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root/OpenMD/trunk/src/brains/ForceManager.cpp

Comparing trunk/src/brains/ForceManager.cpp (file contents):
Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 1993 by gezelter, Tue Apr 29 17:32:31 2014 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, 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
47	<	* @time 10:39am
48	<	* @version 1.0
48	<	*/
43	>	/**
44	>	* @file ForceManager.cpp
45	>	* @author tlin
46	>	* @date 11/09/2004
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 "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	>	initialized_(false) {
72	>	forceField_ = info_->getForceField();
73	>	interactionMan_ = new InteractionManager();
74	>	fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
75	>	thermo = new Thermo(info_);
76	>	}
77
78	<	preCalculation();
78	>	ForceManager::~ForceManager() {
79	>	perturbations_.clear();
80
81	<	calcShortRangeInteraction();
81	>	delete switcher_;
82	>	delete interactionMan_;
83	>	delete fDecomp_;
84	>	delete thermo;
85	>	}
86	>
87	>	/**
88	>	* setupCutoffs
89	>	*
90	>	* Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
91	>	* and cutoffPolicy
92	>	*
93	>	* cutoffRadius : realType
94	>	*  If the cutoffRadius was explicitly set, use that value.
95	>	*  If the cutoffRadius was not explicitly set:
96	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
97	>	*      No electrostatic atoms?  Poll the atom types present in the
98	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
99	>	*      Use the maximum suggested value that was found.
100	>	*
101	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, TAYLOR_SHIFTED,
102	>	*                        SHIFTED_POTENTIAL, or EWALD_FULL)
103	>	*      If cutoffMethod was explicitly set, use that choice.
104	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
105	>	*
106	>	* cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
107	>	*      If cutoffPolicy was explicitly set, use that choice.
108	>	*      If cutoffPolicy was not explicitly set, use TRADITIONAL
109	>	*
110	>	* switchingRadius : realType
111	>	*  If the cutoffMethod was set to SWITCHED:
112	>	*      If the switchingRadius was explicitly set, use that value
113	>	*          (but do a sanity check first).
114	>	*      If the switchingRadius was not explicitly set: use 0.85 *
115	>	*      cutoffRadius_
116	>	*  If the cutoffMethod was not set to SWITCHED:
117	>	*      Set switchingRadius equal to cutoffRadius for safety.
118	>	*/
119	>	void ForceManager::setupCutoffs() {
120	>
121	>	Globals* simParams_ = info_->getSimParams();
122	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
123	>	int mdFileVersion;
124	>	rCut_ = 0.0; //Needs a value for a later max() call;
125	>
126	>	if (simParams_->haveMDfileVersion())
127	>	mdFileVersion = simParams_->getMDfileVersion();
128	>	else
129	>	mdFileVersion = 0;
130	>
131	>	// We need the list of simulated atom types to figure out cutoffs
132	>	// as well as long range corrections.
133
134	<	calcLongRangeInteraction(needPotential, needStress);
134	>	set<AtomType*>::iterator i;
135	>	set<AtomType*> atomTypes_;
136	>	atomTypes_ = info_->getSimulatedAtomTypes();
137
138	<	postCalculation();
138	>	if (simParams_->haveCutoffRadius()) {
139	>	rCut_ = simParams_->getCutoffRadius();
140	>	} else {
141	>	if (info_->usesElectrostaticAtoms()) {
142	>	sprintf(painCave.errMsg,
143	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
144	>	"\tOpenMD will use a default value of 12.0 angstroms"
145	>	"\tfor the cutoffRadius.\n");
146	>	painCave.isFatal = 0;
147	>	painCave.severity = OPENMD_INFO;
148	>	simError();
149	>	rCut_ = 12.0;
150	>	} else {
151	>	RealType thisCut;
152	>	for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
153	>	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
154	>	rCut_ = max(thisCut, rCut_);
155	>	}
156	>	sprintf(painCave.errMsg,
157	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
158	>	"\tOpenMD will use %lf angstroms.\n",
159	>	rCut_);
160	>	painCave.isFatal = 0;
161	>	painCave.severity = OPENMD_INFO;
162	>	simError();
163	>	}
164	>	}
165	>
166	>	fDecomp_->setUserCutoff(rCut_);
167	>	interactionMan_->setCutoffRadius(rCut_);
168	>
169	>	map<string, CutoffMethod> stringToCutoffMethod;
170	>	stringToCutoffMethod["HARD"] = HARD;
171	>	stringToCutoffMethod["SWITCHED"] = SWITCHED;
172	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
173	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
174	>	stringToCutoffMethod["TAYLOR_SHIFTED"] = TAYLOR_SHIFTED;
175	>	stringToCutoffMethod["EWALD_FULL"] = EWALD_FULL;
176	>
177	>	if (simParams_->haveCutoffMethod()) {
178	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
179	>	map<string, CutoffMethod>::iterator i;
180	>	i = stringToCutoffMethod.find(cutMeth);
181	>	if (i == stringToCutoffMethod.end()) {
182	>	sprintf(painCave.errMsg,
183	>	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
184	>	"\tShould be one of: "
185	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, TAYLOR_SHIFTED,\n"
186	>	"\tSHIFTED_FORCE, or EWALD_FULL\n",
187	>	cutMeth.c_str());
188	>	painCave.isFatal = 1;
189	>	painCave.severity = OPENMD_ERROR;
190	>	simError();
191	>	} else {
192	>	cutoffMethod_ = i->second;
193	>	}
194	>	} else {
195	>	if (mdFileVersion > 1) {
196	>	sprintf(painCave.errMsg,
197	>	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
198	>	"\tOpenMD will use SHIFTED_FORCE.\n");
199	>	painCave.isFatal = 0;
200	>	painCave.severity = OPENMD_INFO;
201	>	simError();
202	>	cutoffMethod_ = SHIFTED_FORCE;
203	>	} else {
204	>	// handle the case where the old file version was in play
205	>	// (there should be no cutoffMethod, so we have to deduce it
206	>	// from other data).
