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

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trunk/src/brains/ForceManager.cpp (file contents), Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
branches/development/src/brains/ForceManager.cpp (file contents), Revision 1849 by gezelter, Wed Feb 20 13:52:51 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, 24107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
44		* @file ForceManager.cpp
45		* @author tlin
46		* @date 11/09/2004
46	–	* @time 10:39am
47		* @version 1.0
48		*/
49
50	+
51		#include "brains/ForceManager.hpp"
52		#include "primitives/Molecule.hpp"
53	<	#include "UseTheForce/doForces_interface.h"
53	<	#define __C
54	<	#include "UseTheForce/DarkSide/fInteractionMap.h"
53	>	#define __OPENMD_C
54		#include "utils/simError.h"
55	+	#include "primitives/Bond.hpp"
56		#include "primitives/Bend.hpp"
57	<	#include "primitives/Bend.hpp"
58	<	namespace oopse {
57	>	#include "primitives/Torsion.hpp"
58	>	#include "primitives/Inversion.hpp"
59	>	#include "nonbonded/NonBondedInteraction.hpp"
60	>	#include "perturbations/ElectricField.hpp"
61	>	#include "parallel/ForceMatrixDecomposition.hpp"
62
63	<	/*
64	<	struct BendOrderStruct {
65	<	Bend* bend;
63	<	BendDataSet dataSet;
64	<	};
65	<	struct TorsionOrderStruct {
66	<	Torsion* torsion;
67	<	TorsionDataSet dataSet;
68	<	};
63	>	#include <cstdio>
64	>	#include <iostream>
65	>	#include <iomanip>
66
67	<	bool  BendSortFunctor(const BendOrderStruct& b1, const BendOrderStruct& b2) {
68	<	return b1.dataSet.deltaV < b2.dataSet.deltaV;
67	>	using namespace std;
68	>	namespace OpenMD {
69	>
70	>	ForceManager::ForceManager(SimInfo * info) : info_(info) {
71	>	forceField_ = info_->getForceField();
72	>	interactionMan_ = new InteractionManager();
73	>	fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
74		}
75
76	<	bool  TorsionSortFunctor(const TorsionOrderStruct& t1, const TorsionOrderStruct& t2) {
77	<	return t1.dataSet.deltaV < t2.dataSet.deltaV;
78	<	}
79	<	*/
80	<	void ForceManager::calcForces(bool needPotential, bool needStress) {
76	>	/**
77	>	* setupCutoffs
78	>	*
79	>	* Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
80	>	* and cutoffPolicy
81	>	*
82	>	* cutoffRadius : realType
83	>	*  If the cutoffRadius was explicitly set, use that value.
84	>	*  If the cutoffRadius was not explicitly set:
85	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
86	>	*      No electrostatic atoms?  Poll the atom types present in the
87	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
88	>	*      Use the maximum suggested value that was found.
89	>	*
90	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
91	>	*                        or SHIFTED_POTENTIAL)
92	>	*      If cutoffMethod was explicitly set, use that choice.
93	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
94	>	*
95	>	* cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
96	>	*      If cutoffPolicy was explicitly set, use that choice.
97	>	*      If cutoffPolicy was not explicitly set, use TRADITIONAL
98	>	*
99	>	* switchingRadius : realType
100	>	*  If the cutoffMethod was set to SWITCHED:
101	>	*      If the switchingRadius was explicitly set, use that value
102	>	*          (but do a sanity check first).
103	>	*      If the switchingRadius was not explicitly set: use 0.85 *
104	>	*      cutoffRadius_
105	>	*  If the cutoffMethod was not set to SWITCHED:
106	>	*      Set switchingRadius equal to cutoffRadius for safety.
107	>	*/
108	>	void ForceManager::setupCutoffs() {
109	>
110	>	Globals* simParams_ = info_->getSimParams();
111	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
112	>	int mdFileVersion;
113	>	rCut_ = 0.0; //Needs a value for a later max() call;
114	>
115	>	if (simParams_->haveMDfileVersion())
116	>	mdFileVersion = simParams_->getMDfileVersion();
117	>	else
118	>	mdFileVersion = 0;
119	>
120	>	// We need the list of simulated atom types to figure out cutoffs
121	>	// as well as long range corrections.
