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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 2033 by gezelter, Sat Nov 1 14:12:16 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/UniformField.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	<	std::sort(bendOrderStruct.begin(), bendOrderStruct.end(), std::ptr_fun(BendSortFunctor));
291	<	std::sort(torsionOrderStruct.begin(), torsionOrderStruct.end(), std::ptr_fun(TorsionSortFunctor));
292	<	std::cout << "bend" << std::endl;
293	<	for (std::vector<BendOrderStruct>::iterator k = bendOrderStruct.begin(); k != bendOrderStruct.end(); ++k) {
294	<	Bend* bend = k->bend;
295	<	std::cout << "atom1=" <<bend->getAtomA()->getGlobalIndex() << ",atom2 = "<< bend->getAtomB()->getGlobalIndex() << ",atom3="<<bend->getAtomC()->getGlobalIndex() << " ";
296	<	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;
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	<	std::cout << "torsio" << std::endl;
317	<	for (std::vector<TorsionOrderStruct>::iterator l = torsionOrderStruct.begin(); l != torsionOrderStruct.end(); ++l) {
318	<	Torsion* torsion = l->torsion;
319	<	std::cout << "atom1=" <<torsion->getAtomA()->getGlobalIndex() << ",atom2 = "<< torsion->getAtomB()->getGlobalIndex() << ",atom3="<<torsion->getAtomC()->getGlobalIndex() << ",atom4="<<torsion->getAtomD()->getGlobalIndex()<< " ";
320	<	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;
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	<	*/
369	>
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	>	switcher_->setSwitchType(sft_);
394	>	switcher_->setSwitch(rSwitch_, rCut_);
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	+	doSitePotential_ = info_->getSimParams()->getOutputSitePotential();
418	+
419	+	}
420	+
421	+	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
422	+
423	+	//! Force fields can set options on how to scale van der Waals and
424	+	//! electrostatic interactions for atoms connected via bonds, bends
425	+	//! and torsions in this case the topological distance between
426	+	//! atoms is:
427	+	//! 0 = topologically unconnected
428	+	//! 1 = bonded together
429	+	//! 2 = connected via a bend
430	+	//! 3 = connected via a torsion
431	+
432	+	vdwScale_.reserve(4);
433	+	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
434	+
435	+	electrostaticScale_.reserve(4);
436	+	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
437	+
438	+	vdwScale_[0] = 1.0;
439	+	vdwScale_[1] = fopts.getvdw12scale();
440	+	vdwScale_[2] = fopts.getvdw13scale();
441	+	vdwScale_[3] = fopts.getvdw14scale();
442	+
443	+	electrostaticScale_[0] = 1.0;
444	+	electrostaticScale_[1] = fopts.getelectrostatic12scale();
445	+	electrostaticScale_[2] = fopts.getelectrostatic13scale();
446	+	electrostaticScale_[3] = fopts.getelectrostatic14scale();
447	+
448	+	if (info_->getSimParams()->haveUniformField()) {
449	+	UniformField* eField = new UniformField(info_);
450	+	perturbations_.push_back(eField);
451	+	}
452	+
453	+	usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
454	+
455	+	fDecomp_->distributeInitialData();
456	+
457	+	initialized_ = true;
458	+
459	+	}
460	+
461	+	void ForceManager::calcForces() {
462	+
463	+	if (!initialized_) initialize();
464	+
465	+	preCalculation();
466	+	shortRangeInteractions();
467	+	longRangeInteractions();
468	+	postCalculation();
469	+	}
470	+
471		void ForceManager::preCalculation() {
472		SimInfo::MoleculeIterator mi;
473		Molecule* mol;
#	Line 130 | Line 475 | namespace oopse {
475		Atom* atom;
476		Molecule::RigidBodyIterator rbIter;
477		RigidBody* rb;
478	+	Molecule::CutoffGroupIterator ci;
479	+	CutoffGroup* cg;
480
481	<	// forces are zeroed here, before any are accumulated.
