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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 1866 by gezelter, Thu Apr 25 14:32:56 2013 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
44		* @file ForceManager.cpp
45		* @author tlin
46		* @date 11/09/2004
46	–	* @time 10:39am
47		* @version 1.0
48		*/
49
50	+
51		#include "brains/ForceManager.hpp"
52		#include "primitives/Molecule.hpp"
53	<	#include "UseTheForce/doForces_interface.h"
53	<	#define __C
54	<	#include "UseTheForce/DarkSide/fInteractionMap.h"
53	>	#define __OPENMD_C
54		#include "utils/simError.h"
55	+	#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	>	thermo = new Thermo(info_);
75		}
76
77	<	bool  TorsionSortFunctor(const TorsionOrderStruct& t1, const TorsionOrderStruct& t2) {
78	<	return t1.dataSet.deltaV < t2.dataSet.deltaV;
79	<	}
80	<	*/
81	<	void ForceManager::calcForces(bool needPotential, bool needStress) {
77	>	/**
78	>	* setupCutoffs
79	>	*
80	>	* Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
81	>	* and cutoffPolicy
82	>	*
83	>	* cutoffRadius : realType
84	>	*  If the cutoffRadius was explicitly set, use that value.
85	>	*  If the cutoffRadius was not explicitly set:
86	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
87	>	*      No electrostatic atoms?  Poll the atom types present in the
88	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
89	>	*      Use the maximum suggested value that was found.
90	>	*
91	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
92	>	*                        or SHIFTED_POTENTIAL)
93	>	*      If cutoffMethod was explicitly set, use that choice.
94	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
95	>	*
96	>	* cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
97	>	*      If cutoffPolicy was explicitly set, use that choice.
98	>	*      If cutoffPolicy was not explicitly set, use TRADITIONAL
99	>	*
100	>	* switchingRadius : realType
101	>	*  If the cutoffMethod was set to SWITCHED:
102	>	*      If the switchingRadius was explicitly set, use that value
103	>	*          (but do a sanity check first).
104	>	*      If the switchingRadius was not explicitly set: use 0.85 *
105	>	*      cutoffRadius_
106	>	*  If the cutoffMethod was not set to SWITCHED:
107	>	*      Set switchingRadius equal to cutoffRadius for safety.
108	>	*/
109	>	void ForceManager::setupCutoffs() {
110	>
111	>	Globals* simParams_ = info_->getSimParams();
112	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
113	>	int mdFileVersion;
114	>	rCut_ = 0.0; //Needs a value for a later max() call;
115	>
116	>	if (simParams_->haveMDfileVersion())
117	>	mdFileVersion = simParams_->getMDfileVersion();
118	>	else
119	>	mdFileVersion = 0;
120	>
121	>	// We need the list of simulated atom types to figure out cutoffs
122	>	// as well as long range corrections.
123
124	<	if (!info_->isFortranInitialized()) {
125	<	info_->update();
124	>	set<AtomType*>::iterator i;
125	>	set<AtomType*> atomTypes_;
126	>	atomTypes_ = info_->getSimulatedAtomTypes();
127	>
128	>	if (simParams_->haveCutoffRadius()) {
129	>	rCut_ = simParams_->getCutoffRadius();
130	>	} else {
131	>	if (info_->usesElectrostaticAtoms()) {
132	>	sprintf(painCave.errMsg,
133	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
134	>	"\tOpenMD will use a default value of 12.0 angstroms"
135	>	"\tfor the cutoffRadius.\n");
136	>	painCave.isFatal = 0;
137	>	painCave.severity = OPENMD_INFO;
138	>	simError();
139	>	rCut_ = 12.0;
140	>	} else {
141	>	RealType thisCut;
142	>	for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
143	>	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
144	>	rCut_ = max(thisCut, rCut_);
145	>	}
146	>	sprintf(painCave.errMsg,
147	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
148	>	"\tOpenMD will use %lf angstroms.\n",
149	>	rCut_);
150	>	painCave.isFatal = 0;
151	>	painCave.severity = OPENMD_INFO;
152	>	simError();
153	>	}
154		}
155
156	<	preCalculation();
157	<
86	<	calcShortRangeInteraction();
156	>	fDecomp_->setUserCutoff(rCut_);
157	>	interactionMan_->setCutoffRadius(rCut_);
158
159	<	calcLongRangeInteraction(needPotential, needStress);
159	>	map<string, CutoffMethod> stringToCutoffMethod;
160	>	stringToCutoffMethod["HARD"] = HARD;
161	>	stringToCutoffMethod["SWITCHED"] = SWITCHED;
162	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
163	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
164	>
165	>	if (simParams_->haveCutoffMethod()) {
166	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
167	>	map<string, CutoffMethod>::iterator i;
168	>	i = stringToCutoffMethod.find(cutMeth);
169	>	if (i == stringToCutoffMethod.end()) {
170	>	sprintf(painCave.errMsg,
171	>	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
172	>	"\tShould be one of: "
173	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
174	>	cutMeth.c_str());
175	>	painCave.isFatal = 1;
176	>	painCave.severity = OPENMD_ERROR;
177	>	simError();
178	>	} else {
179	>	cutoffMethod_ = i->second;
180	>	}
181	>	} else {
182	>	if (mdFileVersion > 1) {
183	>	sprintf(painCave.errMsg,
184	>	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
185	>	"\tOpenMD will use SHIFTED_FORCE.\n");
186	>	painCave.isFatal = 0;
187	>	painCave.severity = OPENMD_INFO;
188	>	simError();
189	>	cutoffMethod_ = SHIFTED_FORCE;
190	>	} else {
191	>	// handle the case where the old file version was in play
192	>	// (there should be no cutoffMethod, so we have to deduce it
193	>	// from other data).
