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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 1710 by gezelter, Fri May 18 21:44:02 2012 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 47 | Line 48
48		* @version 1.0
49		*/
50
51	+
52		#include "brains/ForceManager.hpp"
53		#include "primitives/Molecule.hpp"
54	<	#include "UseTheForce/doForces_interface.h"
53	<	#define __C
54	<	#include "UseTheForce/DarkSide/fInteractionMap.h"
54	>	#define __OPENMD_C
55		#include "utils/simError.h"
56	+	#include "primitives/Bond.hpp"
57		#include "primitives/Bend.hpp"
58	<	#include "primitives/Bend.hpp"
59	<	namespace oopse {
58	>	#include "primitives/Torsion.hpp"
59	>	#include "primitives/Inversion.hpp"
60	>	#include "nonbonded/NonBondedInteraction.hpp"
61	>	#include "parallel/ForceMatrixDecomposition.hpp"
62
63	<	/*
64	<	struct BendOrderStruct {
65	<	Bend* bend;
63	<	BendDataSet dataSet;
64	<	};
65	<	struct TorsionOrderStruct {
66	<	Torsion* torsion;
67	<	TorsionDataSet dataSet;
68	<	};
63	>	#include <cstdio>
64	>	#include <iostream>
65	>	#include <iomanip>
66
67	<	bool  BendSortFunctor(const BendOrderStruct& b1, const BendOrderStruct& b2) {
68	<	return b1.dataSet.deltaV < b2.dataSet.deltaV;
67	>	using namespace std;
68	>	namespace OpenMD {
69	>
70	>	ForceManager::ForceManager(SimInfo * info) : info_(info) {
71	>	forceField_ = info_->getForceField();
72	>	interactionMan_ = new InteractionManager();
73	>	fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
74		}
75
76	<	bool  TorsionSortFunctor(const TorsionOrderStruct& t1, const TorsionOrderStruct& t2) {
77	<	return t1.dataSet.deltaV < t2.dataSet.deltaV;
78	<	}
79	<	*/
80	<	void ForceManager::calcForces(bool needPotential, bool needStress) {
81	<
82	<	if (!info_->isFortranInitialized()) {
83	<	info_->update();
76	>	/**
77	>	* setupCutoffs
78	>	*
79	>	* Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
80	>	* and cutoffPolicy
81	>	*
82	>	* cutoffRadius : realType
83	>	*  If the cutoffRadius was explicitly set, use that value.
84	>	*  If the cutoffRadius was not explicitly set:
85	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
86	>	*      No electrostatic atoms?  Poll the atom types present in the
87	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
88	>	*      Use the maximum suggested value that was found.
89	>	*
90	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
91	>	*                        or SHIFTED_POTENTIAL)
92	>	*      If cutoffMethod was explicitly set, use that choice.
93	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
94	>	*
95	>	* cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
96	>	*      If cutoffPolicy was explicitly set, use that choice.
97	>	*      If cutoffPolicy was not explicitly set, use TRADITIONAL
98	>	*
99	>	* switchingRadius : realType
100	>	*  If the cutoffMethod was set to SWITCHED:
101	>	*      If the switchingRadius was explicitly set, use that value
102	>	*          (but do a sanity check first).
103	>	*      If the switchingRadius was not explicitly set: use 0.85 *
104	>	*      cutoffRadius_
105	>	*  If the cutoffMethod was not set to SWITCHED:
106	>	*      Set switchingRadius equal to cutoffRadius for safety.