207	>
208	>	sprintf(painCave.errMsg,
209	>	"ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
210	>	"\tOpenMD found a file which does not set a cutoffMethod.\n"
211	>	"\tOpenMD will attempt to deduce a cutoffMethod using the\n"
212	>	"\tbehavior of the older (version 1) code.  To remove this\n"
213	>	"\twarning, add an explicit cutoffMethod and change the top\n"
214	>	"\tof the file so that it begins with <OpenMD version=2>\n");
215	>	painCave.isFatal = 0;
216	>	painCave.severity = OPENMD_WARNING;
217	>	simError();
218	>
219	>	// The old file version tethered the shifting behavior to the
220	>	// electrostaticSummationMethod keyword.
221
222	<	}
222	>	if (simParams_->haveElectrostaticSummationMethod()) {
223	>	string myMethod = simParams_->getElectrostaticSummationMethod();
224	>	toUpper(myMethod);
225	>
226	>	if (myMethod == "SHIFTED_POTENTIAL") {
227	>	cutoffMethod_ = SHIFTED_POTENTIAL;
228	>	} else if (myMethod == "SHIFTED_FORCE") {
229	>	cutoffMethod_ = SHIFTED_FORCE;
230	>	} else if (myMethod == "TAYLOR_SHIFTED") {
231	>	cutoffMethod_ = TAYLOR_SHIFTED;
232	>	} else if (myMethod == "EWALD_FULL") {
233	>	cutoffMethod_ = EWALD_FULL;
234	>	}
235	>
236	>	if (simParams_->haveSwitchingRadius())
237	>	rSwitch_ = simParams_->getSwitchingRadius();
238
239	<	void ForceManager::preCalculation() {
239	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE" ||
240	>	myMethod == "TAYLOR_SHIFTED" || myMethod == "EWALD_FULL") {
241	>	if (simParams_->haveSwitchingRadius()){
242	>	sprintf(painCave.errMsg,
243	>	"ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
244	>	"\tA value was set for the switchingRadius\n"
245	>	"\teven though the electrostaticSummationMethod was\n"
246	>	"\tset to %s\n", myMethod.c_str());
247	>	painCave.severity = OPENMD_WARNING;
248	>	painCave.isFatal = 1;
249	>	simError();
250	>	}
251	>	}
252	>	if (abs(rCut_ - rSwitch_) < 0.0001) {
253	>	if (cutoffMethod_ == SHIFTED_FORCE) {
254	>	sprintf(painCave.errMsg,
255	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
256	>	"\tcutoffRadius and switchingRadius are set to the\n"
257	>	"\tsame value.  OpenMD will use shifted force\n"
258	>	"\tpotentials instead of switching functions.\n");
259	>	painCave.isFatal = 0;
260	>	painCave.severity = OPENMD_WARNING;
261	>	simError();
262	>	} else {
263	>	cutoffMethod_ = SHIFTED_POTENTIAL;
264	>	sprintf(painCave.errMsg,
265	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
266	>	"\tcutoffRadius and switchingRadius are set to the\n"
267	>	"\tsame value.  OpenMD will use shifted potentials\n"
268	>	"\tinstead of switching functions.\n");
269	>	painCave.isFatal = 0;
270	>	painCave.severity = OPENMD_WARNING;
271	>	simError();
272	>	}
273	>	}
274	>	}
275	>	}
276	>	}
277	>
278	>	map<string, CutoffPolicy> stringToCutoffPolicy;
279	>	stringToCutoffPolicy["MIX"] = MIX;
280	>	stringToCutoffPolicy["MAX"] = MAX;
281	>	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
282	>
283	>	string cutPolicy;
284	>	if (forceFieldOptions_.haveCutoffPolicy()){
285	>	cutPolicy = forceFieldOptions_.getCutoffPolicy();
286	>	}else if (simParams_->haveCutoffPolicy()) {
287	>	cutPolicy = simParams_->getCutoffPolicy();
288	>	}
289	>
290	>	if (!cutPolicy.empty()){
291	>	toUpper(cutPolicy);
292	>	map<string, CutoffPolicy>::iterator i;
293	>	i = stringToCutoffPolicy.find(cutPolicy);
294	>
295	>	if (i == stringToCutoffPolicy.end()) {
296	>	sprintf(painCave.errMsg,
297	>	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
298	>	"\tShould be one of: "
299	>	"MIX, MAX, or TRADITIONAL\n",
300	>	cutPolicy.c_str());
301	>	painCave.isFatal = 1;
302	>	painCave.severity = OPENMD_ERROR;
303	>	simError();
304	>	} else {
305	>	cutoffPolicy_ = i->second;
306	>	}
307	>	} else {
308	>	sprintf(painCave.errMsg,
309	>	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
310	>	"\tOpenMD will use TRADITIONAL.\n");
311	>	painCave.isFatal = 0;
312	>	painCave.severity = OPENMD_INFO;
313	>	simError();
314	>	cutoffPolicy_ = TRADITIONAL;
