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

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trunk/src/brains/ForceManager.cpp (file contents), Revision 998 by chrisfen, Mon Jul 3 13:18:43 2006 UTC vs.
branches/development/src/brains/ForceManager.cpp (file contents), Revision 1808 by gezelter, Mon Oct 22 20:42:10 2012 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]  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	+	#include "primitives/Bond.hpp"
56		#include "primitives/Bend.hpp"
57	<	#include "primitives/Bend.hpp"
58	<	namespace oopse {
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	<	/*
64	<	struct BendOrderStruct {
65	<	Bend* bend;
63	<	BendDataSet dataSet;
64	<	};
65	<	struct TorsionOrderStruct {
66	<	Torsion* torsion;
67	<	TorsionDataSet dataSet;
68	<	};
63	>	#include <cstdio>
64	>	#include <iostream>
65	>	#include <iomanip>
66
67	<	bool  BendSortFunctor(const BendOrderStruct& b1, const BendOrderStruct& b2) {
68	<	return b1.dataSet.deltaV < b2.dataSet.deltaV;
67	>	using namespace std;
68	>	namespace OpenMD {
69	>
70	>	ForceManager::ForceManager(SimInfo * info) : info_(info) {
71	>	forceField_ = info_->getForceField();
72	>	interactionMan_ = new InteractionManager();
73	>	fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
74		}
75
76	<	bool  TorsionSortFunctor(const TorsionOrderStruct& t1, const TorsionOrderStruct& t2) {
77	<	return t1.dataSet.deltaV < t2.dataSet.deltaV;
78	<	}
79	<	*/
80	<	void ForceManager::calcForces(bool needPotential, bool needStress) {
76	>	/**
77	>	* setupCutoffs
78	>	*
79	>	* Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
80	>	* and cutoffPolicy
81	>	*
82	>	* cutoffRadius : realType
83	>	*  If the cutoffRadius was explicitly set, use that value.
84	>	*  If the cutoffRadius was not explicitly set:
85	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
86	>	*      No electrostatic atoms?  Poll the atom types present in the
87	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
88	>	*      Use the maximum suggested value that was found.
89	>	*
90	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
91	>	*                        or SHIFTED_POTENTIAL)
92	>	*      If cutoffMethod was explicitly set, use that choice.
93	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
94	>	*
95	>	* cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
96	>	*      If cutoffPolicy was explicitly set, use that choice.
97	>	*      If cutoffPolicy was not explicitly set, use TRADITIONAL
98	>	*
99	>	* switchingRadius : realType
100	>	*  If the cutoffMethod was set to SWITCHED:
101	>	*      If the switchingRadius was explicitly set, use that value
102	>	*          (but do a sanity check first).
103	>	*      If the switchingRadius was not explicitly set: use 0.85 *
104	>	*      cutoffRadius_
105	>	*  If the cutoffMethod was not set to SWITCHED:
106	>	*      Set switchingRadius equal to cutoffRadius for safety.
107	>	*/
108	>	void ForceManager::setupCutoffs() {
109	>
110	>	Globals* simParams_ = info_->getSimParams();
111	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
112	>	int mdFileVersion;
113	>	rCut_ = 0.0; //Needs a value for a later max() call;
114	>
115	>	if (simParams_->haveMDfileVersion())
116	>	mdFileVersion = simParams_->getMDfileVersion();
117	>	else
118	>	mdFileVersion = 0;
119	>
120	>	if (simParams_->haveCutoffRadius()) {
121	>	rCut_ = simParams_->getCutoffRadius();
122	>	} else {
123	>	if (info_->usesElectrostaticAtoms()) {
124	>	sprintf(painCave.errMsg,
125	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
126	>	"\tOpenMD will use a default value of 12.0 angstroms"
127	>	"\tfor the cutoffRadius.\n");
128	>	painCave.isFatal = 0;
129	>	painCave.severity = OPENMD_INFO;
130	>	simError();
131	>	rCut_ = 12.0;
132	>	} else {
133	>	RealType thisCut;
134	>	set<AtomType*>::iterator i;
135	>	set<AtomType*> atomTypes;
136	>	atomTypes = info_->getSimulatedAtomTypes();
137	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
138	>	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
139	>	rCut_ = max(thisCut, rCut_);
140	>	}
141	>	sprintf(painCave.errMsg,
142	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
143	>	"\tOpenMD will use %lf angstroms.\n",
144	>	rCut_);
145	>	painCave.isFatal = 0;
146	>	painCave.severity = OPENMD_INFO;
147	>	simError();
148	>	}
149	>	}
150
151	<	if (!info_->isFortranInitialized()) {
152	<	info_->update();
151	>	fDecomp_->setUserCutoff(rCut_);
152	>	interactionMan_->setCutoffRadius(rCut_);
153	>
154	>	map<string, CutoffMethod> stringToCutoffMethod;
155	>	stringToCutoffMethod["HARD"] = HARD;
156	>	stringToCutoffMethod["SWITCHED"] = SWITCHED;
157	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
158	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
159	>
160	>	if (simParams_->haveCutoffMethod()) {
161	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
162	>	map<string, CutoffMethod>::iterator i;
163	>	i = stringToCutoffMethod.find(cutMeth);
164	>	if (i == stringToCutoffMethod.end()) {
165	>	sprintf(painCave.errMsg,
166	>	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
167	>	"\tShould be one of: "
168	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
169	>	cutMeth.c_str());
170	>	painCave.isFatal = 1;
171	>	painCave.severity = OPENMD_ERROR;
172	>	simError();
173	>	} else {
174	>	cutoffMethod_ = i->second;
175	>	}
176	>	} else {
177	>	if (mdFileVersion > 1) {
178	>	sprintf(painCave.errMsg,
179	>	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
180	>	"\tOpenMD will use SHIFTED_FORCE.\n");
181	>	painCave.isFatal = 0;
182	>	painCave.severity = OPENMD_INFO;
183	>	simError();
184	>	cutoffMethod_ = SHIFTED_FORCE;
185	>	} else {
186	>	// handle the case where the old file version was in play
187	>	// (there should be no cutoffMethod, so we have to deduce it
188	>	// from other data).
