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

Comparing trunk/src/brains/ForceManager.cpp (file contents):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 2047 by gezelter, Thu Dec 11 16:16:43 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 "perturbations/UniformGradient.hpp"
62	>	#include "parallel/ForceMatrixDecomposition.hpp"
63
64	<	/*
65	<	struct BendOrderStruct {
66	<	Bend* bend;
63	<	BendDataSet dataSet;
64	<	};
65	<	struct TorsionOrderStruct {
66	<	Torsion* torsion;
67	<	TorsionDataSet dataSet;
68	<	};
64	>	#include <cstdio>
65	>	#include <iostream>
66	>	#include <iomanip>
67
68	<	bool  BendSortFunctor(const BendOrderStruct& b1, const BendOrderStruct& b2) {
69	<	return b1.dataSet.deltaV < b2.dataSet.deltaV;
68	>	using namespace std;
69	>	namespace OpenMD {
70	>
71	>	ForceManager::ForceManager(SimInfo * info) : info_(info), switcher_(NULL),
72	>	initialized_(false) {
73	>	forceField_ = info_->getForceField();
74	>	interactionMan_ = new InteractionManager();
75	>	fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
76	>	thermo = new Thermo(info_);
77		}
78
79	<	bool  TorsionSortFunctor(const TorsionOrderStruct& t1, const TorsionOrderStruct& t2) {
80	<	return t1.dataSet.deltaV < t2.dataSet.deltaV;
79	>	ForceManager::~ForceManager() {
80	>	perturbations_.clear();
81	>
82	>	delete switcher_;
83	>	delete interactionMan_;
84	>	delete fDecomp_;
85	>	delete thermo;
86		}
87	<	*/
88	<	void ForceManager::calcForces(bool needPotential, bool needStress) {
87	>
88	>	/**
89	>	* setupCutoffs
90	>	*
91	>	* Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
92	>	* and cutoffPolicy
93	>	*
94	>	* cutoffRadius : realType
95	>	*  If the cutoffRadius was explicitly set, use that value.
96	>	*  If the cutoffRadius was not explicitly set:
97	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
98	>	*      No electrostatic atoms?  Poll the atom types present in the
99	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
100	>	*      Use the maximum suggested value that was found.
101	>	*
102	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, TAYLOR_SHIFTED,
103	>	*                        SHIFTED_POTENTIAL, or EWALD_FULL)
104	>	*      If cutoffMethod was explicitly set, use that choice.
105	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
106	>	*
107	>	* cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
108	>	*      If cutoffPolicy was explicitly set, use that choice.
109	>	*      If cutoffPolicy was not explicitly set, use TRADITIONAL
110	>	*
111	>	* switchingRadius : realType
112	>	*  If the cutoffMethod was set to SWITCHED:
113	>	*      If the switchingRadius was explicitly set, use that value
114	>	*          (but do a sanity check first).
115	>	*      If the switchingRadius was not explicitly set: use 0.85 *
116	>	*      cutoffRadius_
117	>	*  If the cutoffMethod was not set to SWITCHED:
118	>	*      Set switchingRadius equal to cutoffRadius for safety.
119	>	*/
120	>	void ForceManager::setupCutoffs() {
121	>
122	>	Globals* simParams_ = info_->getSimParams();
123	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
124	>	int mdFileVersion;
125	>	rCut_ = 0.0; //Needs a value for a later max() call;
126	>
127	>	if (simParams_->haveMDfileVersion())
128	>	mdFileVersion = simParams_->getMDfileVersion();
129	>	else
130	>	mdFileVersion = 0;
131	>
132	>	// We need the list of simulated atom types to figure out cutoffs
133	>	// as well as long range corrections.
