* @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 __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	>	#include <cstdio>
63	>	#include <iostream>
64	>	#include <iomanip>
65
66	<	if (!info_->isFortranInitialized()) {
67	<	info_->update();
68	<	}
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	<	preCalculation();
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	<	calcShortRangeInteraction();
109	>	Globals* simParams_ = info_->getSimParams();
110	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
111	>
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();
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	<	}
219	>	// create the switching function object:
220
221	<	void ForceManager::preCalculation() {
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	>	longRangeInteractionsRapaport();
352	>	postCalculation();
353	>	}
354	>
355	>	void ForceManager::preCalculation() {
356		SimInfo::MoleculeIterator mi;
357		Molecule* mol;
358		Molecule::AtomIterator ai;
359		Atom* atom;
360		Molecule::RigidBodyIterator rbIter;
361		RigidBody* rb;
362	+	Molecule::CutoffGroupIterator ci;
363	+	CutoffGroup* cg;
364
365		// forces are zeroed here, before any are accumulated.
366	<	// NOTE: do not rezero the forces in Fortran.
367	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
368	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
369	<	atom->zeroForcesAndTorques();
366	>
367	>	for (mol = info_->beginMolecule(mi); mol != NULL;
368	>	mol = info_->nextMolecule(mi)) {
369	>	for(atom = mol->beginAtom(ai); atom != NULL;
370	>	atom = mol->nextAtom(ai)) {
371	>	atom->zeroForcesAndTorques();
372	>	}
373	>
374	>	//change the positions of atoms which belong to the rigidbodies
375	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
376	>	rb = mol->nextRigidBody(rbIter)) {
377	>	rb->zeroForcesAndTorques();
378	>	}
379	>
380	>	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
381	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
382	>	cg = mol->nextCutoffGroup(ci)) {
383	>	//calculate the center of mass of cutoff group
384	>	cg->updateCOM();
385		}
386	<
87	<	//change the positions of atoms which belong to the rigidbodies
88	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
89	<	rb->zeroForcesAndTorques();
90	<	}
386	>	}
387		}
388
389	<	}
390	<
391	<	void ForceManager::calcShortRangeInteraction() {
389	>	// Zero out the stress tensor
390	>	tau *= 0.0;
391	>
392	>	}
393	>
394	>	void ForceManager::shortRangeInteractions() {
395		Molecule* mol;
396		RigidBody* rb;
397		Bond* bond;
398		Bend* bend;
399		Torsion* torsion;
400	+	Inversion* inversion;
401		SimInfo::MoleculeIterator mi;
402		Molecule::RigidBodyIterator rbIter;
403		Molecule::BondIterator bondIter;;
404		Molecule::BendIterator  bendIter;
405		Molecule::TorsionIterator  torsionIter;
406	+	Molecule::InversionIterator  inversionIter;
407	+	RealType bondPotential = 0.0;
408	+	RealType bendPotential = 0.0;
409	+	RealType torsionPotential = 0.0;
410	+	RealType inversionPotential = 0.0;
411
412		//calculate short range interactions
413	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
413	>	for (mol = info_->beginMolecule(mi); mol != NULL;
414	>	mol = info_->nextMolecule(mi)) {
415
416	<	//change the positions of atoms which belong to the rigidbodies
417	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
418	<	rb->updateAtoms();
419	<	}
416	>	//change the positions of atoms which belong to the rigidbodies
417	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
418	>	rb = mol->nextRigidBody(rbIter)) {
419	>	rb->updateAtoms();
420	>	}
421