189	>
190	>	sprintf(painCave.errMsg,
191	>	"ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
192	>	"\tOpenMD found a file which does not set a cutoffMethod.\n"
193	>	"\tOpenMD will attempt to deduce a cutoffMethod using the\n"
194	>	"\tbehavior of the older (version 1) code.  To remove this\n"
195	>	"\twarning, add an explicit cutoffMethod and change the top\n"
196	>	"\tof the file so that it begins with <OpenMD version=2>\n");
197	>	painCave.isFatal = 0;
198	>	painCave.severity = OPENMD_WARNING;
199	>	simError();
200	>
201	>	// The old file version tethered the shifting behavior to the
202	>	// electrostaticSummationMethod keyword.
203	>
204	>	if (simParams_->haveElectrostaticSummationMethod()) {
205	>	string myMethod = simParams_->getElectrostaticSummationMethod();
206	>	toUpper(myMethod);
207	>
208	>	if (myMethod == "SHIFTED_POTENTIAL") {
209	>	cutoffMethod_ = SHIFTED_POTENTIAL;
210	>	} else if (myMethod == "SHIFTED_FORCE") {
211	>	cutoffMethod_ = SHIFTED_FORCE;
212	>	}
213	>
214	>	if (simParams_->haveSwitchingRadius())
215	>	rSwitch_ = simParams_->getSwitchingRadius();
216	>
217	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
218	>	if (simParams_->haveSwitchingRadius()){
219	>	sprintf(painCave.errMsg,
220	>	"ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
221	>	"\tA value was set for the switchingRadius\n"
222	>	"\teven though the electrostaticSummationMethod was\n"
223	>	"\tset to %s\n", myMethod.c_str());
224	>	painCave.severity = OPENMD_WARNING;
225	>	painCave.isFatal = 1;
226	>	simError();
227	>	}
228	>	}
229	>	if (abs(rCut_ - rSwitch_) < 0.0001) {
230	>	if (cutoffMethod_ == SHIFTED_FORCE) {
231	>	sprintf(painCave.errMsg,
232	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
233	>	"\tcutoffRadius and switchingRadius are set to the\n"
234	>	"\tsame value.  OpenMD will use shifted force\n"
235	>	"\tpotentials instead of switching functions.\n");
236	>	painCave.isFatal = 0;
237	>	painCave.severity = OPENMD_WARNING;
238	>	simError();
239	>	} else {
240	>	cutoffMethod_ = SHIFTED_POTENTIAL;
241	>	sprintf(painCave.errMsg,
242	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
243	>	"\tcutoffRadius and switchingRadius are set to the\n"
244	>	"\tsame value.  OpenMD will use shifted potentials\n"
245	>	"\tinstead of switching functions.\n");
246	>	painCave.isFatal = 0;
247	>	painCave.severity = OPENMD_WARNING;
248	>	simError();
249	>	}
250	>	}
251	>	}
252	>	}
253		}
254
255	<	preCalculation();
256	<
257	<	calcShortRangeInteraction();
255	>	map<string, CutoffPolicy> stringToCutoffPolicy;
256	>	stringToCutoffPolicy["MIX"] = MIX;
257	>	stringToCutoffPolicy["MAX"] = MAX;
258	>	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
259
260	<	calcLongRangeInteraction(needPotential, needStress);
260	>	string cutPolicy;
261	>	if (forceFieldOptions_.haveCutoffPolicy()){
262	>	cutPolicy = forceFieldOptions_.getCutoffPolicy();
263	>	}else if (simParams_->haveCutoffPolicy()) {
264	>	cutPolicy = simParams_->getCutoffPolicy();
265	>	}
266
267	<	postCalculation();
267	>	if (!cutPolicy.empty()){
268	>	toUpper(cutPolicy);
269	>	map<string, CutoffPolicy>::iterator i;
270	>	i = stringToCutoffPolicy.find(cutPolicy);
271
272	<	/*
273	<	std::vector<BendOrderStruct> bendOrderStruct;
274	<	for(std::map<Bend*, BendDataSet>::iterator i = bendDataSets.begin(); i != bendDataSets.end(); ++i) {
275	<	BendOrderStruct tmp;
276	<	tmp.bend= const_cast<Bend*>(i->first);
277	<	tmp.dataSet = i->second;
278	<	bendOrderStruct.push_back(tmp);
272	>	if (i == stringToCutoffPolicy.end()) {