315	>	}
316	>
317	>	fDecomp_->setCutoffPolicy(cutoffPolicy_);
318	>
319	>	// create the switching function object:
320	>
321	>	switcher_ = new SwitchingFunction();
322	>
323	>	if (cutoffMethod_ == SWITCHED) {
324	>	if (simParams_->haveSwitchingRadius()) {
325	>	rSwitch_ = simParams_->getSwitchingRadius();
326	>	if (rSwitch_ > rCut_) {
327	>	sprintf(painCave.errMsg,
328	>	"ForceManager::setupCutoffs: switchingRadius (%f) is larger "
329	>	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
330	>	painCave.isFatal = 1;
331	>	painCave.severity = OPENMD_ERROR;
332	>	simError();
333	>	}
334	>	} else {
335	>	rSwitch_ = 0.85 * rCut_;
336	>	sprintf(painCave.errMsg,
337	>	"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
338	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
339	>	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
340	>	painCave.isFatal = 0;
341	>	painCave.severity = OPENMD_WARNING;
342	>	simError();
343	>	}
344	>	} else {
345	>	if (mdFileVersion > 1) {
346	>	// throw an error if we define a switching radius and don't need one.
347	>	// older file versions should not do this.
348	>	if (simParams_->haveSwitchingRadius()) {
349	>	map<string, CutoffMethod>::const_iterator it;
350	>	string theMeth;
351	>	for (it = stringToCutoffMethod.begin();
352	>	it != stringToCutoffMethod.end(); ++it) {
353	>	if (it->second == cutoffMethod_) {
354	>	theMeth = it->first;
355	>	break;
356	>	}
357	>	}
358	>	sprintf(painCave.errMsg,
359	>	"ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
360	>	"\tis not set to SWITCHED, so switchingRadius value\n"
361	>	"\twill be ignored for this simulation\n", theMeth.c_str());
362	>	painCave.isFatal = 0;
363	>	painCave.severity = OPENMD_WARNING;
364	>	simError();
365	>	}
366	>	}
367	>	rSwitch_ = rCut_;
368	>	}
369	>
370	>	// Default to cubic switching function.
371	>	sft_ = cubic;
372	>	if (simParams_->haveSwitchingFunctionType()) {
373	>	string funcType = simParams_->getSwitchingFunctionType();
374	>	toUpper(funcType);
375	>	if (funcType == "CUBIC") {
376	>	sft_ = cubic;
377	>	} else {
378	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
379	>	sft_ = fifth_order_poly;
380	>	} else {
381	>	// throw error
382	>	sprintf( painCave.errMsg,
383	>	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
384	>	"\tswitchingFunctionType must be one of: "
385	>	"\"cubic\" or \"fifth_order_polynomial\".",
386	>	funcType.c_str() );
387	>	painCave.isFatal = 1;
388	>	painCave.severity = OPENMD_ERROR;
389	>	simError();
390	>	}
391	>	}
392	>	}
393	>	switcher_->setSwitchType(sft_);
394	>	switcher_->setSwitch(rSwitch_, rCut_);
395	>	}
396	>
397	>
398	>
399	>
400	>	void ForceManager::initialize() {
401	>
402	>	if (!info_->isTopologyDone()) {
403	>
404	>	info_->update();
405	>	interactionMan_->setSimInfo(info_);
406	>	interactionMan_->initialize();
407	>
408	>	// We want to delay the cutoffs until after the interaction
409	>	// manager has set up the atom-atom interactions so that we can
410	>	// query them for suggested cutoff values
411	>	setupCutoffs();
412	>
413	>	info_->prepareTopology();
414	>
415	>	doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
416	>	doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
417	>	if (doHeatFlux_) doParticlePot_ = true;
418	>
419	>	doElectricField_ = info_->getSimParams()->getOutputElectricField();
420	>	doSitePotential_ = info_->getSimParams()->getOutputSitePotential();
421	>
422	>	}
423	>
424	>	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
425	>
426	>	// Force fields can set options on how to scale van der Waals and
427	>	// electrostatic interactions for atoms connected via bonds, bends
428	>	// and torsions in this case the topological distance between
429	>	// atoms is:
430	>	// 0 = topologically unconnected
431	>	// 1 = bonded together
432	>	// 2 = connected via a bend
433	>	// 3 = connected via a torsion
434	>
435	>	vdwScale_.reserve(4);
436	>	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
437	>