482	<	// NOTE: do not rezero the forces in Fortran.
483	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
484	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
481	>	// forces and potentials are zeroed here, before any are
482	>	// accumulated.
483	>
484	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
485	>
486	>	snap->setBondPotential(0.0);
487	>	snap->setBendPotential(0.0);
488	>	snap->setTorsionPotential(0.0);
489	>	snap->setInversionPotential(0.0);
490	>
491	>	potVec zeroPot(0.0);
492	>	snap->setLongRangePotential(zeroPot);
493	>	snap->setExcludedPotentials(zeroPot);
494	>
495	>	snap->setRestraintPotential(0.0);
496	>	snap->setRawPotential(0.0);
497	>
498	>	for (mol = info_->beginMolecule(mi); mol != NULL;
499	>	mol = info_->nextMolecule(mi)) {
500	>	for(atom = mol->beginAtom(ai); atom != NULL;
501	>	atom = mol->nextAtom(ai)) {
502		atom->zeroForcesAndTorques();
503		}
504	<
504	>
505		//change the positions of atoms which belong to the rigidbodies
506	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
506	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
507	>	rb = mol->nextRigidBody(rbIter)) {
508		rb->zeroForcesAndTorques();
509		}
510	+
511	+	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
512	+	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
513	+	cg = mol->nextCutoffGroup(ci)) {
514	+	//calculate the center of mass of cutoff group
515	+	cg->updateCOM();
516	+	}
517	+	}
518		}
519
520	+	// Zero out the stress tensor
521	+	stressTensor *= 0.0;
522	+	// Zero out the heatFlux
523	+	fDecomp_->setHeatFlux( Vector3d(0.0) );
524		}
525	<
526	<	void ForceManager::calcShortRangeInteraction() {
525	>
526	>	void ForceManager::shortRangeInteractions() {
527		Molecule* mol;
528		RigidBody* rb;
529		Bond* bond;
530		Bend* bend;
531		Torsion* torsion;
532	+	Inversion* inversion;
533		SimInfo::MoleculeIterator mi;
534		Molecule::RigidBodyIterator rbIter;
535		Molecule::BondIterator bondIter;;
536		Molecule::BendIterator  bendIter;
537		Molecule::TorsionIterator  torsionIter;
538	<	double bondPotential = 0.0;
539	<	double bendPotential = 0.0;
540	<	double torsionPotential = 0.0;
538	>	Molecule::InversionIterator  inversionIter;
539	>	RealType bondPotential = 0.0;
540	>	RealType bendPotential = 0.0;
541	>	RealType torsionPotential = 0.0;
542	>	RealType inversionPotential = 0.0;
543
544		//calculate short range interactions
545	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
545	>	for (mol = info_->beginMolecule(mi); mol != NULL;
546	>	mol = info_->nextMolecule(mi)) {
547
548		//change the positions of atoms which belong to the rigidbodies
549	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
550	<	rb->updateAtoms();
549	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
550	>	rb = mol->nextRigidBody(rbIter)) {
551	>	rb->updateAtoms();
552		}
553
554	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
555	<	bond->calcForce();
554	>	for (bond = mol->beginBond(bondIter); bond != NULL;
555	>	bond = mol->nextBond(bondIter)) {
556	>	bond->calcForce(doParticlePot_);
557		bondPotential += bond->getPotential();
558		}
559
560	<
561	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
562	<
563	<	double angle;
564	<	bend->calcForce(angle);
565	<	double currBendPot = bend->getPotential();
566	<	bendPotential += bend->getPotential();