273	>	sprintf(painCave.errMsg,
274	>	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
275	>	"\tShould be one of: "
276	>	"MIX, MAX, or TRADITIONAL\n",
277	>	cutPolicy.c_str());
278	>	painCave.isFatal = 1;
279	>	painCave.severity = OPENMD_ERROR;
280	>	simError();
281	>	} else {
282	>	cutoffPolicy_ = i->second;
283	>	}
284	>	} else {
285	>	sprintf(painCave.errMsg,
286	>	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
287	>	"\tOpenMD will use TRADITIONAL.\n");
288	>	painCave.isFatal = 0;
289	>	painCave.severity = OPENMD_INFO;
290	>	simError();
291	>	cutoffPolicy_ = TRADITIONAL;
292		}
293
294	<	std::vector<TorsionOrderStruct> torsionOrderStruct;
295	<	for(std::map<Torsion*, TorsionDataSet>::iterator j = torsionDataSets.begin(); j != torsionDataSets.end(); ++j) {
296	<	TorsionOrderStruct tmp;
297	<	tmp.torsion = const_cast<Torsion*>(j->first);
298	<	tmp.dataSet = j->second;
299	<	torsionOrderStruct.push_back(tmp);
294	>	fDecomp_->setCutoffPolicy(cutoffPolicy_);
295	>
296	>	// create the switching function object:
297	>
298	>	switcher_ = new SwitchingFunction();
299	>
300	>	if (cutoffMethod_ == SWITCHED) {
301	>	if (simParams_->haveSwitchingRadius()) {
302	>	rSwitch_ = simParams_->getSwitchingRadius();
303	>	if (rSwitch_ > rCut_) {
304	>	sprintf(painCave.errMsg,
305	>	"ForceManager::setupCutoffs: switchingRadius (%f) is larger "
306	>	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
307	>	painCave.isFatal = 1;
308	>	painCave.severity = OPENMD_ERROR;
309	>	simError();
310	>	}
311	>	} else {
312	>	rSwitch_ = 0.85 * rCut_;
313	>	sprintf(painCave.errMsg,
314	>	"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
315	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
316	>	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
317	>	painCave.isFatal = 0;
318	>	painCave.severity = OPENMD_WARNING;
319	>	simError();
320	>	}
321	>	} else {
322	>	if (mdFileVersion > 1) {
323	>	// throw an error if we define a switching radius and don't need one.
324	>	// older file versions should not do this.
325	>	if (simParams_->haveSwitchingRadius()) {
326	>	map<string, CutoffMethod>::const_iterator it;
327	>	string theMeth;
328	>	for (it = stringToCutoffMethod.begin();
329	>	it != stringToCutoffMethod.end(); ++it) {
330	>	if (it->second == cutoffMethod_) {
331	>	theMeth = it->first;
332	>	break;
333	>	}
334	>	}
335	>	sprintf(painCave.errMsg,
336	>	"ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
337	>	"\tis not set to SWITCHED, so switchingRadius value\n"
338	>	"\twill be ignored for this simulation\n", theMeth.c_str());
339	>	painCave.isFatal = 0;
340	>	painCave.severity = OPENMD_WARNING;
341	>	simError();
342	>	}
343	>	}
344	>	rSwitch_ = rCut_;
345		}
346
347	<	std::sort(bendOrderStruct.begin(), bendOrderStruct.end(), std::ptr_fun(BendSortFunctor));
348	<	std::sort(torsionOrderStruct.begin(), torsionOrderStruct.end(), std::ptr_fun(TorsionSortFunctor));
349	<	for (std::vector<BendOrderStruct>::iterator k = bendOrderStruct.begin(); k != bendOrderStruct.end(); ++k) {
350	<	Bend* bend = k->bend;
351	<	std::cout << "Bend: atom1=" <<bend->getAtomA()->getGlobalIndex() << ",atom2 = "<< bend->getAtomB()->getGlobalIndex() << ",atom3="<<bend->getAtomC()->getGlobalIndex() << " ";
352	<	std::cout << "deltaV=" << k->dataSet.deltaV << ",p_theta=" << k->dataSet.prev.angle <<",p_pot=" << k->dataSet.prev.potential<< ",c_theta=" << k->dataSet.curr.angle << ", c_pot = " << k->dataSet.curr.potential <<std::endl;
347	>	// Default to cubic switching function.
