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

Comparing trunk/src/brains/ForceManager.cpp (file contents):
Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
44		* @file ForceManager.cpp
45		* @author tlin
46		* @date 11/09/2004
46	–	* @time 10:39am
47		* @version 1.0
48		*/
49
50	+
51		#include "brains/ForceManager.hpp"
52		#include "primitives/Molecule.hpp"
53	<	#include "UseTheForce/doForces_interface.h"
53	<	#define __C
54	<	#include "UseTheForce/DarkSide/fInteractionMap.h"
53	>	#define __OPENMD_C
54		#include "utils/simError.h"
55	+	#include "primitives/Bond.hpp"
56		#include "primitives/Bend.hpp"
57	<	#include "primitives/Bend.hpp"
58	<	namespace oopse {
57	>	#include "primitives/Torsion.hpp"
58	>	#include "primitives/Inversion.hpp"
59	>	#include "nonbonded/NonBondedInteraction.hpp"
60	>	#include "perturbations/ElectricField.hpp"
61	>	#include "parallel/ForceMatrixDecomposition.hpp"
62
63	<	/*
64	<	struct BendOrderStruct {
65	<	Bend* bend;
63	<	BendDataSet dataSet;
64	<	};
65	<	struct TorsionOrderStruct {
66	<	Torsion* torsion;
67	<	TorsionDataSet dataSet;
68	<	};
63	>	#include <cstdio>
64	>	#include <iostream>
65	>	#include <iomanip>
66
67	<	bool  BendSortFunctor(const BendOrderStruct& b1, const BendOrderStruct& b2) {
68	<	return b1.dataSet.deltaV < b2.dataSet.deltaV;
67	>	using namespace std;
68	>	namespace OpenMD {
69	>
70	>	ForceManager::ForceManager(SimInfo * info) : info_(info), 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	>	*                        or SHIFTED_POTENTIAL)
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	>
176	>	if (simParams_->haveCutoffMethod()) {
177	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
178	>	map<string, CutoffMethod>::iterator i;
179	>	i = stringToCutoffMethod.find(cutMeth);
180	>	if (i == stringToCutoffMethod.end()) {
181	>	sprintf(painCave.errMsg,
182	>	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
183	>	"\tShould be one of: "
184	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, TAYLOR_SHIFTED,\n"
185	>	"\tor SHIFTED_FORCE\n",
186	>	cutMeth.c_str());
187	>	painCave.isFatal = 1;
188	>	painCave.severity = OPENMD_ERROR;
189	>	simError();
190	>	} else {
191	>	cutoffMethod_ = i->second;
192	>	}
193	>	} else {
194	>	if (mdFileVersion > 1) {
195	>	sprintf(painCave.errMsg,
196	>	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
197	>	"\tOpenMD will use SHIFTED_FORCE.\n");
198	>	painCave.isFatal = 0;
199	>	painCave.severity = OPENMD_INFO;
200	>	simError();
201	>	cutoffMethod_ = SHIFTED_FORCE;
202	>	} else {
203	>	// handle the case where the old file version was in play
204	>	// (there should be no cutoffMethod, so we have to deduce it
205	>	// from other data).
206
207	<	postCalculation();
207	>	sprintf(painCave.errMsg,
208	>	"ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
209	>	"\tOpenMD found a file which does not set a cutoffMethod.\n"
210	>	"\tOpenMD will attempt to deduce a cutoffMethod using the\n"
211	>	"\tbehavior of the older (version 1) code.  To remove this\n"
212	>	"\twarning, add an explicit cutoffMethod and change the top\n"
213	>	"\tof the file so that it begins with <OpenMD version=2>\n");
214	>	painCave.isFatal = 0;
215	>	painCave.severity = OPENMD_WARNING;
216	>	simError();
217	>
218	>	// The old file version tethered the shifting behavior to the
219	>	// electrostaticSummationMethod keyword.