194
195	<	postCalculation();
195	>	sprintf(painCave.errMsg,
196	>	"ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
197	>	"\tOpenMD found a file which does not set a cutoffMethod.\n"
198	>	"\tOpenMD will attempt to deduce a cutoffMethod using the\n"
199	>	"\tbehavior of the older (version 1) code.  To remove this\n"
200	>	"\twarning, add an explicit cutoffMethod and change the top\n"
201	>	"\tof the file so that it begins with <OpenMD version=2>\n");
202	>	painCave.isFatal = 0;
203	>	painCave.severity = OPENMD_WARNING;
204	>	simError();
205	>
206	>	// The old file version tethered the shifting behavior to the
207	>	// electrostaticSummationMethod keyword.
208	>
209	>	if (simParams_->haveElectrostaticSummationMethod()) {
210	>	string myMethod = simParams_->getElectrostaticSummationMethod();
211	>	toUpper(myMethod);
212	>
213	>	if (myMethod == "SHIFTED_POTENTIAL") {
214	>	cutoffMethod_ = SHIFTED_POTENTIAL;
215	>	} else if (myMethod == "SHIFTED_FORCE") {
216	>	cutoffMethod_ = SHIFTED_FORCE;
217	>	}
218	>
219	>	if (simParams_->haveSwitchingRadius())
220	>	rSwitch_ = simParams_->getSwitchingRadius();
221
222	<	/*
223	<	std::vector<BendOrderStruct> bendOrderStruct;
224	<	for(std::map<Bend*, BendDataSet>::iterator i = bendDataSets.begin(); i != bendDataSets.end(); ++i) {
225	<	BendOrderStruct tmp;
226	<	tmp.bend= const_cast<Bend*>(i->first);
227	<	tmp.dataSet = i->second;
228	<	bendOrderStruct.push_back(tmp);
222	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
223	>	if (simParams_->haveSwitchingRadius()){
224	>	sprintf(painCave.errMsg,
225	>	"ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
226	>	"\tA value was set for the switchingRadius\n"
227	>	"\teven though the electrostaticSummationMethod was\n"
228	>	"\tset to %s\n", myMethod.c_str());
229	>	painCave.severity = OPENMD_WARNING;
230	>	painCave.isFatal = 1;
231	>	simError();
232	>	}
233	>	}
234	>	if (abs(rCut_ - rSwitch_) < 0.0001) {
235	>	if (cutoffMethod_ == SHIFTED_FORCE) {
236	>	sprintf(painCave.errMsg,
237	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
238	>	"\tcutoffRadius and switchingRadius are set to the\n"
239	>	"\tsame value.  OpenMD will use shifted force\n"
240	>	"\tpotentials instead of switching functions.\n");
241	>	painCave.isFatal = 0;
242	>	painCave.severity = OPENMD_WARNING;
243	>	simError();
244	>	} else {
245	>	cutoffMethod_ = SHIFTED_POTENTIAL;
246	>	sprintf(painCave.errMsg,
247	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
248	>	"\tcutoffRadius and switchingRadius are set to the\n"
249	>	"\tsame value.  OpenMD will use shifted potentials\n"
250	>	"\tinstead of switching functions.\n");
251	>	painCave.isFatal = 0;
252	>	painCave.severity = OPENMD_WARNING;
253	>	simError();
254	>	}
255	>	}
256	>	}
257	>	}
258		}
259
260	<	std::vector<TorsionOrderStruct> torsionOrderStruct;
261	<	for(std::map<Torsion*, TorsionDataSet>::iterator j = torsionDataSets.begin(); j != torsionDataSets.end(); ++j) {
262	<	TorsionOrderStruct tmp;
263	<	tmp.torsion = const_cast<Torsion*>(j->first);
264	<	tmp.dataSet = j->second;
265	<	torsionOrderStruct.push_back(tmp);
266	<	}
267	<
268	<	std::sort(bendOrderStruct.begin(), bendOrderStruct.end(), std::ptr_fun(BendSortFunctor));
269	<	std::sort(torsionOrderStruct.begin(), torsionOrderStruct.end(), std::ptr_fun(TorsionSortFunctor));
270	<	for (std::vector<BendOrderStruct>::iterator k = bendOrderStruct.begin(); k != bendOrderStruct.end(); ++k) {
271	<	Bend* bend = k->bend;
272	<	std::cout << "Bend: atom1=" <<bend->getAtomA()->getGlobalIndex() << ",atom2 = "<< bend->getAtomB()->getGlobalIndex() << ",atom3="<<bend->getAtomC()->getGlobalIndex() << " ";
