ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing trunk/src/brains/ForceManager.cpp (file contents):
Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
Revision 2066 by gezelter, Thu Mar 5 15:22:54 2015 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
44		* @file ForceManager.cpp
45		* @author tlin
46		* @date 11/09/2004
46	–	* @time 10:39am
47		* @version 1.0
48		*/
49
50	+
51		#include "brains/ForceManager.hpp"
52		#include "primitives/Molecule.hpp"
53	<	#include "UseTheForce/doForces_interface.h"
53	<	#define __C
54	<	#include "UseTheForce/DarkSide/fInteractionMap.h"
53	>	#define __OPENMD_C
54		#include "utils/simError.h"
55	+	#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/UniformField.hpp"
61	>	#include "perturbations/UniformGradient.hpp"
62	>	#include "parallel/ForceMatrixDecomposition.hpp"
63
64	<	/*
65	<	struct BendOrderStruct {
66	<	Bend* bend;
63	<	BendDataSet dataSet;
64	<	};
65	<	struct TorsionOrderStruct {
66	<	Torsion* torsion;
67	<	TorsionDataSet dataSet;
68	<	};
64	>	#include <cstdio>
65	>	#include <iostream>
66	>	#include <iomanip>
67
68	<	bool  BendSortFunctor(const BendOrderStruct& b1, const BendOrderStruct& b2) {
69	<	return b1.dataSet.deltaV < b2.dataSet.deltaV;
68	>	using namespace std;
69	>	namespace OpenMD {
70	>
71	>	ForceManager::ForceManager(SimInfo * info) : info_(info),
72	>	initialized_(false),
73	>	switcher_(NULL) {
74	>	forceField_ = info_->getForceField();
75	>	interactionMan_ = new InteractionManager();
76	>	fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
77	>	thermo = new Thermo(info_);
78		}
79
80	<	bool  TorsionSortFunctor(const TorsionOrderStruct& t1, const TorsionOrderStruct& t2) {
81	<	return t1.dataSet.deltaV < t2.dataSet.deltaV;
80	>	ForceManager::~ForceManager() {
81	>	perturbations_.clear();
82	>
83	>	delete switcher_;
84	>	delete interactionMan_;
85	>	delete fDecomp_;
86	>	delete thermo;
87		}
88	<	*/
89	<	void ForceManager::calcForces(bool needPotential, bool needStress) {
88	>
89	>	/**
90	>	* setupCutoffs
91	>	*
92	>	* Sets the values of cutoffRadius, switchingRadius, and cutoffMethod
93	>	*
94	>	* cutoffRadius : realType
95	>	*  If the cutoffRadius was explicitly set, use that value.
96	>	*  If the cutoffRadius was not explicitly set:
97	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
98	>	*      No electrostatic atoms?  Poll the atom types present in the
99	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
100	>	*      Use the maximum suggested value that was found.
101	>	*
102	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, TAYLOR_SHIFTED,
103	>	*                        SHIFTED_POTENTIAL, or EWALD_FULL)
104	>	*      If cutoffMethod was explicitly set, use that choice.
105	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
106	>	*
107	>	* switchingRadius : realType
108	>	*  If the cutoffMethod was set to SWITCHED:
109	>	*      If the switchingRadius was explicitly set, use that value
110	>	*          (but do a sanity check first).
111	>	*      If the switchingRadius was not explicitly set: use 0.85 *
112	>	*      cutoffRadius_
113	>	*  If the cutoffMethod was not set to SWITCHED:
114	>	*      Set switchingRadius equal to cutoffRadius for safety.
115	>	*/
116	>	void ForceManager::setupCutoffs() {
117	>
118	>	Globals* simParams_ = info_->getSimParams();
119	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
120	>	int mdFileVersion;
121	>	rCut_ = 0.0; //Needs a value for a later max() call;
122	>
123	>	if (simParams_->haveMDfileVersion())
124	>	mdFileVersion = simParams_->getMDfileVersion();
125	>	else
126	>	mdFileVersion = 0;
127	>
128	>	// We need the list of simulated atom types to figure out cutoffs
129	>	// as well as long range corrections.