348	>	sft_ = cubic;
349	>	if (simParams_->haveSwitchingFunctionType()) {
350	>	string funcType = simParams_->getSwitchingFunctionType();
351	>	toUpper(funcType);
352	>	if (funcType == "CUBIC") {
353	>	sft_ = cubic;
354	>	} else {
355	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
356	>	sft_ = fifth_order_poly;
357	>	} else {
358	>	// throw error
359	>	sprintf( painCave.errMsg,
360	>	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
361	>	"\tswitchingFunctionType must be one of: "
362	>	"\"cubic\" or \"fifth_order_polynomial\".",
363	>	funcType.c_str() );
364	>	painCave.isFatal = 1;
365	>	painCave.severity = OPENMD_ERROR;
366	>	simError();
367	>	}
368	>	}
369		}
370	<	for (std::vector<TorsionOrderStruct>::iterator l = torsionOrderStruct.begin(); l != torsionOrderStruct.end(); ++l) {
371	<	Torsion* torsion = l->torsion;
372	<	std::cout << "Torsion: atom1=" <<torsion->getAtomA()->getGlobalIndex() << ",atom2 = "<< torsion->getAtomB()->getGlobalIndex() << ",atom3="<<torsion->getAtomC()->getGlobalIndex() << ",atom4="<<torsion->getAtomD()->getGlobalIndex()<< " ";
373	<	std::cout << "deltaV=" << l->dataSet.deltaV << ",p_theta=" << l->dataSet.prev.angle <<",p_pot=" << l->dataSet.prev.potential<< ",c_theta=" << l->dataSet.curr.angle << ", c_pot = " << l->dataSet.curr.potential <<std::endl;
370	>	switcher_->setSwitchType(sft_);
371	>	switcher_->setSwitch(rSwitch_, rCut_);
372	>	}
373	>
374	>
375	>
376	>
377	>	void ForceManager::initialize() {
378	>
379	>	if (!info_->isTopologyDone()) {
380	>
381	>	info_->update();
382	>	interactionMan_->setSimInfo(info_);
383	>	interactionMan_->initialize();
384	>
385	>	// We want to delay the cutoffs until after the interaction
386	>	// manager has set up the atom-atom interactions so that we can
387	>	// query them for suggested cutoff values
388	>	setupCutoffs();
389	>
390	>	info_->prepareTopology();
391	>
392	>	doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
393	>	doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
394	>	if (doHeatFlux_) doParticlePot_ = true;
395	>
396	>	doElectricField_ = info_->getSimParams()->getOutputElectricField();
397	>
398		}
399	<	*/
399	>
400	>	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
401	>
402	>	// Force fields can set options on how to scale van der Waals and
403	>	// electrostatic interactions for atoms connected via bonds, bends
404	>	// and torsions in this case the topological distance between
405	>	// atoms is:
406	>	// 0 = topologically unconnected
407	>	// 1 = bonded together
408	>	// 2 = connected via a bend
409	>	// 3 = connected via a torsion
410	>
411	>	vdwScale_.reserve(4);
412	>	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
413	>
414	>	electrostaticScale_.reserve(4);
415	>	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
416	>
417	>	vdwScale_[0] = 1.0;
418	>	vdwScale_[1] = fopts.getvdw12scale();
419	>	vdwScale_[2] = fopts.getvdw13scale();
420	>	vdwScale_[3] = fopts.getvdw14scale();
421	>
422	>	electrostaticScale_[0] = 1.0;
423	>	electrostaticScale_[1] = fopts.getelectrostatic12scale();
424	>	electrostaticScale_[2] = fopts.getelectrostatic13scale();
425	>	electrostaticScale_[3] = fopts.getelectrostatic14scale();
426	>
427	>	if (info_->getSimParams()->haveElectricField()) {
428	>	ElectricField* eField = new ElectricField(info_);
429	>	perturbations_.push_back(eField);
430	>	}
431	>
432	>	fDecomp_->distributeInitialData();
433	>
434	>	initialized_ = true;
435	>
436		}
437
438	+	void ForceManager::calcForces() {
439	+
440	+	if (!initialized_) initialize();
441	+
442	+	preCalculation();
443	+	shortRangeInteractions();
444	+	longRangeInteractions();
445	+	postCalculation();
446	+	}
447	+
448		void ForceManager::preCalculation() {
449		SimInfo::MoleculeIterator mi;
450		Molecule* mol;
#	Line 128 | Line 452 | namespace oopse {
452		Atom* atom;
453		Molecule::RigidBodyIterator rbIter;
454		RigidBody* rb;
455	+	Molecule::CutoffGroupIterator ci;
456	+	CutoffGroup* cg;
457
458	<	// forces are zeroed here, before any are accumulated.
459	<	// NOTE: do not rezero the forces in Fortran.
460	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
461	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
458	>	// forces and potentials are zeroed here, before any are
459	>	// accumulated.