107	>	*/
108	>	void ForceManager::setupCutoffs() {
109	>
110	>	Globals* simParams_ = info_->getSimParams();
111	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
112	>	int mdFileVersion;
113	>
114	>	if (simParams_->haveMDfileVersion())
115	>	mdFileVersion = simParams_->getMDfileVersion();
116	>	else
117	>	mdFileVersion = 0;
118	>
119	>	if (simParams_->haveCutoffRadius()) {
120	>	rCut_ = simParams_->getCutoffRadius();
121	>	} else {
122	>	if (info_->usesElectrostaticAtoms()) {
123	>	sprintf(painCave.errMsg,
124	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
125	>	"\tOpenMD will use a default value of 12.0 angstroms"
126	>	"\tfor the cutoffRadius.\n");
127	>	painCave.isFatal = 0;
128	>	painCave.severity = OPENMD_INFO;
129	>	simError();
130	>	rCut_ = 12.0;
131	>	} else {
132	>	RealType thisCut;
133	>	set<AtomType*>::iterator i;
134	>	set<AtomType*> atomTypes;
135	>	atomTypes = info_->getSimulatedAtomTypes();
136	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
137	>	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
138	>	rCut_ = max(thisCut, rCut_);
139	>	}
140	>	sprintf(painCave.errMsg,
141	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
142	>	"\tOpenMD will use %lf angstroms.\n",
143	>	rCut_);
144	>	painCave.isFatal = 0;
145	>	painCave.severity = OPENMD_INFO;
146	>	simError();
147	>	}
148		}
149
150	<	preCalculation();
151	<
86	<	calcShortRangeInteraction();
150	>	fDecomp_->setUserCutoff(rCut_);
151	>	interactionMan_->setCutoffRadius(rCut_);
152
153	<	calcLongRangeInteraction(needPotential, needStress);
153	>	map<string, CutoffMethod> stringToCutoffMethod;
154	>	stringToCutoffMethod["HARD"] = HARD;
155	>	stringToCutoffMethod["SWITCHED"] = SWITCHED;
156	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
157	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
158	>
159	>	if (simParams_->haveCutoffMethod()) {
160	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
161	>	map<string, CutoffMethod>::iterator i;
162	>	i = stringToCutoffMethod.find(cutMeth);
163	>	if (i == stringToCutoffMethod.end()) {
164	>	sprintf(painCave.errMsg,
165	>	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
166	>	"\tShould be one of: "
167	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
168	>	cutMeth.c_str());
169	>	painCave.isFatal = 1;
170	>	painCave.severity = OPENMD_ERROR;
171	>	simError();
172	>	} else {
173	>	cutoffMethod_ = i->second;
174	>	}
175	>	} else {
176	>	if (mdFileVersion > 1) {
177	>	sprintf(painCave.errMsg,
178	>	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
179	>	"\tOpenMD will use SHIFTED_FORCE.\n");
180	>	painCave.isFatal = 0;
181	>	painCave.severity = OPENMD_INFO;
182	>	simError();
183	>	cutoffMethod_ = SHIFTED_FORCE;
184	>	} else {
185	>	// handle the case where the old file version was in play
186	>	// (there should be no cutoffMethod, so we have to deduce it
187	>	// from other data).
188
189	<	postCalculation();
189	>	sprintf(painCave.errMsg,
190	>	"ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
191	>	"\tOpenMD found a file which does not set a cutoffMethod.\n"
192	>	"\tOpenMD will attempt to deduce a cutoffMethod using the\n"
193	>	"\tbehavior of the older (version 1) code.  To remove this\n"
194	>	"\twarning, add an explicit cutoffMethod and change the top\n"
195	>	"\tof the file so that it begins with <OpenMD version=2>\n");
196	>	painCave.isFatal = 0;
197	>	painCave.severity = OPENMD_WARNING;
198	>	simError();
199	>
200	>	// The old file version tethered the shifting behavior to the
201	>	// electrostaticSummationMethod keyword.
202	>
203	>	if (simParams_->haveElectrostaticSummationMethod()) {
204	>	string myMethod = simParams_->getElectrostaticSummationMethod();
205	>	toUpper(myMethod);
206	>
207	>	if (myMethod == "SHIFTED_POTENTIAL") {
208	>	cutoffMethod_ = SHIFTED_POTENTIAL;
209	>	} else if (myMethod == "SHIFTED_FORCE") {
210	>	cutoffMethod_ = SHIFTED_FORCE;
211	>	}
212	>
213	>	if (simParams_->haveSwitchingRadius())
214	>	rSwitch_ = simParams_->getSwitchingRadius();
215
216	<	/*
217	<	std::vector<BendOrderStruct> bendOrderStruct;
218	<	for(std::map<Bend*, BendDataSet>::iterator i = bendDataSets.begin(); i != bendDataSets.end(); ++i) {