130
131	<	if (!info_->isFortranInitialized()) {
132	<	info_->update();
131	>	set<AtomType*>::iterator i;
132	>	set<AtomType*> atomTypes_;
133	>	atomTypes_ = info_->getSimulatedAtomTypes();
134	>
135	>	if (simParams_->haveCutoffRadius()) {
136	>	rCut_ = simParams_->getCutoffRadius();
137	>	} else {
138	>	if (info_->usesElectrostaticAtoms()) {
139	>	sprintf(painCave.errMsg,
140	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
141	>	"\tOpenMD will use a default value of 12.0 angstroms"
142	>	"\tfor the cutoffRadius.\n");
143	>	painCave.isFatal = 0;
144	>	painCave.severity = OPENMD_INFO;
145	>	simError();
146	>	rCut_ = 12.0;
147	>	} else {
148	>	RealType thisCut;
149	>	for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
150	>	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
151	>	rCut_ = max(thisCut, rCut_);
152	>	}
153	>	sprintf(painCave.errMsg,
154	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
155	>	"\tOpenMD will use %lf angstroms.\n",
156	>	rCut_);
157	>	painCave.isFatal = 0;
158	>	painCave.severity = OPENMD_INFO;
159	>	simError();
160	>	}
161		}
162
163	<	preCalculation();
164	<
165	<	calcShortRangeInteraction();
163	>	fDecomp_->setCutoffRadius(rCut_);
164	>	interactionMan_->setCutoffRadius(rCut_);
165	>	rCutSq_ = rCut_ * rCut_;
166
167	<	calcLongRangeInteraction(needPotential, needStress);
167	>	map<string, CutoffMethod> stringToCutoffMethod;
168	>	stringToCutoffMethod["HARD"] = HARD;
169	>	stringToCutoffMethod["SWITCHED"] = SWITCHED;
170	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
171	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
172	>	stringToCutoffMethod["TAYLOR_SHIFTED"] = TAYLOR_SHIFTED;
173	>	stringToCutoffMethod["EWALD_FULL"] = EWALD_FULL;
174	>
175	>	if (simParams_->haveCutoffMethod()) {
176	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
177	>	map<string, CutoffMethod>::iterator i;
178	>	i = stringToCutoffMethod.find(cutMeth);
179	>	if (i == stringToCutoffMethod.end()) {
180	>	sprintf(painCave.errMsg,
181	>	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
182	>	"\tShould be one of: "
183	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, TAYLOR_SHIFTED,\n"
184	>	"\tSHIFTED_FORCE, or EWALD_FULL\n",
185	>	cutMeth.c_str());
186	>	painCave.isFatal = 1;
187	>	painCave.severity = OPENMD_ERROR;
188	>	simError();
189	>	} else {
190	>	cutoffMethod_ = i->second;
191	>	}
192	>	} else {
193	>	if (mdFileVersion > 1) {
194	>	sprintf(painCave.errMsg,
195	>	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
196	>	"\tOpenMD will use SHIFTED_FORCE.\n");
197	>	painCave.isFatal = 0;
198	>	painCave.severity = OPENMD_INFO;
199	>	simError();
200	>	cutoffMethod_ = SHIFTED_FORCE;
201	>	} else {
202	>	// handle the case where the old file version was in play
203	>	// (there should be no cutoffMethod, so we have to deduce it
204	>	// from other data).
205
206	<	postCalculation();
206	>	sprintf(painCave.errMsg,
207	>	"ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
208	>	"\tOpenMD found a file which does not set a cutoffMethod.\n"
209	>	"\tOpenMD will attempt to deduce a cutoffMethod using the\n"
210	>	"\tbehavior of the older (version 1) code.  To remove this\n"
211	>	"\twarning, add an explicit cutoffMethod and change the top\n"
212	>	"\tof the file so that it begins with <OpenMD version=2>\n");
213	>	painCave.isFatal = 0;
214	>	painCave.severity = OPENMD_WARNING;
215	>	simError();
216	>
217	>	// The old file version tethered the shifting behavior to the
218	>	// electrostaticSummationMethod keyword.
219	>
220	>	if (simParams_->haveElectrostaticSummationMethod()) {
221	>	string myMethod = simParams_->getElectrostaticSummationMethod();
222	>	toUpper(myMethod);
223	>
224	>	if (myMethod == "SHIFTED_POTENTIAL") {
225	>	cutoffMethod_ = SHIFTED_POTENTIAL;
226	>	} else if (myMethod == "SHIFTED_FORCE") {
227	>	cutoffMethod_ = SHIFTED_FORCE;
228	>	} else if (myMethod == "TAYLOR_SHIFTED") {
229	>	cutoffMethod_ = TAYLOR_SHIFTED;
230	>	} else if (myMethod == "EWALD_FULL") {
231	>	cutoffMethod_ = EWALD_FULL;
232	>	}
233	>
234	>	if (simParams_->haveSwitchingRadius())
235	>	rSwitch_ = simParams_->getSwitchingRadius();
236
237	<	/*
238	<	std::vector<BendOrderStruct> bendOrderStruct;
239	<	for(std::map<Bend*, BendDataSet>::iterator i = bendDataSets.begin(); i != bendDataSets.end(); ++i) {