122
123	<	if (!info_->isFortranInitialized()) {
124	<	info_->update();
123	>	set<AtomType*>::iterator i;
124	>	set<AtomType*> atomTypes_;
125	>	atomTypes_ = info_->getSimulatedAtomTypes();
126	>
127	>	if (simParams_->haveCutoffRadius()) {
128	>	rCut_ = simParams_->getCutoffRadius();
129	>	} else {
130	>	if (info_->usesElectrostaticAtoms()) {
131	>	sprintf(painCave.errMsg,
132	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
133	>	"\tOpenMD will use a default value of 12.0 angstroms"
134	>	"\tfor the cutoffRadius.\n");
135	>	painCave.isFatal = 0;
136	>	painCave.severity = OPENMD_INFO;
137	>	simError();
138	>	rCut_ = 12.0;
139	>	} else {
140	>	RealType thisCut;
141	>	for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
142	>	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
143	>	rCut_ = max(thisCut, rCut_);
144	>	}
145	>	sprintf(painCave.errMsg,
146	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
147	>	"\tOpenMD will use %lf angstroms.\n",
148	>	rCut_);
149	>	painCave.isFatal = 0;
150	>	painCave.severity = OPENMD_INFO;
151	>	simError();
152	>	}
153		}
154
155	<	preCalculation();
156	<
86	<	calcShortRangeInteraction();
155	>	fDecomp_->setUserCutoff(rCut_);
156	>	interactionMan_->setCutoffRadius(rCut_);
157
158	<	calcLongRangeInteraction(needPotential, needStress);
158	>	map<string, CutoffMethod> stringToCutoffMethod;
159	>	stringToCutoffMethod["HARD"] = HARD;
160	>	stringToCutoffMethod["SWITCHED"] = SWITCHED;
161	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
162	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
163	>
164	>	if (simParams_->haveCutoffMethod()) {
165	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
166	>	map<string, CutoffMethod>::iterator i;
167	>	i = stringToCutoffMethod.find(cutMeth);
168	>	if (i == stringToCutoffMethod.end()) {
169	>	sprintf(painCave.errMsg,
170	>	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
171	>	"\tShould be one of: "
172	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
173	>	cutMeth.c_str());
174	>	painCave.isFatal = 1;
175	>	painCave.severity = OPENMD_ERROR;
176	>	simError();
177	>	} else {
178	>	cutoffMethod_ = i->second;
179	>	}
180	>	} else {
181	>	if (mdFileVersion > 1) {
182	>	sprintf(painCave.errMsg,
183	>	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
184	>	"\tOpenMD will use SHIFTED_FORCE.\n");
185	>	painCave.isFatal = 0;
186	>	painCave.severity = OPENMD_INFO;
187	>	simError();
188	>	cutoffMethod_ = SHIFTED_FORCE;
189	>	} else {
190	>	// handle the case where the old file version was in play
191	>	// (there should be no cutoffMethod, so we have to deduce it
192	>	// from other data).
193
194	<	postCalculation();
194	>	sprintf(painCave.errMsg,
195	>	"ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
196	>	"\tOpenMD found a file which does not set a cutoffMethod.\n"
197	>	"\tOpenMD will attempt to deduce a cutoffMethod using the\n"
198	>	"\tbehavior of the older (version 1) code.  To remove this\n"
199	>	"\twarning, add an explicit cutoffMethod and change the top\n"
200	>	"\tof the file so that it begins with <OpenMD version=2>\n");
201	>	painCave.isFatal = 0;
202	>	painCave.severity = OPENMD_WARNING;
203	>	simError();
204	>
205	>	// The old file version tethered the shifting behavior to the
206	>	// electrostaticSummationMethod keyword.
207	>
208	>	if (simParams_->haveElectrostaticSummationMethod()) {
209	>	string myMethod = simParams_->getElectrostaticSummationMethod();
210	>	toUpper(myMethod);
211	>
212	>	if (myMethod == "SHIFTED_POTENTIAL") {
213	>	cutoffMethod_ = SHIFTED_POTENTIAL;
214	>	} else if (myMethod == "SHIFTED_FORCE") {
215	>	cutoffMethod_ = SHIFTED_FORCE;
216	>	}
217	>
218	>	if (simParams_->haveSwitchingRadius())
219	>	rSwitch_ = simParams_->getSwitchingRadius();
220
221	<	/*
222	<	std::vector<BendOrderStruct> bendOrderStruct;
223	<	for(std::map<Bend*, BendDataSet>::iterator i = bendDataSets.begin(); i != bendDataSets.end(); ++i) {
224	<	BendOrderStruct tmp;
225	<	tmp.bend= const_cast<Bend*>(i->first);
226	<	tmp.dataSet = i->second;
227	<	bendOrderStruct.push_back(tmp);
221	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
222	>	if (simParams_->haveSwitchingRadius()){
223	>	sprintf(painCave.errMsg,
224	>	"ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
225	>	"\tA value was set for the switchingRadius\n"
226	>	"\teven though the electrostaticSummationMethod was\n"
227	>	"\tset to %s\n", myMethod.c_str());
228	>	painCave.severity = OPENMD_WARNING;
229	>	painCave.isFatal = 1;
230	>	simError();
231	>	}
232	>	}