134
135	<	if (!info_->isFortranInitialized()) {
136	<	info_->update();
135	>	set<AtomType*>::iterator i;
136	>	set<AtomType*> atomTypes_;
137	>	atomTypes_ = info_->getSimulatedAtomTypes();
138	>
139	>	if (simParams_->haveCutoffRadius()) {
140	>	rCut_ = simParams_->getCutoffRadius();
141	>	} else {
142	>	if (info_->usesElectrostaticAtoms()) {
143	>	sprintf(painCave.errMsg,
144	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
145	>	"\tOpenMD will use a default value of 12.0 angstroms"
146	>	"\tfor the cutoffRadius.\n");
147	>	painCave.isFatal = 0;
148	>	painCave.severity = OPENMD_INFO;
149	>	simError();
150	>	rCut_ = 12.0;
151	>	} else {
152	>	RealType thisCut;
153	>	for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
154	>	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
155	>	rCut_ = max(thisCut, rCut_);
156	>	}
157	>	sprintf(painCave.errMsg,
158	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
159	>	"\tOpenMD will use %lf angstroms.\n",
160	>	rCut_);
161	>	painCave.isFatal = 0;
162	>	painCave.severity = OPENMD_INFO;
163	>	simError();
164	>	}
165		}
166
167	<	preCalculation();
168	<
86	<	calcShortRangeInteraction();
167	>	fDecomp_->setUserCutoff(rCut_);
168	>	interactionMan_->setCutoffRadius(rCut_);
169
170	<	calcLongRangeInteraction(needPotential, needStress);
170	>	map<string, CutoffMethod> stringToCutoffMethod;
171	>	stringToCutoffMethod["HARD"] = HARD;
172	>	stringToCutoffMethod["SWITCHED"] = SWITCHED;
173	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
174	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
175	>	stringToCutoffMethod["TAYLOR_SHIFTED"] = TAYLOR_SHIFTED;
176	>	stringToCutoffMethod["EWALD_FULL"] = EWALD_FULL;
177	>
178	>	if (simParams_->haveCutoffMethod()) {
179	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
180	>	map<string, CutoffMethod>::iterator i;
181	>	i = stringToCutoffMethod.find(cutMeth);
182	>	if (i == stringToCutoffMethod.end()) {
183	>	sprintf(painCave.errMsg,
184	>	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
185	>	"\tShould be one of: "
186	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, TAYLOR_SHIFTED,\n"
187	>	"\tSHIFTED_FORCE, or EWALD_FULL\n",
188	>	cutMeth.c_str());
189	>	painCave.isFatal = 1;
190	>	painCave.severity = OPENMD_ERROR;
191	>	simError();
192	>	} else {
193	>	cutoffMethod_ = i->second;
194	>	}
195	>	} else {
196	>	if (mdFileVersion > 1) {
197	>	sprintf(painCave.errMsg,
198	>	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
199	>	"\tOpenMD will use SHIFTED_FORCE.\n");
200	>	painCave.isFatal = 0;
201	>	painCave.severity = OPENMD_INFO;
202	>	simError();
203	>	cutoffMethod_ = SHIFTED_FORCE;
204	>	} else {
205	>	// handle the case where the old file version was in play
206	>	// (there should be no cutoffMethod, so we have to deduce it
207	>	// from other data).
208
209	<	postCalculation();
209	>	sprintf(painCave.errMsg,
210	>	"ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
211	>	"\tOpenMD found a file which does not set a cutoffMethod.\n"
212	>	"\tOpenMD will attempt to deduce a cutoffMethod using the\n"
213	>	"\tbehavior of the older (version 1) code.  To remove this\n"
214	>	"\twarning, add an explicit cutoffMethod and change the top\n"
215	>	"\tof the file so that it begins with <OpenMD version=2>\n");
216	>	painCave.isFatal = 0;
217	>	painCave.severity = OPENMD_WARNING;
218	>	simError();
219	>
220	>	// The old file version tethered the shifting behavior to the
221	>	// electrostaticSummationMethod keyword.
222	>
223	>	if (simParams_->haveElectrostaticSummationMethod()) {
224	>	string myMethod = simParams_->getElectrostaticSummationMethod();
225	>	toUpper(myMethod);
226	>
227	>	if (myMethod == "SHIFTED_POTENTIAL") {
228	>	cutoffMethod_ = SHIFTED_POTENTIAL;
229	>	} else if (myMethod == "SHIFTED_FORCE") {
230	>	cutoffMethod_ = SHIFTED_FORCE;
231	>	} else if (myMethod == "TAYLOR_SHIFTED") {
232	>	cutoffMethod_ = TAYLOR_SHIFTED;
233	>	} else if (myMethod == "EWALD_FULL") {
234	>	cutoffMethod_ = EWALD_FULL;
235	>	}
236	>
237	>	if (simParams_->haveSwitchingRadius())
238	>	rSwitch_ = simParams_->getSwitchingRadius();
239
240	<	/*
241	<	std::vector<BendOrderStruct> bendOrderStruct;
242	<	for(std::map<Bend*, BendDataSet>::iterator i = bendDataSets.begin(); i != bendDataSets.end(); ++i) {
243	<	BendOrderStruct tmp;
244	<	tmp.bend= const_cast<Bend*>(i->first);
245	<	tmp.dataSet = i->second;
246	<	bendOrderStruct.push_back(tmp);
240	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE" ||
241	>	myMethod == "TAYLOR_SHIFTED" || myMethod == "EWALD_FULL") {