240	<	BendOrderStruct tmp;
241	<	tmp.bend= const_cast<Bend*>(i->first);
242	<	tmp.dataSet = i->second;
243	<	bendOrderStruct.push_back(tmp);
237	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE" ||
238	>	myMethod == "TAYLOR_SHIFTED" || myMethod == "EWALD_FULL") {
239	>	if (simParams_->haveSwitchingRadius()){
240	>	sprintf(painCave.errMsg,
241	>	"ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
242	>	"\tA value was set for the switchingRadius\n"
243	>	"\teven though the electrostaticSummationMethod was\n"
244	>	"\tset to %s\n", myMethod.c_str());
245	>	painCave.severity = OPENMD_WARNING;
246	>	painCave.isFatal = 1;
247	>	simError();
248	>	}
249	>	}
250	>	if (abs(rCut_ - rSwitch_) < 0.0001) {
251	>	if (cutoffMethod_ == SHIFTED_FORCE) {
252	>	sprintf(painCave.errMsg,
253	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
254	>	"\tcutoffRadius and switchingRadius are set to the\n"
255	>	"\tsame value.  OpenMD will use shifted force\n"
256	>	"\tpotentials instead of switching functions.\n");
257	>	painCave.isFatal = 0;
258	>	painCave.severity = OPENMD_WARNING;
259	>	simError();
260	>	} else {
261	>	cutoffMethod_ = SHIFTED_POTENTIAL;
262	>	sprintf(painCave.errMsg,
263	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
264	>	"\tcutoffRadius and switchingRadius are set to the\n"
265	>	"\tsame value.  OpenMD will use shifted potentials\n"
266	>	"\tinstead of switching functions.\n");
267	>	painCave.isFatal = 0;
268	>	painCave.severity = OPENMD_WARNING;
269	>	simError();
270	>	}
271	>	}
272	>	}
273	>	}
274		}
275	+
276	+	// create the switching function object:
277
278	<	std::vector<TorsionOrderStruct> torsionOrderStruct;
279	<	for(std::map<Torsion*, TorsionDataSet>::iterator j = torsionDataSets.begin(); j != torsionDataSets.end(); ++j) {
280	<	TorsionOrderStruct tmp;
281	<	tmp.torsion = const_cast<Torsion*>(j->first);
282	<	tmp.dataSet = j->second;
283	<	torsionOrderStruct.push_back(tmp);
278	>	switcher_ = new SwitchingFunction();
279	>
280	>	if (cutoffMethod_ == SWITCHED) {
281	>	if (simParams_->haveSwitchingRadius()) {
282	>	rSwitch_ = simParams_->getSwitchingRadius();
283	>	if (rSwitch_ > rCut_) {
284	>	sprintf(painCave.errMsg,
285	>	"ForceManager::setupCutoffs: switchingRadius (%f) is larger "
286	>	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
287	>	painCave.isFatal = 1;
288	>	painCave.severity = OPENMD_ERROR;
289	>	simError();
290	>	}
291	>	} else {
292	>	rSwitch_ = 0.85 * rCut_;
293	>	sprintf(painCave.errMsg,
294	>	"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
295	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
296	>	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
297	>	painCave.isFatal = 0;
298	>	painCave.severity = OPENMD_WARNING;
299	>	simError();
300	>	}
301	>	} else {
302	>	if (mdFileVersion > 1) {
303	>	// throw an error if we define a switching radius and don't need one.
304	>	// older file versions should not do this.
305	>	if (simParams_->haveSwitchingRadius()) {
306	>	map<string, CutoffMethod>::const_iterator it;
307	>	string theMeth;
308	>	for (it = stringToCutoffMethod.begin();
309	>	it != stringToCutoffMethod.end(); ++it) {
310	>	if (it->second == cutoffMethod_) {
311	>	theMeth = it->first;
312	>	break;
313	>	}
314	>	}
315	>	sprintf(painCave.errMsg,
316	>	"ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
317	>	"\tis not set to SWITCHED, so switchingRadius value\n"
318	>	"\twill be ignored for this simulation\n", theMeth.c_str());
319	>	painCave.isFatal = 0;
320	>	painCave.severity = OPENMD_WARNING;
321	>	simError();
322	>	}
323	>	}
324	>	rSwitch_ = rCut_;
325		}
326
327	<	std::sort(bendOrderStruct.begin(), bendOrderStruct.end(), std::ptr_fun(BendSortFunctor));
328	<	std::sort(torsionOrderStruct.begin(), torsionOrderStruct.end(), std::ptr_fun(TorsionSortFunctor));
329	<	std::cout << "bend" << std::endl;
330	<	for (std::vector<BendOrderStruct>::iterator k = bendOrderStruct.begin(); k != bendOrderStruct.end(); ++k) {
331	<	Bend* bend = k->bend;
332	<	std::cout << "atom1=" <<bend->getAtomA()->getGlobalIndex() << ",atom2 = "<< bend->getAtomB()->getGlobalIndex() << ",atom3="<<bend->getAtomC()->getGlobalIndex() << " ";
333	<	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;
327	>	// Default to cubic switching function.