273	<	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;
274	<	}
275	<	for (std::vector<TorsionOrderStruct>::iterator l = torsionOrderStruct.begin(); l != torsionOrderStruct.end(); ++l) {
276	<	Torsion* torsion = l->torsion;
277	<	std::cout << "Torsion: atom1=" <<torsion->getAtomA()->getGlobalIndex() << ",atom2 = "<< torsion->getAtomB()->getGlobalIndex() << ",atom3="<<torsion->getAtomC()->getGlobalIndex() << ",atom4="<<torsion->getAtomD()->getGlobalIndex()<< " ";
278	<	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;
279	<	}
280	<	*/
260	>	map<string, CutoffPolicy> stringToCutoffPolicy;
261	>	stringToCutoffPolicy["MIX"] = MIX;
262	>	stringToCutoffPolicy["MAX"] = MAX;
263	>	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
264	>
265	>	string cutPolicy;
266	>	if (forceFieldOptions_.haveCutoffPolicy()){
267	>	cutPolicy = forceFieldOptions_.getCutoffPolicy();
268	>	}else if (simParams_->haveCutoffPolicy()) {
269	>	cutPolicy = simParams_->getCutoffPolicy();
270	>	}
271	>
272	>	if (!cutPolicy.empty()){
273	>	toUpper(cutPolicy);
274	>	map<string, CutoffPolicy>::iterator i;
275	>	i = stringToCutoffPolicy.find(cutPolicy);
276	>
277	>	if (i == stringToCutoffPolicy.end()) {
278	>	sprintf(painCave.errMsg,
279	>	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
280	>	"\tShould be one of: "
281	>	"MIX, MAX, or TRADITIONAL\n",
282	>	cutPolicy.c_str());
283	>	painCave.isFatal = 1;
284	>	painCave.severity = OPENMD_ERROR;
285	>	simError();
286	>	} else {
287	>	cutoffPolicy_ = i->second;
288	>	}
289	>	} else {
290	>	sprintf(painCave.errMsg,
291	>	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
292	>	"\tOpenMD will use TRADITIONAL.\n");
293	>	painCave.isFatal = 0;
294	>	painCave.severity = OPENMD_INFO;
295	>	simError();
296	>	cutoffPolicy_ = TRADITIONAL;
297	>	}
298	>
299	>	fDecomp_->setCutoffPolicy(cutoffPolicy_);
300	>
301	>	// create the switching function object:
302	>
303	>	switcher_ = new SwitchingFunction();
304	>
305	>	if (cutoffMethod_ == SWITCHED) {
306	>	if (simParams_->haveSwitchingRadius()) {
307	>	rSwitch_ = simParams_->getSwitchingRadius();
308	>	if (rSwitch_ > rCut_) {
309	>	sprintf(painCave.errMsg,
310	>	"ForceManager::setupCutoffs: switchingRadius (%f) is larger "
311	>	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
312	>	painCave.isFatal = 1;
313	>	painCave.severity = OPENMD_ERROR;
314	>	simError();
315	>	}
316	>	} else {
317	>	rSwitch_ = 0.85 * rCut_;
318	>	sprintf(painCave.errMsg,
319	>	"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
320	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
321	>	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
322	>	painCave.isFatal = 0;
323	>	painCave.severity = OPENMD_WARNING;
324	>	simError();
325	>	}
326	>	} else {
327	>	if (mdFileVersion > 1) {
328	>	// throw an error if we define a switching radius and don't need one.
329	>	// older file versions should not do this.
330	>	if (simParams_->haveSwitchingRadius()) {
331	>	map<string, CutoffMethod>::const_iterator it;
332	>	string theMeth;
333	>	for (it = stringToCutoffMethod.begin();
334	>	it != stringToCutoffMethod.end(); ++it) {
335	>	if (it->second == cutoffMethod_) {
336	>	theMeth = it->first;
337	>	break;
338	>	}
339	>	}
340	>	sprintf(painCave.errMsg,
341	>	"ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
342	>	"\tis not set to SWITCHED, so switchingRadius value\n"
343	>	"\twill be ignored for this simulation\n", theMeth.c_str());
344	>	painCave.isFatal = 0;
345	>	painCave.severity = OPENMD_WARNING;
346	>	simError();
347	>	}
348	>	}
349	>	rSwitch_ = rCut_;
350	>	}
351	>
352	>	// Default to cubic switching function.