242	>	if (simParams_->haveSwitchingRadius()){
243	>	sprintf(painCave.errMsg,
244	>	"ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
245	>	"\tA value was set for the switchingRadius\n"
246	>	"\teven though the electrostaticSummationMethod was\n"
247	>	"\tset to %s\n", myMethod.c_str());
248	>	painCave.severity = OPENMD_WARNING;
249	>	painCave.isFatal = 1;
250	>	simError();
251	>	}
252	>	}
253	>	if (abs(rCut_ - rSwitch_) < 0.0001) {
254	>	if (cutoffMethod_ == SHIFTED_FORCE) {
255	>	sprintf(painCave.errMsg,
256	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
257	>	"\tcutoffRadius and switchingRadius are set to the\n"
258	>	"\tsame value.  OpenMD will use shifted force\n"
259	>	"\tpotentials instead of switching functions.\n");
260	>	painCave.isFatal = 0;
261	>	painCave.severity = OPENMD_WARNING;
262	>	simError();
263	>	} else {
264	>	cutoffMethod_ = SHIFTED_POTENTIAL;
265	>	sprintf(painCave.errMsg,
266	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
267	>	"\tcutoffRadius and switchingRadius are set to the\n"
268	>	"\tsame value.  OpenMD will use shifted potentials\n"
269	>	"\tinstead of switching functions.\n");
270	>	painCave.isFatal = 0;
271	>	painCave.severity = OPENMD_WARNING;
272	>	simError();
273	>	}
274	>	}
275	>	}
276	>	}
277		}
278
279	<	std::vector<TorsionOrderStruct> torsionOrderStruct;
280	<	for(std::map<Torsion*, TorsionDataSet>::iterator j = torsionDataSets.begin(); j != torsionDataSets.end(); ++j) {
281	<	TorsionOrderStruct tmp;
282	<	tmp.torsion = const_cast<Torsion*>(j->first);
283	<	tmp.dataSet = j->second;
284	<	torsionOrderStruct.push_back(tmp);
279	>	map<string, CutoffPolicy> stringToCutoffPolicy;
280	>	stringToCutoffPolicy["MIX"] = MIX;
281	>	stringToCutoffPolicy["MAX"] = MAX;
282	>	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
283	>
284	>	string cutPolicy;
285	>	if (forceFieldOptions_.haveCutoffPolicy()){
286	>	cutPolicy = forceFieldOptions_.getCutoffPolicy();
287	>	}else if (simParams_->haveCutoffPolicy()) {
288	>	cutPolicy = simParams_->getCutoffPolicy();
289		}
290	<
291	<	std::sort(bendOrderStruct.begin(), bendOrderStruct.end(), std::ptr_fun(BendSortFunctor));
292	<	std::sort(torsionOrderStruct.begin(), torsionOrderStruct.end(), std::ptr_fun(TorsionSortFunctor));
293	<	for (std::vector<BendOrderStruct>::iterator k = bendOrderStruct.begin(); k != bendOrderStruct.end(); ++k) {
294	<	Bend* bend = k->bend;
295	<	std::cout << "Bend: 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;
290	>
291	>	if (!cutPolicy.empty()){
292	>	toUpper(cutPolicy);
293	>	map<string, CutoffPolicy>::iterator i;
294	>	i = stringToCutoffPolicy.find(cutPolicy);
295	>
296	>	if (i == stringToCutoffPolicy.end()) {
297	>	sprintf(painCave.errMsg,
298	>	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
299	>	"\tShould be one of: "
300	>	"MIX, MAX, or TRADITIONAL\n",
301	>	cutPolicy.c_str());
302	>	painCave.isFatal = 1;
303	>	painCave.severity = OPENMD_ERROR;
304	>	simError();
305	>	} else {
306	>	cutoffPolicy_ = i->second;
307	>	}
308	>	} else {
309	>	sprintf(painCave.errMsg,
310	>	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
311	>	"\tOpenMD will use TRADITIONAL.\n");
312	>	painCave.isFatal = 0;
313	>	painCave.severity = OPENMD_INFO;
314	>	simError();
315	>	cutoffPolicy_ = TRADITIONAL;
316		}
317	<	for (std::vector<TorsionOrderStruct>::iterator l = torsionOrderStruct.begin(); l != torsionOrderStruct.end(); ++l) {
318	<	Torsion* torsion = l->torsion;
319	<	std::cout << "Torsion: 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;
317	>
318	>	fDecomp_->setCutoffPolicy(cutoffPolicy_);
319	>
320	>	// create the switching function object:
321	>
322	>	switcher_ = new SwitchingFunction();
323	>
324	>	if (cutoffMethod_ == SWITCHED) {
325	>	if (simParams_->haveSwitchingRadius()) {
326	>	rSwitch_ = simParams_->getSwitchingRadius();
327	>	if (rSwitch_ > rCut_) {
328	>	sprintf(painCave.errMsg,
329	>	"ForceManager::setupCutoffs: switchingRadius (%f) is larger "
330	>	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
331	>	painCave.isFatal = 1;
332	>	painCave.severity = OPENMD_ERROR;
333	>	simError();
334	>	}
335	>	} else {
336	>	rSwitch_ = 0.85 * rCut_;
337	>	sprintf(painCave.errMsg,
338	>	"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
339	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
340	>	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
341	>	painCave.isFatal = 0;
342	>	painCave.severity = OPENMD_WARNING;
343	>	simError();
344	>	}
345	>	} else {
346	>	if (mdFileVersion > 1) {
347	>	// throw an error if we define a switching radius and don't need one.