422	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
423	<	bond->calcForce();
424	<	}
422	>	for (bond = mol->beginBond(bondIter); bond != NULL;
423	>	bond = mol->nextBond(bondIter)) {
424	>	bond->calcForce();
425	>	bondPotential += bond->getPotential();
426	>	}
427
428	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
429	<	bend->calcForce();
428	>	for (bend = mol->beginBend(bendIter); bend != NULL;
429	>	bend = mol->nextBend(bendIter)) {
430	>
431	>	RealType angle;
432	>	bend->calcForce(angle);
433	>	RealType currBendPot = bend->getPotential();
434	>
435	>	bendPotential += bend->getPotential();
436	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
437	>	if (i == bendDataSets.end()) {
438	>	BendDataSet dataSet;
439	>	dataSet.prev.angle = dataSet.curr.angle = angle;
440	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
441	>	dataSet.deltaV = 0.0;
442	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
443	>	dataSet));
444	>	}else {
445	>	i->second.prev.angle = i->second.curr.angle;
446	>	i->second.prev.potential = i->second.curr.potential;
447	>	i->second.curr.angle = angle;
448	>	i->second.curr.potential = currBendPot;
449	>	i->second.deltaV =  fabs(i->second.curr.potential -
450	>	i->second.prev.potential);
451		}
452	<
453	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
454	<	torsion->calcForce();
455	<	}
456	<
452	>	}
453	>
454	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
455	>	torsion = mol->nextTorsion(torsionIter)) {
456	>	RealType angle;
457	>	torsion->calcForce(angle);
458	>	RealType currTorsionPot = torsion->getPotential();
459	>	torsionPotential += torsion->getPotential();
460	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
461	>	if (i == torsionDataSets.end()) {
462	>	TorsionDataSet dataSet;
463	>	dataSet.prev.angle = dataSet.curr.angle = angle;
464	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
465	>	dataSet.deltaV = 0.0;
466	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
467	>	}else {
468	>	i->second.prev.angle = i->second.curr.angle;
469	>	i->second.prev.potential = i->second.curr.potential;
470	>	i->second.curr.angle = angle;
471	>	i->second.curr.potential = currTorsionPot;
472	>	i->second.deltaV =  fabs(i->second.curr.potential -
473	>	i->second.prev.potential);
474	>	}
475	>	}
476	>
477	>	for (inversion = mol->beginInversion(inversionIter);
478	>	inversion != NULL;
479	>	inversion = mol->nextInversion(inversionIter)) {
480	>	RealType angle;
481	>	inversion->calcForce(angle);
482	>	RealType currInversionPot = inversion->getPotential();
483	>	inversionPotential += inversion->getPotential();
484	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
485	>	if (i == inversionDataSets.end()) {
486	>	InversionDataSet dataSet;
487	>	dataSet.prev.angle = dataSet.curr.angle = angle;
488	>	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
489	>	dataSet.deltaV = 0.0;
490	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
491	>	}else {
492	>	i->second.prev.angle = i->second.curr.angle;
493	>	i->second.prev.potential = i->second.curr.potential;
494	>	i->second.curr.angle = angle;
495	>	i->second.curr.potential = currInversionPot;
496	>	i->second.deltaV =  fabs(i->second.curr.potential -
497	>	i->second.prev.potential);
498	>	}
499	>	}
500		}
501
502	<	double  shortRangePotential = 0.0;
503	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
131	<	shortRangePotential += mol->getPotential();
132	<	}
133	<
502	>	RealType  shortRangePotential = bondPotential + bendPotential +
503	>	torsionPotential +  inversionPotential;
504		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