353	>	sft_ = cubic;
354	>	if (simParams_->haveSwitchingFunctionType()) {
355	>	string funcType = simParams_->getSwitchingFunctionType();
356	>	toUpper(funcType);
357	>	if (funcType == "CUBIC") {
358	>	sft_ = cubic;
359	>	} else {
360	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
361	>	sft_ = fifth_order_poly;
362	>	} else {
363	>	// throw error
364	>	sprintf( painCave.errMsg,
365	>	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
366	>	"\tswitchingFunctionType must be one of: "
367	>	"\"cubic\" or \"fifth_order_polynomial\".",
368	>	funcType.c_str() );
369	>	painCave.isFatal = 1;
370	>	painCave.severity = OPENMD_ERROR;
371	>	simError();
372	>	}
373	>	}
374	>	}
375	>	switcher_->setSwitchType(sft_);
376	>	switcher_->setSwitch(rSwitch_, rCut_);
377		}
378
379	+
380	+
381	+
382	+	void ForceManager::initialize() {
383	+
384	+	if (!info_->isTopologyDone()) {
385	+
386	+	info_->update();
387	+	interactionMan_->setSimInfo(info_);
388	+	interactionMan_->initialize();
389	+
390	+	// We want to delay the cutoffs until after the interaction
391	+	// manager has set up the atom-atom interactions so that we can
392	+	// query them for suggested cutoff values
393	+	setupCutoffs();
394	+
395	+	info_->prepareTopology();
396	+
397	+	doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
398	+	doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
399	+	if (doHeatFlux_) doParticlePot_ = true;
400	+
401	+	doElectricField_ = info_->getSimParams()->getOutputElectricField();
402	+
403	+	}
404	+
405	+	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
406	+
407	+	// Force fields can set options on how to scale van der Waals and
408	+	// electrostatic interactions for atoms connected via bonds, bends
409	+	// and torsions in this case the topological distance between
410	+	// atoms is:
411	+	// 0 = topologically unconnected
412	+	// 1 = bonded together
413	+	// 2 = connected via a bend
414	+	// 3 = connected via a torsion
415	+
416	+	vdwScale_.reserve(4);
417	+	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
418	+
419	+	electrostaticScale_.reserve(4);
420	+	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
421	+
422	+	vdwScale_[0] = 1.0;
423	+	vdwScale_[1] = fopts.getvdw12scale();
424	+	vdwScale_[2] = fopts.getvdw13scale();
425	+	vdwScale_[3] = fopts.getvdw14scale();
426	+
427	+	electrostaticScale_[0] = 1.0;
428	+	electrostaticScale_[1] = fopts.getelectrostatic12scale();
429	+	electrostaticScale_[2] = fopts.getelectrostatic13scale();
430	+	electrostaticScale_[3] = fopts.getelectrostatic14scale();
431	+
432	+	if (info_->getSimParams()->haveElectricField()) {
433	+	ElectricField* eField = new ElectricField(info_);
434	+	perturbations_.push_back(eField);
435	+	}
436	+
437	+	usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
438	+
439	+	fDecomp_->distributeInitialData();
440	+
441	+	initialized_ = true;
442	+
443	+	}
444	+
445	+	void ForceManager::calcForces() {
446	+
447	+	if (!initialized_) initialize();
448	+
449	+	preCalculation();
450	+	shortRangeInteractions();
451	+	longRangeInteractions();
452	+	postCalculation();
453	+	}
454	+
455		void ForceManager::preCalculation() {
456		SimInfo::MoleculeIterator mi;
457		Molecule* mol;
#	Line 128 | Line 459 | namespace oopse {
459		Atom* atom;
460		Molecule::RigidBodyIterator rbIter;
461		RigidBody* rb;
462	+	Molecule::CutoffGroupIterator ci;
463	+	CutoffGroup* cg;
464
465	<	// forces are zeroed here, before any are accumulated.
466	<	// NOTE: do not rezero the forces in Fortran.
467	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
468	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
465	>	// forces and potentials are zeroed here, before any are
466	>	// accumulated.
467	>
468	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
469	>
470	>	snap->setBondPotential(0.0);
471	>	snap->setBendPotential(0.0);
472	>	snap->setTorsionPotential(0.0);
473	>	snap->setInversionPotential(0.0);
474	>
475	>	potVec zeroPot(0.0);
476	>	snap->setLongRangePotential(zeroPot);
477	>	snap->setExcludedPotentials(zeroPot);
478	>
479	>	snap->setRestraintPotential(0.0);
480	>	snap->setRawPotential(0.0);
481	>
482	>	for (mol = info_->beginMolecule(mi); mol != NULL;
483	>	mol = info_->nextMolecule(mi)) {
484	>	for(atom = mol->beginAtom(ai); atom != NULL;
485	>	atom = mol->nextAtom(ai)) {
486		atom->zeroForcesAndTorques();
487		}
488	<
488	>
489		//change the positions of atoms which belong to the rigidbodies
490	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
490	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
491	>	rb = mol->nextRigidBody(rbIter)) {
492		rb->zeroForcesAndTorques();
493		}
494	+
495	+	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
496	+	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
497	+	cg = mol->nextCutoffGroup(ci)) {
498	+	//calculate the center of mass of cutoff group
499	+	cg->updateCOM();
500	+	}
501	+	}
502		}
503
504	+	// Zero out the stress tensor
505	+	stressTensor *= 0.0;
506	+	// Zero out the heatFlux
507	+	fDecomp_->setHeatFlux( Vector3d(0.0) );
508		}
509	<
510	<	void ForceManager::calcShortRangeInteraction() {
509	>
510	>	void ForceManager::shortRangeInteractions() {
511		Molecule* mol;
512		RigidBody* rb;
513		Bond* bond;
514		Bend* bend;
515		Torsion* torsion;
516	+	Inversion* inversion;