348	>	// older file versions should not do this.
349	>	if (simParams_->haveSwitchingRadius()) {
350	>	map<string, CutoffMethod>::const_iterator it;
351	>	string theMeth;
352	>	for (it = stringToCutoffMethod.begin();
353	>	it != stringToCutoffMethod.end(); ++it) {
354	>	if (it->second == cutoffMethod_) {
355	>	theMeth = it->first;
356	>	break;
357	>	}
358	>	}
359	>	sprintf(painCave.errMsg,
360	>	"ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
361	>	"\tis not set to SWITCHED, so switchingRadius value\n"
362	>	"\twill be ignored for this simulation\n", theMeth.c_str());
363	>	painCave.isFatal = 0;
364	>	painCave.severity = OPENMD_WARNING;
365	>	simError();
366	>	}
367	>	}
368	>	rSwitch_ = rCut_;
369		}
370	<	*/
370	>
371	>	// Default to cubic switching function.
372	>	sft_ = cubic;
373	>	if (simParams_->haveSwitchingFunctionType()) {
374	>	string funcType = simParams_->getSwitchingFunctionType();
375	>	toUpper(funcType);
376	>	if (funcType == "CUBIC") {
377	>	sft_ = cubic;
378	>	} else {
379	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
380	>	sft_ = fifth_order_poly;
381	>	} else {
382	>	// throw error
383	>	sprintf( painCave.errMsg,
384	>	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
385	>	"\tswitchingFunctionType must be one of: "
386	>	"\"cubic\" or \"fifth_order_polynomial\".",
387	>	funcType.c_str() );
388	>	painCave.isFatal = 1;
389	>	painCave.severity = OPENMD_ERROR;
390	>	simError();
391	>	}
392	>	}
393	>	}
394	>	switcher_->setSwitchType(sft_);
395	>	switcher_->setSwitch(rSwitch_, rCut_);
396		}
397
398	+	void ForceManager::initialize() {
399	+
400	+	if (!info_->isTopologyDone()) {
401	+
402	+	info_->update();
403	+	interactionMan_->setSimInfo(info_);
404	+	interactionMan_->initialize();
405	+
406	+	//! We want to delay the cutoffs until after the interaction
407	+	//! manager has set up the atom-atom interactions so that we can
408	+	//! query them for suggested cutoff values
409	+	setupCutoffs();
410	+
411	+	info_->prepareTopology();
412	+
413	+	doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
414	+	doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
415	+	if (doHeatFlux_) doParticlePot_ = true;
416	+
417	+	doElectricField_ = info_->getSimParams()->getOutputElectricField();
418	+	doSitePotential_ = info_->getSimParams()->getOutputSitePotential();
419	+
420	+	}
421	+
422	+	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
423	+
424	+	//! Force fields can set options on how to scale van der Waals and
425	+	//! electrostatic interactions for atoms connected via bonds, bends
426	+	//! and torsions in this case the topological distance between
427	+	//! atoms is:
428	+	//! 0 = topologically unconnected
429	+	//! 1 = bonded together
430	+	//! 2 = connected via a bend
431	+	//! 3 = connected via a torsion
432	+
433	+	vdwScale_.reserve(4);
434	+	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
435	+
436	+	electrostaticScale_.reserve(4);
437	+	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
438	+
439	+	vdwScale_[0] = 1.0;
440	+	vdwScale_[1] = fopts.getvdw12scale();
441	+	vdwScale_[2] = fopts.getvdw13scale();
442	+	vdwScale_[3] = fopts.getvdw14scale();
443	+
444	+	electrostaticScale_[0] = 1.0;
445	+	electrostaticScale_[1] = fopts.getelectrostatic12scale();
446	+	electrostaticScale_[2] = fopts.getelectrostatic13scale();
447	+	electrostaticScale_[3] = fopts.getelectrostatic14scale();
448	+
449	+	if (info_->getSimParams()->haveUniformField()) {
450	+	UniformField* eField = new UniformField(info_);
451	+	perturbations_.push_back(eField);
452	+	}
453	+	if (info_->getSimParams()->haveUniformGradientStrength() ||
454	+	info_->getSimParams()->haveUniformGradientDirection1() ||
455	+	info_->getSimParams()->haveUniformGradientDirection2() ) {
456	+	UniformGradient* eGrad = new UniformGradient(info_);
457	+	perturbations_.push_back(eGrad);
458	+	}
459	+
460	+	usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