220	>
221	>	if (simParams_->haveElectrostaticSummationMethod()) {
222	>	string myMethod = simParams_->getElectrostaticSummationMethod();
223	>	toUpper(myMethod);
224	>
225	>	if (myMethod == "SHIFTED_POTENTIAL") {
226	>	cutoffMethod_ = SHIFTED_POTENTIAL;
227	>	} else if (myMethod == "SHIFTED_FORCE") {
228	>	cutoffMethod_ = SHIFTED_FORCE;
229	>	} else if (myMethod == "TAYLOR_SHIFTED") {
230	>	cutoffMethod_ = TAYLOR_SHIFTED;
231	>	}
232	>
233	>	if (simParams_->haveSwitchingRadius())
234	>	rSwitch_ = simParams_->getSwitchingRadius();
235
236	<	/*
237	<	std::vector<BendOrderStruct> bendOrderStruct;
238	<	for(std::map<Bend*, BendDataSet>::iterator i = bendDataSets.begin(); i != bendDataSets.end(); ++i) {
239	<	BendOrderStruct tmp;
240	<	tmp.bend= const_cast<Bend*>(i->first);
241	<	tmp.dataSet = i->second;
242	<	bendOrderStruct.push_back(tmp);
236	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE" ||
237	>	myMethod == "TAYLOR_SHIFTED") {
238	>	if (simParams_->haveSwitchingRadius()){
239	>	sprintf(painCave.errMsg,
240	>	"ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
241	>	"\tA value was set for the switchingRadius\n"
242	>	"\teven though the electrostaticSummationMethod was\n"
243	>	"\tset to %s\n", myMethod.c_str());
244	>	painCave.severity = OPENMD_WARNING;
245	>	painCave.isFatal = 1;
246	>	simError();
247	>	}
248	>	}
249	>	if (abs(rCut_ - rSwitch_) < 0.0001) {
250	>	if (cutoffMethod_ == SHIFTED_FORCE) {
251	>	sprintf(painCave.errMsg,
252	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
253	>	"\tcutoffRadius and switchingRadius are set to the\n"
254	>	"\tsame value.  OpenMD will use shifted force\n"
255	>	"\tpotentials instead of switching functions.\n");
256	>	painCave.isFatal = 0;
257	>	painCave.severity = OPENMD_WARNING;
258	>	simError();
259	>	} else {
260	>	cutoffMethod_ = SHIFTED_POTENTIAL;
261	>	sprintf(painCave.errMsg,
262	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
263	>	"\tcutoffRadius and switchingRadius are set to the\n"
264	>	"\tsame value.  OpenMD will use shifted potentials\n"
265	>	"\tinstead of switching functions.\n");
266	>	painCave.isFatal = 0;
267	>	painCave.severity = OPENMD_WARNING;
268	>	simError();
269	>	}
270	>	}
271	>	}
272	>	}
273		}
274
275	<	std::vector<TorsionOrderStruct> torsionOrderStruct;
276	<	for(std::map<Torsion*, TorsionDataSet>::iterator j = torsionDataSets.begin(); j != torsionDataSets.end(); ++j) {
277	<	TorsionOrderStruct tmp;
278	<	tmp.torsion = const_cast<Torsion*>(j->first);
279	<	tmp.dataSet = j->second;
280	<	torsionOrderStruct.push_back(tmp);
275	>	map<string, CutoffPolicy> stringToCutoffPolicy;
276	>	stringToCutoffPolicy["MIX"] = MIX;
277	>	stringToCutoffPolicy["MAX"] = MAX;
278	>	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
279	>
280	>	string cutPolicy;
281	>	if (forceFieldOptions_.haveCutoffPolicy()){
282	>	cutPolicy = forceFieldOptions_.getCutoffPolicy();
283	>	}else if (simParams_->haveCutoffPolicy()) {
284	>	cutPolicy = simParams_->getCutoffPolicy();
285	>	}
286	>
287	>	if (!cutPolicy.empty()){
288	>	toUpper(cutPolicy);
289	>	map<string, CutoffPolicy>::iterator i;
290	>	i = stringToCutoffPolicy.find(cutPolicy);
291	>
292	>	if (i == stringToCutoffPolicy.end()) {
293	>	sprintf(painCave.errMsg,
294	>	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
295	>	"\tShould be one of: "
296	>	"MIX, MAX, or TRADITIONAL\n",
297	>	cutPolicy.c_str());
298	>	painCave.isFatal = 1;
299	>	painCave.severity = OPENMD_ERROR;
300	>	simError();
301	>	} else {
302	>	cutoffPolicy_ = i->second;
303	>	}
304	>	} else {
305	>	sprintf(painCave.errMsg,
306	>	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
307	>	"\tOpenMD will use TRADITIONAL.\n");
308	>	painCave.isFatal = 0;
309	>	painCave.severity = OPENMD_INFO;
310	>	simError();
311	>	cutoffPolicy_ = TRADITIONAL;
312		}
313	+
314	+	fDecomp_->setCutoffPolicy(cutoffPolicy_);
315	+
316	+	// create the switching function object:
317	+
318	+	switcher_ = new SwitchingFunction();
319	+
320	+	if (cutoffMethod_ == SWITCHED) {
321	+	if (simParams_->haveSwitchingRadius()) {
322	+	rSwitch_ = simParams_->getSwitchingRadius();
323	+	if (rSwitch_ > rCut_) {
324	+	sprintf(painCave.errMsg,
325	+	"ForceManager::setupCutoffs: switchingRadius (%f) is larger "
326	+	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
327	+	painCave.isFatal = 1;
328	+	painCave.severity = OPENMD_ERROR;
329	+	simError();
330	+	}
331	+	} else {
332	+	rSwitch_ = 0.85 * rCut_;
333	+	sprintf(painCave.errMsg,
334	+	"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
335	+	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
336	+	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
337	+	painCave.isFatal = 0;
338	+	painCave.severity = OPENMD_WARNING;
339	+	simError();
340	+	}
341	+	} else {
342	+	if (mdFileVersion > 1) {
343	+	// throw an error if we define a switching radius and don't need one.
344	+	// older file versions should not do this.