567	<	std::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(std::map<Bend*, BendDataSet>::value_type(bend, 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 = currBendPot;
579	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
580	<	}
581	<	}
582	<
583	<	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	<	}
560	>	for (bend = mol->beginBend(bendIter); bend != NULL;
561	>	bend = mol->nextBend(bendIter)) {
562	>
563	>	RealType angle;
564	>	bend->calcForce(angle, doParticlePot_);
565	>	RealType currBendPot = bend->getPotential();
566	>
567	>	bendPotential += bend->getPotential();
568	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
569	>	if (i == bendDataSets.end()) {
570	>	BendDataSet dataSet;
571	>	dataSet.prev.angle = dataSet.curr.angle = angle;
572	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
573	>	dataSet.deltaV = 0.0;
574	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
575	>	dataSet));
576	>	}else {
577	>	i->second.prev.angle = i->second.curr.angle;
578	>	i->second.prev.potential = i->second.curr.potential;
579	>	i->second.curr.angle = angle;
580	>	i->second.curr.potential = currBendPot;
581	>	i->second.deltaV =  fabs(i->second.curr.potential -
582	>	i->second.prev.potential);
583	>	}
584		}
585	<
585	>
586	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
587	>	torsion = mol->nextTorsion(torsionIter)) {
588	>	RealType angle;
589	>	torsion->calcForce(angle, doParticlePot_);
590	>	RealType currTorsionPot = torsion->getPotential();
591	>	torsionPotential += torsion->getPotential();
592	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
593	>	if (i == torsionDataSets.end()) {
594	>	TorsionDataSet dataSet;
595	>	dataSet.prev.angle = dataSet.curr.angle = angle;
596	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
597	>	dataSet.deltaV = 0.0;
598	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
599	>	}else {
600	>	i->second.prev.angle = i->second.curr.angle;
601	>	i->second.prev.potential = i->second.curr.potential;
602	>	i->second.curr.angle = angle;
603	>	i->second.curr.potential = currTorsionPot;
604	>	i->second.deltaV =  fabs(i->second.curr.potential -
605	>	i->second.prev.potential);
606	>	}
607	>	}
608	>
609	>	for (inversion = mol->beginInversion(inversionIter);
610	>	inversion != NULL;
611	>	inversion = mol->nextInversion(inversionIter)) {
612	>	RealType angle;
613	>	inversion->calcForce(angle, doParticlePot_);
614	>	RealType currInversionPot = inversion->getPotential();
615	>	inversionPotential += inversion->getPotential();
616	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
617	>	if (i == inversionDataSets.end()) {
618	>	InversionDataSet dataSet;
619	>	dataSet.prev.angle = dataSet.curr.angle = angle;
620	>	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
621	>	dataSet.deltaV = 0.0;
622	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
623	>	}else {
624	>	i->second.prev.angle = i->second.curr.angle;
625	>	i->second.prev.potential = i->second.curr.potential;
626	>	i->second.curr.angle = angle;
627	>	i->second.curr.potential = currInversionPot;
628	>	i->second.deltaV =  fabs(i->second.curr.potential -
629	>	i->second.prev.potential);
630	>	}
631	>	}
632		}
633	<
634	<	double  shortRangePotential = bondPotential + bendPotential + torsionPotential;
633	>
634	>	#ifdef IS_MPI
635	>	// Collect from all nodes.  This should eventually be moved into a
636	>	// SystemDecomposition, but this is a better place than in
637	>	// Thermo to do the collection.