460	>
461	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
462	>
463	>	snap->setBondPotential(0.0);
464	>	snap->setBendPotential(0.0);
465	>	snap->setTorsionPotential(0.0);
466	>	snap->setInversionPotential(0.0);
467	>
468	>	potVec zeroPot(0.0);
469	>	snap->setLongRangePotential(zeroPot);
470	>	snap->setExcludedPotentials(zeroPot);
471	>
472	>	snap->setRestraintPotential(0.0);
473	>	snap->setRawPotential(0.0);
474	>
475	>	for (mol = info_->beginMolecule(mi); mol != NULL;
476	>	mol = info_->nextMolecule(mi)) {
477	>	for(atom = mol->beginAtom(ai); atom != NULL;
478	>	atom = mol->nextAtom(ai)) {
479		atom->zeroForcesAndTorques();
480		}
481	<
481	>
482		//change the positions of atoms which belong to the rigidbodies
483	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
483	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
484	>	rb = mol->nextRigidBody(rbIter)) {
485		rb->zeroForcesAndTorques();
486		}
487	+
488	+	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
489	+	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
490	+	cg = mol->nextCutoffGroup(ci)) {
491	+	//calculate the center of mass of cutoff group
492	+	cg->updateCOM();
493	+	}
494	+	}
495		}
496
497	+	// Zero out the stress tensor
498	+	stressTensor *= 0.0;
499	+	// Zero out the heatFlux
500	+	fDecomp_->setHeatFlux( Vector3d(0.0) );
501		}
502	<
503	<	void ForceManager::calcShortRangeInteraction() {
502	>
503	>	void ForceManager::shortRangeInteractions() {
504		Molecule* mol;
505		RigidBody* rb;
506		Bond* bond;
507		Bend* bend;
508		Torsion* torsion;
509	+	Inversion* inversion;
510		SimInfo::MoleculeIterator mi;
511		Molecule::RigidBodyIterator rbIter;
512		Molecule::BondIterator bondIter;;
513		Molecule::BendIterator  bendIter;
514		Molecule::TorsionIterator  torsionIter;
515	+	Molecule::InversionIterator  inversionIter;
516		RealType bondPotential = 0.0;
517		RealType bendPotential = 0.0;
518		RealType torsionPotential = 0.0;
519	+	RealType inversionPotential = 0.0;
520
521		//calculate short range interactions
522	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
522	>	for (mol = info_->beginMolecule(mi); mol != NULL;
523	>	mol = info_->nextMolecule(mi)) {
524
525		//change the positions of atoms which belong to the rigidbodies
526	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
527	<	rb->updateAtoms();
526	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
527	>	rb = mol->nextRigidBody(rbIter)) {
528	>	rb->updateAtoms();
529		}
530
531	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
532	<	bond->calcForce();
531	>	for (bond = mol->beginBond(bondIter); bond != NULL;
532	>	bond = mol->nextBond(bondIter)) {
533	>	bond->calcForce(doParticlePot_);
534		bondPotential += bond->getPotential();
173	–	}
174	–
175	–
176	–	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
177	–
178	–	RealType angle;
179	–	bend->calcForce(angle);
180	–	RealType currBendPot = bend->getPotential();
181	–	bendPotential += bend->getPotential();
182	–	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
183	–	if (i == bendDataSets.end()) {
184	–	BendDataSet dataSet;
185	–	dataSet.prev.angle = dataSet.curr.angle = angle;
186	–	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
187	–	dataSet.deltaV = 0.0;
188	–	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
189	–	}else {
190	–	i->second.prev.angle = i->second.curr.angle;
191	–	i->second.prev.potential = i->second.curr.potential;
192	–	i->second.curr.angle = angle;
193	–	i->second.curr.potential = currBendPot;
194	–	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
195	–	}
535		}
536
537	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
537	>	for (bend = mol->beginBend(bendIter); bend != NULL;
538	>	bend = mol->nextBend(bendIter)) {
539	>
540		RealType angle;
541	<	torsion->calcForce(angle);
542	<	RealType currTorsionPot = torsion->getPotential();
543	<	torsionPotential += torsion->getPotential();
544	<	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
545	<	if (i == torsionDataSets.end()) {
546	<	TorsionDataSet dataSet;
547	<	dataSet.prev.angle = dataSet.curr.angle = angle;
548	<	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
549	<	dataSet.deltaV = 0.0;
550	<	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
551	<	}else {
552	<	i->second.prev.angle = i->second.curr.angle;
553	<	i->second.prev.potential = i->second.curr.potential;
554	<	i->second.curr.angle = angle;
555	<	i->second.curr.potential = currTorsionPot;
556	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
557	<	}
541	>	bend->calcForce(angle, doParticlePot_);
542	>	RealType currBendPot = bend->getPotential();
543	>
544	>	bendPotential += bend->getPotential();
545	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
546	>	if (i == bendDataSets.end()) {
547	>	BendDataSet dataSet;
548	>	dataSet.prev.angle = dataSet.curr.angle = angle;
549	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
550	>	dataSet.deltaV = 0.0;
551	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
552	>	dataSet));
553	>	}else {
554	>	i->second.prev.angle = i->second.curr.angle;
555	>	i->second.prev.potential = i->second.curr.potential;
556	>	i->second.curr.angle = angle;
557	>	i->second.curr.potential = currBendPot;
558	>	i->second.deltaV =  fabs(i->second.curr.potential -
559	>	i->second.prev.potential);
560	>	}
561		}
562	<
562	>
563	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
564	>	torsion = mol->nextTorsion(torsionIter)) {
565	>	RealType angle;
566	>	torsion->calcForce(angle, doParticlePot_);
567	>	RealType currTorsionPot = torsion->getPotential();
568	>	torsionPotential += torsion->getPotential();
569	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
570	>	if (i == torsionDataSets.end()) {
571	>	TorsionDataSet dataSet;
572	>	dataSet.prev.angle = dataSet.curr.angle = angle;
573	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
574	>	dataSet.deltaV = 0.0;
575	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
576	>	}else {
577	>	i->second.prev.angle = i->second.curr.angle;
578	>	i->second.prev.potential = i->second.curr.potential;
579	>	i->second.curr.angle = angle;
580	>	i->second.curr.potential = currTorsionPot;
581	>	i->second.deltaV =  fabs(i->second.curr.potential -
582	>	i->second.prev.potential);
583	>	}
584	>	}
585	>
586	>	for (inversion = mol->beginInversion(inversionIter);
587	>	inversion != NULL;
588	>	inversion = mol->nextInversion(inversionIter)) {
589	>	RealType angle;
590	>	inversion->calcForce(angle, doParticlePot_);
591	>	RealType currInversionPot = inversion->getPotential();
592	>	inversionPotential += inversion->getPotential();
593	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
594	>	if (i == inversionDataSets.end()) {
595	>	InversionDataSet dataSet;
596	>	dataSet.prev.angle = dataSet.curr.angle = angle;
597	>	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
598	>	dataSet.deltaV = 0.0;
599	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
600	>	}else {
601	>	i->second.prev.angle = i->second.curr.angle;
602	>	i->second.prev.potential = i->second.curr.potential;
603	>	i->second.curr.angle = angle;
604	>	i->second.curr.potential = currInversionPot;
605	>	i->second.deltaV =  fabs(i->second.curr.potential -
606	>	i->second.prev.potential);
607	>	}
608	>	}
609		}
610	<
611	<	RealType  shortRangePotential = bondPotential + bendPotential + torsionPotential;
610	>
611	>	#ifdef IS_MPI
612	>	// Collect from all nodes.  This should eventually be moved into a
613	>	// SystemDecomposition, but this is a better place than in
614	>	// Thermo to do the collection.