345	+	if (simParams_->haveSwitchingRadius()) {
346	+	map<string, CutoffMethod>::const_iterator it;
347	+	string theMeth;
348	+	for (it = stringToCutoffMethod.begin();
349	+	it != stringToCutoffMethod.end(); ++it) {
350	+	if (it->second == cutoffMethod_) {
351	+	theMeth = it->first;
352	+	break;
353	+	}
354	+	}
355	+	sprintf(painCave.errMsg,
356	+	"ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
357	+	"\tis not set to SWITCHED, so switchingRadius value\n"
358	+	"\twill be ignored for this simulation\n", theMeth.c_str());
359	+	painCave.isFatal = 0;
360	+	painCave.severity = OPENMD_WARNING;
361	+	simError();
362	+	}
363	+	}
364	+	rSwitch_ = rCut_;
365	+	}
366
367	<	std::sort(bendOrderStruct.begin(), bendOrderStruct.end(), std::ptr_fun(BendSortFunctor));
368	<	std::sort(torsionOrderStruct.begin(), torsionOrderStruct.end(), std::ptr_fun(TorsionSortFunctor));
369	<	std::cout << "bend" << std::endl;
370	<	for (std::vector<BendOrderStruct>::iterator k = bendOrderStruct.begin(); k != bendOrderStruct.end(); ++k) {
371	<	Bend* bend = k->bend;
372	<	std::cout << "atom1=" <<bend->getAtomA()->getGlobalIndex() << ",atom2 = "<< bend->getAtomB()->getGlobalIndex() << ",atom3="<<bend->getAtomC()->getGlobalIndex() << " ";
373	<	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;
367	>	// Default to cubic switching function.
368	>	sft_ = cubic;
369	>	if (simParams_->haveSwitchingFunctionType()) {
370	>	string funcType = simParams_->getSwitchingFunctionType();
371	>	toUpper(funcType);
372	>	if (funcType == "CUBIC") {
373	>	sft_ = cubic;
374	>	} else {
375	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
376	>	sft_ = fifth_order_poly;
377	>	} else {
378	>	// throw error
379	>	sprintf( painCave.errMsg,
380	>	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
381	>	"\tswitchingFunctionType must be one of: "
382	>	"\"cubic\" or \"fifth_order_polynomial\".",
383	>	funcType.c_str() );
384	>	painCave.isFatal = 1;
385	>	painCave.severity = OPENMD_ERROR;
386	>	simError();
387	>	}
388	>	}
389		}
390	<	std::cout << "torsio" << std::endl;
391	<	for (std::vector<TorsionOrderStruct>::iterator l = torsionOrderStruct.begin(); l != torsionOrderStruct.end(); ++l) {
119	<	Torsion* torsion = l->torsion;
120	<	std::cout << "atom1=" <<torsion->getAtomA()->getGlobalIndex() << ",atom2 = "<< torsion->getAtomB()->getGlobalIndex() << ",atom3="<<torsion->getAtomC()->getGlobalIndex() << ",atom4="<<torsion->getAtomD()->getGlobalIndex()<< " ";
121	<	std::cout << "deltaV=" << l->dataSet.deltaV << ",p_theta=" << l->dataSet.prev.angle <<",p_pot=" << l->dataSet.prev.potential<< ",c_theta=" << l->dataSet.curr.angle << ", c_pot = " << l->dataSet.curr.potential <<std::endl;
122	<	}
123	<	*/
390	>	switcher_->setSwitchType(sft_);
391	>	switcher_->setSwitch(rSwitch_, rCut_);
392		}
393
394	+
395	+
396	+
397	+	void ForceManager::initialize() {
398	+
399	+	if (!info_->isTopologyDone()) {
400	+
401	+	info_->update();
402	+	interactionMan_->setSimInfo(info_);
403	+	interactionMan_->initialize();
404	+
405	+	// We want to delay the cutoffs until after the interaction
406	+	// manager has set up the atom-atom interactions so that we can
407	+	// query them for suggested cutoff values
408	+	setupCutoffs();
409	+
410	+	info_->prepareTopology();
411	+
412	+	doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
413	+	doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
414	+	if (doHeatFlux_) doParticlePot_ = true;
415	+
416	+	doElectricField_ = info_->getSimParams()->getOutputElectricField();
417	+
418	+	}
419	+
420	+	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
421	+
422	+	// Force fields can set options on how to scale van der Waals and
423	+	// electrostatic interactions for atoms connected via bonds, bends
424	+	// and torsions in this case the topological distance between
425	+	// atoms is:
426	+	// 0 = topologically unconnected
427	+	// 1 = bonded together
428	+	// 2 = connected via a bend
429	+	// 3 = connected via a torsion
430	+
431	+	vdwScale_.reserve(4);
432	+	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
433	+
434	+	electrostaticScale_.reserve(4);
435	+	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
436	+
437	+	vdwScale_[0] = 1.0;
438	+	vdwScale_[1] = fopts.getvdw12scale();
439	+	vdwScale_[2] = fopts.getvdw13scale();
440	+	vdwScale_[3] = fopts.getvdw14scale();
441	+
442	+	electrostaticScale_[0] = 1.0;
443	+	electrostaticScale_[1] = fopts.getelectrostatic12scale();
444	+	electrostaticScale_[2] = fopts.getelectrostatic13scale();
445	+	electrostaticScale_[3] = fopts.getelectrostatic14scale();
446	+
447	+	if (info_->getSimParams()->haveElectricField()) {
448	+	ElectricField* eField = new ElectricField(info_);
449	+	perturbations_.push_back(eField);
450	+	}
451	+
452	+	usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
453	+
454	+	fDecomp_->distributeInitialData();
455	+
456	+	initialized_ = true;
457	+
458	+	}
459	+
460	+	void ForceManager::calcForces() {
461	+
462	+	if (!initialized_) initialize();
463	+
464	+	preCalculation();
465	+	shortRangeInteractions();
466	+	longRangeInteractions();
467	+	postCalculation();
468	+	}
469	+
470		void ForceManager::preCalculation() {
471		SimInfo::MoleculeIterator mi;
472		Molecule* mol;
#	Line 130 | Line 474 | namespace oopse {
474		Atom* atom;
475		Molecule::RigidBodyIterator rbIter;
476		RigidBody* rb;
477	+	Molecule::CutoffGroupIterator ci;
478	+	CutoffGroup* cg;
479
480	<	// forces are zeroed here, before any are accumulated.