461	+
462	+	fDecomp_->distributeInitialData();
463	+
464	+	initialized_ = true;
465	+
466	+	}
467	+
468	+	void ForceManager::calcForces() {
469	+
470	+	if (!initialized_) initialize();
471	+
472	+	preCalculation();
473	+	shortRangeInteractions();
474	+	longRangeInteractions();
475	+	postCalculation();
476	+	}
477	+
478		void ForceManager::preCalculation() {
479		SimInfo::MoleculeIterator mi;
480		Molecule* mol;
#	Line 128 | Line 482 | namespace oopse {
482		Atom* atom;
483		Molecule::RigidBodyIterator rbIter;
484		RigidBody* rb;
485	+	Molecule::CutoffGroupIterator ci;
486	+	CutoffGroup* cg;
487
488	<	// forces are zeroed here, before any are accumulated.
489	<	// NOTE: do not rezero the forces in Fortran.
490	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
491	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
488	>	// forces and potentials are zeroed here, before any are
489	>	// accumulated.
490	>
491	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
492	>
493	>	snap->setBondPotential(0.0);
494	>	snap->setBendPotential(0.0);
495	>	snap->setTorsionPotential(0.0);
496	>	snap->setInversionPotential(0.0);
497	>
498	>	potVec zeroPot(0.0);
499	>	snap->setLongRangePotential(zeroPot);
500	>	snap->setExcludedPotentials(zeroPot);
501	>
502	>	snap->setRestraintPotential(0.0);
503	>	snap->setRawPotential(0.0);
504	>
505	>	for (mol = info_->beginMolecule(mi); mol != NULL;
506	>	mol = info_->nextMolecule(mi)) {
507	>	for(atom = mol->beginAtom(ai); atom != NULL;
508	>	atom = mol->nextAtom(ai)) {
509		atom->zeroForcesAndTorques();
510		}
511	<
511	>
512		//change the positions of atoms which belong to the rigidbodies
513	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
513	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
514	>	rb = mol->nextRigidBody(rbIter)) {
515		rb->zeroForcesAndTorques();
516		}
517	+
518	+	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
519	+	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
520	+	cg = mol->nextCutoffGroup(ci)) {
521	+	//calculate the center of mass of cutoff group
522	+	cg->updateCOM();
523	+	}
524	+	}
525		}
526
527	+	// Zero out the stress tensor
528	+	stressTensor *= 0.0;
529	+	// Zero out the heatFlux
530	+	fDecomp_->setHeatFlux( Vector3d(0.0) );
531		}
532	<
533	<	void ForceManager::calcShortRangeInteraction() {
532	>
533	>	void ForceManager::shortRangeInteractions() {
534		Molecule* mol;
535		RigidBody* rb;
536		Bond* bond;
537		Bend* bend;
538		Torsion* torsion;
539	+	Inversion* inversion;
540		SimInfo::MoleculeIterator mi;
541		Molecule::RigidBodyIterator rbIter;
542		Molecule::BondIterator bondIter;;
543		Molecule::BendIterator  bendIter;
544		Molecule::TorsionIterator  torsionIter;
545	+	Molecule::InversionIterator  inversionIter;
546		RealType bondPotential = 0.0;
547		RealType bendPotential = 0.0;
548		RealType torsionPotential = 0.0;
549	+	RealType inversionPotential = 0.0;
550
551		//calculate short range interactions
552	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
552	>	for (mol = info_->beginMolecule(mi); mol != NULL;
553	>	mol = info_->nextMolecule(mi)) {
554
555		//change the positions of atoms which belong to the rigidbodies
556	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
557	<	rb->updateAtoms();
556	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
557	>	rb = mol->nextRigidBody(rbIter)) {
558	>	rb->updateAtoms();
559		}
560
561	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
562	<	bond->calcForce();
561	>	for (bond = mol->beginBond(bondIter); bond != NULL;
562	>	bond = mol->nextBond(bondIter)) {
563	>	bond->calcForce(doParticlePot_);
564		bondPotential += bond->getPotential();
173	–	}
174	–
175	–
176	–	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
177	–
178	–	RealType angle;
179	–	bend->calcForce(angle);
180	–	RealType 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	–	}
565		}
566
567	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