438	>	electrostaticScale_.reserve(4);
439	>	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
440	>
441	>	vdwScale_[0] = 1.0;
442	>	vdwScale_[1] = fopts.getvdw12scale();
443	>	vdwScale_[2] = fopts.getvdw13scale();
444	>	vdwScale_[3] = fopts.getvdw14scale();
445	>
446	>	electrostaticScale_[0] = 1.0;
447	>	electrostaticScale_[1] = fopts.getelectrostatic12scale();
448	>	electrostaticScale_[2] = fopts.getelectrostatic13scale();
449	>	electrostaticScale_[3] = fopts.getelectrostatic14scale();
450	>
451	>	if (info_->getSimParams()->haveElectricField()) {
452	>	ElectricField* eField = new ElectricField(info_);
453	>	perturbations_.push_back(eField);
454	>	}
455	>
456	>	usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
457	>
458	>	fDecomp_->distributeInitialData();
459	>
460	>	initialized_ = true;
461	>
462	>	}
463	>
464	>	void ForceManager::calcForces() {
465	>
466	>	if (!initialized_) initialize();
467	>
468	>	preCalculation();
469	>	shortRangeInteractions();
470	>	longRangeInteractions();
471	>	postCalculation();
472	>	}
473	>
474	>	void ForceManager::preCalculation() {
475		SimInfo::MoleculeIterator mi;
476		Molecule* mol;
477		Molecule::AtomIterator ai;
478		Atom* atom;
479		Molecule::RigidBodyIterator rbIter;
480		RigidBody* rb;
481	+	Molecule::CutoffGroupIterator ci;
482	+	CutoffGroup* cg;
483
484	<	// forces are zeroed here, before any are accumulated.
485	<	// NOTE: do not rezero the forces in Fortran.
486	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
487	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
488	<	atom->zeroForcesAndTorques();
484	>	// forces and potentials are zeroed here, before any are
485	>	// accumulated.
486	>
487	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
488	>
489	>	snap->setBondPotential(0.0);
490	>	snap->setBendPotential(0.0);
491	>	snap->setTorsionPotential(0.0);
492	>	snap->setInversionPotential(0.0);
493	>
494	>	potVec zeroPot(0.0);
495	>	snap->setLongRangePotential(zeroPot);
496	>	snap->setExcludedPotentials(zeroPot);
497	>
498	>	snap->setRestraintPotential(0.0);
499	>	snap->setRawPotential(0.0);
500	>
501	>	for (mol = info_->beginMolecule(mi); mol != NULL;
502	>	mol = info_->nextMolecule(mi)) {
503	>	for(atom = mol->beginAtom(ai); atom != NULL;
504	>	atom = mol->nextAtom(ai)) {
505	>	atom->zeroForcesAndTorques();
506	>	}
507	>
508	>	//change the positions of atoms which belong to the rigidbodies
509	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
510	>	rb = mol->nextRigidBody(rbIter)) {
511	>	rb->zeroForcesAndTorques();
512	>	}
513	>
514	>	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
515	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
516	>	cg = mol->nextCutoffGroup(ci)) {
517	>	//calculate the center of mass of cutoff group
518	>	cg->updateCOM();
519		}
520	<
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	<	}
520	>	}
521		}
522
523	<	}
524	<
525	<	void ForceManager::calcShortRangeInteraction() {
523	>	// Zero out the stress tensor
524	>	stressTensor *= 0.0;
525	>	// Zero out the heatFlux
526	>	fDecomp_->setHeatFlux( Vector3d(0.0) );
527	>	}
528	>
529	>	void ForceManager::shortRangeInteractions() {
530		Molecule* mol;
531		RigidBody* rb;
532		Bond* bond;
533		Bend* bend;
534		Torsion* torsion;
535	+	Inversion* inversion;
536		SimInfo::MoleculeIterator mi;
537		Molecule::RigidBodyIterator rbIter;
538		Molecule::BondIterator bondIter;;
539		Molecule::BendIterator  bendIter;
540		Molecule::TorsionIterator  torsionIter;
541	+	Molecule::InversionIterator  inversionIter;
542	+	RealType bondPotential = 0.0;
543	+	RealType bendPotential = 0.0;
544	+	RealType torsionPotential = 0.0;
545	+	RealType inversionPotential = 0.0;
546
547		//calculate short range interactions
548	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
548	>	for (mol = info_->beginMolecule(mi); mol != NULL;
549	>	mol = info_->nextMolecule(mi)) {
550
551	<	//change the positions of atoms which belong to the rigidbodies