615	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
616	>	MPI::SUM);
617	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
618	>	MPI::SUM);
619	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
620	>	MPI::REALTYPE, MPI::SUM);
621	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
622	>	MPI::REALTYPE, MPI::SUM);
623	>	#endif
624	>
625		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
626	<	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
627	<	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
628	<	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
629	<	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
626	>
627	>	curSnapshot->setBondPotential(bondPotential);
628	>	curSnapshot->setBendPotential(bendPotential);
629	>	curSnapshot->setTorsionPotential(torsionPotential);
630	>	curSnapshot->setInversionPotential(inversionPotential);
631
632	+	// RealType shortRangePotential = bondPotential + bendPotential +
633	+	//   torsionPotential +  inversionPotential;
634	+
635	+	// curSnapshot->setShortRangePotential(shortRangePotential);
636		}
637	+
638	+	void ForceManager::longRangeInteractions() {
639
230	–	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
231	–	Snapshot* curSnapshot;
232	–	DataStorage* config;
233	–	RealType* frc;
234	–	RealType* pos;
235	–	RealType* trq;
236	–	RealType* A;
237	–	RealType* electroFrame;
238	–	RealType* rc;
239	–
240	–	//get current snapshot from SimInfo
241	–	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
640
641	<	//get array pointers
642	<	config = &(curSnapshot->atomData);
643	<	frc = config->getArrayPointer(DataStorage::dslForce);
246	<	pos = config->getArrayPointer(DataStorage::dslPosition);
247	<	trq = config->getArrayPointer(DataStorage::dslTorque);
248	<	A   = config->getArrayPointer(DataStorage::dslAmat);
249	<	electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
641	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
642	>	DataStorage* config = &(curSnapshot->atomData);
643	>	DataStorage* cgConfig = &(curSnapshot->cgData);
644
645		//calculate the center of mass of cutoff group
646	+
647		SimInfo::MoleculeIterator mi;
648		Molecule* mol;
649		Molecule::CutoffGroupIterator ci;
650		CutoffGroup* cg;
256	–	Vector3d com;
257	–	std::vector<Vector3d> rcGroup;
651
652	<	if(info_->getNCutoffGroups() > 0){
653	<
654	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
655	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
656	<	cg->getCOM(com);
657	<	rcGroup.push_back(com);
652	>	if(info_->getNCutoffGroups() > 0){
653	>	for (mol = info_->beginMolecule(mi); mol != NULL;
654	>	mol = info_->nextMolecule(mi)) {
655	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
656	>	cg = mol->nextCutoffGroup(ci)) {
657	>	cg->updateCOM();
658		}
659	<	}// end for (mol)
267	<
268	<	rc = rcGroup[0].getArrayPointer();
659	>	}
660		} else {
661	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
662	<	rc = pos;
661	>	// center of mass of the group is the same as position of the atom
662	>	// if cutoff group does not exist
663	>	cgConfig->position = config->position;
664	>	cgConfig->velocity = config->velocity;
665		}
273	–
274	–	//initialize data before passing to fortran
275	–	RealType longRangePotential[LR_POT_TYPES];
276	–	RealType lrPot = 0.0;
277	–	Vector3d totalDipole;
278	–	Mat3x3d tau;
279	–	short int passedCalcPot = needPotential;
280	–	short int passedCalcStress = needStress;
281	–	int isError = 0;
666
667	<	for (int i=0; i<LR_POT_TYPES;i++){
668	<	longRangePotential[i]=0.0; //Initialize array
669	<	}
667	>	fDecomp_->zeroWorkArrays();
668	>	fDecomp_->distributeData();
669	>
670	>	int cg1, cg2, atom1, atom2, topoDist;
671	>	Vector3d d_grp, dag, d, gvel2, vel2;
672	>	RealType rgrpsq, rgrp, r2, r;
673	>	RealType electroMult, vdwMult;
674	>	RealType vij;
675	>	Vector3d fij, fg, f1;
676	>	tuple3<RealType, RealType, RealType> cuts;
677	>	RealType rCutSq;
678	>	bool in_switching_region;
679	>	RealType sw, dswdr, swderiv;
680	>	vector<int> atomListColumn, atomListRow, atomListLocal;
681	>	InteractionData idat;
682	>	SelfData sdat;
683	>	RealType mf;
684	>	RealType vpair;
685	>	RealType dVdFQ1(0.0);
686	>	RealType dVdFQ2(0.0);
687	>	potVec longRangePotential(0.0);
688	>	potVec workPot(0.0);
689	>	potVec exPot(0.0);
690	>	Vector3d eField1(0.0);
691	>	Vector3d eField2(0.0);
692	>	vector<int>::iterator ia, jb;
693
694	<	doForceLoop( pos,
288	<	rc,
289	<	A,
290	<	electroFrame,
291	<	frc,
292	<	trq,
293	<	tau.getArrayPointer(),
294	<	longRangePotential,
295	<	&passedCalcPot,
296	<	&passedCalcStress,
297	<	&isError );