328	>	sft_ = cubic;
329	>	if (simParams_->haveSwitchingFunctionType()) {
330	>	string funcType = simParams_->getSwitchingFunctionType();
331	>	toUpper(funcType);
332	>	if (funcType == "CUBIC") {
333	>	sft_ = cubic;
334	>	} else {
335	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
336	>	sft_ = fifth_order_poly;
337	>	} else {
338	>	// throw error
339	>	sprintf( painCave.errMsg,
340	>	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
341	>	"\tswitchingFunctionType must be one of: "
342	>	"\"cubic\" or \"fifth_order_polynomial\".",
343	>	funcType.c_str() );
344	>	painCave.isFatal = 1;
345	>	painCave.severity = OPENMD_ERROR;
346	>	simError();
347	>	}
348	>	}
349		}
350	<	std::cout << "torsio" << std::endl;
351	<	for (std::vector<TorsionOrderStruct>::iterator l = torsionOrderStruct.begin(); l != torsionOrderStruct.end(); ++l) {
119	<	Torsion* torsion = l->torsion;
120	<	std::cout << "atom1=" <<torsion->getAtomA()->getGlobalIndex() << ",atom2 = "<< torsion->getAtomB()->getGlobalIndex() << ",atom3="<<torsion->getAtomC()->getGlobalIndex() << ",atom4="<<torsion->getAtomD()->getGlobalIndex()<< " ";
121	<	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;
122	<	}
123	<	*/
350	>	switcher_->setSwitchType(sft_);
351	>	switcher_->setSwitch(rSwitch_, rCut_);
352		}
353
354	+	void ForceManager::initialize() {
355	+
356	+	if (!info_->isTopologyDone()) {
357	+
358	+	info_->update();
359	+	interactionMan_->setSimInfo(info_);
360	+	interactionMan_->initialize();
361	+
362	+	//! We want to delay the cutoffs until after the interaction
363	+	//! manager has set up the atom-atom interactions so that we can
364	+	//! query them for suggested cutoff values
365	+	setupCutoffs();
366	+
367	+	info_->prepareTopology();
368	+
369	+	doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
370	+	doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
371	+	if (doHeatFlux_) doParticlePot_ = true;
372	+
373	+	doElectricField_ = info_->getSimParams()->getOutputElectricField();
374	+	doSitePotential_ = info_->getSimParams()->getOutputSitePotential();
375	+
376	+	}
377	+
378	+	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
379	+
380	+	//! Force fields can set options on how to scale van der Waals and
381	+	//! electrostatic interactions for atoms connected via bonds, bends
382	+	//! and torsions in this case the topological distance between
383	+	//! atoms is:
384	+	//! 0 = topologically unconnected
385	+	//! 1 = bonded together
386	+	//! 2 = connected via a bend
387	+	//! 3 = connected via a torsion
388	+
389	+	vdwScale_.reserve(4);
390	+	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
391	+
392	+	electrostaticScale_.reserve(4);
393	+	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
394	+
395	+	vdwScale_[0] = 1.0;
396	+	vdwScale_[1] = fopts.getvdw12scale();
397	+	vdwScale_[2] = fopts.getvdw13scale();
398	+	vdwScale_[3] = fopts.getvdw14scale();
399	+
400	+	electrostaticScale_[0] = 1.0;
401	+	electrostaticScale_[1] = fopts.getelectrostatic12scale();
402	+	electrostaticScale_[2] = fopts.getelectrostatic13scale();
403	+	electrostaticScale_[3] = fopts.getelectrostatic14scale();
404	+
405	+	if (info_->getSimParams()->haveUniformField()) {
406	+	UniformField* eField = new UniformField(info_);
407	+	perturbations_.push_back(eField);
408	+	}
409	+	if (info_->getSimParams()->haveUniformGradientStrength() ||
410	+	info_->getSimParams()->haveUniformGradientDirection1() ||
411	+	info_->getSimParams()->haveUniformGradientDirection2() ) {
412	+	UniformGradient* eGrad = new UniformGradient(info_);
413	+	perturbations_.push_back(eGrad);
414	+	}
415	+
416	+	usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
417	+
418	+	fDecomp_->distributeInitialData();
419	+
420	+	initialized_ = true;
421	+
422	+	}
423	+
424	+	void ForceManager::calcForces() {
425	+
426	+	if (!initialized_) initialize();
427	+
428	+	preCalculation();
429	+	shortRangeInteractions();
430	+	longRangeInteractions();
431	+	postCalculation();
432	+	}
433	+
434		void ForceManager::preCalculation() {
435		SimInfo::MoleculeIterator mi;
436		Molecule* mol;
#	Line 130 | Line 438 | namespace oopse {
438		Atom* atom;
439		Molecule::RigidBodyIterator rbIter;
440		RigidBody* rb;
441	+	Molecule::CutoffGroupIterator ci;
442	+	CutoffGroup* cg;
443
444	<	// forces are zeroed here, before any are accumulated.
445	<	// NOTE: do not rezero the forces in Fortran.
446	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
447	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
444	>	// forces and potentials are zeroed here, before any are
445	>	// accumulated.
446	>
447	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
448	>
449	>	snap->setBondPotential(0.0);
450	>	snap->setBendPotential(0.0);
451	>	snap->setTorsionPotential(0.0);
452	>	snap->setInversionPotential(0.0);
453	>
454	>	potVec zeroPot(0.0);
455	>	snap->setLongRangePotential(zeroPot);
456	>	snap->setExcludedPotentials(zeroPot);
457	>
458	>	snap->setRestraintPotential(0.0);
459	>	snap->setRawPotential(0.0);
460	>
461	>	for (mol = info_->beginMolecule(mi); mol != NULL;
462	>	mol = info_->nextMolecule(mi)) {
463	>	for(atom = mol->beginAtom(ai); atom != NULL;
464	>	atom = mol->nextAtom(ai)) {
465		atom->zeroForcesAndTorques();
466		}
467	<
467	>
468		//change the positions of atoms which belong to the rigidbodies
469	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
469	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
470	>	rb = mol->nextRigidBody(rbIter)) {
471		rb->zeroForcesAndTorques();
472		}
473	+
474	+	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
475	+	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
476	+	cg = mol->nextCutoffGroup(ci)) {
477	+	//calculate the center of mass of cutoff group
478	+	cg->updateCOM();
479	+	}
480	+	}
481		}
482
483	+	// Zero out the stress tensor
484	+	stressTensor *= 0.0;
485	+	// Zero out the heatFlux
486	+	fDecomp_->setHeatFlux( Vector3d(0.0) );
487		}
488	<
489	<	void ForceManager::calcShortRangeInteraction() {
488	>
489	>	void ForceManager::shortRangeInteractions() {
490		Molecule* mol;
491		RigidBody* rb;
492		Bond* bond;
493		Bend* bend;