638	>
639	>	MPI_Allreduce(MPI_IN_PLACE, &bondPotential, 1, MPI_REALTYPE,
640	>	MPI_SUM, MPI_COMM_WORLD);
641	>	MPI_Allreduce(MPI_IN_PLACE, &bendPotential, 1, MPI_REALTYPE,
642	>	MPI_SUM, MPI_COMM_WORLD);
643	>	MPI_Allreduce(MPI_IN_PLACE, &torsionPotential, 1,
644	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
645	>	MPI_Allreduce(MPI_IN_PLACE, &inversionPotential, 1,
646	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
647	>	#endif
648	>
649		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
650	<	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
651	<	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
652	<	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
653	<	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
650	>
651	>	curSnapshot->setBondPotential(bondPotential);
652	>	curSnapshot->setBendPotential(bendPotential);
653	>	curSnapshot->setTorsionPotential(torsionPotential);
654	>	curSnapshot->setInversionPotential(inversionPotential);
655
656	+	// RealType shortRangePotential = bondPotential + bendPotential +
657	+	//   torsionPotential +  inversionPotential;
658	+
659	+	// curSnapshot->setShortRangePotential(shortRangePotential);
660		}
661	+
662	+	void ForceManager::longRangeInteractions() {
663
664	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
665	<	Snapshot* curSnapshot;
666	<	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();
664	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
665	>	DataStorage* config = &(curSnapshot->atomData);
666	>	DataStorage* cgConfig = &(curSnapshot->cgData);
667
245	–	//get array pointers
246	–	config = &(curSnapshot->atomData);
247	–	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);
668
669		//calculate the center of mass of cutoff group
670	+
671		SimInfo::MoleculeIterator mi;
672		Molecule* mol;
673		Molecule::CutoffGroupIterator ci;
674		CutoffGroup* cg;
258	–	Vector3d com;
259	–	std::vector<Vector3d> rcGroup;
675
676	<	if(info_->getNCutoffGroups() > 0){
677	<
678	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
679	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
680	<	cg->getCOM(com);
681	<	rcGroup.push_back(com);
676	>	if(info_->getNCutoffGroups() > 0){
677	>	for (mol = info_->beginMolecule(mi); mol != NULL;
678	>	mol = info_->nextMolecule(mi)) {
679	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
680	>	cg = mol->nextCutoffGroup(ci)) {
681	>	cg->updateCOM();
682		}
683	<	}// end for (mol)
269	<
270	<	rc = rcGroup[0].getArrayPointer();
683	>	}
684		} else {
685	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
686	<	rc = pos;
685	>	// center of mass of the group is the same as position of the atom
686	>	// if cutoff group does not exist
687	>	cgConfig->position = config->position;
688	>	cgConfig->velocity = config->velocity;
689		}
690	<
691	<	//initialize data before passing to fortran
692	<	double longRangePotential[LR_POT_TYPES];
278	<	double lrPot = 0.0;
690	>
691	>	fDecomp_->zeroWorkArrays();
692	>	fDecomp_->distributeData();
693
694	<	Mat3x3d tau;
695	<	short int passedCalcPot = needPotential;
696	<	short int passedCalcStress = needStress;
697	<	int isError = 0;
694	>	int cg1, cg2, atom1, atom2, topoDist;
695	>	Vector3d d_grp, dag, d, gvel2, vel2;
696	>	RealType rgrpsq, rgrp, r2, r;
697	>	RealType electroMult, vdwMult;
698	>	RealType vij;
699	>	Vector3d fij, fg, f1;
700	>	tuple3<RealType, RealType, RealType> cuts;
701	>	RealType rCut, rCutSq, rListSq;
702	>	bool in_switching_region;
703	>	RealType sw, dswdr, swderiv;
704	>	vector<int> atomListColumn, atomListRow;
705	>	InteractionData idat;
706	>	SelfData sdat;