552	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
553	<	rb->updateAtoms();
554	<	}
551	>	//change the positions of atoms which belong to the rigidbodies
552	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
553	>	rb = mol->nextRigidBody(rbIter)) {
554	>	rb->updateAtoms();
555	>	}
556
557	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
558	<	bond->calcForce();
559	<	}
560	<
561	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
120	<	bend->calcForce();
121	<	}
557	>	for (bond = mol->beginBond(bondIter); bond != NULL;
558	>	bond = mol->nextBond(bondIter)) {
559	>	bond->calcForce(doParticlePot_);
560	>	bondPotential += bond->getPotential();
561	>	}
562
563	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
564	<	torsion->calcForce();
563	>	for (bend = mol->beginBend(bendIter); bend != NULL;
564	>	bend = mol->nextBend(bendIter)) {
565	>
566	>	RealType angle;
567	>	bend->calcForce(angle, doParticlePot_);
568	>	RealType currBendPot = bend->getPotential();
569	>
570	>	bendPotential += bend->getPotential();
571	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
572	>	if (i == bendDataSets.end()) {
573	>	BendDataSet dataSet;
574	>	dataSet.prev.angle = dataSet.curr.angle = angle;
575	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
576	>	dataSet.deltaV = 0.0;
577	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
578	>	dataSet));
579	>	}else {
580	>	i->second.prev.angle = i->second.curr.angle;
581	>	i->second.prev.potential = i->second.curr.potential;
582	>	i->second.curr.angle = angle;
583	>	i->second.curr.potential = currBendPot;
584	>	i->second.deltaV =  fabs(i->second.curr.potential -
585	>	i->second.prev.potential);
586		}
587	<
587	>	}
588	>
589	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
590	>	torsion = mol->nextTorsion(torsionIter)) {
591	>	RealType angle;
592	>	torsion->calcForce(angle, doParticlePot_);
593	>	RealType currTorsionPot = torsion->getPotential();
594	>	torsionPotential += torsion->getPotential();
595	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
596	>	if (i == torsionDataSets.end()) {
597	>	TorsionDataSet dataSet;
598	>	dataSet.prev.angle = dataSet.curr.angle = angle;
599	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
600	>	dataSet.deltaV = 0.0;
601	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
602	>	}else {
603	>	i->second.prev.angle = i->second.curr.angle;
604	>	i->second.prev.potential = i->second.curr.potential;
605	>	i->second.curr.angle = angle;
606	>	i->second.curr.potential = currTorsionPot;
607	>	i->second.deltaV =  fabs(i->second.curr.potential -
608	>	i->second.prev.potential);
609	>	}
610	>	}
611	>
612	>	for (inversion = mol->beginInversion(inversionIter);
613	>	inversion != NULL;
614	>	inversion = mol->nextInversion(inversionIter)) {
615	>	RealType angle;
616	>	inversion->calcForce(angle, doParticlePot_);
617	>	RealType currInversionPot = inversion->getPotential();
618	>	inversionPotential += inversion->getPotential();
619	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
620	>	if (i == inversionDataSets.end()) {
621	>	InversionDataSet dataSet;
622	>	dataSet.prev.angle = dataSet.curr.angle = angle;
623	>	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
624	>	dataSet.deltaV = 0.0;
625	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
626	>	}else {
627	>	i->second.prev.angle = i->second.curr.angle;
628	>	i->second.prev.potential = i->second.curr.potential;
629	>	i->second.curr.angle = angle;
630	>	i->second.curr.potential = currInversionPot;
631	>	i->second.deltaV =  fabs(i->second.curr.potential -
632	>	i->second.prev.potential);
633	>	}
634	>	}
635		}
128	–
129	–	double  shortRangePotential = 0.0;
130	–	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
131	–	shortRangePotential += mol->getPotential();
132	–	}
636
637	+	#ifdef IS_MPI
638	+	// Collect from all nodes.  This should eventually be moved into a
639	+	// SystemDecomposition, but this is a better place than in
640	+	// Thermo to do the collection.