481	<	// NOTE: do not rezero the forces in Fortran.
482	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
483	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
480	>	// forces and potentials are zeroed here, before any are
481	>	// accumulated.
482	>
483	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
484	>
485	>	snap->setBondPotential(0.0);
486	>	snap->setBendPotential(0.0);
487	>	snap->setTorsionPotential(0.0);
488	>	snap->setInversionPotential(0.0);
489	>
490	>	potVec zeroPot(0.0);
491	>	snap->setLongRangePotential(zeroPot);
492	>	snap->setExcludedPotentials(zeroPot);
493	>
494	>	snap->setRestraintPotential(0.0);
495	>	snap->setRawPotential(0.0);
496	>
497	>	for (mol = info_->beginMolecule(mi); mol != NULL;
498	>	mol = info_->nextMolecule(mi)) {
499	>	for(atom = mol->beginAtom(ai); atom != NULL;
500	>	atom = mol->nextAtom(ai)) {
501		atom->zeroForcesAndTorques();
502		}
503	<
503	>
504		//change the positions of atoms which belong to the rigidbodies
505	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
505	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
506	>	rb = mol->nextRigidBody(rbIter)) {
507		rb->zeroForcesAndTorques();
508		}
509	+
510	+	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
511	+	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
512	+	cg = mol->nextCutoffGroup(ci)) {
513	+	//calculate the center of mass of cutoff group
514	+	cg->updateCOM();
515	+	}
516	+	}
517		}
518
519	+	// Zero out the stress tensor
520	+	stressTensor *= 0.0;
521	+	// Zero out the heatFlux
522	+	fDecomp_->setHeatFlux( Vector3d(0.0) );
523		}
524	<
525	<	void ForceManager::calcShortRangeInteraction() {
524	>
525	>	void ForceManager::shortRangeInteractions() {
526		Molecule* mol;
527		RigidBody* rb;
528		Bond* bond;
529		Bend* bend;
530		Torsion* torsion;
531	+	Inversion* inversion;
532		SimInfo::MoleculeIterator mi;
533		Molecule::RigidBodyIterator rbIter;
534		Molecule::BondIterator bondIter;;
535		Molecule::BendIterator  bendIter;
536		Molecule::TorsionIterator  torsionIter;
537	<	double bondPotential = 0.0;
538	<	double bendPotential = 0.0;
539	<	double torsionPotential = 0.0;
537	>	Molecule::InversionIterator  inversionIter;
538	>	RealType bondPotential = 0.0;
539	>	RealType bendPotential = 0.0;
540	>	RealType torsionPotential = 0.0;
541	>	RealType inversionPotential = 0.0;
542
543		//calculate short range interactions
544	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
544	>	for (mol = info_->beginMolecule(mi); mol != NULL;
545	>	mol = info_->nextMolecule(mi)) {
546
547		//change the positions of atoms which belong to the rigidbodies
548	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
549	<	rb->updateAtoms();
548	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
549	>	rb = mol->nextRigidBody(rbIter)) {
550	>	rb->updateAtoms();
551		}
552
553	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
554	<	bond->calcForce();
553	>	for (bond = mol->beginBond(bondIter); bond != NULL;
554	>	bond = mol->nextBond(bondIter)) {
555	>	bond->calcForce(doParticlePot_);
556		bondPotential += bond->getPotential();
175	–	}
176	–
177	–
178	–	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
179	–
180	–	double angle;
181	–	bend->calcForce(angle);
182	–	double currBendPot = bend->getPotential();
183	–	bendPotential += bend->getPotential();
184	–	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
185	–	if (i == bendDataSets.end()) {
186	–	BendDataSet dataSet;
187	–	dataSet.prev.angle = dataSet.curr.angle = angle;
188	–	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
189	–	dataSet.deltaV = 0.0;
190	–	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
191	–	}else {
192	–	i->second.prev.angle = i->second.curr.angle;
193	–	i->second.prev.potential = i->second.curr.potential;
194	–	i->second.curr.angle = angle;
195	–	i->second.curr.potential = currBendPot;
196	–	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
197	–	}
557		}
558