219	<	BendOrderStruct tmp;
220	<	tmp.bend= const_cast<Bend*>(i->first);
221	<	tmp.dataSet = i->second;
222	<	bendOrderStruct.push_back(tmp);
216	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
217	>	if (simParams_->haveSwitchingRadius()){
218	>	sprintf(painCave.errMsg,
219	>	"ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
220	>	"\tA value was set for the switchingRadius\n"
221	>	"\teven though the electrostaticSummationMethod was\n"
222	>	"\tset to %s\n", myMethod.c_str());
223	>	painCave.severity = OPENMD_WARNING;
224	>	painCave.isFatal = 1;
225	>	simError();
226	>	}
227	>	}
228	>	if (abs(rCut_ - rSwitch_) < 0.0001) {
229	>	if (cutoffMethod_ == SHIFTED_FORCE) {
230	>	sprintf(painCave.errMsg,
231	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
232	>	"\tcutoffRadius and switchingRadius are set to the\n"
233	>	"\tsame value.  OpenMD will use shifted force\n"
234	>	"\tpotentials instead of switching functions.\n");
235	>	painCave.isFatal = 0;
236	>	painCave.severity = OPENMD_WARNING;
237	>	simError();
238	>	} else {
239	>	cutoffMethod_ = SHIFTED_POTENTIAL;
240	>	sprintf(painCave.errMsg,
241	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
242	>	"\tcutoffRadius and switchingRadius are set to the\n"
243	>	"\tsame value.  OpenMD will use shifted potentials\n"
244	>	"\tinstead of switching functions.\n");
245	>	painCave.isFatal = 0;
246	>	painCave.severity = OPENMD_WARNING;
247	>	simError();
248	>	}
249	>	}
250	>	}
251	>	}
252		}
253
254	<	std::vector<TorsionOrderStruct> torsionOrderStruct;
255	<	for(std::map<Torsion*, TorsionDataSet>::iterator j = torsionDataSets.begin(); j != torsionDataSets.end(); ++j) {
256	<	TorsionOrderStruct tmp;
257	<	tmp.torsion = const_cast<Torsion*>(j->first);
258	<	tmp.dataSet = j->second;
259	<	torsionOrderStruct.push_back(tmp);
254	>	map<string, CutoffPolicy> stringToCutoffPolicy;
255	>	stringToCutoffPolicy["MIX"] = MIX;
256	>	stringToCutoffPolicy["MAX"] = MAX;
257	>	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
258	>
259	>	string cutPolicy;
260	>	if (forceFieldOptions_.haveCutoffPolicy()){
261	>	cutPolicy = forceFieldOptions_.getCutoffPolicy();
262	>	}else if (simParams_->haveCutoffPolicy()) {
263	>	cutPolicy = simParams_->getCutoffPolicy();
264		}
265	+
266	+	if (!cutPolicy.empty()){
267	+	toUpper(cutPolicy);
268	+	map<string, CutoffPolicy>::iterator i;
269	+	i = stringToCutoffPolicy.find(cutPolicy);
270	+
271	+	if (i == stringToCutoffPolicy.end()) {
272	+	sprintf(painCave.errMsg,
273	+	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
274	+	"\tShould be one of: "
275	+	"MIX, MAX, or TRADITIONAL\n",
276	+	cutPolicy.c_str());
277	+	painCave.isFatal = 1;
278	+	painCave.severity = OPENMD_ERROR;
279	+	simError();
280	+	} else {
281	+	cutoffPolicy_ = i->second;
282	+	}
283	+	} else {
284	+	sprintf(painCave.errMsg,
285	+	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
286	+	"\tOpenMD will use TRADITIONAL.\n");
287	+	painCave.isFatal = 0;
288	+	painCave.severity = OPENMD_INFO;
289	+	simError();
290	+	cutoffPolicy_ = TRADITIONAL;
291	+	}
292	+
293	+	fDecomp_->setCutoffPolicy(cutoffPolicy_);
294	+
295	+	// create the switching function object:
296	+
297	+	switcher_ = new SwitchingFunction();
298	+
299	+	if (cutoffMethod_ == SWITCHED) {
300	+	if (simParams_->haveSwitchingRadius()) {
301	+	rSwitch_ = simParams_->getSwitchingRadius();
302	+	if (rSwitch_ > rCut_) {
303	+	sprintf(painCave.errMsg,
304	+	"ForceManager::setupCutoffs: switchingRadius (%f) is larger "
305	+	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
306	+	painCave.isFatal = 1;
307	+	painCave.severity = OPENMD_ERROR;
308	+	simError();
309	+	}
310	+	} else {
311	+	rSwitch_ = 0.85 * rCut_;
312	+	sprintf(painCave.errMsg,
313	+	"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
314	+	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
315	+	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
316	+	painCave.isFatal = 0;
317	+	painCave.severity = OPENMD_WARNING;
318	+	simError();
319	+	}
320	+	} else {
321	+	if (mdFileVersion > 1) {
322	+	// throw an error if we define a switching radius and don't need one.
323	+	// older file versions should not do this.