505		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
506	<	}
506	>	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
507	>	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
508	>	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
509	>	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
510	>	}
511	>
512	>	void ForceManager::longRangeInteractionsRapaport() {
513
514	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
515	<	Snapshot* curSnapshot;
516	<	DataStorage* config;
141	<	double* frc;
142	<	double* pos;
143	<	double* trq;
144	<	double* A;
145	<	double* electroFrame;
146	<	double* rc;
147	<
148	<	//get current snapshot from SimInfo
149	<	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
514	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
515	>	DataStorage* config = &(curSnapshot->atomData);
516	>	DataStorage* cgConfig = &(curSnapshot->cgData);
517
151	–	//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);
158	–
518		//calculate the center of mass of cutoff group
519	+
520		SimInfo::MoleculeIterator mi;
521		Molecule* mol;
522		Molecule::CutoffGroupIterator ci;
523		CutoffGroup* cg;
164	–	Vector3d com;
165	–	std::vector<Vector3d> rcGroup;
166	–
167	–	if(info_->getNCutoffGroups() > 0){
524
525	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
526	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
527	<	cg->getCOM(com);
528	<	rcGroup.push_back(com);
529	<	}
530	<	}// end for (mol)
531	<
532	<	rc = rcGroup[0].getArrayPointer();
533	<	} else {
534	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
535	<	rc = pos;
525	>	if(info_->getNCutoffGroups() > 0){
526	>	for (mol = info_->beginMolecule(mi); mol != NULL;
527	>	mol = info_->nextMolecule(mi)) {
528	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
529	>	cg = mol->nextCutoffGroup(ci)) {
530	>	cerr << "branch1\n";
531	>	cerr << "globind = " << cg->getGlobalIndex() << "\n";
532	>	cg->updateCOM();
533	>	}
534	>	}
535	>	} else {
536	>	// center of mass of the group is the same as position of the atom
537	>	// if cutoff group does not exist
538	>	cerr << "branch2\n";
539	>	cgConfig->position = config->position;
540		}
181	–
182	–	//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;
541
542	<	doForceLoop( pos,
543	<	rc,
191	<	A,
192	<	electroFrame,
193	<	frc,
194	<	trq,
195	<	tau.getArrayPointer(),
196	<	&longRangePotential,
197	<	&passedCalcPot,
198	<	&passedCalcStress,
199	<	&isError );
542	>	fDecomp_->zeroWorkArrays();
543	>	fDecomp_->distributeData();
544
545	<	if( isError ){
546	<	sprintf( painCave.errMsg,
547	<	"Error returned from the fortran force calculation.\n" );
548	<	painCave.isFatal = 1;
549	<	simError();
545	>	int cg1, cg2, atom1, atom2, topoDist;
546	>	Vector3d d_grp, dag, d;
547	>	RealType rgrpsq, rgrp, r2, r;
548	>	RealType electroMult, vdwMult;
549	>	RealType vij;
550	>	Vector3d fij, fg, f1;
551	>	tuple3<RealType, RealType, RealType> cuts;
552	>	RealType rCutSq;
553	>	bool in_switching_region;
554	>	RealType sw, dswdr, swderiv;
555	>	vector<int> atomListColumn, atomListRow, atomListLocal;
556	>	InteractionData idat;
557	>	SelfData sdat;
558	>	RealType mf;
559	>	RealType lrPot;
560	>	RealType vpair;
561	>	potVec longRangePotential(0.0);
562	>	potVec workPot(0.0);
563	>
564	>	int loopStart, loopEnd;
565	>
566	>	idat.vdwMult = &vdwMult;
567	>	idat.electroMult = &electroMult;
568	>	idat.pot = &workPot;
569	>	sdat.pot = fDecomp_->getEmbeddingPotential();
570	>	idat.vpair = &vpair;
571	>	idat.f1 = &f1;
572	>	idat.sw = &sw;
573	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