567	>	for (bend = mol->beginBend(bendIter); bend != NULL;
568	>	bend = mol->nextBend(bendIter)) {
569	>
570		RealType angle;
571	<	torsion->calcForce(angle);
572	<	RealType currTorsionPot = torsion->getPotential();
573	<	torsionPotential += torsion->getPotential();
574	<	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
575	<	if (i == torsionDataSets.end()) {
576	<	TorsionDataSet dataSet;
577	<	dataSet.prev.angle = dataSet.curr.angle = angle;
578	<	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
579	<	dataSet.deltaV = 0.0;
580	<	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
581	<	}else {
582	<	i->second.prev.angle = i->second.curr.angle;
583	<	i->second.prev.potential = i->second.curr.potential;
584	<	i->second.curr.angle = angle;
585	<	i->second.curr.potential = currTorsionPot;
586	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
587	<	}
571	>	bend->calcForce(angle, doParticlePot_);
572	>	RealType currBendPot = bend->getPotential();
573	>
574	>	bendPotential += bend->getPotential();
575	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
576	>	if (i == bendDataSets.end()) {
577	>	BendDataSet dataSet;
578	>	dataSet.prev.angle = dataSet.curr.angle = angle;
579	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
580	>	dataSet.deltaV = 0.0;
581	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
582	>	dataSet));
583	>	}else {
584	>	i->second.prev.angle = i->second.curr.angle;
585	>	i->second.prev.potential = i->second.curr.potential;
586	>	i->second.curr.angle = angle;
587	>	i->second.curr.potential = currBendPot;
588	>	i->second.deltaV =  fabs(i->second.curr.potential -
589	>	i->second.prev.potential);
590	>	}
591		}
592	<
592	>
593	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
594	>	torsion = mol->nextTorsion(torsionIter)) {
595	>	RealType angle;
596	>	torsion->calcForce(angle, doParticlePot_);
597	>	RealType currTorsionPot = torsion->getPotential();
598	>	torsionPotential += torsion->getPotential();
599	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
600	>	if (i == torsionDataSets.end()) {
601	>	TorsionDataSet dataSet;
602	>	dataSet.prev.angle = dataSet.curr.angle = angle;
603	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
604	>	dataSet.deltaV = 0.0;
605	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
606	>	}else {
607	>	i->second.prev.angle = i->second.curr.angle;
608	>	i->second.prev.potential = i->second.curr.potential;
609	>	i->second.curr.angle = angle;
610	>	i->second.curr.potential = currTorsionPot;
611	>	i->second.deltaV =  fabs(i->second.curr.potential -
612	>	i->second.prev.potential);
613	>	}
614	>	}
615	>
616	>	for (inversion = mol->beginInversion(inversionIter);
617	>	inversion != NULL;
618	>	inversion = mol->nextInversion(inversionIter)) {
619	>	RealType angle;
620	>	inversion->calcForce(angle, doParticlePot_);
621	>	RealType currInversionPot = inversion->getPotential();
622	>	inversionPotential += inversion->getPotential();
623	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
624	>	if (i == inversionDataSets.end()) {
625	>	InversionDataSet dataSet;
626	>	dataSet.prev.angle = dataSet.curr.angle = angle;
627	>	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
628	>	dataSet.deltaV = 0.0;
629	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
630	>	}else {
631	>	i->second.prev.angle = i->second.curr.angle;
632	>	i->second.prev.potential = i->second.curr.potential;
633	>	i->second.curr.angle = angle;
634	>	i->second.curr.potential = currInversionPot;
635	>	i->second.deltaV =  fabs(i->second.curr.potential -
636	>	i->second.prev.potential);
637	>	}
638	>	}
639		}
640	<
641	<	RealType  shortRangePotential = bondPotential + bendPotential + torsionPotential;
640	>
641	>	#ifdef IS_MPI
642	>	// Collect from all nodes.  This should eventually be moved into a
643	>	// SystemDecomposition, but this is a better place than in
644	>	// Thermo to do the collection.