324	+	if (simParams_->haveSwitchingRadius()) {
325	+	map<string, CutoffMethod>::const_iterator it;
326	+	string theMeth;
327	+	for (it = stringToCutoffMethod.begin();
328	+	it != stringToCutoffMethod.end(); ++it) {
329	+	if (it->second == cutoffMethod_) {
330	+	theMeth = it->first;
331	+	break;
332	+	}
333	+	}
334	+	sprintf(painCave.errMsg,
335	+	"ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
336	+	"\tis not set to SWITCHED, so switchingRadius value\n"
337	+	"\twill be ignored for this simulation\n", theMeth.c_str());
338	+	painCave.isFatal = 0;
339	+	painCave.severity = OPENMD_WARNING;
340	+	simError();
341	+	}
342	+	}
343	+	rSwitch_ = rCut_;
344	+	}
345
346	<	std::sort(bendOrderStruct.begin(), bendOrderStruct.end(), std::ptr_fun(BendSortFunctor));
347	<	std::sort(torsionOrderStruct.begin(), torsionOrderStruct.end(), std::ptr_fun(TorsionSortFunctor));
348	<	for (std::vector<BendOrderStruct>::iterator k = bendOrderStruct.begin(); k != bendOrderStruct.end(); ++k) {
349	<	Bend* bend = k->bend;
350	<	std::cout << "Bend: atom1=" <<bend->getAtomA()->getGlobalIndex() << ",atom2 = "<< bend->getAtomB()->getGlobalIndex() << ",atom3="<<bend->getAtomC()->getGlobalIndex() << " ";
351	<	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;
346	>	// Default to cubic switching function.
347	>	sft_ = cubic;
348	>	if (simParams_->haveSwitchingFunctionType()) {
349	>	string funcType = simParams_->getSwitchingFunctionType();
350	>	toUpper(funcType);
351	>	if (funcType == "CUBIC") {
352	>	sft_ = cubic;
353	>	} else {
354	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
355	>	sft_ = fifth_order_poly;
356	>	} else {
357	>	// throw error
358	>	sprintf( painCave.errMsg,
359	>	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
360	>	"\tswitchingFunctionType must be one of: "
361	>	"\"cubic\" or \"fifth_order_polynomial\".",
362	>	funcType.c_str() );
363	>	painCave.isFatal = 1;
364	>	painCave.severity = OPENMD_ERROR;
365	>	simError();
366	>	}
367	>	}
368		}
369	<	for (std::vector<TorsionOrderStruct>::iterator l = torsionOrderStruct.begin(); l != torsionOrderStruct.end(); ++l) {
370	<	Torsion* torsion = l->torsion;
371	<	std::cout << "Torsion: atom1=" <<torsion->getAtomA()->getGlobalIndex() << ",atom2 = "<< torsion->getAtomB()->getGlobalIndex() << ",atom3="<<torsion->getAtomC()->getGlobalIndex() << ",atom4="<<torsion->getAtomD()->getGlobalIndex()<< " ";
372	<	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;
369	>	switcher_->setSwitchType(sft_);
370	>	switcher_->setSwitch(rSwitch_, rCut_);
371	>	interactionMan_->setSwitchingRadius(rSwitch_);
372	>	}
373	>
374	>
375	>
376	>
377	>	void ForceManager::initialize() {
378	>
379	>	if (!info_->isTopologyDone()) {
380	>
381	>	info_->update();
382	>	interactionMan_->setSimInfo(info_);
383	>	interactionMan_->initialize();
384	>
385	>	// We want to delay the cutoffs until after the interaction
386	>	// manager has set up the atom-atom interactions so that we can
387	>	// query them for suggested cutoff values
388	>	setupCutoffs();
389	>
390	>	info_->prepareTopology();
391		}
392	<	*/
392	>
393	>	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
394	>
395	>	// Force fields can set options on how to scale van der Waals and
396	>	// electrostatic interactions for atoms connected via bonds, bends
397	>	// and torsions in this case the topological distance between
398	>	// atoms is:
399	>	// 0 = topologically unconnected
400	>	// 1 = bonded together
401	>	// 2 = connected via a bend
402	>	// 3 = connected via a torsion
403	>
404	>	vdwScale_.reserve(4);
405	>	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
406	>
407	>	electrostaticScale_.reserve(4);
408	>	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
409	>
410	>	vdwScale_[0] = 1.0;
411	>	vdwScale_[1] = fopts.getvdw12scale();
412	>	vdwScale_[2] = fopts.getvdw13scale();
413	>	vdwScale_[3] = fopts.getvdw14scale();
414	>
415	>	electrostaticScale_[0] = 1.0;
416	>	electrostaticScale_[1] = fopts.getelectrostatic12scale();
417	>	electrostaticScale_[2] = fopts.getelectrostatic13scale();
418	>	electrostaticScale_[3] = fopts.getelectrostatic14scale();
419	>
420	>	fDecomp_->distributeInitialData();
421	>
422	>	initialized_ = true;
423	>
424		}
425
426	+	void ForceManager::calcForces() {
427	+
428	+	if (!initialized_) initialize();
429	+
430	+	preCalculation();
431	+	shortRangeInteractions();
432	+	longRangeInteractions();
433	+	postCalculation();
434	+	}
435	+
436		void ForceManager::preCalculation() {
437		SimInfo::MoleculeIterator mi;
438		Molecule* mol;
#	Line 128 | Line 440 | namespace oopse {
440		Atom* atom;
441		Molecule::RigidBodyIterator rbIter;
442		RigidBody* rb;
443	+	Molecule::CutoffGroupIterator ci;
444	+	CutoffGroup* cg;
445
446		// forces are zeroed here, before any are accumulated.