574	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
575	>
576	>	loopEnd = PAIR_LOOP;
577	>	if (info_->requiresPrepair() ) {
578	>	loopStart = PREPAIR_LOOP;
579	>	} else {
580	>	loopStart = PAIR_LOOP;
581		}
582
583	<	//store the tau and long range potential
209	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential;
210	<	curSnapshot->statData.setTau(tau);
211	<	}
583	>	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
584
585	+	if (iLoop == loopStart) {
586	+	bool update_nlist = fDecomp_->checkNeighborList();
587	+	if (update_nlist)
588	+	neighborMatW = fDecomp_->buildLayerBasedNeighborList();
589	+	}
590
591	<	void ForceManager::postCalculation() {
591	>	int i;
592	>	#pragma omp parallel for num_threads(2) private(i)
593	>	for(i = 0; i < neighborMatW.size(); ++i)
594	>	for(vector<int>::iterator j = neighborMatW[i].begin(); j != neighborMatW[i].end(); ++j)
595	>	{
596	>	cg1 = i;
597	>	cg2 = *j;
598	>
599	>	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
600	>
601	>	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
602	>	curSnapshot->wrapVector(d_grp);
603	>	rgrpsq = d_grp.lengthSquare();
604	>
605	>	rCutSq = cuts.second;
606	>
607	>	if (rgrpsq < rCutSq) {
608	>	idat.rcut = &cuts.first;
609	>	if (iLoop == PAIR_LOOP) {
610	>	vij = 0.0;
611	>	fij = V3Zero;
612	>	}
613	>
614	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
615	>	rgrp);
616	>
617	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
618	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
619	>
620	>	for (vector<int>::iterator ia = atomListRow.begin();
621	>	ia != atomListRow.end(); ++ia) {
622	>	atom1 = (*ia);
623	>
624	>	for (vector<int>::iterator jb = atomListColumn.begin();
625	>	jb != atomListColumn.end(); ++jb) {
626	>	atom2 = (*jb);
627	>
628	>	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
629	>	vpair = 0.0;
630	>	workPot = 0.0;
631	>	f1 = V3Zero;
632	>
633	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
634	>
635	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
636	>	vdwMult = vdwScale_[topoDist];
637	>	electroMult = electrostaticScale_[topoDist];
638	>
639	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
640	>	idat.d = &d_grp;
641	>	idat.r2 = &rgrpsq;
642	>	cerr << "dgrp = " << d_grp << "\n";
643	>	} else {
644	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
645	>	curSnapshot->wrapVector( d );
646	>	r2 = d.lengthSquare();
647	>	cerr << "datm = " << d<< "\n";
648	>	idat.d = &d;
649	>	idat.r2 = &r2;
650	>	}
651	>
652	>	cerr << "idat.d = " << *(idat.d) << "\n";
653	>	r = sqrt( *(idat.r2) );
654	>	idat.rij = &r;
655	>
656	>	if (iLoop == PREPAIR_LOOP) {
657	>	interactionMan_->doPrePair(idat);
658	>	} else {
659	>	interactionMan_->doPair(idat);
660	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
661	>
662	>	cerr << "d = " << *(idat.d) << "\tv=" << vpair << "\tf=" << f1 << "\n";
663	>	vij += vpair;
664	>	fij += f1;
665	>	tau -= outProduct( *(idat.d), f1);
666	>	}
667	>	}
668	>	}
669	>	}
670	>
671	>	if (iLoop == PAIR_LOOP) {
672	>	if (in_switching_region) {
673	>	swderiv = vij * dswdr / rgrp;
674	>	fg = swderiv * d_grp;
675	>	fij += fg;
676	>
677	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
678	>	tau -= outProduct( *(idat.d), fg);
679	>	}
680	>
681	>	for (vector<int>::iterator ia = atomListRow.begin();
682	>	ia != atomListRow.end(); ++ia) {
683	>	atom1 = (*ia);
684	>	mf = fDecomp_->getMassFactorRow(atom1);
685	>	// fg is the force on atom ia due to cutoff group's
686	>	// presence in switching region
687	>	fg = swderiv * d_grp * mf;
688	>	fDecomp_->addForceToAtomRow(atom1, fg);
689	>
690	>	if (atomListRow.size() > 1) {