494		Torsion* torsion;
495	+	Inversion* inversion;
496		SimInfo::MoleculeIterator mi;
497		Molecule::RigidBodyIterator rbIter;
498		Molecule::BondIterator bondIter;;
499		Molecule::BendIterator  bendIter;
500		Molecule::TorsionIterator  torsionIter;
501	<	double bondPotential = 0.0;
502	<	double bendPotential = 0.0;
503	<	double torsionPotential = 0.0;
501	>	Molecule::InversionIterator  inversionIter;
502	>	RealType bondPotential = 0.0;
503	>	RealType bendPotential = 0.0;
504	>	RealType torsionPotential = 0.0;
505	>	RealType inversionPotential = 0.0;
506
507		//calculate short range interactions
508	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
508	>	for (mol = info_->beginMolecule(mi); mol != NULL;
509	>	mol = info_->nextMolecule(mi)) {
510
511		//change the positions of atoms which belong to the rigidbodies
512	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
513	<	rb->updateAtoms();
512	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
513	>	rb = mol->nextRigidBody(rbIter)) {
514	>	rb->updateAtoms();
515		}
516
517	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
518	<	bond->calcForce();
517	>	for (bond = mol->beginBond(bondIter); bond != NULL;
518	>	bond = mol->nextBond(bondIter)) {
519	>	bond->calcForce(doParticlePot_);
520		bondPotential += bond->getPotential();
521		}
522
523	<
524	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
525	<
526	<	double angle;
527	<	bend->calcForce(angle);
528	<	double currBendPot = bend->getPotential();
529	<	bendPotential += bend->getPotential();
530	<	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
531	<	if (i == bendDataSets.end()) {
532	<	BendDataSet dataSet;
533	<	dataSet.prev.angle = dataSet.curr.angle = angle;
534	<	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
535	<	dataSet.deltaV = 0.0;
536	<	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
537	<	}else {
538	<	i->second.prev.angle = i->second.curr.angle;
539	<	i->second.prev.potential = i->second.curr.potential;
540	<	i->second.curr.angle = angle;
541	<	i->second.curr.potential = currBendPot;
542	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
543	<	}
544	<	}
545	<
546	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
201	<	double angle;
202	<	torsion->calcForce(angle);
203	<	double currTorsionPot = torsion->getPotential();
204	<	torsionPotential += torsion->getPotential();
205	<	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
206	<	if (i == torsionDataSets.end()) {
207	<	TorsionDataSet dataSet;
208	<	dataSet.prev.angle = dataSet.curr.angle = angle;
209	<	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
210	<	dataSet.deltaV = 0.0;
211	<	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
212	<	}else {
213	<	i->second.prev.angle = i->second.curr.angle;
214	<	i->second.prev.potential = i->second.curr.potential;
215	<	i->second.curr.angle = angle;
216	<	i->second.curr.potential = currTorsionPot;
217	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
218	<	}
523	>	for (bend = mol->beginBend(bendIter); bend != NULL;
524	>	bend = mol->nextBend(bendIter)) {
525	>
526	>	RealType angle;
527	>	bend->calcForce(angle, doParticlePot_);
528	>	RealType currBendPot = bend->getPotential();
529	>
530	>	bendPotential += bend->getPotential();
531	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
532	>	if (i == bendDataSets.end()) {
533	>	BendDataSet dataSet;
534	>	dataSet.prev.angle = dataSet.curr.angle = angle;
535	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
536	>	dataSet.deltaV = 0.0;
537	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
538	>	dataSet));
539	>	}else {
540	>	i->second.prev.angle = i->second.curr.angle;
541	>	i->second.prev.potential = i->second.curr.potential;
542	>	i->second.curr.angle = angle;
543	>	i->second.curr.potential = currBendPot;
544	>	i->second.deltaV =  fabs(i->second.curr.potential -
545	>	i->second.prev.potential);
546	>	}
547		}
548	<
548	>
549	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
550	>	torsion = mol->nextTorsion(torsionIter)) {
551	>	RealType angle;
552	>	torsion->calcForce(angle, doParticlePot_);
553	>	RealType currTorsionPot = torsion->getPotential();
554	>	torsionPotential += torsion->getPotential();
555	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
556	>	if (i == torsionDataSets.end()) {
557	>	TorsionDataSet dataSet;
558	>	dataSet.prev.angle = dataSet.curr.angle = angle;
559	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
560	>	dataSet.deltaV = 0.0;
561	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
562	>	}else {
563	>	i->second.prev.angle = i->second.curr.angle;
564	>	i->second.prev.potential = i->second.curr.potential;
565	>	i->second.curr.angle = angle;
566	>	i->second.curr.potential = currTorsionPot;
567	>	i->second.deltaV =  fabs(i->second.curr.potential -
568	>	i->second.prev.potential);
569	>	}
570	>	}
571	>
572	>	for (inversion = mol->beginInversion(inversionIter);
573	>	inversion != NULL;
574	>	inversion = mol->nextInversion(inversionIter)) {
575	>	RealType angle;
576	>	inversion->calcForce(angle, doParticlePot_);
577	>	RealType currInversionPot = inversion->getPotential();
578	>	inversionPotential += inversion->getPotential();
579	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
580	>	if (i == inversionDataSets.end()) {
581	>	InversionDataSet dataSet;
582	>	dataSet.prev.angle = dataSet.curr.angle = angle;
583	>	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
584	>	dataSet.deltaV = 0.0;
585	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
586	>	}else {
587	>	i->second.prev.angle = i->second.curr.angle;
588	>	i->second.prev.potential = i->second.curr.potential;
589	>	i->second.curr.angle = angle;
590	>	i->second.curr.potential = currInversionPot;
591	>	i->second.deltaV =  fabs(i->second.curr.potential -
592	>	i->second.prev.potential);
593	>	}
594	>	}
595		}
596	<
597	<	double  shortRangePotential = bondPotential + bendPotential + torsionPotential;
596	>
597	>	#ifdef IS_MPI
598	>	// Collect from all nodes.  This should eventually be moved into a
599	>	// SystemDecomposition, but this is a better place than in
600	>	// Thermo to do the collection.