233	>	if (abs(rCut_ - rSwitch_) < 0.0001) {
234	>	if (cutoffMethod_ == SHIFTED_FORCE) {
235	>	sprintf(painCave.errMsg,
236	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
237	>	"\tcutoffRadius and switchingRadius are set to the\n"
238	>	"\tsame value.  OpenMD will use shifted force\n"
239	>	"\tpotentials instead of switching functions.\n");
240	>	painCave.isFatal = 0;
241	>	painCave.severity = OPENMD_WARNING;
242	>	simError();
243	>	} else {
244	>	cutoffMethod_ = SHIFTED_POTENTIAL;
245	>	sprintf(painCave.errMsg,
246	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
247	>	"\tcutoffRadius and switchingRadius are set to the\n"
248	>	"\tsame value.  OpenMD will use shifted potentials\n"
249	>	"\tinstead of switching functions.\n");
250	>	painCave.isFatal = 0;
251	>	painCave.severity = OPENMD_WARNING;
252	>	simError();
253	>	}
254	>	}
255	>	}
256	>	}
257		}
258
259	<	std::vector<TorsionOrderStruct> torsionOrderStruct;
260	<	for(std::map<Torsion*, TorsionDataSet>::iterator j = torsionDataSets.begin(); j != torsionDataSets.end(); ++j) {
261	<	TorsionOrderStruct tmp;
262	<	tmp.torsion = const_cast<Torsion*>(j->first);
263	<	tmp.dataSet = j->second;
264	<	torsionOrderStruct.push_back(tmp);
265	<	}
266	<
267	<	std::sort(bendOrderStruct.begin(), bendOrderStruct.end(), std::ptr_fun(BendSortFunctor));
268	<	std::sort(torsionOrderStruct.begin(), torsionOrderStruct.end(), std::ptr_fun(TorsionSortFunctor));
269	<	std::cout << "bend" << std::endl;
270	<	for (std::vector<BendOrderStruct>::iterator k = bendOrderStruct.begin(); k != bendOrderStruct.end(); ++k) {
271	<	Bend* bend = k->bend;
272	<	std::cout << "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	<	std::cout << "torsio" << std::endl;
276	<	for (std::vector<TorsionOrderStruct>::iterator l = torsionOrderStruct.begin(); l != torsionOrderStruct.end(); ++l) {
277	<	Torsion* torsion = l->torsion;
278	<	std::cout << "atom1=" <<torsion->getAtomA()->getGlobalIndex() << ",atom2 = "<< torsion->getAtomB()->getGlobalIndex() << ",atom3="<<torsion->getAtomC()->getGlobalIndex() << ",atom4="<<torsion->getAtomD()->getGlobalIndex()<< " ";
279	<	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;
280	<	}
281	<	*/
259	>	map<string, CutoffPolicy> stringToCutoffPolicy;
260	>	stringToCutoffPolicy["MIX"] = MIX;
261	>	stringToCutoffPolicy["MAX"] = MAX;
262	>	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
263	>
264	>	string cutPolicy;
265	>	if (forceFieldOptions_.haveCutoffPolicy()){
266	>	cutPolicy = forceFieldOptions_.getCutoffPolicy();
267	>	}else if (simParams_->haveCutoffPolicy()) {
268	>	cutPolicy = simParams_->getCutoffPolicy();
269	>	}
270	>
271	>	if (!cutPolicy.empty()){
272	>	toUpper(cutPolicy);
273	>	map<string, CutoffPolicy>::iterator i;
274	>	i = stringToCutoffPolicy.find(cutPolicy);
275	>
276	>	if (i == stringToCutoffPolicy.end()) {
277	>	sprintf(painCave.errMsg,
278	>	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
279	>	"\tShould be one of: "
280	>	"MIX, MAX, or TRADITIONAL\n",
281	>	cutPolicy.c_str());
282	>	painCave.isFatal = 1;
283	>	painCave.severity = OPENMD_ERROR;
284	>	simError();
285	>	} else {
286	>	cutoffPolicy_ = i->second;
287	>	}
288	>	} else {
289	>	sprintf(painCave.errMsg,
290	>	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
291	>	"\tOpenMD will use TRADITIONAL.\n");
292	>	painCave.isFatal = 0;
293	>	painCave.severity = OPENMD_INFO;
294	>	simError();
295	>	cutoffPolicy_ = TRADITIONAL;
296	>	}
297	>
298	>	fDecomp_->setCutoffPolicy(cutoffPolicy_);
299	>
300	>	// create the switching function object:
301	>
302	>	switcher_ = new SwitchingFunction();
303	>
304	>	if (cutoffMethod_ == SWITCHED) {
305	>	if (simParams_->haveSwitchingRadius()) {
306	>	rSwitch_ = simParams_->getSwitchingRadius();
307	>	if (rSwitch_ > rCut_) {
308	>	sprintf(painCave.errMsg,
309	>	"ForceManager::setupCutoffs: switchingRadius (%f) is larger "
310	>	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
311	>	painCave.isFatal = 1;
312	>	painCave.severity = OPENMD_ERROR;
313	>	simError();
314	>	}
315	>	} else {
316	>	rSwitch_ = 0.85 * rCut_;
317	>	sprintf(painCave.errMsg,
318	>	"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
319	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
320	>	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
321	>	painCave.isFatal = 0;
322	>	painCave.severity = OPENMD_WARNING;
323	>	simError();
324	>	}
325	>	} else {
326	>	if (mdFileVersion > 1) {
327	>	// throw an error if we define a switching radius and don't need one.
328	>	// older file versions should not do this.
329	>	if (simParams_->haveSwitchingRadius()) {
330	>	map<string, CutoffMethod>::const_iterator it;
331	>	string theMeth;
332	>	for (it = stringToCutoffMethod.begin();
333	>	it != stringToCutoffMethod.end(); ++it) {
334	>	if (it->second == cutoffMethod_) {
335	>	theMeth = it->first;
336	>	break;
337	>	}
338	>	}
339	>	sprintf(painCave.errMsg,
340	>	"ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
341	>	"\tis not set to SWITCHED, so switchingRadius value\n"
342	>	"\twill be ignored for this simulation\n", theMeth.c_str());
343	>	painCave.isFatal = 0;
344	>	painCave.severity = OPENMD_WARNING;
345	>	simError();
346	>	}
347	>	}
348	>	rSwitch_ = rCut_;
349	>	}
350	>
351	>	// Default to cubic switching function.
352	>	sft_ = cubic;
353	>	if (simParams_->haveSwitchingFunctionType()) {
354	>	string funcType = simParams_->getSwitchingFunctionType();
355	>	toUpper(funcType);
356	>	if (funcType == "CUBIC") {
357	>	sft_ = cubic;
358	>	} else {
359	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
360	>	sft_ = fifth_order_poly;
361	>	} else {
362	>	// throw error
363	>	sprintf( painCave.errMsg,
364	>	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
365	>	"\tswitchingFunctionType must be one of: "
366	>	"\"cubic\" or \"fifth_order_polynomial\".",
367	>	funcType.c_str() );
368	>	painCave.isFatal = 1;
369	>	painCave.severity = OPENMD_ERROR;
370	>	simError();
371	>	}
372	>	}
373	>	}
374	>	switcher_->setSwitchType(sft_);
375	>	switcher_->setSwitch(rSwitch_, rCut_);
376		}
377
378	+
379	+
380	+
381	+	void ForceManager::initialize() {
382	+
383	+	if (!info_->isTopologyDone()) {
384	+
385	+	info_->update();
386	+	interactionMan_->setSimInfo(info_);
387	+	interactionMan_->initialize();
388	+
389	+	// We want to delay the cutoffs until after the interaction
390	+	// manager has set up the atom-atom interactions so that we can
391	+	// query them for suggested cutoff values
392	+	setupCutoffs();
393	+
394	+	info_->prepareTopology();
395	+
396	+	doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
397	+	doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
398	+	if (doHeatFlux_) doParticlePot_ = true;
399	+
400	+	doElectricField_ = info_->getSimParams()->getOutputElectricField();
401	+
402	+	}
403	+
404	+	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
405	+
406	+	// Force fields can set options on how to scale van der Waals and
407	+	// electrostatic interactions for atoms connected via bonds, bends
408	+	// and torsions in this case the topological distance between
409	+	// atoms is:
410	+	// 0 = topologically unconnected
411	+	// 1 = bonded together
412	+	// 2 = connected via a bend
413	+	// 3 = connected via a torsion
414	+
415	+	vdwScale_.reserve(4);
416	+	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
417	+
418	+	electrostaticScale_.reserve(4);
419	+	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
420	+
421	+	vdwScale_[0] = 1.0;
422	+	vdwScale_[1] = fopts.getvdw12scale();
423	+	vdwScale_[2] = fopts.getvdw13scale();
424	+	vdwScale_[3] = fopts.getvdw14scale();
425	+
426	+	electrostaticScale_[0] = 1.0;
427	+	electrostaticScale_[1] = fopts.getelectrostatic12scale();
428	+	electrostaticScale_[2] = fopts.getelectrostatic13scale();
429	+	electrostaticScale_[3] = fopts.getelectrostatic14scale();
430	+
431	+	if (info_->getSimParams()->haveElectricField()) {
432	+	ElectricField* eField = new ElectricField(info_);
433	+	perturbations_.push_back(eField);
434	+	}
435	+
436	+	fDecomp_->distributeInitialData();
437	+
438	+	initialized_ = true;
439	+
440	+	}
441	+
442	+	void ForceManager::calcForces() {
443	+
444	+	if (!initialized_) initialize();
445	+
446	+	preCalculation();
447	+	shortRangeInteractions();
448	+	longRangeInteractions();
449	+	postCalculation();
450	+	}
451	+
452		void ForceManager::preCalculation() {
453		SimInfo::MoleculeIterator mi;
454		Molecule* mol;
#	Line 130 | Line 456 | namespace oopse {
456		Atom* atom;
457		Molecule::RigidBodyIterator rbIter;
458		RigidBody* rb;
459	+	Molecule::CutoffGroupIterator ci;
460	+	CutoffGroup* cg;
461
462	<	// forces are zeroed here, before any are accumulated.
463	<	// NOTE: do not rezero the forces in Fortran.
464	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
465	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
462	>	// forces and potentials are zeroed here, before any are
463	>	// accumulated.
464	>
465	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
466	>
467	>	snap->setBondPotential(0.0);
468	>	snap->setBendPotential(0.0);
469	>	snap->setTorsionPotential(0.0);
470	>	snap->setInversionPotential(0.0);
471	>
472	>	potVec zeroPot(0.0);
473	>	snap->setLongRangePotential(zeroPot);
474	>	snap->setExcludedPotentials(zeroPot);
475	>
476	>	snap->setRestraintPotential(0.0);
477	>	snap->setRawPotential(0.0);
478	>
479	>	for (mol = info_->beginMolecule(mi); mol != NULL;
480	>	mol = info_->nextMolecule(mi)) {
481	>	for(atom = mol->beginAtom(ai); atom != NULL;
482	>	atom = mol->nextAtom(ai)) {
483		atom->zeroForcesAndTorques();
484		}
485	<
485	>
486		//change the positions of atoms which belong to the rigidbodies
487	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
487	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
488	>	rb = mol->nextRigidBody(rbIter)) {
489		rb->zeroForcesAndTorques();
490		}
491	+
492	+	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
493	+	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
494	+	cg = mol->nextCutoffGroup(ci)) {
495	+	//calculate the center of mass of cutoff group
496	+	cg->updateCOM();
497	+	}
498	+	}
499		}
500
501	+	// Zero out the stress tensor
502	+	stressTensor *= 0.0;
503	+	// Zero out the heatFlux
504	+	fDecomp_->setHeatFlux( Vector3d(0.0) );
505		}
506	<
507	<	void ForceManager::calcShortRangeInteraction() {
506	>
507	>	void ForceManager::shortRangeInteractions() {
508		Molecule* mol;
509		RigidBody* rb;
510		Bond* bond;
511		Bend* bend;
512		Torsion* torsion;
513	+	Inversion* inversion;
514		SimInfo::MoleculeIterator mi;
515		Molecule::RigidBodyIterator rbIter;
516		Molecule::BondIterator bondIter;;
517		Molecule::BendIterator  bendIter;
518		Molecule::TorsionIterator  torsionIter;
519	<	double bondPotential = 0.0;
520	<	double bendPotential = 0.0;
521	<	double torsionPotential = 0.0;
519	>	Molecule::InversionIterator  inversionIter;
520	>	RealType bondPotential = 0.0;
521	>	RealType bendPotential = 0.0;
522	>	RealType torsionPotential = 0.0;
523	>	RealType inversionPotential = 0.0;
524
525		//calculate short range interactions
526	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
526	>	for (mol = info_->beginMolecule(mi); mol != NULL;
527	>	mol = info_->nextMolecule(mi)) {
528
529		//change the positions of atoms which belong to the rigidbodies
530	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
531	<	rb->updateAtoms();
530	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
531	>	rb = mol->nextRigidBody(rbIter)) {
532	>	rb->updateAtoms();
533		}
534
535	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
536	<	bond->calcForce();
535	>	for (bond = mol->beginBond(bondIter); bond != NULL;
536	>	bond = mol->nextBond(bondIter)) {
537	>	bond->calcForce(doParticlePot_);
538		bondPotential += bond->getPotential();
539		}
540
541	<
542	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
543	<
544	<	double angle;
545	<	bend->calcForce(angle);
546	<	double currBendPot = bend->getPotential();
547	<	bendPotential += bend->getPotential();
548	<	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
549	<	if (i == bendDataSets.end()) {
550	<	BendDataSet dataSet;
551	<	dataSet.prev.angle = dataSet.curr.angle = angle;
552	<	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
553	<	dataSet.deltaV = 0.0;
554	<	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
555	<	}else {
556	<	i->second.prev.angle = i->second.curr.angle;
557	<	i->second.prev.potential = i->second.curr.potential;
558	<	i->second.curr.angle = angle;
559	<	i->second.curr.potential = currBendPot;
560	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
561	<	}
562	<	}
563	<
564	<	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	<	}
541	>	for (bend = mol->beginBend(bendIter); bend != NULL;
542	>	bend = mol->nextBend(bendIter)) {
543	>
544	>	RealType angle;
545	>	bend->calcForce(angle, doParticlePot_);
546	>	RealType currBendPot = bend->getPotential();
547	>
548	>	bendPotential += bend->getPotential();
549	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
550	>	if (i == bendDataSets.end()) {
551	>	BendDataSet dataSet;
552	>	dataSet.prev.angle = dataSet.curr.angle = angle;
553	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
554	>	dataSet.deltaV = 0.0;
555	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
556	>	dataSet));
557	>	}else {
558	>	i->second.prev.angle = i->second.curr.angle;
559	>	i->second.prev.potential = i->second.curr.potential;
560	>	i->second.curr.angle = angle;
561	>	i->second.curr.potential = currBendPot;
562	>	i->second.deltaV =  fabs(i->second.curr.potential -
563	>	i->second.prev.potential);
564	>	}
565		}
566	<
566	>
567	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
568	>	torsion = mol->nextTorsion(torsionIter)) {
569	>	RealType angle;
570	>	torsion->calcForce(angle, doParticlePot_);
571	>	RealType currTorsionPot = torsion->getPotential();
572	>	torsionPotential += torsion->getPotential();
573	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
574	>	if (i == torsionDataSets.end()) {
575	>	TorsionDataSet dataSet;
576	>	dataSet.prev.angle = dataSet.curr.angle = angle;
577	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
578	>	dataSet.deltaV = 0.0;
579	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
580	>	}else {
581	>	i->second.prev.angle = i->second.curr.angle;
582	>	i->second.prev.potential = i->second.curr.potential;
583	>	i->second.curr.angle = angle;
584	>	i->second.curr.potential = currTorsionPot;
585	>	i->second.deltaV =  fabs(i->second.curr.potential -
586	>	i->second.prev.potential);
587	>	}
588	>	}
589	>
590	>	for (inversion = mol->beginInversion(inversionIter);
591	>	inversion != NULL;
592	>	inversion = mol->nextInversion(inversionIter)) {
593	>	RealType angle;
594	>	inversion->calcForce(angle, doParticlePot_);
595	>	RealType currInversionPot = inversion->getPotential();
596	>	inversionPotential += inversion->getPotential();
597	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
598	>	if (i == inversionDataSets.end()) {
599	>	InversionDataSet dataSet;
600	>	dataSet.prev.angle = dataSet.curr.angle = angle;
601	>	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
602	>	dataSet.deltaV = 0.0;
603	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
604	>	}else {
605	>	i->second.prev.angle = i->second.curr.angle;
606	>	i->second.prev.potential = i->second.curr.potential;
607	>	i->second.curr.angle = angle;
608	>	i->second.curr.potential = currInversionPot;
609	>	i->second.deltaV =  fabs(i->second.curr.potential -
610	>	i->second.prev.potential);
611	>	}
612	>	}
613		}
614	<
615	<	double  shortRangePotential = bondPotential + bendPotential + torsionPotential;
614	>
615	>	#ifdef IS_MPI
616	>	// Collect from all nodes.  This should eventually be moved into a
617	>	// SystemDecomposition, but this is a better place than in
618	>	// Thermo to do the collection.
619	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
620	>	MPI::SUM);
621	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
622	>	MPI::SUM);
623	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
624	>	MPI::REALTYPE, MPI::SUM);
625	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
626	>	MPI::REALTYPE, MPI::SUM);
627	>	#endif
628	>
629		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
630	<	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
631	<	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
632	<	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
633	<	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
630	>
631	>	curSnapshot->setBondPotential(bondPotential);
632	>	curSnapshot->setBendPotential(bendPotential);
633	>	curSnapshot->setTorsionPotential(torsionPotential);
634	>	curSnapshot->setInversionPotential(inversionPotential);
635
636	+	// RealType shortRangePotential = bondPotential + bendPotential +
637	+	//   torsionPotential +  inversionPotential;
638	+
639	+	// curSnapshot->setShortRangePotential(shortRangePotential);
640		}
641	+
642	+	void ForceManager::longRangeInteractions() {
643
232	–	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
233	–	Snapshot* curSnapshot;
234	–	DataStorage* config;
235	–	double* frc;
236	–	double* pos;
237	–	double* trq;
238	–	double* A;
239	–	double* electroFrame;
240	–	double* rc;
241	–
242	–	//get current snapshot from SimInfo
243	–	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
644
645	<	//get array pointers
646	<	config = &(curSnapshot->atomData);
647	<	frc = config->getArrayPointer(DataStorage::dslForce);
248	<	pos = config->getArrayPointer(DataStorage::dslPosition);
249	<	trq = config->getArrayPointer(DataStorage::dslTorque);
250	<	A   = config->getArrayPointer(DataStorage::dslAmat);
251	<	electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
645	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
646	>	DataStorage* config = &(curSnapshot->atomData);
647	>	DataStorage* cgConfig = &(curSnapshot->cgData);
648
649		//calculate the center of mass of cutoff group
650	+
651		SimInfo::MoleculeIterator mi;
652		Molecule* mol;
653		Molecule::CutoffGroupIterator ci;
654		CutoffGroup* cg;
258	–	Vector3d com;
259	–	std::vector<Vector3d> rcGroup;
655
656	<	if(info_->getNCutoffGroups() > 0){
657	<
658	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
659	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
660	<	cg->getCOM(com);
661	<	rcGroup.push_back(com);
656	>	if(info_->getNCutoffGroups() > 0){
657	>	for (mol = info_->beginMolecule(mi); mol != NULL;
658	>	mol = info_->nextMolecule(mi)) {
659	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
660	>	cg = mol->nextCutoffGroup(ci)) {
661	>	cg->updateCOM();
662		}
663	<	}// end for (mol)
269	<
270	<	rc = rcGroup[0].getArrayPointer();
663	>	}
664		} else {
665	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
666	<	rc = pos;
665	>	// center of mass of the group is the same as position of the atom
666	>	// if cutoff group does not exist
667	>	cgConfig->position = config->position;
668	>	cgConfig->velocity = config->velocity;
669		}
670	<
671	<	//initialize data before passing to fortran
672	<	double longRangePotential[LR_POT_TYPES];
278	<	double lrPot = 0.0;
670	>
671	>	fDecomp_->zeroWorkArrays();
672	>	fDecomp_->distributeData();
673
674	<	Mat3x3d tau;
675	<	short int passedCalcPot = needPotential;
676	<	short int passedCalcStress = needStress;
677	<	int isError = 0;
674	>	int cg1, cg2, atom1, atom2, topoDist;
675	>	Vector3d d_grp, dag, d, gvel2, vel2;
676	>	RealType rgrpsq, rgrp, r2, r;
677	>	RealType electroMult, vdwMult;
678	>	RealType vij;
679	>	Vector3d fij, fg, f1;
680	>	tuple3<RealType, RealType, RealType> cuts;
681	>	RealType rCutSq;
682	>	bool in_switching_region;
683	>	RealType sw, dswdr, swderiv;
684	>	vector<int> atomListColumn, atomListRow, atomListLocal;
685	>	InteractionData idat;
686	>	SelfData sdat;
687	>	RealType mf;
688	>	RealType vpair;
689	>	RealType dVdFQ1(0.0);
690	>	RealType dVdFQ2(0.0);
691	>	potVec longRangePotential(0.0);
692	>	potVec workPot(0.0);
693	>	potVec exPot(0.0);
694	>	Vector3d eField1(0.0);
695	>	Vector3d eField2(0.0);
696	>	vector<int>::iterator ia, jb;
697
698	<	for (int i=0; i<LR_POT_TYPES;i++){
699	<	longRangePotential[i]=0.0; //Initialize array
698	>	int loopStart, loopEnd;
699	>
700	>	idat.vdwMult = &vdwMult;
701	>	idat.electroMult = &electroMult;
702	>	idat.pot = &workPot;
703	>	idat.excludedPot = &exPot;
704	>	sdat.pot = fDecomp_->getEmbeddingPotential();
705	>	sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
706	>	idat.vpair = &vpair;
707	>	idat.dVdFQ1 = &dVdFQ1;
708	>	idat.dVdFQ2 = &dVdFQ2;
709	>	idat.eField1 = &eField1;
710	>	idat.eField2 = &eField2;
711	>	idat.f1 = &f1;
712	>	idat.sw = &sw;
713	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
714	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
715	>	idat.doParticlePot = doParticlePot_;
716	>	idat.doElectricField = doElectricField_;
717	>	sdat.doParticlePot = doParticlePot_;
718	>
719	>	loopEnd = PAIR_LOOP;
720	>	if (info_->requiresPrepair() ) {
721	>	loopStart = PREPAIR_LOOP;
722	>	} else {
723	>	loopStart = PAIR_LOOP;
724		}
725	+	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
726	+
727	+	if (iLoop == loopStart) {
728	+	bool update_nlist = fDecomp_->checkNeighborList();
729	+	if (update_nlist)
730	+	neighborList = fDecomp_->buildNeighborList();
731	+	}
732
733	<	doForceLoop( pos,
734	<	rc,
735	<	A,
736	<	electroFrame,
737	<	frc,
738	<	trq,
739	<	tau.getArrayPointer(),
740	<	longRangePotential,
741	<	&passedCalcPot,
742	<	&passedCalcStress,
743	<	&isError );
744	<
745	<	if( isError ){
746	<	sprintf( painCave.errMsg,
747	<	"Error returned from the fortran force calculation.\n" );
748	<	painCave.isFatal = 1;
749	<	simError();
733	>	for (vector<pair<int, int> >::iterator it = neighborList.begin();
734	>	it != neighborList.end(); ++it) {
735	>
736	>	cg1 = (*it).first;
737	>	cg2 = (*it).second;
738	>
739	>	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
740	>
741	>	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
742	>
743	>	curSnapshot->wrapVector(d_grp);
744	>	rgrpsq = d_grp.lengthSquare();
745	>	rCutSq = cuts.second;
746	>
747	>	if (rgrpsq < rCutSq) {
748	>	idat.rcut = &cuts.first;
749	>	if (iLoop == PAIR_LOOP) {
750	>	vij = 0.0;
751	>	fij = V3Zero;
752	>	eField1 = V3Zero;
753	>	eField2 = V3Zero;
754	>	}
755	>
756	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
757	>	rgrp);
758	>
759	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
760	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
761	>
762	>	if (doHeatFlux_)
763	>	gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
764	>
765	>	for (ia = atomListRow.begin();
766	>	ia != atomListRow.end(); ++ia) {
767	>	atom1 = (*ia);
768	>
769	>	for (jb = atomListColumn.begin();
770	>	jb != atomListColumn.end(); ++jb) {
771	>	atom2 = (*jb);
772	>
773	>	if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
774	>
775	>	vpair = 0.0;
776	>	workPot = 0.0;
777	>	exPot = 0.0;
778	>	f1 = V3Zero;
779	>	dVdFQ1 = 0.0;
780	>	dVdFQ2 = 0.0;
781	>
782	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
783	>
784	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
785	>	vdwMult = vdwScale_[topoDist];
786	>	electroMult = electrostaticScale_[topoDist];
787	>
788	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
789	>	idat.d = &d_grp;
790	>	idat.r2 = &rgrpsq;
791	>	if (doHeatFlux_)
792	>	vel2 = gvel2;
793	>	} else {
794	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
795	>	curSnapshot->wrapVector( d );
796	>	r2 = d.lengthSquare();
797	>	idat.d = &d;
798	>	idat.r2 = &r2;
799	>	if (doHeatFlux_)
800	>	vel2 = fDecomp_->getAtomVelocityColumn(atom2);
801	>	}
802	>
803	>	r = sqrt( *(idat.r2) );
804	>	idat.rij = &r;
805	>
806	>	if (iLoop == PREPAIR_LOOP) {
807	>	interactionMan_->doPrePair(idat);
808	>	} else {
809	>	interactionMan_->doPair(idat);
810	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
811	>	vij += vpair;
812	>	fij += f1;
813	>	stressTensor -= outProduct( *(idat.d), f1);
814	>	if (doHeatFlux_)
815	>	fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
816	>	}
817	>	}
818	>	}
819	>	}
820	>
821	>	if (iLoop == PAIR_LOOP) {
822	>	if (in_switching_region) {
823	>	swderiv = vij * dswdr / rgrp;
824	>	fg = swderiv * d_grp;
825	>	fij += fg;
826	>
827	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
828	>	if (!fDecomp_->skipAtomPair(atomListRow[0],
829	>	atomListColumn[0],
830	>	cg1, cg2)) {
831	>	stressTensor -= outProduct( *(idat.d), fg);
832	>	if (doHeatFlux_)
833	>	fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
834	>	}
835	>	}
836	>
837	>	for (ia = atomListRow.begin();
838	>	ia != atomListRow.end(); ++ia) {
839	>	atom1 = (*ia);
840	>	mf = fDecomp_->getMassFactorRow(atom1);
841	>	// fg is the force on atom ia due to cutoff group's
842	>	// presence in switching region
843	>	fg = swderiv * d_grp * mf;
844	>	fDecomp_->addForceToAtomRow(atom1, fg);
845	>	if (atomListRow.size() > 1) {
846	>	if (info_->usesAtomicVirial()) {
847	>	// find the distance between the atom
848	>	// and the center of the cutoff group:
849	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
850	>	stressTensor -= outProduct(dag, fg);
851	>	if (doHeatFlux_)
852	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
853	>	}
854	>	}
855	>	}
856	>	for (jb = atomListColumn.begin();
857	>	jb != atomListColumn.end(); ++jb) {
858	>	atom2 = (*jb);
859	>	mf = fDecomp_->getMassFactorColumn(atom2);
860	>	// fg is the force on atom jb due to cutoff group's
861	>	// presence in switching region
862	>	fg = -swderiv * d_grp * mf;
863	>	fDecomp_->addForceToAtomColumn(atom2, fg);
864	>
865	>	if (atomListColumn.size() > 1) {
866	>	if (info_->usesAtomicVirial()) {
867	>	// find the distance between the atom
868	>	// and the center of the cutoff group:
869	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
870	>	stressTensor -= outProduct(dag, fg);
871	>	if (doHeatFlux_)
872	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
873	>	}
874	>	}
875	>	}
876	>	}
877	>	//if (!info_->usesAtomicVirial()) {
878	>	//  stressTensor -= outProduct(d_grp, fij);
879	>	//  if (doHeatFlux_)
880	>	//     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
881	>	//}
882	>	}
883	>	}
884	>	}
885	>
886	>	if (iLoop == PREPAIR_LOOP) {
887	>	if (info_->requiresPrepair()) {
888	>
889	>	fDecomp_->collectIntermediateData();
890	>
891	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
892	>	fDecomp_->fillSelfData(sdat, atom1);
893	>	interactionMan_->doPreForce(sdat);
894	>	}
895	>
896	>	fDecomp_->distributeIntermediateData();
897	>
898	>	}
899	>	}
900		}
901	<	for (int i=0; i<LR_POT_TYPES;i++){
902	<	lrPot += longRangePotential[i]; //Quick hack
901	>
902	>	// collects pairwise information
903	>	fDecomp_->collectData();
904	>
905	>	if (info_->requiresSelfCorrection()) {
906	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
907	>	fDecomp_->fillSelfData(sdat, atom1);
908	>	interactionMan_->doSelfCorrection(sdat);
909	>	}
910		}
911
912	<	//store the tau and long range potential
913	<	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];
912	>	// collects single-atom information
913	>	fDecomp_->collectSelfData();
914
915	<	curSnapshot->statData.setTau(tau);
916	<	}
915	>	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
916	>	*(fDecomp_->getPairwisePotential());
917
918	+	curSnapshot->setLongRangePotential(longRangePotential);
919	+
920	+	curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
921	+	*(fDecomp_->getExcludedPotential()));
922
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::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
952	+	MPI::REALTYPE, MPI::SUM);
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.
branches/development/src/brains/ForceManager.cpp (property svn:keywords), Revision 1849 by gezelter, Wed Feb 20 13:52:51 2013 UTC

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