694	>	int loopStart, loopEnd;
695
696	<	if( isError ){
697	<	sprintf( painCave.errMsg,
698	<	"Error returned from the fortran force calculation.\n" );
699	<	painCave.isFatal = 1;
700	<	simError();
701	<	}
702	<	for (int i=0; i<LR_POT_TYPES;i++){
703	<	lrPot += longRangePotential[i]; //Quick hack
704	<	}
705	<
706	<	// grab the simulation box dipole moment if specified
707	<	if (info_->getCalcBoxDipole()){
708	<	getAccumulatedBoxDipole(totalDipole.getArrayPointer());
696	>	idat.vdwMult = &vdwMult;
697	>	idat.electroMult = &electroMult;
698	>	idat.pot = &workPot;
699	>	idat.excludedPot = &exPot;
700	>	sdat.pot = fDecomp_->getEmbeddingPotential();
701	>	sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
702	>	idat.vpair = &vpair;
703	>	idat.dVdFQ1 = &dVdFQ1;
704	>	idat.dVdFQ2 = &dVdFQ2;
705	>	idat.eField1 = &eField1;
706	>	idat.eField2 = &eField2;
707	>	idat.f1 = &f1;
708	>	idat.sw = &sw;
709	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
710	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
711	>	idat.doParticlePot = doParticlePot_;
712	>	idat.doElectricField = doElectricField_;
713	>	sdat.doParticlePot = doParticlePot_;
714	>
715	>	loopEnd = PAIR_LOOP;
716	>	if (info_->requiresPrepair() ) {
717	>	loopStart = PREPAIR_LOOP;
718	>	} else {
719	>	loopStart = PAIR_LOOP;
720	>	}
721	>	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
722	>
723	>	if (iLoop == loopStart) {
724	>	bool update_nlist = fDecomp_->checkNeighborList();
725	>	if (update_nlist)
726	>	neighborList = fDecomp_->buildNeighborList();
727	>	}
728
729	<	curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
730	<	curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
731	<	curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
729	>	for (vector<pair<int, int> >::iterator it = neighborList.begin();
730	>	it != neighborList.end(); ++it) {
731	>
732	>	cg1 = (*it).first;
733	>	cg2 = (*it).second;
734	>
735	>	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
736	>
737	>	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
738	>
739	>	curSnapshot->wrapVector(d_grp);
740	>	rgrpsq = d_grp.lengthSquare();
741	>	rCutSq = cuts.second;
742	>
743	>	if (rgrpsq < rCutSq) {
744	>	idat.rcut = &cuts.first;
745	>	if (iLoop == PAIR_LOOP) {
746	>	vij = 0.0;
747	>	fij = V3Zero;
748	>	}
749	>
750	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
751	>	rgrp);
752	>
753	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
754	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
755	>
756	>	if (doHeatFlux_)
757	>	gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
758	>
759	>	for (ia = atomListRow.begin();
760	>	ia != atomListRow.end(); ++ia) {
761	>	atom1 = (*ia);
762	>
763	>	for (jb = atomListColumn.begin();
764	>	jb != atomListColumn.end(); ++jb) {
765	>	atom2 = (*jb);
766	>
767	>	if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
768	>
769	>	vpair = 0.0;
770	>	workPot = 0.0;
771	>	exPot = 0.0;
772	>	f1 = V3Zero;
773	>	dVdFQ1 = 0.0;
774	>	dVdFQ2 = 0.0;
775	>
776	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
777	>
778	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
779	>	vdwMult = vdwScale_[topoDist];
780	>	electroMult = electrostaticScale_[topoDist];
781	>
782	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
783	>	idat.d = &d_grp;
784	>	idat.r2 = &rgrpsq;
785	>	if (doHeatFlux_)
786	>	vel2 = gvel2;
787	>	} else {
788	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
789	>	curSnapshot->wrapVector( d );
790	>	r2 = d.lengthSquare();
791	>	idat.d = &d;
792	>	idat.r2 = &r2;
793	>	if (doHeatFlux_)
794	>	vel2 = fDecomp_->getAtomVelocityColumn(atom2);
795	>	}
796	>
797	>	r = sqrt( *(idat.r2) );
798	>	idat.rij = &r;
799	>
800	>	if (iLoop == PREPAIR_LOOP) {
801	>	interactionMan_->doPrePair(idat);
802	>	} else {
803	>	interactionMan_->doPair(idat);
804	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
805	>	vij += vpair;
806	>	fij += f1;
807	>	stressTensor -= outProduct( *(idat.d), f1);
808	>	if (doHeatFlux_)
809	>	fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
810	>	}
811	>	}
812	>	}
813	>	}
814	>
815	>	if (iLoop == PAIR_LOOP) {
816	>	if (in_switching_region) {
817	>	swderiv = vij * dswdr / rgrp;
818	>	fg = swderiv * d_grp;
819	>	fij += fg;
820	>
821	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
822	>	stressTensor -= outProduct( *(idat.d), fg);
823	>	if (doHeatFlux_)
824	>	fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
825	>
826	>	}
827	>
828	>	for (ia = atomListRow.begin();
829	>	ia != atomListRow.end(); ++ia) {
830	>	atom1 = (*ia);
831	>	mf = fDecomp_->getMassFactorRow(atom1);