559	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
560	<	double angle;
561	<	torsion->calcForce(angle);
562	<	double currTorsionPot = torsion->getPotential();
563	<	torsionPotential += torsion->getPotential();
564	<	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
565	<	if (i == torsionDataSets.end()) {
566	<	TorsionDataSet dataSet;
567	<	dataSet.prev.angle = dataSet.curr.angle = angle;
568	<	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
569	<	dataSet.deltaV = 0.0;
570	<	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
571	<	}else {
572	<	i->second.prev.angle = i->second.curr.angle;
573	<	i->second.prev.potential = i->second.curr.potential;
574	<	i->second.curr.angle = angle;
575	<	i->second.curr.potential = currTorsionPot;
576	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
577	<	}
559	>	for (bend = mol->beginBend(bendIter); bend != NULL;
560	>	bend = mol->nextBend(bendIter)) {
561	>
562	>	RealType angle;
563	>	bend->calcForce(angle, doParticlePot_);
564	>	RealType currBendPot = bend->getPotential();
565	>
566	>	bendPotential += bend->getPotential();
567	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
568	>	if (i == bendDataSets.end()) {
569	>	BendDataSet dataSet;
570	>	dataSet.prev.angle = dataSet.curr.angle = angle;
571	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
572	>	dataSet.deltaV = 0.0;
573	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
574	>	dataSet));
575	>	}else {
576	>	i->second.prev.angle = i->second.curr.angle;
577	>	i->second.prev.potential = i->second.curr.potential;
578	>	i->second.curr.angle = angle;
579	>	i->second.curr.potential = currBendPot;
580	>	i->second.deltaV =  fabs(i->second.curr.potential -
581	>	i->second.prev.potential);
582	>	}
583		}
584	<
584	>
585	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
586	>	torsion = mol->nextTorsion(torsionIter)) {
587	>	RealType angle;
588	>	torsion->calcForce(angle, doParticlePot_);
589	>	RealType currTorsionPot = torsion->getPotential();
590	>	torsionPotential += torsion->getPotential();
591	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
592	>	if (i == torsionDataSets.end()) {
593	>	TorsionDataSet dataSet;
594	>	dataSet.prev.angle = dataSet.curr.angle = angle;
595	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
596	>	dataSet.deltaV = 0.0;
597	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
598	>	}else {
599	>	i->second.prev.angle = i->second.curr.angle;
600	>	i->second.prev.potential = i->second.curr.potential;
601	>	i->second.curr.angle = angle;
602	>	i->second.curr.potential = currTorsionPot;
603	>	i->second.deltaV =  fabs(i->second.curr.potential -
604	>	i->second.prev.potential);
605	>	}
606	>	}
607	>
608	>	for (inversion = mol->beginInversion(inversionIter);
609	>	inversion != NULL;
610	>	inversion = mol->nextInversion(inversionIter)) {
611	>	RealType angle;
612	>	inversion->calcForce(angle, doParticlePot_);
613	>	RealType currInversionPot = inversion->getPotential();
614	>	inversionPotential += inversion->getPotential();
615	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
616	>	if (i == inversionDataSets.end()) {
617	>	InversionDataSet dataSet;
618	>	dataSet.prev.angle = dataSet.curr.angle = angle;
619	>	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
620	>	dataSet.deltaV = 0.0;
621	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
622	>	}else {
623	>	i->second.prev.angle = i->second.curr.angle;
624	>	i->second.prev.potential = i->second.curr.potential;
625	>	i->second.curr.angle = angle;
626	>	i->second.curr.potential = currInversionPot;
627	>	i->second.deltaV =  fabs(i->second.curr.potential -
628	>	i->second.prev.potential);
629	>	}
630	>	}
631		}
632	<
633	<	double  shortRangePotential = bondPotential + bendPotential + torsionPotential;
632	>
633	>	#ifdef IS_MPI
634	>	// Collect from all nodes.  This should eventually be moved into a
635	>	// SystemDecomposition, but this is a better place than in
636	>	// Thermo to do the collection.