691	>	if (info_->usesAtomicVirial()) {
692	>	// find the distance between the atom
693	>	// and the center of the cutoff group:
694	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
695	>	tau -= outProduct(dag, fg);
696	>	}
697	>	}
698	>	}
699	>	for (vector<int>::iterator jb = atomListColumn.begin();
700	>	jb != atomListColumn.end(); ++jb) {
701	>	atom2 = (*jb);
702	>	mf = fDecomp_->getMassFactorColumn(atom2);
703	>	// fg is the force on atom jb due to cutoff group's
704	>	// presence in switching region
705	>	fg = -swderiv * d_grp * mf;
706	>	fDecomp_->addForceToAtomColumn(atom2, fg);
707	>
708	>	if (atomListColumn.size() > 1) {
709	>	if (info_->usesAtomicVirial()) {
710	>	// find the distance between the atom
711	>	// and the center of the cutoff group:
712	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
713	>	tau -= outProduct(dag, fg);
714	>	}
715	>	}
716	>	}
717	>	}
718	>	//if (!SIM_uses_AtomicVirial) {
719	>	//  tau -= outProduct(d_grp, fij);
720	>	//}
721	>	}
722	>	}
723	>	}
724	>
725	>	if (iLoop == PREPAIR_LOOP) {
726	>	if (info_->requiresPrepair()) {
727	>
728	>	fDecomp_->collectIntermediateData();
729	>
730	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
731	>	fDecomp_->fillSelfData(sdat, atom1);
732	>	interactionMan_->doPreForce(sdat);
733	>	}
734	>
735	>	fDecomp_->distributeIntermediateData();
736	>
737	>	}
738	>	}
739	>
740	>	}
741	>
742	>	fDecomp_->collectData();
743	>
744	>	if (info_->requiresSelfCorrection()) {
745	>
746	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
747	>	fDecomp_->fillSelfData(sdat, atom1);
748	>	interactionMan_->doSelfCorrection(sdat);
749	>	}
750	>
751	>	}
752	>
753	>	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
754	>	*(fDecomp_->getPairwisePotential());
755	>
756	>	lrPot = longRangePotential.sum();
757	>
758	>	//store the tau and long range potential
759	>	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
760	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
761	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
762	>	}
763	>
764	>	void ForceManager::longRangeInteractions() {
765	>
766	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
767	>	DataStorage* config = &(curSnapshot->atomData);
768	>	DataStorage* cgConfig = &(curSnapshot->cgData);
769	>
770	>	//calculate the center of mass of cutoff group
771	>
772	>	SimInfo::MoleculeIterator mi;
773	>	Molecule* mol;
774	>	Molecule::CutoffGroupIterator ci;
775	>	CutoffGroup* cg;
776	>
777	>	if(info_->getNCutoffGroups() > 0){
778	>	for (mol = info_->beginMolecule(mi); mol != NULL;
779	>	mol = info_->nextMolecule(mi)) {
780	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
781	>	cg = mol->nextCutoffGroup(ci)) {
782	>	cerr << "branch1\n";
783	>	cerr << "globind = " << cg->getGlobalIndex() << "\n";
784	>	cg->updateCOM();
785	>	}
786	>	}
787	>	} else {
788	>	// center of mass of the group is the same as position of the atom
789	>	// if cutoff group does not exist
790	>	cerr << "branch2\n";
791	>	cgConfig->position = config->position;
792	>	}
793	>
794	>	fDecomp_->zeroWorkArrays();
795	>	fDecomp_->distributeData();
796	>
797	>	int cg1, cg2, atom1, atom2, topoDist;
798	>	Vector3d d_grp, dag, d;
799	>	RealType rgrpsq, rgrp, r2, r;
800	>	RealType electroMult, vdwMult;
801	>	RealType vij;
802	>	Vector3d fij, fg, f1;
803	>	tuple3<RealType, RealType, RealType> cuts;
804	>	RealType rCutSq;
805	>	bool in_switching_region;
806	>	RealType sw, dswdr, swderiv;
807	>	vector<int> atomListColumn, atomListRow, atomListLocal;
808	>	InteractionData idat;
809	>	SelfData sdat;
810	>	RealType mf;
811	>	RealType lrPot;