447	<	// NOTE: do not rezero the forces in Fortran.
448	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
449	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
447	>
448	>	for (mol = info_->beginMolecule(mi); mol != NULL;
449	>	mol = info_->nextMolecule(mi)) {
450	>	for(atom = mol->beginAtom(ai); atom != NULL;
451	>	atom = mol->nextAtom(ai)) {
452		atom->zeroForcesAndTorques();
453		}
454	<
454	>
455		//change the positions of atoms which belong to the rigidbodies
456	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
456	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
457	>	rb = mol->nextRigidBody(rbIter)) {
458		rb->zeroForcesAndTorques();
459		}
460	+
461	+	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
462	+	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
463	+	cg = mol->nextCutoffGroup(ci)) {
464	+	//calculate the center of mass of cutoff group
465	+	cg->updateCOM();
466	+	}
467	+	}
468		}
469
470	+	// Zero out the stress tensor
471	+	tau *= 0.0;
472	+
473		}
474	<
475	<	void ForceManager::calcShortRangeInteraction() {
474	>
475	>	void ForceManager::shortRangeInteractions() {
476		Molecule* mol;
477		RigidBody* rb;
478		Bond* bond;
479		Bend* bend;
480		Torsion* torsion;
481	+	Inversion* inversion;
482		SimInfo::MoleculeIterator mi;
483		Molecule::RigidBodyIterator rbIter;
484		Molecule::BondIterator bondIter;;
485		Molecule::BendIterator  bendIter;
486		Molecule::TorsionIterator  torsionIter;
487	+	Molecule::InversionIterator  inversionIter;
488		RealType bondPotential = 0.0;
489		RealType bendPotential = 0.0;
490		RealType torsionPotential = 0.0;
491	+	RealType inversionPotential = 0.0;
492
493		//calculate short range interactions
494	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
494	>	for (mol = info_->beginMolecule(mi); mol != NULL;
495	>	mol = info_->nextMolecule(mi)) {
496
497		//change the positions of atoms which belong to the rigidbodies
498	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
499	<	rb->updateAtoms();
498	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
499	>	rb = mol->nextRigidBody(rbIter)) {
500	>	rb->updateAtoms();
501		}
502
503	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
503	>	for (bond = mol->beginBond(bondIter); bond != NULL;
504	>	bond = mol->nextBond(bondIter)) {
505		bond->calcForce();
506		bondPotential += bond->getPotential();
507		}
508
509	<
510	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
511	<
512	<	RealType angle;
513	<	bend->calcForce(angle);
514	<	RealType currBendPot = bend->getPotential();
515	<	bendPotential += bend->getPotential();
516	<	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
517	<	if (i == bendDataSets.end()) {
518	<	BendDataSet dataSet;
519	<	dataSet.prev.angle = dataSet.curr.angle = angle;
520	<	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
521	<	dataSet.deltaV = 0.0;
522	<	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
523	<	}else {
524	<	i->second.prev.angle = i->second.curr.angle;
525	<	i->second.prev.potential = i->second.curr.potential;
526	<	i->second.curr.angle = angle;
527	<	i->second.curr.potential = currBendPot;
528	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
529	<	}
509	>	for (bend = mol->beginBend(bendIter); bend != NULL;
510	>	bend = mol->nextBend(bendIter)) {
511	>
512	>	RealType angle;
513	>	bend->calcForce(angle);
514	>	RealType currBendPot = bend->getPotential();
515	>
516	>	bendPotential += bend->getPotential();
517	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
518	>	if (i == bendDataSets.end()) {
519	>	BendDataSet dataSet;
520	>	dataSet.prev.angle = dataSet.curr.angle = angle;
521	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
522	>	dataSet.deltaV = 0.0;
523	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
524	>	dataSet));
525	>	}else {
526	>	i->second.prev.angle = i->second.curr.angle;
527	>	i->second.prev.potential = i->second.curr.potential;
528	>	i->second.curr.angle = angle;
529	>	i->second.curr.potential = currBendPot;
530	>	i->second.deltaV =  fabs(i->second.curr.potential -
531	>	i->second.prev.potential);
532	>	}
533		}
534	<
535	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
534	>
535	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
536	>	torsion = mol->nextTorsion(torsionIter)) {
537		RealType angle;
538	<	torsion->calcForce(angle);
538	>	torsion->calcForce(angle);