832	>	// fg is the force on atom ia due to cutoff group's
833	>	// presence in switching region
834	>	fg = swderiv * d_grp * mf;
835	>	fDecomp_->addForceToAtomRow(atom1, fg);
836	>	if (atomListRow.size() > 1) {
837	>	if (info_->usesAtomicVirial()) {
838	>	// find the distance between the atom
839	>	// and the center of the cutoff group:
840	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
841	>	stressTensor -= outProduct(dag, fg);
842	>	if (doHeatFlux_)
843	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
844	>	}
845	>	}
846	>	}
847	>	for (jb = atomListColumn.begin();
848	>	jb != atomListColumn.end(); ++jb) {
849	>	atom2 = (*jb);
850	>	mf = fDecomp_->getMassFactorColumn(atom2);
851	>	// fg is the force on atom jb due to cutoff group's
852	>	// presence in switching region
853	>	fg = -swderiv * d_grp * mf;
854	>	fDecomp_->addForceToAtomColumn(atom2, fg);
855	>
856	>	if (atomListColumn.size() > 1) {
857	>	if (info_->usesAtomicVirial()) {
858	>	// find the distance between the atom
859	>	// and the center of the cutoff group:
860	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
861	>	stressTensor -= outProduct(dag, fg);
862	>	if (doHeatFlux_)
863	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
864	>	}
865	>	}
866	>	}
867	>	}
868	>	//if (!info_->usesAtomicVirial()) {
869	>	//  stressTensor -= outProduct(d_grp, fij);
870	>	//  if (doHeatFlux_)
871	>	//     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
872	>	//}
873	>	}
874	>	}
875	>	}
876	>
877	>	if (iLoop == PREPAIR_LOOP) {
878	>	if (info_->requiresPrepair()) {
879	>
880	>	fDecomp_->collectIntermediateData();
881	>
882	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
883	>	fDecomp_->fillSelfData(sdat, atom1);
884	>	interactionMan_->doPreForce(sdat);
885	>	}
886	>
887	>	fDecomp_->distributeIntermediateData();
888	>
889	>	}
890	>	}
891		}
892	+
893	+	// collects pairwise information
894	+	fDecomp_->collectData();
895	+
896	+	if (info_->requiresSelfCorrection()) {
897	+	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
898	+	fDecomp_->fillSelfData(sdat, atom1);
899	+	interactionMan_->doSelfCorrection(sdat);
900	+	}
901	+	}
902
903	<	//store the tau and long range potential
904	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
320	<	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
321	<	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
903	>	// collects single-atom information
904	>	fDecomp_->collectSelfData();
905
906	<	curSnapshot->statData.setTau(tau);
907	<	}
906	>	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
907	>	*(fDecomp_->getPairwisePotential());
908
909	+	curSnapshot->setLongRangePotential(longRangePotential);
910
911	+	// collects single-atom information
912	+	fDecomp_->collectSelfData();
913	+
914	+	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
915	+	*(fDecomp_->getPairwisePotential());
916	+
917	+	curSnapshot->setLongRangePotential(longRangePotential);
918	+
919	+	curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
920	+	*(fDecomp_->getExcludedPotential()));
921	+
922	+	}
923	+
924	+
925		void ForceManager::postCalculation() {
926	+
927	+	vector<Perturbation*>::iterator pi;
928	+	for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
929	+	(*pi)->applyPerturbation();
930	+	}
931	+
932		SimInfo::MoleculeIterator mi;
933		Molecule* mol;
934		Molecule::RigidBodyIterator rbIter;
935		RigidBody* rb;
936	<
936	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
937	>
938		// collect the atomic forces onto rigid bodies
939	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
940	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
941	<	rb->calcForcesAndTorques();
939	>
940	>	for (mol = info_->beginMolecule(mi); mol != NULL;
941	>	mol = info_->nextMolecule(mi)) {
942	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
943	>	rb = mol->nextRigidBody(rbIter)) {
944	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
945	>	stressTensor += rbTau;
946		}
947	<	}
948	<
947	>	}
948	>
949	>	#ifdef IS_MPI
950	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
951	>	MPI::REALTYPE, MPI::SUM);
952	>	#endif
953	>	curSnapshot->setStressTensor(stressTensor);
954	>
955		}
956	<
342	<	} //end namespace oopse
956	>	} //end namespace OpenMD

Comparing:
trunk/src/brains/ForceManager.cpp (property svn:keywords), Revision 998 by chrisfen, Mon Jul 3 13:18:43 2006 UTC vs.
branches/development/src/brains/ForceManager.cpp (property svn:keywords), Revision 1808 by gezelter, Mon Oct 22 20:42:10 2012 UTC

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