645	>
646	>	MPI_Allreduce(MPI_IN_PLACE, &bondPotential, 1, MPI_REALTYPE,
647	>	MPI_SUM, MPI_COMM_WORLD);
648	>	MPI_Allreduce(MPI_IN_PLACE, &bendPotential, 1, MPI_REALTYPE,
649	>	MPI_SUM, MPI_COMM_WORLD);
650	>	MPI_Allreduce(MPI_IN_PLACE, &torsionPotential, 1,
651	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
652	>	MPI_Allreduce(MPI_IN_PLACE, &inversionPotential, 1,
653	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
654	>	#endif
655	>
656		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
657	<	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
658	<	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
659	<	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
660	<	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
657	>
658	>	curSnapshot->setBondPotential(bondPotential);
659	>	curSnapshot->setBendPotential(bendPotential);
660	>	curSnapshot->setTorsionPotential(torsionPotential);
661	>	curSnapshot->setInversionPotential(inversionPotential);
662
663	+	// RealType shortRangePotential = bondPotential + bendPotential +
664	+	//   torsionPotential +  inversionPotential;
665	+
666	+	// curSnapshot->setShortRangePotential(shortRangePotential);
667		}
668	+
669	+	void ForceManager::longRangeInteractions() {
670
671	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
672	<	Snapshot* curSnapshot;
673	<	DataStorage* config;
233	<	RealType* frc;
234	<	RealType* pos;
235	<	RealType* trq;
236	<	RealType* A;
237	<	RealType* electroFrame;
238	<	RealType* rc;
239	<
240	<	//get current snapshot from SimInfo
241	<	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
671	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
672	>	DataStorage* config = &(curSnapshot->atomData);
673	>	DataStorage* cgConfig = &(curSnapshot->cgData);
674
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);
675
676		//calculate the center of mass of cutoff group
677	+
678		SimInfo::MoleculeIterator mi;
679		Molecule* mol;
680		Molecule::CutoffGroupIterator ci;
681		CutoffGroup* cg;
256	–	Vector3d com;
257	–	std::vector<Vector3d> rcGroup;
682
683	<	if(info_->getNCutoffGroups() > 0){
684	<
685	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
686	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
687	<	cg->getCOM(com);
688	<	rcGroup.push_back(com);
683	>	if(info_->getNCutoffGroups() > 0){
684	>	for (mol = info_->beginMolecule(mi); mol != NULL;
685	>	mol = info_->nextMolecule(mi)) {
686	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
687	>	cg = mol->nextCutoffGroup(ci)) {
688	>	cg->updateCOM();
689		}
690	<	}// end for (mol)
267	<
268	<	rc = rcGroup[0].getArrayPointer();
690	>	}
691		} else {
692	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
693	<	rc = pos;
692	>	// center of mass of the group is the same as position of the atom
693	>	// if cutoff group does not exist
694	>	cgConfig->position = config->position;
695	>	cgConfig->velocity = config->velocity;
696		}
697	<
698	<	//initialize data before passing to fortran
699	<	RealType longRangePotential[LR_POT_TYPES];
276	<	RealType lrPot = 0.0;
697	>
698	>	fDecomp_->zeroWorkArrays();
699	>	fDecomp_->distributeData();
700
701	<	Mat3x3d tau;
702	<	short int passedCalcPot = needPotential;
703	<	short int passedCalcStress = needStress;
704	<	int isError = 0;
701	>	int cg1, cg2, atom1, atom2, topoDist;
702	>	Vector3d d_grp, dag, d, gvel2, vel2;
703	>	RealType rgrpsq, rgrp, r2, r;
704	>	RealType electroMult, vdwMult;
705	>	RealType vij;
706	>	Vector3d fij, fg, f1;
707	>	tuple3<RealType, RealType, RealType> cuts;
708	>	RealType rCut, rCutSq, rListSq;
709	>	bool in_switching_region;
710	>	RealType sw, dswdr, swderiv;
711	>	vector<int> atomListColumn, atomListRow;
712	>	InteractionData idat;
713	>	SelfData sdat;
714	>	RealType mf;
715	>	RealType vpair;
716	>	RealType dVdFQ1(0.0);
717	>	RealType dVdFQ2(0.0);
718	>	potVec longRangePotential(0.0);
719	>	RealType reciprocalPotential(0.0);
720	>	potVec workPot(0.0);
721	>	potVec exPot(0.0);
722	>	Vector3d eField1(0.0);
723	>	Vector3d eField2(0.0);
724	>	RealType sPot1(0.0);
725	>	RealType sPot2(0.0);
726	>
727	>	vector<int>::iterator ia, jb;