517		SimInfo::MoleculeIterator mi;
518		Molecule::RigidBodyIterator rbIter;
519		Molecule::BondIterator bondIter;;
520		Molecule::BendIterator  bendIter;
521		Molecule::TorsionIterator  torsionIter;
522	+	Molecule::InversionIterator  inversionIter;
523		RealType bondPotential = 0.0;
524		RealType bendPotential = 0.0;
525		RealType torsionPotential = 0.0;
526	+	RealType inversionPotential = 0.0;
527
528		//calculate short range interactions
529	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
529	>	for (mol = info_->beginMolecule(mi); mol != NULL;
530	>	mol = info_->nextMolecule(mi)) {
531
532		//change the positions of atoms which belong to the rigidbodies
533	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
534	<	rb->updateAtoms();
533	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
534	>	rb = mol->nextRigidBody(rbIter)) {
535	>	rb->updateAtoms();
536		}
537
538	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
539	<	bond->calcForce();
538	>	for (bond = mol->beginBond(bondIter); bond != NULL;
539	>	bond = mol->nextBond(bondIter)) {
540	>	bond->calcForce(doParticlePot_);
541		bondPotential += bond->getPotential();
542		}
543
544	<
545	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
546	<
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	<	}
196	<	}
197	<
198	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
544	>	for (bend = mol->beginBend(bendIter); bend != NULL;
545	>	bend = mol->nextBend(bendIter)) {
546	>
547		RealType angle;
548	<	torsion->calcForce(angle);
549	<	RealType currTorsionPot = torsion->getPotential();
550	<	torsionPotential += torsion->getPotential();
551	<	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
552	<	if (i == torsionDataSets.end()) {
553	<	TorsionDataSet dataSet;
554	<	dataSet.prev.angle = dataSet.curr.angle = angle;
555	<	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
556	<	dataSet.deltaV = 0.0;
557	<	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
558	<	}else {
559	<	i->second.prev.angle = i->second.curr.angle;
560	<	i->second.prev.potential = i->second.curr.potential;
561	<	i->second.curr.angle = angle;
562	<	i->second.curr.potential = currTorsionPot;
563	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
564	<	}
548	>	bend->calcForce(angle, doParticlePot_);
549	>	RealType currBendPot = bend->getPotential();
550	>
551	>	bendPotential += bend->getPotential();
552	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
553	>	if (i == bendDataSets.end()) {
554	>	BendDataSet dataSet;
555	>	dataSet.prev.angle = dataSet.curr.angle = angle;
556	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
557	>	dataSet.deltaV = 0.0;
558	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
559	>	dataSet));
560	>	}else {
561	>	i->second.prev.angle = i->second.curr.angle;
562	>	i->second.prev.potential = i->second.curr.potential;
563	>	i->second.curr.angle = angle;
564	>	i->second.curr.potential = currBendPot;
565	>	i->second.deltaV =  fabs(i->second.curr.potential -
566	>	i->second.prev.potential);
567	>	}
568		}
569	<
569	>
570	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
571	>	torsion = mol->nextTorsion(torsionIter)) {
572	>	RealType angle;
573	>	torsion->calcForce(angle, doParticlePot_);
574	>	RealType currTorsionPot = torsion->getPotential();
575	>	torsionPotential += torsion->getPotential();
576	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
577	>	if (i == torsionDataSets.end()) {
578	>	TorsionDataSet dataSet;
579	>	dataSet.prev.angle = dataSet.curr.angle = angle;
580	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
581	>	dataSet.deltaV = 0.0;
582	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
583	>	}else {
584	>	i->second.prev.angle = i->second.curr.angle;
585	>	i->second.prev.potential = i->second.curr.potential;
586	>	i->second.curr.angle = angle;
587	>	i->second.curr.potential = currTorsionPot;
588	>	i->second.deltaV =  fabs(i->second.curr.potential -
589	>	i->second.prev.potential);
590	>	}
591	>	}
592	>
593	>	for (inversion = mol->beginInversion(inversionIter);
594	>	inversion != NULL;
595	>	inversion = mol->nextInversion(inversionIter)) {
596	>	RealType angle;
597	>	inversion->calcForce(angle, doParticlePot_);
598	>	RealType currInversionPot = inversion->getPotential();
599	>	inversionPotential += inversion->getPotential();
600	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
601	>	if (i == inversionDataSets.end()) {
602	>	InversionDataSet dataSet;
603	>	dataSet.prev.angle = dataSet.curr.angle = angle;
604	>	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
605	>	dataSet.deltaV = 0.0;
606	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
607	>	}else {
608	>	i->second.prev.angle = i->second.curr.angle;
609	>	i->second.prev.potential = i->second.curr.potential;
610	>	i->second.curr.angle = angle;
611	>	i->second.curr.potential = currInversionPot;
612	>	i->second.deltaV =  fabs(i->second.curr.potential -
613	>	i->second.prev.potential);
614	>	}
615	>	}
616		}
617	<
618	<	RealType  shortRangePotential = bondPotential + bendPotential + torsionPotential;
617	>
618	>	#ifdef IS_MPI
619	>	// Collect from all nodes.  This should eventually be moved into a
620	>	// SystemDecomposition, but this is a better place than in
621	>	// Thermo to do the collection.