601	>
602	>	MPI_Allreduce(MPI_IN_PLACE, &bondPotential, 1, MPI_REALTYPE,
603	>	MPI_SUM, MPI_COMM_WORLD);
604	>	MPI_Allreduce(MPI_IN_PLACE, &bendPotential, 1, MPI_REALTYPE,
605	>	MPI_SUM, MPI_COMM_WORLD);
606	>	MPI_Allreduce(MPI_IN_PLACE, &torsionPotential, 1,
607	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
608	>	MPI_Allreduce(MPI_IN_PLACE, &inversionPotential, 1,
609	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
610	>	#endif
611	>
612		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
225	–	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
226	–	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
227	–	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
228	–	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
229	–
230	–	}
613
614	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
615	<	Snapshot* curSnapshot;
616	<	DataStorage* config;
617	<	double* frc;
236	<	double* pos;
237	<	double* trq;
238	<	double* A;
239	<	double* electroFrame;
240	<	double* rc;
614	>	curSnapshot->setBondPotential(bondPotential);
615	>	curSnapshot->setBendPotential(bendPotential);
616	>	curSnapshot->setTorsionPotential(torsionPotential);
617	>	curSnapshot->setInversionPotential(inversionPotential);
618
619	<	//get current snapshot from SimInfo
620	<	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
619	>	// RealType shortRangePotential = bondPotential + bendPotential +
620	>	//   torsionPotential +  inversionPotential;
621
622	<	//get array pointers
623	<	config = &(curSnapshot->atomData);
624	<	frc = config->getArrayPointer(DataStorage::dslForce);
625	<	pos = config->getArrayPointer(DataStorage::dslPosition);
249	<	trq = config->getArrayPointer(DataStorage::dslTorque);
250	<	A   = config->getArrayPointer(DataStorage::dslAmat);
251	<	electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
622	>	// curSnapshot->setShortRangePotential(shortRangePotential);
623	>	}
624	>
625	>	void ForceManager::longRangeInteractions() {
626
627	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
628	+	DataStorage* config = &(curSnapshot->atomData);
629	+	DataStorage* cgConfig = &(curSnapshot->cgData);
630	+
631		//calculate the center of mass of cutoff group
632	+
633		SimInfo::MoleculeIterator mi;
634		Molecule* mol;
635		Molecule::CutoffGroupIterator ci;
636		CutoffGroup* cg;
637	<	Vector3d com;
638	<	std::vector<Vector3d> rcGroup;
639	<
640	<	if(info_->getNCutoffGroups() > 0){
641	<
642	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
643	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
265	<	cg->getCOM(com);
266	<	rcGroup.push_back(com);
637	>
638	>	if(info_->getNCutoffGroups() != info_->getNAtoms()){
639	>	for (mol = info_->beginMolecule(mi); mol != NULL;
640	>	mol = info_->nextMolecule(mi)) {
641	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
642	>	cg = mol->nextCutoffGroup(ci)) {
643	>	cg->updateCOM();
644		}
645	<	}// end for (mol)
269	<
270	<	rc = rcGroup[0].getArrayPointer();
645	>	}
646		} else {
647	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
648	<	rc = pos;
647	>	// center of mass of the group is the same as position of the atom
648	>	// if cutoff group does not exist
649	>	cgConfig->position = config->position;
650	>	cgConfig->velocity = config->velocity;
651		}
652	<
653	<	//initialize data before passing to fortran
654	<	double longRangePotential[LR_POT_TYPES];
278	<	double lrPot = 0.0;
652	>
653	>	fDecomp_->zeroWorkArrays();
654	>	fDecomp_->distributeData();
655
656	<	Mat3x3d tau;
657	<	short int passedCalcPot = needPotential;
658	<	short int passedCalcStress = needStress;
659	<	int isError = 0;
656	>	int cg1, cg2, atom1, atom2, topoDist;
657	>	Vector3d d_grp, dag, d, gvel2, vel2;
658	>	RealType rgrpsq, rgrp, r2, r;
659	>	RealType electroMult, vdwMult;
660	>	RealType vij;
661	>	Vector3d fij, fg, f1;
662	>	bool in_switching_region;
663	>	RealType sw, dswdr, swderiv;
664	>	vector<int> atomListColumn, atomListRow;
665	>	InteractionData idat;
666	>	SelfData sdat;
667	>	RealType mf;
668	>	RealType vpair;
669	>	RealType dVdFQ1(0.0);
670	>	RealType dVdFQ2(0.0);
671	>	potVec longRangePotential(0.0);
672	>	RealType reciprocalPotential(0.0);
673	>	potVec workPot(0.0);
674	>	potVec exPot(0.0);
675	>	Vector3d eField1(0.0);
676	>	Vector3d eField2(0.0);
677	>	RealType sPot1(0.0);
678	>	RealType sPot2(0.0);
679	>	bool newAtom1;
680	>
681	>	vector<int>::iterator ia, jb;
682
683	<	for (int i=0; i<LR_POT_TYPES;i++){