707	>	RealType mf;
708	>	RealType vpair;
709	>	RealType dVdFQ1(0.0);
710	>	RealType dVdFQ2(0.0);
711	>	potVec longRangePotential(0.0);
712	>	RealType reciprocalPotential(0.0);
713	>	potVec workPot(0.0);
714	>	potVec exPot(0.0);
715	>	Vector3d eField1(0.0);
716	>	Vector3d eField2(0.0);
717	>	RealType sPot1(0.0);
718	>	RealType sPot2(0.0);
719	>
720	>	vector<int>::iterator ia, jb;
721
722	<	for (int i=0; i<LR_POT_TYPES;i++){
723	<	longRangePotential[i]=0.0; //Initialize array
722	>	int loopStart, loopEnd;
723	>
724	>	idat.rcut = &rCut;
725	>	idat.vdwMult = &vdwMult;
726	>	idat.electroMult = &electroMult;
727	>	idat.pot = &workPot;
728	>	idat.excludedPot = &exPot;
729	>	sdat.pot = fDecomp_->getEmbeddingPotential();
730	>	sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
731	>	idat.vpair = &vpair;
732	>	idat.dVdFQ1 = &dVdFQ1;
733	>	idat.dVdFQ2 = &dVdFQ2;
734	>	idat.eField1 = &eField1;
735	>	idat.eField2 = &eField2;
736	>	idat.sPot1 = &sPot1;
737	>	idat.sPot2 = &sPot2;
738	>	idat.f1 = &f1;
739	>	idat.sw = &sw;
740	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
741	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE ||
742	>	cutoffMethod_ == TAYLOR_SHIFTED) ? true : false;
743	>	idat.doParticlePot = doParticlePot_;
744	>	idat.doElectricField = doElectricField_;
745	>	idat.doSitePotential = doSitePotential_;
746	>	sdat.doParticlePot = doParticlePot_;
747	>
748	>	loopEnd = PAIR_LOOP;
749	>	if (info_->requiresPrepair() ) {
750	>	loopStart = PREPAIR_LOOP;
751	>	} else {
752	>	loopStart = PAIR_LOOP;
753		}
754	+	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
755	+
756	+	if (iLoop == loopStart) {
757	+	bool update_nlist = fDecomp_->checkNeighborList();
758	+	if (update_nlist) {
759	+	if (!usePeriodicBoundaryConditions_)
760	+	Mat3x3d bbox = thermo->getBoundingBox();
761	+	fDecomp_->buildNeighborList(neighborList_);
762	+	}
763	+	}
764
765	<	doForceLoop( pos,
766	<	rc,
767	<	A,
768	<	electroFrame,
769	<	frc,
770	<	trq,
771	<	tau.getArrayPointer(),
296	<	longRangePotential,
297	<	&passedCalcPot,
298	<	&passedCalcStress,
299	<	&isError );
765	>	for (vector<pair<int, int> >::iterator it = neighborList_.begin();
766	>	it != neighborList_.end(); ++it) {
767	>
768	>	cg1 = (*it).first;
769	>	cg2 = (*it).second;
770	>
771	>	fDecomp_->getGroupCutoffs(cg1, cg2, rCut, rCutSq, rListSq);
772
773	<	if( isError ){
774	<	sprintf( painCave.errMsg,
775	<	"Error returned from the fortran force calculation.\n" );
776	<	painCave.isFatal = 1;
777	<	simError();
773	>	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
774	>
775	>	// already wrapped in the getIntergroupVector call:
776	>	// curSnapshot->wrapVector(d_grp);
777	>	rgrpsq = d_grp.lengthSquare();
778	>
779	>	if (rgrpsq < rCutSq) {
780	>	if (iLoop == PAIR_LOOP) {
781	>	vij = 0.0;
782	>	fij.zero();
783	>	eField1.zero();
784	>	eField2.zero();
785	>	sPot1 = 0.0;
786	>	sPot2 = 0.0;
787	>	}
788	>
789	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
790	>	rgrp);
791	>
792	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
793	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
794	>
795	>	if (doHeatFlux_)
796	>	gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
797	>
798	>	for (ia = atomListRow.begin();
799	>	ia != atomListRow.end(); ++ia) {
800	>	atom1 = (*ia);
801	>
802	>	for (jb = atomListColumn.begin();
803	>	jb != atomListColumn.end(); ++jb) {
804	>	atom2 = (*jb);
805	>
806	>	if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
807	>
808	>	vpair = 0.0;
809	>	workPot = 0.0;
810	>	exPot = 0.0;
811	>	f1.zero();
812	>	dVdFQ1 = 0.0;
813	>	dVdFQ2 = 0.0;
814	>