622	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
623	>	MPI::SUM);
624	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
625	>	MPI::SUM);
626	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
627	>	MPI::REALTYPE, MPI::SUM);
628	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
629	>	MPI::REALTYPE, MPI::SUM);
630	>	#endif
631	>
632		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
633	<	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
634	<	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
635	<	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
636	<	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
633	>
634	>	curSnapshot->setBondPotential(bondPotential);
635	>	curSnapshot->setBendPotential(bendPotential);
636	>	curSnapshot->setTorsionPotential(torsionPotential);
637	>	curSnapshot->setInversionPotential(inversionPotential);
638
639	+	// RealType shortRangePotential = bondPotential + bendPotential +
640	+	//   torsionPotential +  inversionPotential;
641	+
642	+	// curSnapshot->setShortRangePotential(shortRangePotential);
643		}
644	+
645	+	void ForceManager::longRangeInteractions() {
646
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();
647
648	<	//get array pointers
649	<	config = &(curSnapshot->atomData);
650	<	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);
648	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
649	>	DataStorage* config = &(curSnapshot->atomData);
650	>	DataStorage* cgConfig = &(curSnapshot->cgData);
651
652		//calculate the center of mass of cutoff group
653	+
654		SimInfo::MoleculeIterator mi;
655		Molecule* mol;
656		Molecule::CutoffGroupIterator ci;
657		CutoffGroup* cg;
256	–	Vector3d com;
257	–	std::vector<Vector3d> rcGroup;
658
659	<	if(info_->getNCutoffGroups() > 0){
660	<
661	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
662	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
663	<	cg->getCOM(com);
664	<	rcGroup.push_back(com);
659	>	if(info_->getNCutoffGroups() > 0){
660	>	for (mol = info_->beginMolecule(mi); mol != NULL;
661	>	mol = info_->nextMolecule(mi)) {
662	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
663	>	cg = mol->nextCutoffGroup(ci)) {
664	>	cg->updateCOM();
665		}
666	<	}// end for (mol)
267	<
268	<	rc = rcGroup[0].getArrayPointer();
666	>	}
667		} else {
668	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
669	<	rc = pos;
668	>	// center of mass of the group is the same as position of the atom
669	>	// if cutoff group does not exist
670	>	cgConfig->position = config->position;
671	>	cgConfig->velocity = config->velocity;
672		}
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;
673
674	<	for (int i=0; i<LR_POT_TYPES;i++){
675	<	longRangePotential[i]=0.0; //Initialize array
676	<	}
674	>	fDecomp_->zeroWorkArrays();
675	>	fDecomp_->distributeData();
676	>
677	>	int cg1, cg2, atom1, atom2, topoDist;
678	>	Vector3d d_grp, dag, d, gvel2, vel2;
679	>	RealType rgrpsq, rgrp, r2, r;
680	>	RealType electroMult, vdwMult;
681	>	RealType vij;
682	>	Vector3d fij, fg, f1;
683	>	tuple3<RealType, RealType, RealType> cuts;
684	>	RealType rCutSq;
685	>	bool in_switching_region;
686	>	RealType sw, dswdr, swderiv;
687	>	vector<int> atomListColumn, atomListRow, atomListLocal;
688	>	InteractionData idat;
689	>	SelfData sdat;
690	>	RealType mf;
691	>	RealType vpair;
692	>	RealType dVdFQ1(0.0);
693	>	RealType dVdFQ2(0.0);
694	>	potVec longRangePotential(0.0);
695	>	potVec workPot(0.0);
696	>	potVec exPot(0.0);
697	>	Vector3d eField1(0.0);
698	>	Vector3d eField2(0.0);
699	>	vector<int>::iterator ia, jb;
700
701	<	doForceLoop( pos,
288	<	rc,
289	<	A,
290	<	electroFrame,
291	<	frc,
292	<	trq,
293	<	tau.getArrayPointer(),
294	<	longRangePotential,
295	<	&passedCalcPot,
296	<	&passedCalcStress,
297	<	&isError );
701	>	int loopStart, loopEnd;
702
703	<	if( isError ){
704	<	sprintf( painCave.errMsg,
705	<	"Error returned from the fortran force calculation.\n" );
706	<	painCave.isFatal = 1;
707	<	simError();
703	>	idat.vdwMult = &vdwMult;
704	>	idat.electroMult = &electroMult;
705	>	idat.pot = &workPot;
706	>	idat.excludedPot = &exPot;
707	>	sdat.pot = fDecomp_->getEmbeddingPotential();
708	>	sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
709	>	idat.vpair = &vpair;
710	>	idat.dVdFQ1 = &dVdFQ1;
711	>	idat.dVdFQ2 = &dVdFQ2;
712	>	idat.eField1 = &eField1;
713	>	idat.eField2 = &eField2;
714	>	idat.f1 = &f1;
715	>	idat.sw = &sw;
716	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
717	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
718	>	idat.doParticlePot = doParticlePot_;