539		RealType currTorsionPot = torsion->getPotential();
540	<	torsionPotential += torsion->getPotential();
541	<	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
542	<	if (i == torsionDataSets.end()) {
543	<	TorsionDataSet dataSet;
544	<	dataSet.prev.angle = dataSet.curr.angle = angle;
545	<	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
546	<	dataSet.deltaV = 0.0;
547	<	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
548	<	}else {
549	<	i->second.prev.angle = i->second.curr.angle;
550	<	i->second.prev.potential = i->second.curr.potential;
551	<	i->second.curr.angle = angle;
552	<	i->second.curr.potential = currTorsionPot;
553	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
554	<	}
555	<	}
556	<
540	>	torsionPotential += torsion->getPotential();
541	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
542	>	if (i == torsionDataSets.end()) {
543	>	TorsionDataSet dataSet;
544	>	dataSet.prev.angle = dataSet.curr.angle = angle;
545	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
546	>	dataSet.deltaV = 0.0;
547	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
548	>	}else {
549	>	i->second.prev.angle = i->second.curr.angle;
550	>	i->second.prev.potential = i->second.curr.potential;
551	>	i->second.curr.angle = angle;
552	>	i->second.curr.potential = currTorsionPot;
553	>	i->second.deltaV =  fabs(i->second.curr.potential -
554	>	i->second.prev.potential);
555	>	}
556	>	}
557	>
558	>	for (inversion = mol->beginInversion(inversionIter);
559	>	inversion != NULL;
560	>	inversion = mol->nextInversion(inversionIter)) {
561	>	RealType angle;
562	>	inversion->calcForce(angle);
563	>	RealType currInversionPot = inversion->getPotential();
564	>	inversionPotential += inversion->getPotential();
565	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
566	>	if (i == inversionDataSets.end()) {
567	>	InversionDataSet dataSet;
568	>	dataSet.prev.angle = dataSet.curr.angle = angle;
569	>	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
570	>	dataSet.deltaV = 0.0;
571	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
572	>	}else {
573	>	i->second.prev.angle = i->second.curr.angle;
574	>	i->second.prev.potential = i->second.curr.potential;
575	>	i->second.curr.angle = angle;
576	>	i->second.curr.potential = currInversionPot;
577	>	i->second.deltaV =  fabs(i->second.curr.potential -
578	>	i->second.prev.potential);
579	>	}
580	>	}
581		}
582
583	<	RealType  shortRangePotential = bondPotential + bendPotential + torsionPotential;
583	>	RealType  shortRangePotential = bondPotential + bendPotential +
584	>	torsionPotential +  inversionPotential;
585		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
586		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
587		curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
588		curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
589		curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
590	<
590	>	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
591		}
592	+
593	+	void ForceManager::longRangeInteractions() {
594
595	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
596	<	Snapshot* curSnapshot;
597	<	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();
595	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
596	>	DataStorage* config = &(curSnapshot->atomData);
597	>	DataStorage* cgConfig = &(curSnapshot->cgData);
598
243	–	//get array pointers
244	–	config = &(curSnapshot->atomData);
245	–	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);
250	–
599		//calculate the center of mass of cutoff group
600	+
601		SimInfo::MoleculeIterator mi;
602		Molecule* mol;
603		Molecule::CutoffGroupIterator ci;
604		CutoffGroup* cg;
256	–	Vector3d com;
257	–	std::vector<Vector3d> rcGroup;
605
606	<	if(info_->getNCutoffGroups() > 0){
607	<
608	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
609	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
610	<	cg->getCOM(com);
611	<	rcGroup.push_back(com);
606	>	if(info_->getNCutoffGroups() > 0){
607	>	for (mol = info_->beginMolecule(mi); mol != NULL;
608	>	mol = info_->nextMolecule(mi)) {
609	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
610	>	cg = mol->nextCutoffGroup(ci)) {
611	>	cg->updateCOM();
612		}
613	<	}// end for (mol)
267	<
268	<	rc = rcGroup[0].getArrayPointer();
613	>	}
614		} else {
615	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
616	<	rc = pos;