641	+
642	+	MPI_Allreduce(MPI_IN_PLACE, &bondPotential, 1, MPI_REALTYPE,
643	+	MPI_SUM, MPI_COMM_WORLD);
644	+	MPI_Allreduce(MPI_IN_PLACE, &bendPotential, 1, MPI_REALTYPE,
645	+	MPI_SUM, MPI_COMM_WORLD);
646	+	MPI_Allreduce(MPI_IN_PLACE, &torsionPotential, 1,
647	+	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
648	+	MPI_Allreduce(MPI_IN_PLACE, &inversionPotential, 1,
649	+	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
650	+	#endif
651	+
652		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
135	–	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
136	–	}
653
654	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
655	<	Snapshot* curSnapshot;
656	<	DataStorage* config;
657	<	double* frc;
142	<	double* pos;
143	<	double* trq;
144	<	double* A;
145	<	double* electroFrame;
146	<	double* rc;
654	>	curSnapshot->setBondPotential(bondPotential);
655	>	curSnapshot->setBendPotential(bendPotential);
656	>	curSnapshot->setTorsionPotential(torsionPotential);
657	>	curSnapshot->setInversionPotential(inversionPotential);
658
659	<	//get current snapshot from SimInfo
660	<	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
659	>	// RealType shortRangePotential = bondPotential + bendPotential +
660	>	//   torsionPotential +  inversionPotential;
661
662	<	//get array pointers
663	<	config = &(curSnapshot->atomData);
664	<	frc = config->getArrayPointer(DataStorage::dslForce);
665	<	pos = config->getArrayPointer(DataStorage::dslPosition);
155	<	trq = config->getArrayPointer(DataStorage::dslTorque);
156	<	A   = config->getArrayPointer(DataStorage::dslAmat);
157	<	electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
662	>	// curSnapshot->setShortRangePotential(shortRangePotential);
663	>	}
664	>
665	>	void ForceManager::longRangeInteractions() {
666
667	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
668	+	DataStorage* config = &(curSnapshot->atomData);
669	+	DataStorage* cgConfig = &(curSnapshot->cgData);
670	+
671	+
672		//calculate the center of mass of cutoff group
673	+
674		SimInfo::MoleculeIterator mi;
675		Molecule* mol;
676		Molecule::CutoffGroupIterator ci;
677		CutoffGroup* cg;
164	–	Vector3d com;
165	–	std::vector<Vector3d> rcGroup;
166	–
167	–	if(info_->getNCutoffGroups() > 0){
678
679	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
680	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
681	<	cg->getCOM(com);
682	<	rcGroup.push_back(com);
679	>	if(info_->getNCutoffGroups() > 0){
680	>	for (mol = info_->beginMolecule(mi); mol != NULL;
681	>	mol = info_->nextMolecule(mi)) {
682	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
683	>	cg = mol->nextCutoffGroup(ci)) {
684	>	cg->updateCOM();
685		}
686	<	}// end for (mol)
175	<
176	<	rc = rcGroup[0].getArrayPointer();
686	>	}
687		} else {
688	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
689	<	rc = pos;
688	>	// center of mass of the group is the same as position of the atom
689	>	// if cutoff group does not exist
690	>	cgConfig->position = config->position;
691	>	cgConfig->velocity = config->velocity;
692		}
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;
693
694	<	doForceLoop( pos,
695	<	rc,
696	<	A,
697	<	electroFrame,
698	<	frc,
699	<	trq,
700	<	tau.getArrayPointer(),
701	<	&longRangePotential,
702	<	&passedCalcPot,
703	<	&passedCalcStress,
704	<	&isError );
694	>	fDecomp_->zeroWorkArrays();
695	>	fDecomp_->distributeData();
696	>
697	>	int cg1, cg2, atom1, atom2, topoDist;
698	>	Vector3d d_grp, dag, d, gvel2, vel2;
699	>	RealType rgrpsq, rgrp, r2, r;
700	>	RealType electroMult, vdwMult;
701	>	RealType vij;
702	>	Vector3d fij, fg, f1;
703	>	tuple3<RealType, RealType, RealType> cuts;
704	>	RealType rCut, rCutSq, rListSq;
705	>	bool in_switching_region;
706	>	RealType sw, dswdr, swderiv;
707	>	vector<int> atomListColumn, atomListRow;
708	>	InteractionData idat;
709	>	SelfData sdat;
710	>	RealType mf;
711	>	RealType vpair;
712	>	RealType dVdFQ1(0.0);
713	>	RealType dVdFQ2(0.0);
714	>	potVec longRangePotential(0.0);
715	>	RealType reciprocalPotential(0.0);
716	>	potVec workPot(0.0);
717	>	potVec exPot(0.0);
718	>	Vector3d eField1(0.0);
719	>	Vector3d eField2(0.0);
720	>	RealType sPot1(0.0);
721	>	RealType sPot2(0.0);
722	>
723	>	vector<int>::iterator ia, jb;
724
725	<	if( isError ){
726	<	sprintf( painCave.errMsg,
727	<	"Error returned from the fortran force calculation.\n" );
728	<	painCave.isFatal = 1;
729	<	simError();
725	>	int loopStart, loopEnd;
726	>
727	>	idat.rcut = &rCut;
728	>	idat.vdwMult = &vdwMult;
729	>	idat.electroMult = &electroMult;
730	>	idat.pot = &workPot;
731	>	idat.excludedPot = &exPot;
732	>	sdat.pot = fDecomp_->getEmbeddingPotential();
733	>	sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
734	>	idat.vpair = &vpair;
735	>	idat.dVdFQ1 = &dVdFQ1;