637	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
638	>	MPI::SUM);
639	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
640	>	MPI::SUM);
641	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
642	>	MPI::REALTYPE, MPI::SUM);
643	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
644	>	MPI::REALTYPE, MPI::SUM);
645	>	#endif
646	>
647		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
225	–	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
226	–	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
227	–	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
228	–	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
229	–
230	–	}
648
649	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
650	<	Snapshot* curSnapshot;
651	<	DataStorage* config;
652	<	double* frc;
236	<	double* pos;
237	<	double* trq;
238	<	double* A;
239	<	double* electroFrame;
240	<	double* rc;
649	>	curSnapshot->setBondPotential(bondPotential);
650	>	curSnapshot->setBendPotential(bendPotential);
651	>	curSnapshot->setTorsionPotential(torsionPotential);
652	>	curSnapshot->setInversionPotential(inversionPotential);
653
654	<	//get current snapshot from SimInfo
655	<	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
654	>	// RealType shortRangePotential = bondPotential + bendPotential +
655	>	//   torsionPotential +  inversionPotential;
656
657	<	//get array pointers
658	<	config = &(curSnapshot->atomData);
659	<	frc = config->getArrayPointer(DataStorage::dslForce);
660	<	pos = config->getArrayPointer(DataStorage::dslPosition);
249	<	trq = config->getArrayPointer(DataStorage::dslTorque);
250	<	A   = config->getArrayPointer(DataStorage::dslAmat);
251	<	electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
657	>	// curSnapshot->setShortRangePotential(shortRangePotential);
658	>	}
659	>
660	>	void ForceManager::longRangeInteractions() {
661
662	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
663	+	DataStorage* config = &(curSnapshot->atomData);
664	+	DataStorage* cgConfig = &(curSnapshot->cgData);
665	+
666		//calculate the center of mass of cutoff group
667	+
668		SimInfo::MoleculeIterator mi;
669		Molecule* mol;
670		Molecule::CutoffGroupIterator ci;
671		CutoffGroup* cg;
258	–	Vector3d com;
259	–	std::vector<Vector3d> rcGroup;
672
673	<	if(info_->getNCutoffGroups() > 0){
674	<
675	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
676	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
677	<	cg->getCOM(com);
678	<	rcGroup.push_back(com);
673	>	if(info_->getNCutoffGroups() > 0){
674	>	for (mol = info_->beginMolecule(mi); mol != NULL;
675	>	mol = info_->nextMolecule(mi)) {
676	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
677	>	cg = mol->nextCutoffGroup(ci)) {
678	>	cg->updateCOM();
679		}
680	<	}// end for (mol)
269	<
270	<	rc = rcGroup[0].getArrayPointer();
680	>	}
681		} else {
682	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
683	<	rc = pos;
682	>	// center of mass of the group is the same as position of the atom
683	>	// if cutoff group does not exist
684	>	cgConfig->position = config->position;
685	>	cgConfig->velocity = config->velocity;
686		}
687	<
688	<	//initialize data before passing to fortran
689	<	double longRangePotential[LR_POT_TYPES];
278	<	double lrPot = 0.0;
687	>
688	>	fDecomp_->zeroWorkArrays();
689	>	fDecomp_->distributeData();
690
691	<	Mat3x3d tau;
692	<	short int passedCalcPot = needPotential;
693	<	short int passedCalcStress = needStress;
694	<	int isError = 0;
691	>	int cg1, cg2, atom1, atom2, topoDist;
692	>	Vector3d d_grp, dag, d, gvel2, vel2;
693	>	RealType rgrpsq, rgrp, r2, r;
694	>	RealType electroMult, vdwMult;
695	>	RealType vij;
696	>	Vector3d fij, fg, f1;
697	>	tuple3<RealType, RealType, RealType> cuts;
698	>	RealType rCutSq;
699	>	bool in_switching_region;
700	>	RealType sw, dswdr, swderiv;
701	>	vector<int> atomListColumn, atomListRow;
702	>	InteractionData idat;
703	>	SelfData sdat;
704	>	RealType mf;
705	>	RealType vpair;
706	>	RealType dVdFQ1(0.0);
707	>	RealType dVdFQ2(0.0);
708	>	Vector3d eField1(0.0);
709	>	Vector3d eField2(0.0);
710	>	potVec longRangePotential(0.0);
711	>	potVec workPot(0.0);
712	>	potVec exPot(0.0);
713	>	vector<int>::iterator ia, jb;
714
715	<	for (int i=0; i<LR_POT_TYPES;i++){
716	<	longRangePotential[i]=0.0; //Initialize array
715	>	int loopStart, loopEnd;
716	>
717	>	idat.vdwMult = &vdwMult;
718	>	idat.electroMult = &electroMult;
719	>	idat.pot = &workPot;
720	>	idat.excludedPot = &exPot;
721	>	sdat.pot = fDecomp_->getEmbeddingPotential();
722	>	sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
723	>	idat.vpair = &vpair;
724	>	idat.dVdFQ1 = &dVdFQ1;
725	>	idat.dVdFQ2 = &dVdFQ2;
726	>	idat.eField1 = &eField1;
727	>	idat.eField2 = &eField2;