815	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
816	>
817	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
818	>	vdwMult = vdwScale_[topoDist];
819	>	electroMult = electrostaticScale_[topoDist];
820	>
821	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
822	>	idat.d = &d_grp;
823	>	idat.r2 = &rgrpsq;
824	>	if (doHeatFlux_)
825	>	vel2 = gvel2;
826	>	} else {
827	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
828	>	curSnapshot->wrapVector( d );
829	>	r2 = d.lengthSquare();
830	>	idat.d = &d;
831	>	idat.r2 = &r2;
832	>	if (doHeatFlux_)
833	>	vel2 = fDecomp_->getAtomVelocityColumn(atom2);
834	>	}
835	>
836	>	r = sqrt( *(idat.r2) );
837	>	idat.rij = &r;
838	>
839	>	if (iLoop == PREPAIR_LOOP) {
840	>	interactionMan_->doPrePair(idat);
841	>	} else {
842	>	interactionMan_->doPair(idat);
843	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
844	>	vij += vpair;
845	>	fij += f1;
846	>	stressTensor -= outProduct( *(idat.d), f1);
847	>	if (doHeatFlux_)
848	>	fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
849	>	}
850	>	}
851	>	}
852	>	}
853	>
854	>	if (iLoop == PAIR_LOOP) {
855	>	if (in_switching_region) {
856	>	swderiv = vij * dswdr / rgrp;
857	>	fg = swderiv * d_grp;
858	>	fij += fg;
859	>
860	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
861	>	if (!fDecomp_->skipAtomPair(atomListRow[0],
862	>	atomListColumn[0],
863	>	cg1, cg2)) {
864	>	stressTensor -= outProduct( *(idat.d), fg);
865	>	if (doHeatFlux_)
866	>	fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
867	>	}
868	>	}
869	>
870	>	for (ia = atomListRow.begin();
871	>	ia != atomListRow.end(); ++ia) {
872	>	atom1 = (*ia);
873	>	mf = fDecomp_->getMassFactorRow(atom1);
874	>	// fg is the force on atom ia due to cutoff group's
875	>	// presence in switching region
876	>	fg = swderiv * d_grp * mf;
877	>	fDecomp_->addForceToAtomRow(atom1, fg);
878	>	if (atomListRow.size() > 1) {
879	>	if (info_->usesAtomicVirial()) {
880	>	// find the distance between the atom
881	>	// and the center of the cutoff group:
882	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
883	>	stressTensor -= outProduct(dag, fg);
884	>	if (doHeatFlux_)
885	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
886	>	}
887	>	}
888	>	}
889	>	for (jb = atomListColumn.begin();
890	>	jb != atomListColumn.end(); ++jb) {
891	>	atom2 = (*jb);
892	>	mf = fDecomp_->getMassFactorColumn(atom2);
893	>	// fg is the force on atom jb due to cutoff group's
894	>	// presence in switching region
895	>	fg = -swderiv * d_grp * mf;
896	>	fDecomp_->addForceToAtomColumn(atom2, fg);
897	>
898	>	if (atomListColumn.size() > 1) {
899	>	if (info_->usesAtomicVirial()) {
900	>	// find the distance between the atom
901	>	// and the center of the cutoff group:
902	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
903	>	stressTensor -= outProduct(dag, fg);
904	>	if (doHeatFlux_)
905	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
906	>	}
907	>	}
908	>	}
909	>	}
910	>	//if (!info_->usesAtomicVirial()) {
911	>	//  stressTensor -= outProduct(d_grp, fij);
912	>	//  if (doHeatFlux_)
913	>	//     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
914	>	//}
915	>	}
916	>	}
917	>	}
918	>
919	>	if (iLoop == PREPAIR_LOOP) {
920	>	if (info_->requiresPrepair()) {
921	>
922	>	fDecomp_->collectIntermediateData();
923	>
924	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
925	>	fDecomp_->fillSelfData(sdat, atom1);
926	>	interactionMan_->doPreForce(sdat);
927	>	}
928	>
929	>	fDecomp_->distributeIntermediateData();
930	>
931	>	}
932	>	}
933		}
934	<	for (int i=0; i<LR_POT_TYPES;i++){
935	<	lrPot += longRangePotential[i]; //Quick hack