736	>	idat.dVdFQ2 = &dVdFQ2;
737	>	idat.eField1 = &eField1;
738	>	idat.eField2 = &eField2;
739	>	idat.sPot1 = &sPot1;
740	>	idat.sPot2 = &sPot2;
741	>	idat.f1 = &f1;
742	>	idat.sw = &sw;
743	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
744	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE || cutoffMethod_ == TAYLOR_SHIFTED) ? true : false;
745	>	idat.doParticlePot = doParticlePot_;
746	>	idat.doElectricField = doElectricField_;
747	>	idat.doSitePotential = doSitePotential_;
748	>	sdat.doParticlePot = doParticlePot_;
749	>
750	>	loopEnd = PAIR_LOOP;
751	>	if (info_->requiresPrepair() ) {
752	>	loopStart = PREPAIR_LOOP;
753	>	} else {
754	>	loopStart = PAIR_LOOP;
755		}
756	+	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
757	+
758	+	if (iLoop == loopStart) {
759	+	bool update_nlist = fDecomp_->checkNeighborList();
760	+	if (update_nlist) {
761	+	if (!usePeriodicBoundaryConditions_)
762	+	Mat3x3d bbox = thermo->getBoundingBox();
763	+	fDecomp_->buildNeighborList(neighborList_);
764	+	}
765	+	}
766
767	<	//store the tau and long range potential
768	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential;
769	<	curSnapshot->statData.setTau(tau);
770	<	}
767	>	for (vector<pair<int, int> >::iterator it = neighborList_.begin();
768	>	it != neighborList_.end(); ++it) {
769	>
770	>	cg1 = (*it).first;
771	>	cg2 = (*it).second;
772	>
773	>	fDecomp_->getGroupCutoffs(cg1, cg2, rCut, rCutSq, rListSq);
774
775	+	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
776
777	<	void ForceManager::postCalculation() {
777	>	// already wrapped in the getIntergroupVector call:
778	>	// curSnapshot->wrapVector(d_grp);
779	>	rgrpsq = d_grp.lengthSquare();
780	>
781	>	if (rgrpsq < rCutSq) {
782	>	if (iLoop == PAIR_LOOP) {
783	>	vij = 0.0;
784	>	fij.zero();
785	>	eField1.zero();
786	>	eField2.zero();
787	>	sPot1 = 0.0;
788	>	sPot2 = 0.0;
789	>	}
790	>
791	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
792	>	rgrp);
793	>
794	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
795	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
796	>
797	>	if (doHeatFlux_)
798	>	gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
799	>
800	>	for (ia = atomListRow.begin();
801	>	ia != atomListRow.end(); ++ia) {
802	>	atom1 = (*ia);
803	>
804	>	for (jb = atomListColumn.begin();
805	>	jb != atomListColumn.end(); ++jb) {
806	>	atom2 = (*jb);
807	>
808	>	if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
809	>
810	>	vpair = 0.0;
811	>	workPot = 0.0;
812	>	exPot = 0.0;
813	>	f1.zero();
814	>	dVdFQ1 = 0.0;
815	>	dVdFQ2 = 0.0;
816	>
817	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
818	>
819	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
820	>	vdwMult = vdwScale_[topoDist];
821	>	electroMult = electrostaticScale_[topoDist];
822	>
823	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
824	>	idat.d = &d_grp;
825	>	idat.r2 = &rgrpsq;
826	>	if (doHeatFlux_)
827	>	vel2 = gvel2;
828	>	} else {
829	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
830	>	curSnapshot->wrapVector( d );
831	>	r2 = d.lengthSquare();
832	>	idat.d = &d;
833	>	idat.r2 = &r2;
834	>	if (doHeatFlux_)
835	>	vel2 = fDecomp_->getAtomVelocityColumn(atom2);
836	>	}
837	>
838	>	r = sqrt( *(idat.r2) );
839	>	idat.rij = &r;
840	>
841	>	if (iLoop == PREPAIR_LOOP) {
842	>	interactionMan_->doPrePair(idat);
843	>	} else {
844	>	interactionMan_->doPair(idat);
845	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
846	>	vij += vpair;
847	>	fij += f1;
848	>	stressTensor -= outProduct( *(idat.d), f1);
849	>	if (doHeatFlux_)
850	>	fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
851	>	}
852	>	}
853	>	}
854	>	}
855	>
856	>	if (iLoop == PAIR_LOOP) {
857	>	if (in_switching_region) {
858	>	swderiv = vij * dswdr / rgrp;
859	>	fg = swderiv * d_grp;
860	>	fij += fg;
861	>
862	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
863	>	if (!fDecomp_->skipAtomPair(atomListRow[0],
864	>	atomListColumn[0],
865	>	cg1, cg2)) {
866	>	stressTensor -= outProduct( *(idat.d), fg);
867	>	if (doHeatFlux_)
868	>	fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
869	>	}
870	>	}
871	>
872	>	for (ia = atomListRow.begin();
873	>	ia != atomListRow.end(); ++ia) {
874	>	atom1 = (*ia);
875	>	mf = fDecomp_->getMassFactorRow(atom1);
876	>	// fg is the force on atom ia due to cutoff group's
877	>	// presence in switching region
878	>	fg = swderiv * d_grp * mf;
879	>	fDecomp_->addForceToAtomRow(atom1, fg);
880	>	if (atomListRow.size() > 1) {
881	>	if (info_->usesAtomicVirial()) {
882	>	// find the distance between the atom
883	>	// and the center of the cutoff group:
884	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
885	>	stressTensor -= outProduct(dag, fg);
886	>	if (doHeatFlux_)
887	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
888	>	}