728	>	idat.f1 = &f1;
729	>	idat.sw = &sw;
730	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
731	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE || cutoffMethod_ == TAYLOR_SHIFTED) ? true : false;
732	>	idat.doParticlePot = doParticlePot_;
733	>	idat.doElectricField = doElectricField_;
734	>	sdat.doParticlePot = doParticlePot_;
735	>
736	>	loopEnd = PAIR_LOOP;
737	>	if (info_->requiresPrepair() ) {
738	>	loopStart = PREPAIR_LOOP;
739	>	} else {
740	>	loopStart = PAIR_LOOP;
741		}
742	+	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
743	+
744	+	if (iLoop == loopStart) {
745	+	bool update_nlist = fDecomp_->checkNeighborList();
746	+	if (update_nlist) {
747	+	if (!usePeriodicBoundaryConditions_)
748	+	Mat3x3d bbox = thermo->getBoundingBox();
749	+	neighborList = fDecomp_->buildNeighborList();
750	+	}
751	+	}
752
753	<	doForceLoop( pos,
754	<	rc,
755	<	A,
756	<	electroFrame,
757	<	frc,
758	<	trq,
759	<	tau.getArrayPointer(),
296	<	longRangePotential,
297	<	&passedCalcPot,
298	<	&passedCalcStress,
299	<	&isError );
753	>	for (vector<pair<int, int> >::iterator it = neighborList.begin();
754	>	it != neighborList.end(); ++it) {
755	>
756	>	cg1 = (*it).first;
757	>	cg2 = (*it).second;
758	>
759	>	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
760
761	<	if( isError ){
762	<	sprintf( painCave.errMsg,
763	<	"Error returned from the fortran force calculation.\n" );
764	<	painCave.isFatal = 1;
765	<	simError();
761	>	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
762	>
763	>	curSnapshot->wrapVector(d_grp);
764	>	rgrpsq = d_grp.lengthSquare();
765	>	rCutSq = cuts.second;
766	>
767	>	if (rgrpsq < rCutSq) {
768	>	idat.rcut = &cuts.first;
769	>	if (iLoop == PAIR_LOOP) {
770	>	vij = 0.0;
771	>	fij.zero();
772	>	eField1.zero();
773	>	eField2.zero();
774	>	}
775	>
776	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
777	>	rgrp);
778	>
779	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
780	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
781	>
782	>	if (doHeatFlux_)
783	>	gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
784	>
785	>	for (ia = atomListRow.begin();
786	>	ia != atomListRow.end(); ++ia) {
787	>	atom1 = (*ia);
788	>
789	>	for (jb = atomListColumn.begin();
790	>	jb != atomListColumn.end(); ++jb) {
791	>	atom2 = (*jb);
792	>
793	>	if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
794	>
795	>	vpair = 0.0;
796	>	workPot = 0.0;
797	>	exPot = 0.0;
798	>	f1.zero();
799	>	dVdFQ1 = 0.0;
800	>	dVdFQ2 = 0.0;
801	>
802	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
803	>
804	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
805	>	vdwMult = vdwScale_[topoDist];
806	>	electroMult = electrostaticScale_[topoDist];
807	>
808	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
809	>	idat.d = &d_grp;
810	>	idat.r2 = &rgrpsq;
811	>	if (doHeatFlux_)
812	>	vel2 = gvel2;
813	>	} else {
814	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
815	>	curSnapshot->wrapVector( d );
816	>	r2 = d.lengthSquare();
817	>	idat.d = &d;
818	>	idat.r2 = &r2;
819	>	if (doHeatFlux_)
820	>	vel2 = fDecomp_->getAtomVelocityColumn(atom2);
821	>	}
822	>
823	>	r = sqrt( *(idat.r2) );
824	>	idat.rij = &r;
825	>
826	>	if (iLoop == PREPAIR_LOOP) {
827	>	interactionMan_->doPrePair(idat);
828	>	} else {
829	>	interactionMan_->doPair(idat);
830	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
831	>	vij += vpair;
832	>	fij += f1;
833	>	stressTensor -= outProduct( *(idat.d), f1);
834	>	if (doHeatFlux_)
835	>	fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
836	>	}
837	>	}
838	>	}
839	>	}
840	>
841	>	if (iLoop == PAIR_LOOP) {
842	>	if (in_switching_region) {
843	>	swderiv = vij * dswdr / rgrp;
844	>	fg = swderiv * d_grp;
845	>	fij += fg;
846	>
847	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
848	>	if (!fDecomp_->skipAtomPair(atomListRow[0],
849	>	atomListColumn[0],
850	>	cg1, cg2)) {
851	>	stressTensor -= outProduct( *(idat.d), fg);
852	>	if (doHeatFlux_)
853	>	fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
854	>	}
855	>	}
856	>
857	>	for (ia = atomListRow.begin();
858	>	ia != atomListRow.end(); ++ia) {
859	>	atom1 = (*ia);
860	>	mf = fDecomp_->getMassFactorRow(atom1);
861	>	// fg is the force on atom ia due to cutoff group's
862	>	// presence in switching region
863	>	fg = swderiv * d_grp * mf;
864	>	fDecomp_->addForceToAtomRow(atom1, fg);
865	>	if (atomListRow.size() > 1) {
866	>	if (info_->usesAtomicVirial()) {
867	>	// find the distance between the atom
868	>	// and the center of the cutoff group:
869	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
870	>	stressTensor -= outProduct(dag, fg);
871	>	if (doHeatFlux_)
872	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
873	>	}