615	>	// center of mass of the group is the same as position of the atom
616	>	// if cutoff group does not exist
617	>	cgConfig->position = config->position;
618		}
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;
619
620	<	for (int i=0; i<LR_POT_TYPES;i++){
621	<	longRangePotential[i]=0.0; //Initialize array
620	>	fDecomp_->zeroWorkArrays();
621	>	fDecomp_->distributeData();
622	>
623	>	int cg1, cg2, atom1, atom2, topoDist;
624	>	Vector3d d_grp, dag, d;
625	>	RealType rgrpsq, rgrp, r2, r;
626	>	RealType electroMult, vdwMult;
627	>	RealType vij;
628	>	Vector3d fij, fg, f1;
629	>	tuple3<RealType, RealType, RealType> cuts;
630	>	RealType rCutSq;
631	>	bool in_switching_region;
632	>	RealType sw, dswdr, swderiv;
633	>	vector<int> atomListColumn, atomListRow, atomListLocal;
634	>	InteractionData idat;
635	>	SelfData sdat;
636	>	RealType mf;
637	>	RealType lrPot;
638	>	RealType vpair;
639	>	potVec longRangePotential(0.0);
640	>	potVec workPot(0.0);
641	>
642	>	int loopStart, loopEnd;
643	>
644	>	idat.vdwMult = &vdwMult;
645	>	idat.electroMult = &electroMult;
646	>	idat.pot = &workPot;
647	>	sdat.pot = fDecomp_->getEmbeddingPotential();
648	>	idat.vpair = &vpair;
649	>	idat.f1 = &f1;
650	>	idat.sw = &sw;
651	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
652	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
653	>
654	>	loopEnd = PAIR_LOOP;
655	>	if (info_->requiresPrepair() ) {
656	>	loopStart = PREPAIR_LOOP;
657	>	} else {
658	>	loopStart = PAIR_LOOP;
659		}
660	+
661	+	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
662	+
663	+	if (iLoop == loopStart) {
664	+	bool update_nlist = fDecomp_->checkNeighborList();
665	+	if (update_nlist)
666	+	neighborList = fDecomp_->buildNeighborList();
667	+	}
668
669	<	doForceLoop( pos,
670	<	rc,
671	<	A,
672	<	electroFrame,
673	<	frc,
674	<	trq,
675	<	tau.getArrayPointer(),
294	<	longRangePotential,
295	<	&passedCalcPot,
296	<	&passedCalcStress,
297	<	&isError );
669	>	for (vector<pair<int, int> >::iterator it = neighborList.begin();
670	>	it != neighborList.end(); ++it) {
671	>
672	>	cg1 = (*it).first;
673	>	cg2 = (*it).second;
674	>
675	>	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
676
677	<	if( isError ){
678	<	sprintf( painCave.errMsg,
679	<	"Error returned from the fortran force calculation.\n" );
680	<	painCave.isFatal = 1;
681	<	simError();
677	>	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
678	>
679	>	curSnapshot->wrapVector(d_grp);
680	>	rgrpsq = d_grp.lengthSquare();
681	>	rCutSq = cuts.second;
682	>
683	>	if (rgrpsq < rCutSq) {
684	>	idat.rcut = &cuts.first;
685	>	if (iLoop == PAIR_LOOP) {
686	>	vij = 0.0;
687	>	fij = V3Zero;
688	>	}
689	>
690	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
691	>	rgrp);
692	>
693	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
694	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
695	>
696	>	for (vector<int>::iterator ia = atomListRow.begin();
697	>	ia != atomListRow.end(); ++ia) {
698	>	atom1 = (*ia);
699	>
700	>	for (vector<int>::iterator jb = atomListColumn.begin();
701	>	jb != atomListColumn.end(); ++jb) {
702	>	atom2 = (*jb);
703	>
704	>	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
705	>	vpair = 0.0;
706	>	workPot = 0.0;
707	>	f1 = V3Zero;
708	>
709	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
710	>
711	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
712	>	vdwMult = vdwScale_[topoDist];
713	>	electroMult = electrostaticScale_[topoDist];
714	>
715	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
716	>	idat.d = &d_grp;
717	>	idat.r2 = &rgrpsq;
718	>	} else {
719	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
720	>	curSnapshot->wrapVector( d );
721	>	r2 = d.lengthSquare();
722	>	idat.d = &d;
723	>	idat.r2 = &r2;
724	>	}
725	>
726	>	r = sqrt( *(idat.r2) );
727	>	idat.rij = &r;
728	>
729	>	if (iLoop == PREPAIR_LOOP) {
730	>	interactionMan_->doPrePair(idat);
731	>	} else {
732	>	interactionMan_->doPair(idat);
733	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
734	>	vij += vpair;
735	>	fij += f1;
736	>	tau -= outProduct( *(idat.d), f1);
737	>	}
738	>	}
739	>	}
740	>	}
741	>
742	>	if (iLoop == PAIR_LOOP) {
743	>	if (in_switching_region) {
744	>	swderiv = vij * dswdr / rgrp;
745	>	fg = swderiv * d_grp;
746	>	fij += fg;
747	>
748	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
749	>	tau -= outProduct( *(idat.d), fg);
750	>	}