889	>	}
890	>	}
891	>	for (jb = atomListColumn.begin();
892	>	jb != atomListColumn.end(); ++jb) {
893	>	atom2 = (*jb);
894	>	mf = fDecomp_->getMassFactorColumn(atom2);
895	>	// fg is the force on atom jb due to cutoff group's
896	>	// presence in switching region
897	>	fg = -swderiv * d_grp * mf;
898	>	fDecomp_->addForceToAtomColumn(atom2, fg);
899	>
900	>	if (atomListColumn.size() > 1) {
901	>	if (info_->usesAtomicVirial()) {
902	>	// find the distance between the atom
903	>	// and the center of the cutoff group:
904	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
905	>	stressTensor -= outProduct(dag, fg);
906	>	if (doHeatFlux_)
907	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
908	>	}
909	>	}
910	>	}
911	>	}
912	>	//if (!info_->usesAtomicVirial()) {
913	>	//  stressTensor -= outProduct(d_grp, fij);
914	>	//  if (doHeatFlux_)
915	>	//     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
916	>	//}
917	>	}
918	>	}
919	>	}
920	>
921	>	if (iLoop == PREPAIR_LOOP) {
922	>	if (info_->requiresPrepair()) {
923	>
924	>	fDecomp_->collectIntermediateData();
925	>
926	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
927	>	fDecomp_->fillSelfData(sdat, atom1);
928	>	interactionMan_->doPreForce(sdat);
929	>	}
930	>
931	>	fDecomp_->distributeIntermediateData();
932	>
933	>	}
934	>	}
935	>	}
936	>
937	>	// collects pairwise information
938	>	fDecomp_->collectData();
939	>	if (cutoffMethod_ == EWALD_FULL) {
940	>	interactionMan_->doReciprocalSpaceSum(reciprocalPotential);
941	>
942	>	curSnapshot->setReciprocalPotential(reciprocalPotential);
943	>	}
944	>
945	>	if (info_->requiresSelfCorrection()) {
946	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
947	>	fDecomp_->fillSelfData(sdat, atom1);
948	>	interactionMan_->doSelfCorrection(sdat);
949	>	}
950	>	}
951	>
952	>	// collects single-atom information
953	>	fDecomp_->collectSelfData();
954	>
955	>	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
956	>	*(fDecomp_->getPairwisePotential());
957	>
958	>	curSnapshot->setLongRangePotential(longRangePotential);
959	>
960	>	curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
961	>	*(fDecomp_->getExcludedPotential()));
962	>
963	>	}
964	>
965	>	void ForceManager::postCalculation() {
966	>
967	>	vector<Perturbation*>::iterator pi;
968	>	for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
969	>	(*pi)->applyPerturbation();
970	>	}
971	>
972		SimInfo::MoleculeIterator mi;
973		Molecule* mol;
974		Molecule::RigidBodyIterator rbIter;
975		RigidBody* rb;
976	<
976	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
977	>
978		// collect the atomic forces onto rigid bodies
979	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
980	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
981	<	rb->calcForcesAndTorques();
982	<	}
979	>
980	>	for (mol = info_->beginMolecule(mi); mol != NULL;
981	>	mol = info_->nextMolecule(mi)) {
982	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
983	>	rb = mol->nextRigidBody(rbIter)) {
984	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
985	>	stressTensor += rbTau;
986	>	}
987		}
988	+
989	+	#ifdef IS_MPI
990	+	MPI_Allreduce(MPI_IN_PLACE, stressTensor.getArrayPointer(), 9,
991	+	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
992	+	#endif
993	+	curSnapshot->setStressTensor(stressTensor);
994	+
995	+	if (info_->getSimParams()->getUseLongRangeCorrections()) {
996	+	/*
997	+	RealType vol = curSnapshot->getVolume();
998	+	RealType Elrc(0.0);
999	+	RealType Wlrc(0.0);
1000
1001	<	}
1001	>	set<AtomType*>::iterator i;
1002	>	set<AtomType*>::iterator j;
1003	>
1004	>	RealType n_i, n_j;
1005	>	RealType rho_i, rho_j;
1006	>	pair<RealType, RealType> LRI;
1007	>
1008	>	for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
1009	>	n_i = RealType(info_->getGlobalCountOfType(*i));
1010	>	rho_i = n_i /  vol;
1011	>	for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) {
1012	>	n_j = RealType(info_->getGlobalCountOfType(*j));
1013	>	rho_j = n_j / vol;
1014	>
1015	>	LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) );
1016
1017	<	} //end namespace oopse
1017	>	Elrc += n_i   * rho_j * LRI.first;
1018	>	Wlrc -= rho_i * rho_j * LRI.second;
1019	>	}
1020	>	}
1021	>	Elrc *= 2.0 * NumericConstant::PI;
1022	>	Wlrc *= 2.0 * NumericConstant::PI;
1023	>
1024	>	RealType lrp = curSnapshot->getLongRangePotential();
1025	>	curSnapshot->setLongRangePotential(lrp + Elrc);
1026	>	stressTensor += Wlrc * SquareMatrix3<RealType>::identity();
1027	>	curSnapshot->setStressTensor(stressTensor);
1028	>	*/
1029	>
1030	>	}
1031	>	}
1032	>	}

Comparing trunk/src/brains/ForceManager.cpp (property svn:keywords):
Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 1993 by gezelter, Tue Apr 29 17:32:31 2014 UTC

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