812	>	RealType vpair;
813	>	potVec longRangePotential(0.0);
814	>	potVec workPot(0.0);
815	>
816	>	int loopStart, loopEnd;
817	>
818	>	idat.vdwMult = &vdwMult;
819	>	idat.electroMult = &electroMult;
820	>	idat.pot = &workPot;
821	>	sdat.pot = fDecomp_->getEmbeddingPotential();
822	>	idat.vpair = &vpair;
823	>	idat.f1 = &f1;
824	>	idat.sw = &sw;
825	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
826	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
827	>
828	>	loopEnd = PAIR_LOOP;
829	>	if (info_->requiresPrepair() ) {
830	>	loopStart = PREPAIR_LOOP;
831	>	} else {
832	>	loopStart = PAIR_LOOP;
833	>	}
834	>
835	>	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
836	>
837	>	if (iLoop == loopStart) {
838	>	bool update_nlist = fDecomp_->checkNeighborList();
839	>	if (update_nlist)
840	>	neighborList = fDecomp_->buildNeighborList();
841	>
842	>	}
843	>
844	>	for (vector<pair<int, int> >::iterator it = neighborList.begin();
845	>	it != neighborList.end(); ++it)
846	>	{
847	>	cg1 = (*it).first;
848	>	cg2 = (*it).second;
849	>
850	>	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
851	>
852	>	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
853	>	curSnapshot->wrapVector(d_grp);
854	>	rgrpsq = d_grp.lengthSquare();
855	>
856	>	rCutSq = cuts.second;
857	>
858	>	if (rgrpsq < rCutSq) {
859	>	idat.rcut = &cuts.first;
860	>	if (iLoop == PAIR_LOOP) {
861	>	vij = 0.0;
862	>	fij = V3Zero;
863	>	}
864	>
865	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
866	>	rgrp);
867	>
868	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
869	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
870	>
871	>	for (vector<int>::iterator ia = atomListRow.begin();
872	>	ia != atomListRow.end(); ++ia) {
873	>	atom1 = (*ia);
874	>
875	>	for (vector<int>::iterator jb = atomListColumn.begin();
876	>	jb != atomListColumn.end(); ++jb) {
877	>	atom2 = (*jb);
878	>
879	>	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
880	>	vpair = 0.0;
881	>	workPot = 0.0;
882	>	f1 = V3Zero;
883	>
884	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
885	>
886	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
887	>	vdwMult = vdwScale_[topoDist];
888	>	electroMult = electrostaticScale_[topoDist];
889	>
890	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
891	>	idat.d = &d_grp;
892	>	idat.r2 = &rgrpsq;
893	>	cerr << "dgrp = " << d_grp << "\n";
894	>	} else {
895	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
896	>	curSnapshot->wrapVector( d );
897	>	r2 = d.lengthSquare();
898	>	cerr << "datm = " << d<< "\n";
899	>	idat.d = &d;
900	>	idat.r2 = &r2;
901	>	}
902	>
903	>	cerr << "idat.d = " << *(idat.d) << "\n";
904	>	r = sqrt( *(idat.r2) );
905	>	idat.rij = &r;
906	>
907	>	if (iLoop == PREPAIR_LOOP) {
908	>	interactionMan_->doPrePair(idat);
909	>	} else {
910	>	interactionMan_->doPair(idat);
911	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
912	>
913	>	cerr << "d = " << *(idat.d) << "\tv=" << vpair << "\tf=" << f1 << "\n";
914	>	vij += vpair;
915	>	fij += f1;
916	>	tau -= outProduct( *(idat.d), f1);
917	>	}
918	>	}
919	>	}
920	>	}
921	>
922	>	if (iLoop == PAIR_LOOP) {
923	>	if (in_switching_region) {
924	>	swderiv = vij * dswdr / rgrp;
925	>	fg = swderiv * d_grp;
926	>	fij += fg;
927	>
928	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
929	>	tau -= outProduct( *(idat.d), fg);
930	>	}
931	>
932	>	for (vector<int>::iterator ia = atomListRow.begin();
933	>	ia != atomListRow.end(); ++ia) {
934	>	atom1 = (*ia);
935	>	mf = fDecomp_->getMassFactorRow(atom1);
936	>	// fg is the force on atom ia due to cutoff group's