684	<	longRangePotential[i]=0.0; //Initialize array
683	>	int loopStart, loopEnd;
684	>
685	>	idat.rcut = &rCut_;
686	>	idat.vdwMult = &vdwMult;
687	>	idat.electroMult = &electroMult;
688	>	idat.pot = &workPot;
689	>	idat.excludedPot = &exPot;
690	>	sdat.pot = fDecomp_->getEmbeddingPotential();
691	>	sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
692	>	idat.vpair = &vpair;
693	>	idat.dVdFQ1 = &dVdFQ1;
694	>	idat.dVdFQ2 = &dVdFQ2;
695	>	idat.eField1 = &eField1;
696	>	idat.eField2 = &eField2;
697	>	idat.sPot1 = &sPot1;
698	>	idat.sPot2 = &sPot2;
699	>	idat.f1 = &f1;
700	>	idat.sw = &sw;
701	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
702	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE ||
703	>	cutoffMethod_ == TAYLOR_SHIFTED) ? true : false;
704	>	idat.doParticlePot = doParticlePot_;
705	>	idat.doElectricField = doElectricField_;
706	>	idat.doSitePotential = doSitePotential_;
707	>	sdat.doParticlePot = doParticlePot_;
708	>
709	>	loopEnd = PAIR_LOOP;
710	>	if (info_->requiresPrepair() ) {
711	>	loopStart = PREPAIR_LOOP;
712	>	} else {
713	>	loopStart = PAIR_LOOP;
714		}
715	+	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
716	+
717	+	if (iLoop == loopStart) {
718	+	bool update_nlist = fDecomp_->checkNeighborList();
719	+	if (update_nlist) {
720	+	if (!usePeriodicBoundaryConditions_)
721	+	Mat3x3d bbox = thermo->getBoundingBox();
722	+	fDecomp_->buildNeighborList(neighborList_, point_);
723	+	}
724	+	}
725
726	<	doForceLoop( pos,
727	<	rc,
728	<	A,
729	<	electroFrame,
730	<	frc,
731	<	trq,
295	<	tau.getArrayPointer(),
296	<	longRangePotential,
297	<	&passedCalcPot,
298	<	&passedCalcStress,
299	<	&isError );
726	>	for (cg1 = 0; cg1 < point_.size() - 1; cg1++) {
727	>
728	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
729	>	newAtom1 = true;
730	>
731	>	for (int m2 = point_[cg1]; m2 < point_[cg1+1]; m2++) {
732
733	<	if( isError ){
734	<	sprintf( painCave.errMsg,
735	<	"Error returned from the fortran force calculation.\n" );
736	<	painCave.isFatal = 1;
737	<	simError();
733	>	cg2 = neighborList_[m2];
734	>
735	>	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
736	>
737	>	// already wrapped in the getIntergroupVector call:
738	>	// curSnapshot->wrapVector(d_grp);
739	>	rgrpsq = d_grp.lengthSquare();
740	>
741	>	if (rgrpsq < rCutSq_) {
742	>	if (iLoop == PAIR_LOOP) {
743	>	vij = 0.0;
744	>	fij.zero();
745	>	eField1.zero();
746	>	eField2.zero();
747	>	sPot1 = 0.0;
748	>	sPot2 = 0.0;
749	>	}
750	>
751	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
752	>	rgrp);
753	>
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.zero();
773	>	dVdFQ1 = 0.0;
774	>	dVdFQ2 = 0.0;
775	>
776	>	fDecomp_->fillInteractionData(idat, atom1, atom2, newAtom1);
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	>	if (!fDecomp_->skipAtomPair(atomListRow[0],
823	>	atomListColumn[0],
824	>	cg1, cg2)) {
825	>	stressTensor -= outProduct( *(idat.d), fg);
826	>	if (doHeatFlux_)
827	>	fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
828	>	}
829	>	}
830	>
831	>	for (ia = atomListRow.begin();
832	>	ia != atomListRow.end(); ++ia) {
833	>	atom1 = (*ia);
834	>	mf = fDecomp_->getMassFactorRow(atom1);
835	>	// fg is the force on atom ia due to cutoff group's
836	>	// presence in switching region
837	>	fg = swderiv * d_grp * mf;
838	>	fDecomp_->addForceToAtomRow(atom1, fg);
839	>	if (atomListRow.size() > 1) {
840	>	if (info_->usesAtomicVirial()) {
841	>	// find the distance between the atom
842	>	// and the center of the cutoff group:
843	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
844	>	stressTensor -= outProduct(dag, fg);
845	>	if (doHeatFlux_)
846	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
847	>	}
848	>	}
849	>	}
850	>	for (jb = atomListColumn.begin();
851	>	jb != atomListColumn.end(); ++jb) {
852	>	atom2 = (*jb);
853	>	mf = fDecomp_->getMassFactorColumn(atom2);
854	>	// fg is the force on atom jb due to cutoff group's
855	>	// presence in switching region
856	>	fg = -swderiv * d_grp * mf;
857	>	fDecomp_->addForceToAtomColumn(atom2, fg);
858	>
859	>	if (atomListColumn.size() > 1) {
860	>	if (info_->usesAtomicVirial()) {
861	>	// find the distance between the atom
862	>	// and the center of the cutoff group:
863	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
864	>	stressTensor -= outProduct(dag, fg);
865	>	if (doHeatFlux_)
866	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
867	>	}