719	>	idat.doElectricField = doElectricField_;
720	>	sdat.doParticlePot = doParticlePot_;
721	>
722	>	loopEnd = PAIR_LOOP;
723	>	if (info_->requiresPrepair() ) {
724	>	loopStart = PREPAIR_LOOP;
725	>	} else {
726	>	loopStart = PAIR_LOOP;
727		}
728	<	for (int i=0; i<LR_POT_TYPES;i++){
729	<	lrPot += longRangePotential[i]; //Quick hack
730	<	}
728	>	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
729	>
730	>	if (iLoop == loopStart) {
731	>	bool update_nlist = fDecomp_->checkNeighborList();
732	>	if (update_nlist) {
733	>	if (!usePeriodicBoundaryConditions_)
734	>	Mat3x3d bbox = thermo->getBoundingBox();
735	>	neighborList = fDecomp_->buildNeighborList();
736	>	}
737	>	}
738
739	<	// grab the simulation box dipole moment if specified
740	<	if (info_->getCalcBoxDipole()){
741	<	getAccumulatedBoxDipole(totalDipole.getArrayPointer());
739	>	for (vector<pair<int, int> >::iterator it = neighborList.begin();
740	>	it != neighborList.end(); ++it) {
741	>
742	>	cg1 = (*it).first;
743	>	cg2 = (*it).second;
744	>
745	>	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
746
747	<	curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
748	<	curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
749	<	curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
747	>	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
748	>
749	>	curSnapshot->wrapVector(d_grp);
750	>	rgrpsq = d_grp.lengthSquare();
751	>	rCutSq = cuts.second;
752	>
753	>	if (rgrpsq < rCutSq) {
754	>	idat.rcut = &cuts.first;
755	>	if (iLoop == PAIR_LOOP) {
756	>	vij = 0.0;
757	>	fij = V3Zero;
758	>	eField1 = V3Zero;
759	>	eField2 = V3Zero;
760	>	}
761	>
762	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
763	>	rgrp);
764	>
765	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
766	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
767	>
768	>	if (doHeatFlux_)
769	>	gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
770	>
771	>	for (ia = atomListRow.begin();
772	>	ia != atomListRow.end(); ++ia) {
773	>	atom1 = (*ia);
774	>
775	>	for (jb = atomListColumn.begin();
776	>	jb != atomListColumn.end(); ++jb) {
777	>	atom2 = (*jb);
778	>
779	>	if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
780	>
781	>	vpair = 0.0;
782	>	workPot = 0.0;
783	>	exPot = 0.0;
784	>	f1 = V3Zero;
785	>	dVdFQ1 = 0.0;
786	>	dVdFQ2 = 0.0;
787	>
788	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
789	>
790	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
791	>	vdwMult = vdwScale_[topoDist];
792	>	electroMult = electrostaticScale_[topoDist];
793	>
794	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
795	>	idat.d = &d_grp;
796	>	idat.r2 = &rgrpsq;
797	>	if (doHeatFlux_)
798	>	vel2 = gvel2;
799	>	} else {
800	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
801	>	curSnapshot->wrapVector( d );
802	>	r2 = d.lengthSquare();
803	>	idat.d = &d;
804	>	idat.r2 = &r2;
805	>	if (doHeatFlux_)
806	>	vel2 = fDecomp_->getAtomVelocityColumn(atom2);
807	>	}
808	>
809	>	r = sqrt( *(idat.r2) );
810	>	idat.rij = &r;
811	>
812	>	if (iLoop == PREPAIR_LOOP) {
813	>	interactionMan_->doPrePair(idat);
814	>	} else {
815	>	interactionMan_->doPair(idat);
816	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
817	>	vij += vpair;
818	>	fij += f1;
819	>	stressTensor -= outProduct( *(idat.d), f1);
820	>	if (doHeatFlux_)
821	>	fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
822	>	}
823	>	}
824	>	}
825	>	}
826	>
827	>	if (iLoop == PAIR_LOOP) {
828	>	if (in_switching_region) {
829	>	swderiv = vij * dswdr / rgrp;
830	>	fg = swderiv * d_grp;
831	>	fij += fg;
832	>
833	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
834	>	if (!fDecomp_->skipAtomPair(atomListRow[0],
835	>	atomListColumn[0],
836	>	cg1, cg2)) {
837	>	stressTensor -= outProduct( *(idat.d), fg);
838	>	if (doHeatFlux_)
839	>	fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
840	>	}
841	>	}
842	>
843	>	for (ia = atomListRow.begin();
844	>	ia != atomListRow.end(); ++ia) {
845	>	atom1 = (*ia);
846	>	mf = fDecomp_->getMassFactorRow(atom1);
847	>	// fg is the force on atom ia due to cutoff group's
848	>	// presence in switching region
849	>	fg = swderiv * d_grp * mf;
850	>	fDecomp_->addForceToAtomRow(atom1, fg);
851	>	if (atomListRow.size() > 1) {
852	>	if (info_->usesAtomicVirial()) {
853	>	// find the distance between the atom
854	>	// and the center of the cutoff group:
855	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
856	>	stressTensor -= outProduct(dag, fg);
857	>	if (doHeatFlux_)
858	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
859	>	}
860	>	}
861	>	}