937	>	// presence in switching region
938	>	fg = swderiv * d_grp * mf;
939	>	fDecomp_->addForceToAtomRow(atom1, fg);
940	>
941	>	if (atomListRow.size() > 1) {
942	>	if (info_->usesAtomicVirial()) {
943	>	// find the distance between the atom
944	>	// and the center of the cutoff group:
945	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
946	>	tau -= outProduct(dag, fg);
947	>	}
948	>	}
949	>	}
950	>	for (vector<int>::iterator jb = atomListColumn.begin();
951	>	jb != atomListColumn.end(); ++jb) {
952	>	atom2 = (*jb);
953	>	mf = fDecomp_->getMassFactorColumn(atom2);
954	>	// fg is the force on atom jb due to cutoff group's
955	>	// presence in switching region
956	>	fg = -swderiv * d_grp * mf;
957	>	fDecomp_->addForceToAtomColumn(atom2, fg);
958	>
959	>	if (atomListColumn.size() > 1) {
960	>	if (info_->usesAtomicVirial()) {
961	>	// find the distance between the atom
962	>	// and the center of the cutoff group:
963	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
964	>	tau -= outProduct(dag, fg);
965	>	}
966	>	}
967	>	}
968	>	}
969	>	//if (!SIM_uses_AtomicVirial) {
970	>	//  tau -= outProduct(d_grp, fij);
971	>	//}
972	>	}
973	>	}
974	>	}
975	>
976	>	if (iLoop == PREPAIR_LOOP) {
977	>	if (info_->requiresPrepair()) {
978	>
979	>	fDecomp_->collectIntermediateData();
980	>
981	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
982	>	fDecomp_->fillSelfData(sdat, atom1);
983	>	interactionMan_->doPreForce(sdat);
984	>	}
985	>
986	>	fDecomp_->distributeIntermediateData();
987	>
988	>	}
989	>	}
990	>
991	>	}
992	>
993	>	fDecomp_->collectData();
994	>
995	>	if (info_->requiresSelfCorrection()) {
996	>
997	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
998	>	fDecomp_->fillSelfData(sdat, atom1);
999	>	interactionMan_->doSelfCorrection(sdat);
1000	>	}
1001	>
1002	>	}
1003	>
1004	>	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
1005	>	*(fDecomp_->getPairwisePotential());
1006	>
1007	>	lrPot = longRangePotential.sum();
1008	>
1009	>	//store the tau and long range potential
1010	>	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
1011	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
1012	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
1013	>	}
1014	>
1015	>
1016	>	void ForceManager::postCalculation() {
1017		SimInfo::MoleculeIterator mi;
1018		Molecule* mol;
1019		Molecule::RigidBodyIterator rbIter;
1020		RigidBody* rb;
1021	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
1022
1023		// collect the atomic forces onto rigid bodies
1024	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
1025	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
1026	<	rb->calcForcesAndTorques();
1027	<	}
1024	>
1025	>	for (mol = info_->beginMolecule(mi); mol != NULL;
1026	>	mol = info_->nextMolecule(mi)) {
1027	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1028	>	rb = mol->nextRigidBody(rbIter)) {
1029	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
1030	>	tau += rbTau;
1031	>	}
1032		}
1033	+
1034	+	#ifdef IS_MPI
1035	+	Mat3x3d tmpTau(tau);
1036	+	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
1037	+	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1038	+	#endif
1039	+	curSnapshot->statData.setTau(tau);
1040	+	}
1041
1042	<	}
228	<
229	<	} //end namespace oopse
1042	>	} //end namespace OpenMD

Comparing:
trunk/src/brains/ForceManager.cpp (property svn:keywords), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/devel_omp/src/brains/ForceManager.cpp (property svn:keywords), Revision 1595 by chuckv, Tue Jul 19 18:50:04 2011 UTC

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