751	>
752	>	for (vector<int>::iterator ia = atomListRow.begin();
753	>	ia != atomListRow.end(); ++ia) {
754	>	atom1 = (*ia);
755	>	mf = fDecomp_->getMassFactorRow(atom1);
756	>	// fg is the force on atom ia due to cutoff group's
757	>	// presence in switching region
758	>	fg = swderiv * d_grp * mf;
759	>	fDecomp_->addForceToAtomRow(atom1, fg);
760	>	if (atomListRow.size() > 1) {
761	>	if (info_->usesAtomicVirial()) {
762	>	// find the distance between the atom
763	>	// and the center of the cutoff group:
764	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
765	>	tau -= outProduct(dag, fg);
766	>	}
767	>	}
768	>	}
769	>	for (vector<int>::iterator jb = atomListColumn.begin();
770	>	jb != atomListColumn.end(); ++jb) {
771	>	atom2 = (*jb);
772	>	mf = fDecomp_->getMassFactorColumn(atom2);
773	>	// fg is the force on atom jb due to cutoff group's
774	>	// presence in switching region
775	>	fg = -swderiv * d_grp * mf;
776	>	fDecomp_->addForceToAtomColumn(atom2, fg);
777	>
778	>	if (atomListColumn.size() > 1) {
779	>	if (info_->usesAtomicVirial()) {
780	>	// find the distance between the atom
781	>	// and the center of the cutoff group:
782	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
783	>	tau -= outProduct(dag, fg);
784	>	}
785	>	}
786	>	}
787	>	}
788	>	//if (!info_->usesAtomicVirial()) {
789	>	//  tau -= outProduct(d_grp, fij);
790	>	//}
791	>	}
792	>	}
793	>	}
794	>
795	>	if (iLoop == PREPAIR_LOOP) {
796	>	if (info_->requiresPrepair()) {
797	>
798	>	fDecomp_->collectIntermediateData();
799	>
800	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
801	>	fDecomp_->fillSelfData(sdat, atom1);
802	>	interactionMan_->doPreForce(sdat);
803	>	}
804	>
805	>	fDecomp_->distributeIntermediateData();
806	>
807	>	}
808	>	}
809		}
810	<	for (int i=0; i<LR_POT_TYPES;i++){
811	<	lrPot += longRangePotential[i]; //Quick hack
812	<	}
810	>
811	>	fDecomp_->collectData();
812	>
813	>	if (info_->requiresSelfCorrection()) {
814
815	<	// grab the simulation box dipole moment if specified
816	<	if (info_->getCalcBoxDipole()){
817	<	getAccumulatedBoxDipole(totalDipole.getArrayPointer());
815	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
816	>	fDecomp_->fillSelfData(sdat, atom1);
817	>	interactionMan_->doSelfCorrection(sdat);
818	>	}
819
313	–	curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
314	–	curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
315	–	curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
820		}
821
822	+	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
823	+	*(fDecomp_->getPairwisePotential());
824	+
825	+	lrPot = longRangePotential.sum();
826	+
827		//store the tau and long range potential
828		curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
829	<	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
830	<	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
322	<
323	<	curSnapshot->statData.setTau(tau);
829	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
830	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
831		}
832
833	<
833	>
834		void ForceManager::postCalculation() {
835		SimInfo::MoleculeIterator mi;
836		Molecule* mol;
837		Molecule::RigidBodyIterator rbIter;
838		RigidBody* rb;
839	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
840
841		// collect the atomic forces onto rigid bodies
842	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
843	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
844	<	rb->calcForcesAndTorques();
842	>
843	>	for (mol = info_->beginMolecule(mi); mol != NULL;
844	>	mol = info_->nextMolecule(mi)) {
845	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
846	>	rb = mol->nextRigidBody(rbIter)) {
847	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
848	>	tau += rbTau;
849		}
850	<	}
851	<
850	>	}
851	>
852	>	#ifdef IS_MPI
853	>	Mat3x3d tmpTau(tau);
854	>	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
855	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
856	>	#endif
857	>	curSnapshot->setTau(tau);
858		}
859
860	<	} //end namespace oopse
860	>	} //end namespace OpenMD

Comparing:
trunk/src/brains/ForceManager.cpp (property svn:keywords), Revision 998 by chrisfen, Mon Jul 3 13:18:43 2006 UTC vs.
branches/development/src/brains/ForceManager.cpp (property svn:keywords), Revision 1710 by gezelter, Fri May 18 21:44:02 2012 UTC

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