868	>	}
869	>	}
870	>	}
871	>	//if (!info_->usesAtomicVirial()) {
872	>	//  stressTensor -= outProduct(d_grp, fij);
873	>	//  if (doHeatFlux_)
874	>	//     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
875	>	//}
876	>	}
877	>	}
878	>	}
879	>	newAtom1 = false;
880	>	}
881	>
882	>	if (iLoop == PREPAIR_LOOP) {
883	>	if (info_->requiresPrepair()) {
884	>
885	>	fDecomp_->collectIntermediateData();
886	>
887	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
888	>	fDecomp_->fillSelfData(sdat, atom1);
889	>	interactionMan_->doPreForce(sdat);
890	>	}
891	>
892	>	fDecomp_->distributeIntermediateData();
893	>
894	>	}
895	>	}
896		}
897	<	for (int i=0; i<LR_POT_TYPES;i++){
898	<	lrPot += longRangePotential[i]; //Quick hack
897	>
898	>	// collects pairwise information
899	>	fDecomp_->collectData();
900	>	if (cutoffMethod_ == EWALD_FULL) {
901	>	interactionMan_->doReciprocalSpaceSum(reciprocalPotential);
902	>
903	>	curSnapshot->setReciprocalPotential(reciprocalPotential);
904		}
905	+
906	+	if (info_->requiresSelfCorrection()) {
907	+	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
908	+	fDecomp_->fillSelfData(sdat, atom1);
909	+	interactionMan_->doSelfCorrection(sdat);
910	+	}
911	+	}
912
913	<	//store the tau and long range potential
914	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
313	<	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
314	<	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
913	>	// collects single-atom information
914	>	fDecomp_->collectSelfData();
915
916	<	curSnapshot->statData.setTau(tau);
917	<	}
916	>	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
917	>	*(fDecomp_->getPairwisePotential());
918
919	+	curSnapshot->setLongRangePotential(longRangePotential);
920	+
921	+	curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
922	+	*(fDecomp_->getExcludedPotential()));
923
924	+	}
925	+
926		void ForceManager::postCalculation() {
927	+
928	+	vector<Perturbation*>::iterator pi;
929	+	for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
930	+	(*pi)->applyPerturbation();
931	+	}
932	+
933		SimInfo::MoleculeIterator mi;
934		Molecule* mol;
935		Molecule::RigidBodyIterator rbIter;
936		RigidBody* rb;
937	<
937	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
938	>
939		// collect the atomic forces onto rigid bodies
940	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
941	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
942	<	rb->calcForcesAndTorques();
940	>
941	>	for (mol = info_->beginMolecule(mi); mol != NULL;
942	>	mol = info_->nextMolecule(mi)) {
943	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
944	>	rb = mol->nextRigidBody(rbIter)) {
945	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
946	>	stressTensor += rbTau;
947		}
948		}
949	+
950	+	#ifdef IS_MPI
951	+	MPI_Allreduce(MPI_IN_PLACE, stressTensor.getArrayPointer(), 9,
952	+	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
953	+	#endif
954	+	curSnapshot->setStressTensor(stressTensor);
955	+
956	+	if (info_->getSimParams()->getUseLongRangeCorrections()) {
957	+	/*
958	+	RealType vol = curSnapshot->getVolume();
959	+	RealType Elrc(0.0);
960	+	RealType Wlrc(0.0);
961
962	<	}
962	>	set<AtomType*>::iterator i;
963	>	set<AtomType*>::iterator j;
964	>
965	>	RealType n_i, n_j;
966	>	RealType rho_i, rho_j;
967	>	pair<RealType, RealType> LRI;
968	>
969	>	for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
970	>	n_i = RealType(info_->getGlobalCountOfType(*i));
971	>	rho_i = n_i /  vol;
972	>	for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) {
973	>	n_j = RealType(info_->getGlobalCountOfType(*j));
974	>	rho_j = n_j / vol;
975	>
976	>	LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) );
977
978	<	} //end namespace oopse
978	>	Elrc += n_i   * rho_j * LRI.first;
979	>	Wlrc -= rho_i * rho_j * LRI.second;
980	>	}
981	>	}
982	>	Elrc *= 2.0 * NumericConstant::PI;
983	>	Wlrc *= 2.0 * NumericConstant::PI;
984	>
985	>	RealType lrp = curSnapshot->getLongRangePotential();
986	>	curSnapshot->setLongRangePotential(lrp + Elrc);
987	>	stressTensor += Wlrc * SquareMatrix3<RealType>::identity();
988	>	curSnapshot->setStressTensor(stressTensor);
989	>	*/
990	>
991	>	}
992	>	}
993	>	}

Comparing trunk/src/brains/ForceManager.cpp (property svn:keywords):
Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
Revision 2066 by gezelter, Thu Mar 5 15:22:54 2015 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines