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

Comparing trunk/src/brains/ForceManager.cpp (file contents):
Revision 776 by gezelter, Fri Dec 2 20:10:49 2005 UTC vs.
Revision 1987 by gezelter, Thu Apr 17 19:07:31 2014 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), switcher_(NULL),
71	>	initialized_(false) {
72	>	forceField_ = info_->getForceField();
73	>	interactionMan_ = new InteractionManager();
74	>	fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
75	>	thermo = new Thermo(info_);
76		}
77
78	<	bool  TorsionSortFunctor(const TorsionOrderStruct& t1, const TorsionOrderStruct& t2) {
79	<	return t1.dataSet.deltaV < t2.dataSet.deltaV;
78	>	ForceManager::~ForceManager() {
79	>	perturbations_.clear();
80	>
81	>	delete switcher_;
82	>	delete interactionMan_;
83	>	delete fDecomp_;
84	>	delete thermo;
85		}
86	<	*/
87	<	void ForceManager::calcForces(bool needPotential, bool needStress) {
86	>
87	>	/**
88	>	* setupCutoffs
89	>	*
90	>	* Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
91	>	* and cutoffPolicy
92	>	*
93	>	* cutoffRadius : realType
94	>	*  If the cutoffRadius was explicitly set, use that value.
95	>	*  If the cutoffRadius was not explicitly set:
96	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
97	>	*      No electrostatic atoms?  Poll the atom types present in the
98	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
99	>	*      Use the maximum suggested value that was found.
100	>	*
101	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, TAYLOR_SHIFTED,
102	>	*                        SHIFTED_POTENTIAL, or EWALD_FULL)
103	>	*      If cutoffMethod was explicitly set, use that choice.
104	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
105	>	*
106	>	* cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
107	>	*      If cutoffPolicy was explicitly set, use that choice.
108	>	*      If cutoffPolicy was not explicitly set, use TRADITIONAL
109	>	*
110	>	* switchingRadius : realType
111	>	*  If the cutoffMethod was set to SWITCHED:
112	>	*      If the switchingRadius was explicitly set, use that value
113	>	*          (but do a sanity check first).
114	>	*      If the switchingRadius was not explicitly set: use 0.85 *
115	>	*      cutoffRadius_
116	>	*  If the cutoffMethod was not set to SWITCHED:
117	>	*      Set switchingRadius equal to cutoffRadius for safety.
118	>	*/
119	>	void ForceManager::setupCutoffs() {
120	>
121	>	Globals* simParams_ = info_->getSimParams();
122	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
123	>	int mdFileVersion;
124	>	rCut_ = 0.0; //Needs a value for a later max() call;
125	>
126	>	if (simParams_->haveMDfileVersion())
127	>	mdFileVersion = simParams_->getMDfileVersion();
128	>	else
129	>	mdFileVersion = 0;
130	>
131	>	// We need the list of simulated atom types to figure out cutoffs
132	>	// as well as long range corrections.
133
134	<	if (!info_->isFortranInitialized()) {
135	<	info_->update();
134	>	set<AtomType*>::iterator i;
135	>	set<AtomType*> atomTypes_;
136	>	atomTypes_ = info_->getSimulatedAtomTypes();
137	>
138	>	if (simParams_->haveCutoffRadius()) {
139	>	rCut_ = simParams_->getCutoffRadius();
140	>	} else {
141	>	if (info_->usesElectrostaticAtoms()) {
142	>	sprintf(painCave.errMsg,
143	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
144	>	"\tOpenMD will use a default value of 12.0 angstroms"
145	>	"\tfor the cutoffRadius.\n");
146	>	painCave.isFatal = 0;
147	>	painCave.severity = OPENMD_INFO;
148	>	simError();
149	>	rCut_ = 12.0;
150	>	} else {
151	>	RealType thisCut;
152	>	for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
153	>	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
154	>	rCut_ = max(thisCut, rCut_);
155	>	}
156	>	sprintf(painCave.errMsg,
157	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
158	>	"\tOpenMD will use %lf angstroms.\n",
159	>	rCut_);
160	>	painCave.isFatal = 0;
161	>	painCave.severity = OPENMD_INFO;
162	>	simError();
163	>	}
164		}
165
166	<	preCalculation();
167	<
86	<	calcShortRangeInteraction();
166	>	fDecomp_->setUserCutoff(rCut_);
167	>	interactionMan_->setCutoffRadius(rCut_);
168
169	<	calcLongRangeInteraction(needPotential, needStress);
169	>	map<string, CutoffMethod> stringToCutoffMethod;
170	>	stringToCutoffMethod["HARD"] = HARD;
171	>	stringToCutoffMethod["SWITCHED"] = SWITCHED;
172	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
173	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
174	>	stringToCutoffMethod["TAYLOR_SHIFTED"] = TAYLOR_SHIFTED;
175	>	stringToCutoffMethod["EWALD_FULL"] = EWALD_FULL;
176	>
177	>	if (simParams_->haveCutoffMethod()) {
178	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
179	>	map<string, CutoffMethod>::iterator i;
180	>	i = stringToCutoffMethod.find(cutMeth);
181	>	if (i == stringToCutoffMethod.end()) {
182	>	sprintf(painCave.errMsg,
183	>	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
184	>	"\tShould be one of: "
185	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, TAYLOR_SHIFTED,\n"
186	>	"\tSHIFTED_FORCE, or EWALD_FULL\n",
187	>	cutMeth.c_str());
188	>	painCave.isFatal = 1;
189	>	painCave.severity = OPENMD_ERROR;
190	>	simError();
191	>	} else {
192	>	cutoffMethod_ = i->second;
193	>	}
194	>	} else {
195	>	if (mdFileVersion > 1) {
196	>	sprintf(painCave.errMsg,
197	>	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
198	>	"\tOpenMD will use SHIFTED_FORCE.\n");
199	>	painCave.isFatal = 0;
200	>	painCave.severity = OPENMD_INFO;
201	>	simError();
202	>	cutoffMethod_ = SHIFTED_FORCE;
203	>	} else {
204	>	// handle the case where the old file version was in play
205	>	// (there should be no cutoffMethod, so we have to deduce it
206	>	// from other data).
207
208	<	postCalculation();
208	>	sprintf(painCave.errMsg,
209	>	"ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
210	>	"\tOpenMD found a file which does not set a cutoffMethod.\n"
211	>	"\tOpenMD will attempt to deduce a cutoffMethod using the\n"
212	>	"\tbehavior of the older (version 1) code.  To remove this\n"
213	>	"\twarning, add an explicit cutoffMethod and change the top\n"
214	>	"\tof the file so that it begins with <OpenMD version=2>\n");
215	>	painCave.isFatal = 0;
216	>	painCave.severity = OPENMD_WARNING;
217	>	simError();
218	>
219	>	// The old file version tethered the shifting behavior to the
220	>	// electrostaticSummationMethod keyword.
221	>
222	>	if (simParams_->haveElectrostaticSummationMethod()) {
223	>	string myMethod = simParams_->getElectrostaticSummationMethod();
224	>	toUpper(myMethod);
225	>
226	>	if (myMethod == "SHIFTED_POTENTIAL") {
227	>	cutoffMethod_ = SHIFTED_POTENTIAL;
228	>	} else if (myMethod == "SHIFTED_FORCE") {
229	>	cutoffMethod_ = SHIFTED_FORCE;
230	>	} else if (myMethod == "TAYLOR_SHIFTED") {
231	>	cutoffMethod_ = TAYLOR_SHIFTED;
232	>	} else if (myMethod == "EWALD_FULL") {
233	>	cutoffMethod_ = EWALD_FULL;
234	>	}
235	>
236	>	if (simParams_->haveSwitchingRadius())
237	>	rSwitch_ = simParams_->getSwitchingRadius();
238
239	<	/*
240	<	std::vector<BendOrderStruct> bendOrderStruct;
241	<	for(std::map<Bend*, BendDataSet>::iterator i = bendDataSets.begin(); i != bendDataSets.end(); ++i) {
242	<	BendOrderStruct tmp;
243	<	tmp.bend= const_cast<Bend*>(i->first);
244	<	tmp.dataSet = i->second;
245	<	bendOrderStruct.push_back(tmp);
239	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE" ||
240	>	myMethod == "TAYLOR_SHIFTED" || myMethod == "EWALD_FULL") {
241	>	if (simParams_->haveSwitchingRadius()){
242	>	sprintf(painCave.errMsg,
243	>	"ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
244	>	"\tA value was set for the switchingRadius\n"
245	>	"\teven though the electrostaticSummationMethod was\n"
246	>	"\tset to %s\n", myMethod.c_str());
247	>	painCave.severity = OPENMD_WARNING;
248	>	painCave.isFatal = 1;
249	>	simError();
250	>	}
251	>	}
252	>	if (abs(rCut_ - rSwitch_) < 0.0001) {
253	>	if (cutoffMethod_ == SHIFTED_FORCE) {
254	>	sprintf(painCave.errMsg,
255	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
256	>	"\tcutoffRadius and switchingRadius are set to the\n"
257	>	"\tsame value.  OpenMD will use shifted force\n"
258	>	"\tpotentials instead of switching functions.\n");
259	>	painCave.isFatal = 0;
260	>	painCave.severity = OPENMD_WARNING;
261	>	simError();
262	>	} else {
263	>	cutoffMethod_ = SHIFTED_POTENTIAL;
264	>	sprintf(painCave.errMsg,
265	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
266	>	"\tcutoffRadius and switchingRadius are set to the\n"
267	>	"\tsame value.  OpenMD will use shifted potentials\n"
268	>	"\tinstead of switching functions.\n");
269	>	painCave.isFatal = 0;
270	>	painCave.severity = OPENMD_WARNING;
271	>	simError();
272	>	}
273	>	}
274	>	}
275	>	}
276		}
277
278	<	std::vector<TorsionOrderStruct> torsionOrderStruct;
279	<	for(std::map<Torsion*, TorsionDataSet>::iterator j = torsionDataSets.begin(); j != torsionDataSets.end(); ++j) {
280	<	TorsionOrderStruct tmp;
281	<	tmp.torsion = const_cast<Torsion*>(j->first);
282	<	tmp.dataSet = j->second;
283	<	torsionOrderStruct.push_back(tmp);
278	>	map<string, CutoffPolicy> stringToCutoffPolicy;
279	>	stringToCutoffPolicy["MIX"] = MIX;
280	>	stringToCutoffPolicy["MAX"] = MAX;
281	>	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
282	>
283	>	string cutPolicy;
284	>	if (forceFieldOptions_.haveCutoffPolicy()){
285	>	cutPolicy = forceFieldOptions_.getCutoffPolicy();
286	>	}else if (simParams_->haveCutoffPolicy()) {
287	>	cutPolicy = simParams_->getCutoffPolicy();
288	>	}
289	>
290	>	if (!cutPolicy.empty()){
291	>	toUpper(cutPolicy);
292	>	map<string, CutoffPolicy>::iterator i;
293	>	i = stringToCutoffPolicy.find(cutPolicy);
294	>
295	>	if (i == stringToCutoffPolicy.end()) {
296	>	sprintf(painCave.errMsg,
297	>	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
298	>	"\tShould be one of: "
299	>	"MIX, MAX, or TRADITIONAL\n",
300	>	cutPolicy.c_str());
301	>	painCave.isFatal = 1;
302	>	painCave.severity = OPENMD_ERROR;
303	>	simError();
304	>	} else {
305	>	cutoffPolicy_ = i->second;
306	>	}
307	>	} else {
308	>	sprintf(painCave.errMsg,
309	>	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
310	>	"\tOpenMD will use TRADITIONAL.\n");
311	>	painCave.isFatal = 0;
312	>	painCave.severity = OPENMD_INFO;
313	>	simError();
314	>	cutoffPolicy_ = TRADITIONAL;
315		}
316	+
317	+	fDecomp_->setCutoffPolicy(cutoffPolicy_);
318	+
319	+	// create the switching function object:
320	+
321	+	switcher_ = new SwitchingFunction();
322	+
323	+	if (cutoffMethod_ == SWITCHED) {
324	+	if (simParams_->haveSwitchingRadius()) {
325	+	rSwitch_ = simParams_->getSwitchingRadius();
326	+	if (rSwitch_ > rCut_) {
327	+	sprintf(painCave.errMsg,
328	+	"ForceManager::setupCutoffs: switchingRadius (%f) is larger "
329	+	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
330	+	painCave.isFatal = 1;
331	+	painCave.severity = OPENMD_ERROR;
332	+	simError();
333	+	}
334	+	} else {
335	+	rSwitch_ = 0.85 * rCut_;
336	+	sprintf(painCave.errMsg,
337	+	"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
338	+	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
339	+	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
340	+	painCave.isFatal = 0;
341	+	painCave.severity = OPENMD_WARNING;
342	+	simError();
343	+	}
344	+	} else {
345	+	if (mdFileVersion > 1) {
346	+	// throw an error if we define a switching radius and don't need one.
347	+	// older file versions should not do this.
348	+	if (simParams_->haveSwitchingRadius()) {
349	+	map<string, CutoffMethod>::const_iterator it;
350	+	string theMeth;
351	+	for (it = stringToCutoffMethod.begin();
352	+	it != stringToCutoffMethod.end(); ++it) {
353	+	if (it->second == cutoffMethod_) {
354	+	theMeth = it->first;
355	+	break;
356	+	}
357	+	}
358	+	sprintf(painCave.errMsg,
359	+	"ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
360	+	"\tis not set to SWITCHED, so switchingRadius value\n"
361	+	"\twill be ignored for this simulation\n", theMeth.c_str());
362	+	painCave.isFatal = 0;
363	+	painCave.severity = OPENMD_WARNING;
364	+	simError();
365	+	}
366	+	}
367	+	rSwitch_ = rCut_;
368	+	}
369
370	<	std::sort(bendOrderStruct.begin(), bendOrderStruct.end(), std::ptr_fun(BendSortFunctor));
371	<	std::sort(torsionOrderStruct.begin(), torsionOrderStruct.end(), std::ptr_fun(TorsionSortFunctor));
372	<	for (std::vector<BendOrderStruct>::iterator k = bendOrderStruct.begin(); k != bendOrderStruct.end(); ++k) {
373	<	Bend* bend = k->bend;
374	<	std::cout << "Bend: atom1=" <<bend->getAtomA()->getGlobalIndex() << ",atom2 = "<< bend->getAtomB()->getGlobalIndex() << ",atom3="<<bend->getAtomC()->getGlobalIndex() << " ";
375	<	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;
370	>	// Default to cubic switching function.
371	>	sft_ = cubic;
372	>	if (simParams_->haveSwitchingFunctionType()) {
373	>	string funcType = simParams_->getSwitchingFunctionType();
374	>	toUpper(funcType);
375	>	if (funcType == "CUBIC") {
376	>	sft_ = cubic;
377	>	} else {
378	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
379	>	sft_ = fifth_order_poly;
380	>	} else {
381	>	// throw error
382	>	sprintf( painCave.errMsg,
383	>	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
384	>	"\tswitchingFunctionType must be one of: "
385	>	"\"cubic\" or \"fifth_order_polynomial\".",
386	>	funcType.c_str() );
387	>	painCave.isFatal = 1;
388	>	painCave.severity = OPENMD_ERROR;
389	>	simError();
390	>	}
391	>	}
392		}
393	<	for (std::vector<TorsionOrderStruct>::iterator l = torsionOrderStruct.begin(); l != torsionOrderStruct.end(); ++l) {
394	<	Torsion* torsion = l->torsion;
118	<	std::cout << "Torsion: atom1=" <<torsion->getAtomA()->getGlobalIndex() << ",atom2 = "<< torsion->getAtomB()->getGlobalIndex() << ",atom3="<<torsion->getAtomC()->getGlobalIndex() << ",atom4="<<torsion->getAtomD()->getGlobalIndex()<< " ";
119	<	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;
120	<	}
121	<	*/
393	>	switcher_->setSwitchType(sft_);
394	>	switcher_->setSwitch(rSwitch_, rCut_);
395		}
396
397	+
398	+
399	+
400	+	void ForceManager::initialize() {
401	+
402	+	if (!info_->isTopologyDone()) {
403	+
404	+	info_->update();
405	+	interactionMan_->setSimInfo(info_);
406	+	interactionMan_->initialize();
407	+
408	+	// We want to delay the cutoffs until after the interaction
409	+	// manager has set up the atom-atom interactions so that we can
410	+	// query them for suggested cutoff values
411	+	setupCutoffs();
412	+
413	+	info_->prepareTopology();
414	+
415	+	doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
416	+	doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
417	+	if (doHeatFlux_) doParticlePot_ = true;
418	+
419	+	doElectricField_ = info_->getSimParams()->getOutputElectricField();
420	+
421	+	}
422	+
423	+	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
424	+
425	+	// Force fields can set options on how to scale van der Waals and
426	+	// electrostatic interactions for atoms connected via bonds, bends
427	+	// and torsions in this case the topological distance between
428	+	// atoms is:
429	+	// 0 = topologically unconnected
430	+	// 1 = bonded together
431	+	// 2 = connected via a bend
432	+	// 3 = connected via a torsion
433	+
434	+	vdwScale_.reserve(4);
435	+	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
436	+
437	+	electrostaticScale_.reserve(4);
438	+	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
439	+
440	+	vdwScale_[0] = 1.0;
441	+	vdwScale_[1] = fopts.getvdw12scale();
442	+	vdwScale_[2] = fopts.getvdw13scale();
443	+	vdwScale_[3] = fopts.getvdw14scale();
444	+
445	+	electrostaticScale_[0] = 1.0;
446	+	electrostaticScale_[1] = fopts.getelectrostatic12scale();
447	+	electrostaticScale_[2] = fopts.getelectrostatic13scale();
448	+	electrostaticScale_[3] = fopts.getelectrostatic14scale();
449	+
450	+	if (info_->getSimParams()->haveElectricField()) {
451	+	ElectricField* eField = new ElectricField(info_);
452	+	perturbations_.push_back(eField);
453	+	}
454	+
455	+	usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
456	+
457	+	fDecomp_->distributeInitialData();
458	+
459	+	initialized_ = true;
460	+
461	+	}
462	+
463	+	void ForceManager::calcForces() {
464	+
465	+	if (!initialized_) initialize();
466	+
467	+	preCalculation();
468	+	shortRangeInteractions();
469	+	longRangeInteractions();
470	+	postCalculation();
471	+	}
472	+
473		void ForceManager::preCalculation() {
474		SimInfo::MoleculeIterator mi;
475		Molecule* mol;
#	Line 128 | Line 477 | namespace oopse {
477		Atom* atom;
478		Molecule::RigidBodyIterator rbIter;
479		RigidBody* rb;
480	+	Molecule::CutoffGroupIterator ci;
481	+	CutoffGroup* cg;
482
483	<	// forces are zeroed here, before any are accumulated.
484	<	// NOTE: do not rezero the forces in Fortran.
485	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
486	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
483	>	// forces and potentials are zeroed here, before any are
484	>	// accumulated.
485	>
486	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
487	>
488	>	snap->setBondPotential(0.0);
489	>	snap->setBendPotential(0.0);
490	>	snap->setTorsionPotential(0.0);
491	>	snap->setInversionPotential(0.0);
492	>
493	>	potVec zeroPot(0.0);
494	>	snap->setLongRangePotential(zeroPot);
495	>	snap->setExcludedPotentials(zeroPot);
496	>
497	>	snap->setRestraintPotential(0.0);
498	>	snap->setRawPotential(0.0);
499	>
500	>	for (mol = info_->beginMolecule(mi); mol != NULL;
501	>	mol = info_->nextMolecule(mi)) {
502	>	for(atom = mol->beginAtom(ai); atom != NULL;
503	>	atom = mol->nextAtom(ai)) {
504		atom->zeroForcesAndTorques();
505		}
506	<
506	>
507		//change the positions of atoms which belong to the rigidbodies
508	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
508	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
509	>	rb = mol->nextRigidBody(rbIter)) {
510		rb->zeroForcesAndTorques();
511		}
512	+
513	+	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
514	+	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
515	+	cg = mol->nextCutoffGroup(ci)) {
516	+	//calculate the center of mass of cutoff group
517	+	cg->updateCOM();
518	+	}
519	+	}
520		}
521
522	+	// Zero out the stress tensor
523	+	stressTensor *= 0.0;
524	+	// Zero out the heatFlux
525	+	fDecomp_->setHeatFlux( Vector3d(0.0) );
526		}
527	<
528	<	void ForceManager::calcShortRangeInteraction() {
527	>
528	>	void ForceManager::shortRangeInteractions() {
529		Molecule* mol;
530		RigidBody* rb;
531		Bond* bond;
532		Bend* bend;
533		Torsion* torsion;
534	+	Inversion* inversion;
535		SimInfo::MoleculeIterator mi;
536		Molecule::RigidBodyIterator rbIter;
537		Molecule::BondIterator bondIter;;
538		Molecule::BendIterator  bendIter;
539		Molecule::TorsionIterator  torsionIter;
540	<	double bondPotential = 0.0;
541	<	double bendPotential = 0.0;
542	<	double torsionPotential = 0.0;
540	>	Molecule::InversionIterator  inversionIter;
541	>	RealType bondPotential = 0.0;
542	>	RealType bendPotential = 0.0;
543	>	RealType torsionPotential = 0.0;
544	>	RealType inversionPotential = 0.0;
545
546		//calculate short range interactions
547	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
547	>	for (mol = info_->beginMolecule(mi); mol != NULL;
548	>	mol = info_->nextMolecule(mi)) {
549
550		//change the positions of atoms which belong to the rigidbodies
551	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
552	<	rb->updateAtoms();
551	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
552	>	rb = mol->nextRigidBody(rbIter)) {
553	>	rb->updateAtoms();
554		}
555
556	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
557	<	bond->calcForce();
556	>	for (bond = mol->beginBond(bondIter); bond != NULL;
557	>	bond = mol->nextBond(bondIter)) {
558	>	bond->calcForce(doParticlePot_);
559		bondPotential += bond->getPotential();
173	–	}
174	–
175	–
176	–	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
177	–
178	–	double angle;
179	–	bend->calcForce(angle);
180	–	double 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	–	}
560		}
561
562	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
563	<	double angle;
564	<	torsion->calcForce(angle);
565	<	double currTorsionPot = torsion->getPotential();
566	<	torsionPotential += torsion->getPotential();
567	<	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
568	<	if (i == torsionDataSets.end()) {
569	<	TorsionDataSet dataSet;
570	<	dataSet.prev.angle = dataSet.curr.angle = angle;
571	<	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
572	<	dataSet.deltaV = 0.0;
573	<	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
574	<	}else {
575	<	i->second.prev.angle = i->second.curr.angle;
576	<	i->second.prev.potential = i->second.curr.potential;
577	<	i->second.curr.angle = angle;
578	<	i->second.curr.potential = currTorsionPot;
579	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
580	<	}
562	>	for (bend = mol->beginBend(bendIter); bend != NULL;
563	>	bend = mol->nextBend(bendIter)) {
564	>
565	>	RealType angle;
566	>	bend->calcForce(angle, doParticlePot_);
567	>	RealType currBendPot = bend->getPotential();
568	>
569	>	bendPotential += bend->getPotential();
570	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
571	>	if (i == bendDataSets.end()) {
572	>	BendDataSet dataSet;
573	>	dataSet.prev.angle = dataSet.curr.angle = angle;
574	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
575	>	dataSet.deltaV = 0.0;
576	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
577	>	dataSet));
578	>	}else {
579	>	i->second.prev.angle = i->second.curr.angle;
580	>	i->second.prev.potential = i->second.curr.potential;
581	>	i->second.curr.angle = angle;
582	>	i->second.curr.potential = currBendPot;
583	>	i->second.deltaV =  fabs(i->second.curr.potential -
584	>	i->second.prev.potential);
585	>	}
586		}
587	<
587	>
588	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
589	>	torsion = mol->nextTorsion(torsionIter)) {
590	>	RealType angle;
591	>	torsion->calcForce(angle, doParticlePot_);
592	>	RealType currTorsionPot = torsion->getPotential();
593	>	torsionPotential += torsion->getPotential();
594	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
595	>	if (i == torsionDataSets.end()) {
596	>	TorsionDataSet dataSet;
597	>	dataSet.prev.angle = dataSet.curr.angle = angle;
598	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
599	>	dataSet.deltaV = 0.0;
600	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
601	>	}else {
602	>	i->second.prev.angle = i->second.curr.angle;
603	>	i->second.prev.potential = i->second.curr.potential;
604	>	i->second.curr.angle = angle;
605	>	i->second.curr.potential = currTorsionPot;
606	>	i->second.deltaV =  fabs(i->second.curr.potential -
607	>	i->second.prev.potential);
608	>	}
609	>	}
610	>
611	>	for (inversion = mol->beginInversion(inversionIter);
612	>	inversion != NULL;
613	>	inversion = mol->nextInversion(inversionIter)) {
614	>	RealType angle;
615	>	inversion->calcForce(angle, doParticlePot_);
616	>	RealType currInversionPot = inversion->getPotential();
617	>	inversionPotential += inversion->getPotential();
618	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
619	>	if (i == inversionDataSets.end()) {
620	>	InversionDataSet dataSet;
621	>	dataSet.prev.angle = dataSet.curr.angle = angle;
622	>	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
623	>	dataSet.deltaV = 0.0;
624	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
625	>	}else {
626	>	i->second.prev.angle = i->second.curr.angle;
627	>	i->second.prev.potential = i->second.curr.potential;
628	>	i->second.curr.angle = angle;
629	>	i->second.curr.potential = currInversionPot;
630	>	i->second.deltaV =  fabs(i->second.curr.potential -
631	>	i->second.prev.potential);
632	>	}
633	>	}
634		}
635	<
636	<	double  shortRangePotential = bondPotential + bendPotential + torsionPotential;
635	>
636	>	#ifdef IS_MPI
637	>	// Collect from all nodes.  This should eventually be moved into a
638	>	// SystemDecomposition, but this is a better place than in
639	>	// Thermo to do the collection.
640	>
641	>	MPI_Allreduce(MPI_IN_PLACE, &bondPotential, 1, MPI_REALTYPE,
642	>	MPI_SUM, MPI_COMM_WORLD);
643	>	MPI_Allreduce(MPI_IN_PLACE, &bendPotential, 1, MPI_REALTYPE,
644	>	MPI_SUM, MPI_COMM_WORLD);
645	>	MPI_Allreduce(MPI_IN_PLACE, &torsionPotential, 1,
646	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
647	>	MPI_Allreduce(MPI_IN_PLACE, &inversionPotential, 1,
648	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
649	>	#endif
650	>
651		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
652	<	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
653	<	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
654	<	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
655	<	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
652	>
653	>	curSnapshot->setBondPotential(bondPotential);
654	>	curSnapshot->setBendPotential(bendPotential);
655	>	curSnapshot->setTorsionPotential(torsionPotential);
656	>	curSnapshot->setInversionPotential(inversionPotential);
657
658	+	// RealType shortRangePotential = bondPotential + bendPotential +
659	+	//   torsionPotential +  inversionPotential;
660	+
661	+	// curSnapshot->setShortRangePotential(shortRangePotential);
662		}
663	+
664	+	void ForceManager::longRangeInteractions() {
665
666	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
667	<	Snapshot* curSnapshot;
668	<	DataStorage* config;
233	<	double* frc;
234	<	double* pos;
235	<	double* trq;
236	<	double* A;
237	<	double* electroFrame;
238	<	double* rc;
239	<
240	<	//get current snapshot from SimInfo
241	<	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
666	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
667	>	DataStorage* config = &(curSnapshot->atomData);
668	>	DataStorage* cgConfig = &(curSnapshot->cgData);
669
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);
670
671		//calculate the center of mass of cutoff group
672	+
673		SimInfo::MoleculeIterator mi;
674		Molecule* mol;
675		Molecule::CutoffGroupIterator ci;
676		CutoffGroup* cg;
256	–	Vector3d com;
257	–	std::vector<Vector3d> rcGroup;
677
678	<	if(info_->getNCutoffGroups() > 0){
679	<
680	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
681	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
682	<	cg->getCOM(com);
683	<	rcGroup.push_back(com);
678	>	if(info_->getNCutoffGroups() > 0){
679	>	for (mol = info_->beginMolecule(mi); mol != NULL;
680	>	mol = info_->nextMolecule(mi)) {
681	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
682	>	cg = mol->nextCutoffGroup(ci)) {
683	>	cg->updateCOM();
684		}
685	<	}// end for (mol)
267	<
268	<	rc = rcGroup[0].getArrayPointer();
685	>	}
686		} else {
687	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
688	<	rc = pos;
687	>	// center of mass of the group is the same as position of the atom
688	>	// if cutoff group does not exist
689	>	cgConfig->position = config->position;
690	>	cgConfig->velocity = config->velocity;
691		}
692	<
693	<	//initialize data before passing to fortran
694	<	double longRangePotential[LR_POT_TYPES];
276	<	double lrPot = 0.0;
692	>
693	>	fDecomp_->zeroWorkArrays();
694	>	fDecomp_->distributeData();
695
696	<	Mat3x3d tau;
697	<	short int passedCalcPot = needPotential;
698	<	short int passedCalcStress = needStress;
699	<	int isError = 0;
696	>	int cg1, cg2, atom1, atom2, topoDist;
697	>	Vector3d d_grp, dag, d, gvel2, vel2;
698	>	RealType rgrpsq, rgrp, r2, r;
699	>	RealType electroMult, vdwMult;
700	>	RealType vij;
701	>	Vector3d fij, fg, f1;
702	>	tuple3<RealType, RealType, RealType> cuts;
703	>	RealType rCut, rCutSq, rListSq;
704	>	bool in_switching_region;
705	>	RealType sw, dswdr, swderiv;
706	>	vector<int> atomListColumn, atomListRow;
707	>	InteractionData idat;
708	>	SelfData sdat;
709	>	RealType mf;
710	>	RealType vpair;
711	>	RealType dVdFQ1(0.0);
712	>	RealType dVdFQ2(0.0);
713	>	potVec longRangePotential(0.0);
714	>	RealType reciprocalPotential(0.0);
715	>	potVec workPot(0.0);
716	>	potVec exPot(0.0);
717	>	Vector3d eField1(0.0);
718	>	Vector3d eField2(0.0);
719	>	vector<int>::iterator ia, jb;
720
721	<	for (int i=0; i<LR_POT_TYPES;i++){
722	<	longRangePotential[i]=0.0; //Initialize array
721	>	int loopStart, loopEnd;
722	>
723	>	idat.rcut = &rCut;
724	>	idat.vdwMult = &vdwMult;
725	>	idat.electroMult = &electroMult;
726	>	idat.pot = &workPot;
727	>	idat.excludedPot = &exPot;
728	>	sdat.pot = fDecomp_->getEmbeddingPotential();
729	>	sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
730	>	idat.vpair = &vpair;
731	>	idat.dVdFQ1 = &dVdFQ1;
732	>	idat.dVdFQ2 = &dVdFQ2;
733	>	idat.eField1 = &eField1;
734	>	idat.eField2 = &eField2;
735	>	idat.f1 = &f1;
736	>	idat.sw = &sw;
737	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
738	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE || cutoffMethod_ == TAYLOR_SHIFTED) ? true : false;
739	>	idat.doParticlePot = doParticlePot_;
740	>	idat.doElectricField = doElectricField_;
741	>	sdat.doParticlePot = doParticlePot_;
742	>
743	>	loopEnd = PAIR_LOOP;
744	>	if (info_->requiresPrepair() ) {
745	>	loopStart = PREPAIR_LOOP;
746	>	} else {
747	>	loopStart = PAIR_LOOP;
748		}
749	+	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
750	+
751	+	if (iLoop == loopStart) {
752	+	bool update_nlist = fDecomp_->checkNeighborList();
753	+	if (update_nlist) {
754	+	if (!usePeriodicBoundaryConditions_)
755	+	Mat3x3d bbox = thermo->getBoundingBox();
756	+	fDecomp_->buildNeighborList(neighborList_);
757	+	}
758	+	}
759
760	<	doForceLoop( pos,
761	<	rc,
762	<	A,
763	<	electroFrame,
764	<	frc,
765	<	trq,
766	<	tau.getArrayPointer(),
767	<	longRangePotential,
768	<	&passedCalcPot,
769	<	&passedCalcStress,
770	<	&isError );
771	<
772	<	if( isError ){
773	<	sprintf( painCave.errMsg,
774	<	"Error returned from the fortran force calculation.\n" );
775	<	painCave.isFatal = 1;
776	<	simError();
760	>	for (vector<pair<int, int> >::iterator it = neighborList_.begin();
761	>	it != neighborList_.end(); ++it) {
762	>
763	>	cg1 = (*it).first;
764	>	cg2 = (*it).second;
765	>
766	>	fDecomp_->getGroupCutoffs(cg1, cg2, rCut, rCutSq, rListSq);
767	>
768	>	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
769	>
770	>	// already wrapped in the getIntergroupVector call:
771	>	// curSnapshot->wrapVector(d_grp);
772	>	rgrpsq = d_grp.lengthSquare();
773	>
774	>	if (rgrpsq < rCutSq) {
775	>	if (iLoop == PAIR_LOOP) {
776	>	vij = 0.0;
777	>	fij.zero();
778	>	eField1.zero();
779	>	eField2.zero();
780	>	}
781	>
782	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
783	>	rgrp);
784	>
785	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
786	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
787	>
788	>	if (doHeatFlux_)
789	>	gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
790	>
791	>	for (ia = atomListRow.begin();
792	>	ia != atomListRow.end(); ++ia) {
793	>	atom1 = (*ia);
794	>
795	>	for (jb = atomListColumn.begin();
796	>	jb != atomListColumn.end(); ++jb) {
797	>	atom2 = (*jb);
798	>
799	>	if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
800	>
801	>	vpair = 0.0;
802	>	workPot = 0.0;
803	>	exPot = 0.0;
804	>	f1.zero();
805	>	dVdFQ1 = 0.0;
806	>	dVdFQ2 = 0.0;
807	>
808	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
809	>
810	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
811	>	vdwMult = vdwScale_[topoDist];
812	>	electroMult = electrostaticScale_[topoDist];
813	>
814	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
815	>	idat.d = &d_grp;
816	>	idat.r2 = &rgrpsq;
817	>	if (doHeatFlux_)
818	>	vel2 = gvel2;
819	>	} else {
820	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
821	>	curSnapshot->wrapVector( d );
822	>	r2 = d.lengthSquare();
823	>	idat.d = &d;
824	>	idat.r2 = &r2;
825	>	if (doHeatFlux_)
826	>	vel2 = fDecomp_->getAtomVelocityColumn(atom2);
827	>	}
828	>
829	>	r = sqrt( *(idat.r2) );
830	>	idat.rij = &r;
831	>
832	>	if (iLoop == PREPAIR_LOOP) {
833	>	interactionMan_->doPrePair(idat);
834	>	} else {
835	>	interactionMan_->doPair(idat);
836	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
837	>	vij += vpair;
838	>	fij += f1;
839	>	stressTensor -= outProduct( *(idat.d), f1);
840	>	if (doHeatFlux_)
841	>	fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
842	>	}
843	>	}
844	>	}
845	>	}
846	>
847	>	if (iLoop == PAIR_LOOP) {
848	>	if (in_switching_region) {
849	>	swderiv = vij * dswdr / rgrp;
850	>	fg = swderiv * d_grp;
851	>	fij += fg;
852	>
853	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
854	>	if (!fDecomp_->skipAtomPair(atomListRow[0],
855	>	atomListColumn[0],
856	>	cg1, cg2)) {
857	>	stressTensor -= outProduct( *(idat.d), fg);
858	>	if (doHeatFlux_)
859	>	fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
860	>	}
861	>	}
862	>
863	>	for (ia = atomListRow.begin();
864	>	ia != atomListRow.end(); ++ia) {
865	>	atom1 = (*ia);
866	>	mf = fDecomp_->getMassFactorRow(atom1);
867	>	// fg is the force on atom ia due to cutoff group's
868	>	// presence in switching region
869	>	fg = swderiv * d_grp * mf;
870	>	fDecomp_->addForceToAtomRow(atom1, fg);
871	>	if (atomListRow.size() > 1) {
872	>	if (info_->usesAtomicVirial()) {
873	>	// find the distance between the atom
874	>	// and the center of the cutoff group:
875	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
876	>	stressTensor -= outProduct(dag, fg);
877	>	if (doHeatFlux_)
878	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
879	>	}
880	>	}
881	>	}
882	>	for (jb = atomListColumn.begin();
883	>	jb != atomListColumn.end(); ++jb) {
884	>	atom2 = (*jb);
885	>	mf = fDecomp_->getMassFactorColumn(atom2);
886	>	// fg is the force on atom jb due to cutoff group's
887	>	// presence in switching region
888	>	fg = -swderiv * d_grp * mf;
889	>	fDecomp_->addForceToAtomColumn(atom2, fg);
890	>
891	>	if (atomListColumn.size() > 1) {
892	>	if (info_->usesAtomicVirial()) {
893	>	// find the distance between the atom
894	>	// and the center of the cutoff group:
895	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
896	>	stressTensor -= outProduct(dag, fg);
897	>	if (doHeatFlux_)
898	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
899	>	}
900	>	}
901	>	}
902	>	}
903	>	//if (!info_->usesAtomicVirial()) {
904	>	//  stressTensor -= outProduct(d_grp, fij);
905	>	//  if (doHeatFlux_)
906	>	//     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
907	>	//}
908	>	}
909	>	}
910	>	}
911	>
912	>	if (iLoop == PREPAIR_LOOP) {
913	>	if (info_->requiresPrepair()) {
914	>
915	>	fDecomp_->collectIntermediateData();
916	>
917	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
918	>	fDecomp_->fillSelfData(sdat, atom1);
919	>	interactionMan_->doPreForce(sdat);
920	>	}
921	>
922	>	fDecomp_->distributeIntermediateData();
923	>
924	>	}
925	>	}
926		}
927	<	for (int i=0; i<LR_POT_TYPES;i++){
928	<	lrPot += longRangePotential[i]; //Quick hack
927	>
928	>	// collects pairwise information
929	>	fDecomp_->collectData();
930	>	if (cutoffMethod_ == EWALD_FULL) {
931	>	interactionMan_->doReciprocalSpaceSum(reciprocalPotential);
932	>
933	>	curSnapshot->setReciprocalPotential(reciprocalPotential);
934		}
935	+
936	+	if (info_->requiresSelfCorrection()) {
937	+	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
938	+	fDecomp_->fillSelfData(sdat, atom1);
939	+	interactionMan_->doSelfCorrection(sdat);
940	+	}
941	+	}
942
943	<	//store the tau and long range potential
944	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
311	<	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
312	<	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
943	>	// collects single-atom information
944	>	fDecomp_->collectSelfData();
945
946	<	curSnapshot->statData.setTau(tau);
947	<	}
946	>	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
947	>	*(fDecomp_->getPairwisePotential());
948
949	+	curSnapshot->setLongRangePotential(longRangePotential);
950	+
951	+	curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
952	+	*(fDecomp_->getExcludedPotential()));
953
954	+	}
955	+
956		void ForceManager::postCalculation() {
957	+
958	+	vector<Perturbation*>::iterator pi;
959	+	for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
960	+	(*pi)->applyPerturbation();
961	+	}
962	+
963		SimInfo::MoleculeIterator mi;
964		Molecule* mol;
965		Molecule::RigidBodyIterator rbIter;
966		RigidBody* rb;
967	<
967	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
968	>
969		// collect the atomic forces onto rigid bodies
970	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
971	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
972	<	rb->calcForcesAndTorques();
970	>
971	>	for (mol = info_->beginMolecule(mi); mol != NULL;
972	>	mol = info_->nextMolecule(mi)) {
973	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
974	>	rb = mol->nextRigidBody(rbIter)) {
975	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
976	>	stressTensor += rbTau;
977		}
978		}
979	+
980	+	#ifdef IS_MPI
981	+	MPI_Allreduce(MPI_IN_PLACE, stressTensor.getArrayPointer(), 9,
982	+	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
983	+	#endif
984	+	curSnapshot->setStressTensor(stressTensor);
985	+
986	+	if (info_->getSimParams()->getUseLongRangeCorrections()) {
987	+	/*
988	+	RealType vol = curSnapshot->getVolume();
989	+	RealType Elrc(0.0);
990	+	RealType Wlrc(0.0);
991
992	<	}
992	>	set<AtomType*>::iterator i;
993	>	set<AtomType*>::iterator j;
994	>
995	>	RealType n_i, n_j;
996	>	RealType rho_i, rho_j;
997	>	pair<RealType, RealType> LRI;
998	>
999	>	for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
1000	>	n_i = RealType(info_->getGlobalCountOfType(*i));
1001	>	rho_i = n_i /  vol;
1002	>	for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) {
1003	>	n_j = RealType(info_->getGlobalCountOfType(*j));
1004	>	rho_j = n_j / vol;
1005	>
1006	>	LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) );
1007
1008	<	} //end namespace oopse
1008	>	Elrc += n_i   * rho_j * LRI.first;
1009	>	Wlrc -= rho_i * rho_j * LRI.second;
1010	>	}
1011	>	}
1012	>	Elrc *= 2.0 * NumericConstant::PI;
1013	>	Wlrc *= 2.0 * NumericConstant::PI;
1014	>
1015	>	RealType lrp = curSnapshot->getLongRangePotential();
1016	>	curSnapshot->setLongRangePotential(lrp + Elrc);
1017	>	stressTensor += Wlrc * SquareMatrix3<RealType>::identity();
1018	>	curSnapshot->setStressTensor(stressTensor);
1019	>	*/
1020	>
1021	>	}
1022	>	}
1023	>	}

Comparing trunk/src/brains/ForceManager.cpp (property svn:keywords):
Revision 776 by gezelter, Fri Dec 2 20:10:49 2005 UTC vs.
Revision 1987 by gezelter, Thu Apr 17 19:07:31 2014 UTC

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