874	>	}
875	>	}
876	>	for (jb = atomListColumn.begin();
877	>	jb != atomListColumn.end(); ++jb) {
878	>	atom2 = (*jb);
879	>	mf = fDecomp_->getMassFactorColumn(atom2);
880	>	// fg is the force on atom jb due to cutoff group's
881	>	// presence in switching region
882	>	fg = -swderiv * d_grp * mf;
883	>	fDecomp_->addForceToAtomColumn(atom2, fg);
884	>
885	>	if (atomListColumn.size() > 1) {
886	>	if (info_->usesAtomicVirial()) {
887	>	// find the distance between the atom
888	>	// and the center of the cutoff group:
889	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
890	>	stressTensor -= outProduct(dag, fg);
891	>	if (doHeatFlux_)
892	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
893	>	}
894	>	}
895	>	}
896	>	}
897	>	//if (!info_->usesAtomicVirial()) {
898	>	//  stressTensor -= outProduct(d_grp, fij);
899	>	//  if (doHeatFlux_)
900	>	//     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
901	>	//}
902	>	}
903	>	}
904	>	}
905	>
906	>	if (iLoop == PREPAIR_LOOP) {
907	>	if (info_->requiresPrepair()) {
908	>
909	>	fDecomp_->collectIntermediateData();
910	>
911	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
912	>	fDecomp_->fillSelfData(sdat, atom1);
913	>	interactionMan_->doPreForce(sdat);
914	>	}
915	>
916	>	fDecomp_->distributeIntermediateData();
917	>
918	>	}
919	>	}
920		}
921	<	for (int i=0; i<LR_POT_TYPES;i++){
922	<	lrPot += longRangePotential[i]; //Quick hack
921	>
922	>	// collects pairwise information
923	>	fDecomp_->collectData();
924	>
925	>	if (info_->requiresSelfCorrection()) {
926	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
927	>	fDecomp_->fillSelfData(sdat, atom1);
928	>	interactionMan_->doSelfCorrection(sdat);
929	>	}
930		}
931
932	<	//store the tau and long range potential
933	<	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];
932	>	// collects single-atom information
933	>	fDecomp_->collectSelfData();
934
935	<	curSnapshot->statData.setTau(tau);
936	<	}
935	>	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
936	>	*(fDecomp_->getPairwisePotential());
937
938	+	curSnapshot->setLongRangePotential(longRangePotential);
939	+
940	+	curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
941	+	*(fDecomp_->getExcludedPotential()));
942
943	+	}
944	+
945	+
946		void ForceManager::postCalculation() {
947	+
948	+	vector<Perturbation*>::iterator pi;
949	+	for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
950	+	(*pi)->applyPerturbation();
951	+	}
952	+
953		SimInfo::MoleculeIterator mi;
954		Molecule* mol;
955		Molecule::RigidBodyIterator rbIter;
956		RigidBody* rb;
957	<
957	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
958	>
959		// collect the atomic forces onto rigid bodies
960	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
961	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
962	<	rb->calcForcesAndTorques();
960	>
961	>	for (mol = info_->beginMolecule(mi); mol != NULL;
962	>	mol = info_->nextMolecule(mi)) {
963	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
964	>	rb = mol->nextRigidBody(rbIter)) {
965	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
966	>	stressTensor += rbTau;
967		}
968		}
969	+
970	+	#ifdef IS_MPI
971	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
972	+	MPI::REALTYPE, MPI::SUM);
973	+	#endif
974	+	curSnapshot->setStressTensor(stressTensor);
975	+
976	+	if (info_->getSimParams()->getUseLongRangeCorrections()) {
977	+	/*
978	+	RealType vol = curSnapshot->getVolume();
979	+	RealType Elrc(0.0);
980	+	RealType Wlrc(0.0);
981
982	<	}
982	>	set<AtomType*>::iterator i;
983	>	set<AtomType*>::iterator j;
984	>
985	>	RealType n_i, n_j;
986	>	RealType rho_i, rho_j;
987	>	pair<RealType, RealType> LRI;
988	>
989	>	for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
990	>	n_i = RealType(info_->getGlobalCountOfType(*i));
991	>	rho_i = n_i /  vol;
992	>	for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) {
993	>	n_j = RealType(info_->getGlobalCountOfType(*j));
994	>	rho_j = n_j / vol;
995	>
996	>	LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) );
997
998	<	} //end namespace oopse
998	>	Elrc += n_i   * rho_j * LRI.first;
999	>	Wlrc -= rho_i * rho_j * LRI.second;
1000	>	}
1001	>	}
1002	>	Elrc *= 2.0 * NumericConstant::PI;
1003	>	Wlrc *= 2.0 * NumericConstant::PI;
1004	>
1005	>	RealType lrp = curSnapshot->getLongRangePotential();
1006	>	curSnapshot->setLongRangePotential(lrp + Elrc);
1007	>	stressTensor += Wlrc * SquareMatrix3<RealType>::identity();
1008	>	curSnapshot->setStressTensor(stressTensor);
1009	>	*/
1010	>
1011	>	}
1012	>	}
1013	>	}

Comparing trunk/src/brains/ForceManager.cpp (property svn:keywords):
Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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