862	>	for (jb = atomListColumn.begin();
863	>	jb != atomListColumn.end(); ++jb) {
864	>	atom2 = (*jb);
865	>	mf = fDecomp_->getMassFactorColumn(atom2);
866	>	// fg is the force on atom jb due to cutoff group's
867	>	// presence in switching region
868	>	fg = -swderiv * d_grp * mf;
869	>	fDecomp_->addForceToAtomColumn(atom2, fg);
870	>
871	>	if (atomListColumn.size() > 1) {
872	>	if (info_->usesAtomicVirial()) {
873	>	// find the distance between the atom
874	>	// and the center of the cutoff group:
875	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
876	>	stressTensor -= outProduct(dag, fg);
877	>	if (doHeatFlux_)
878	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
879	>	}
880	>	}
881	>	}
882	>	}
883	>	//if (!info_->usesAtomicVirial()) {
884	>	//  stressTensor -= outProduct(d_grp, fij);
885	>	//  if (doHeatFlux_)
886	>	//     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
887	>	//}
888	>	}
889	>	}
890	>	}
891	>
892	>	if (iLoop == PREPAIR_LOOP) {
893	>	if (info_->requiresPrepair()) {
894	>
895	>	fDecomp_->collectIntermediateData();
896	>
897	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
898	>	fDecomp_->fillSelfData(sdat, atom1);
899	>	interactionMan_->doPreForce(sdat);
900	>	}
901	>
902	>	fDecomp_->distributeIntermediateData();
903	>
904	>	}
905	>	}
906		}
907	+
908	+	// collects pairwise information
909	+	fDecomp_->collectData();
910	+
911	+	if (info_->requiresSelfCorrection()) {
912	+	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
913	+	fDecomp_->fillSelfData(sdat, atom1);
914	+	interactionMan_->doSelfCorrection(sdat);
915	+	}
916	+	}
917
918	<	//store the tau and long range potential
919	<	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];
918	>	// collects single-atom information
919	>	fDecomp_->collectSelfData();
920
921	<	curSnapshot->statData.setTau(tau);
922	<	}
921	>	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
922	>	*(fDecomp_->getPairwisePotential());
923
924	+	curSnapshot->setLongRangePotential(longRangePotential);
925	+
926	+	curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
927	+	*(fDecomp_->getExcludedPotential()));
928
929	+	}
930	+
931	+
932		void ForceManager::postCalculation() {
933	+
934	+	vector<Perturbation*>::iterator pi;
935	+	for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
936	+	(*pi)->applyPerturbation();
937	+	}
938	+
939		SimInfo::MoleculeIterator mi;
940		Molecule* mol;
941		Molecule::RigidBodyIterator rbIter;
942		RigidBody* rb;
943	<
943	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
944	>
945		// collect the atomic forces onto rigid bodies
946	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
947	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
948	<	rb->calcForcesAndTorques();
946	>
947	>	for (mol = info_->beginMolecule(mi); mol != NULL;
948	>	mol = info_->nextMolecule(mi)) {
949	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
950	>	rb = mol->nextRigidBody(rbIter)) {
951	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
952	>	stressTensor += rbTau;
953		}
954	<	}
954	>	}
955	>
956	>	#ifdef IS_MPI
957	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
958	>	MPI::REALTYPE, MPI::SUM);
959	>	#endif
960	>	curSnapshot->setStressTensor(stressTensor);
961	>
962	>	if (info_->getSimParams()->getUseLongRangeCorrections()) {
963	>	/*
964	>	RealType vol = curSnapshot->getVolume();
965	>	RealType Elrc(0.0);
966	>	RealType Wlrc(0.0);
967
968	<	}
968	>	set<AtomType*>::iterator i;
969	>	set<AtomType*>::iterator j;
970	>
971	>	RealType n_i, n_j;
972	>	RealType rho_i, rho_j;
973	>	pair<RealType, RealType> LRI;
974	>
975	>	for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
976	>	n_i = RealType(info_->getGlobalCountOfType(*i));
977	>	rho_i = n_i /  vol;
978	>	for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) {
979	>	n_j = RealType(info_->getGlobalCountOfType(*j));
980	>	rho_j = n_j / vol;
981	>
982	>	LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) );
983
984	<	} //end namespace oopse
984	>	Elrc += n_i   * rho_j * LRI.first;
985	>	Wlrc -= rho_i * rho_j * LRI.second;
986	>	}
987	>	}
988	>	Elrc *= 2.0 * NumericConstant::PI;
989	>	Wlrc *= 2.0 * NumericConstant::PI;
990	>
991	>	RealType lrp = curSnapshot->getLongRangePotential();
992	>	curSnapshot->setLongRangePotential(lrp + Elrc);
993	>	stressTensor += Wlrc * SquareMatrix3<RealType>::identity();
994	>	curSnapshot->setStressTensor(stressTensor);
995	>	*/
996	>
997	>	}
998	>	}
999	>	}

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 1866 by gezelter, Thu Apr 25 14:32:56 2013 UTC

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