934	>
935	>	// collects pairwise information
936	>	fDecomp_->collectData();
937	>	if (cutoffMethod_ == EWALD_FULL) {
938	>	interactionMan_->doReciprocalSpaceSum(reciprocalPotential);
939	>
940	>	curSnapshot->setReciprocalPotential(reciprocalPotential);
941		}
942	+
943	+	if (info_->requiresSelfCorrection()) {
944	+	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
945	+	fDecomp_->fillSelfData(sdat, atom1);
946	+	interactionMan_->doSelfCorrection(sdat);
947	+	}
948	+	}
949
950	<	//store the tau and long range potential
951	<	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];
950	>	// collects single-atom information
951	>	fDecomp_->collectSelfData();
952
953	<	curSnapshot->statData.setTau(tau);
954	<	}
953	>	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
954	>	*(fDecomp_->getPairwisePotential());
955
956	+	curSnapshot->setLongRangePotential(longRangePotential);
957	+
958	+	curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
959	+	*(fDecomp_->getExcludedPotential()));
960
961	+	}
962	+
963		void ForceManager::postCalculation() {
964	+
965	+	vector<Perturbation*>::iterator pi;
966	+	for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
967	+	(*pi)->applyPerturbation();
968	+	}
969	+
970		SimInfo::MoleculeIterator mi;
971		Molecule* mol;
972		Molecule::RigidBodyIterator rbIter;
973		RigidBody* rb;
974	<
974	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
975	>
976		// collect the atomic forces onto rigid bodies
977	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
978	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
979	<	rb->calcForcesAndTorques();
977	>
978	>	for (mol = info_->beginMolecule(mi); mol != NULL;
979	>	mol = info_->nextMolecule(mi)) {
980	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
981	>	rb = mol->nextRigidBody(rbIter)) {
982	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
983	>	stressTensor += rbTau;
984		}
985		}
986	+
987	+	#ifdef IS_MPI
988	+	MPI_Allreduce(MPI_IN_PLACE, stressTensor.getArrayPointer(), 9,
989	+	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
990	+	#endif
991	+	curSnapshot->setStressTensor(stressTensor);
992	+
993	+	if (info_->getSimParams()->getUseLongRangeCorrections()) {
994	+	/*
995	+	RealType vol = curSnapshot->getVolume();
996	+	RealType Elrc(0.0);
997	+	RealType Wlrc(0.0);
998
999	<	}
999	>	set<AtomType*>::iterator i;
1000	>	set<AtomType*>::iterator j;
1001	>
1002	>	RealType n_i, n_j;
1003	>	RealType rho_i, rho_j;
1004	>	pair<RealType, RealType> LRI;
1005	>
1006	>	for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
1007	>	n_i = RealType(info_->getGlobalCountOfType(*i));
1008	>	rho_i = n_i /  vol;
1009	>	for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) {
1010	>	n_j = RealType(info_->getGlobalCountOfType(*j));
1011	>	rho_j = n_j / vol;
1012	>
1013	>	LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) );
1014
1015	<	} //end namespace oopse
1015	>	Elrc += n_i   * rho_j * LRI.first;
1016	>	Wlrc -= rho_i * rho_j * LRI.second;
1017	>	}
1018	>	}
1019	>	Elrc *= 2.0 * NumericConstant::PI;
1020	>	Wlrc *= 2.0 * NumericConstant::PI;
1021	>
1022	>	RealType lrp = curSnapshot->getLongRangePotential();
1023	>	curSnapshot->setLongRangePotential(lrp + Elrc);
1024	>	stressTensor += Wlrc * SquareMatrix3<RealType>::identity();
1025	>	curSnapshot->setStressTensor(stressTensor);
1026	>	*/
1027	>
1028	>	}
1029	>	}
1030	>	}

Comparing trunk/src/brains/ForceManager.cpp (property svn:keywords):
Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
Revision 2033 by gezelter, Sat Nov 1 14:12:16 2014 UTC

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