728
729	<	for (int i=0; i<LR_POT_TYPES;i++){
730	<	longRangePotential[i]=0.0; //Initialize array
729	>	int loopStart, loopEnd;
730	>
731	>	idat.rcut = &rCut;
732	>	idat.vdwMult = &vdwMult;
733	>	idat.electroMult = &electroMult;
734	>	idat.pot = &workPot;
735	>	idat.excludedPot = &exPot;
736	>	sdat.pot = fDecomp_->getEmbeddingPotential();
737	>	sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
738	>	idat.vpair = &vpair;
739	>	idat.dVdFQ1 = &dVdFQ1;
740	>	idat.dVdFQ2 = &dVdFQ2;
741	>	idat.eField1 = &eField1;
742	>	idat.eField2 = &eField2;
743	>	idat.sPot1 = &sPot1;
744	>	idat.sPot2 = &sPot2;
745	>	idat.f1 = &f1;
746	>	idat.sw = &sw;
747	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
748	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE ||
749	>	cutoffMethod_ == TAYLOR_SHIFTED) ? true : false;
750	>	idat.doParticlePot = doParticlePot_;
751	>	idat.doElectricField = doElectricField_;
752	>	idat.doSitePotential = doSitePotential_;
753	>	sdat.doParticlePot = doParticlePot_;
754	>
755	>	loopEnd = PAIR_LOOP;
756	>	if (info_->requiresPrepair() ) {
757	>	loopStart = PREPAIR_LOOP;
758	>	} else {
759	>	loopStart = PAIR_LOOP;
760		}
761	+	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
762	+
763	+	if (iLoop == loopStart) {
764	+	bool update_nlist = fDecomp_->checkNeighborList();
765	+	if (update_nlist) {
766	+	if (!usePeriodicBoundaryConditions_)
767	+	Mat3x3d bbox = thermo->getBoundingBox();
768	+	fDecomp_->buildNeighborList(neighborList_);
769	+	}
770	+	}
771
772	<	doForceLoop( pos,
773	<	rc,
774	<	A,
775	<	electroFrame,
776	<	frc,
777	<	trq,
778	<	tau.getArrayPointer(),
294	<	longRangePotential,
295	<	&passedCalcPot,
296	<	&passedCalcStress,
297	<	&isError );
772	>	for (vector<pair<int, int> >::iterator it = neighborList_.begin();
773	>	it != neighborList_.end(); ++it) {
774	>
775	>	cg1 = (*it).first;
776	>	cg2 = (*it).second;
777	>
778	>	fDecomp_->getGroupCutoffs(cg1, cg2, rCut, rCutSq, rListSq);
779
780	<	if( isError ){
781	<	sprintf( painCave.errMsg,
782	<	"Error returned from the fortran force calculation.\n" );
783	<	painCave.isFatal = 1;
784	<	simError();
780	>	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
781	>
782	>	// already wrapped in the getIntergroupVector call:
783	>	// curSnapshot->wrapVector(d_grp);
784	>	rgrpsq = d_grp.lengthSquare();
785	>
786	>	if (rgrpsq < rCutSq) {
787	>	if (iLoop == PAIR_LOOP) {
788	>	vij = 0.0;
789	>	fij.zero();
790	>	eField1.zero();
791	>	eField2.zero();
792	>	sPot1 = 0.0;
793	>	sPot2 = 0.0;
794	>	}
795	>
796	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
797	>	rgrp);
798	>
799	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
800	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
801	>
802	>	if (doHeatFlux_)
803	>	gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
804	>
805	>	for (ia = atomListRow.begin();
806	>	ia != atomListRow.end(); ++ia) {
807	>	atom1 = (*ia);
808	>
809	>	for (jb = atomListColumn.begin();
810	>	jb != atomListColumn.end(); ++jb) {
811	>	atom2 = (*jb);
812	>
813	>	if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
814	>
815	>	vpair = 0.0;
816	>	workPot = 0.0;
817	>	exPot = 0.0;
818	>	f1.zero();
819	>	dVdFQ1 = 0.0;
820	>	dVdFQ2 = 0.0;
821	>
822	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
823	>
824	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
825	>	vdwMult = vdwScale_[topoDist];
826	>	electroMult = electrostaticScale_[topoDist];
827	>
828	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
829	>	idat.d = &d_grp;
830	>	idat.r2 = &rgrpsq;
831	>	if (doHeatFlux_)
832	>	vel2 = gvel2;
833	>	} else {
834	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
835	>	curSnapshot->wrapVector( d );
836	>	r2 = d.lengthSquare();
837	>	idat.d = &d;
838	>	idat.r2 = &r2;
839	>	if (doHeatFlux_)
840	>	vel2 = fDecomp_->getAtomVelocityColumn(atom2);
841	>	}
842	>
843	>	r = sqrt( *(idat.r2) );
844	>	idat.rij = &r;
845	>
846	>	if (iLoop == PREPAIR_LOOP) {
847	>	interactionMan_->doPrePair(idat);
848	>	} else {
849	>	interactionMan_->doPair(idat);
850	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
851	>	vij += vpair;
852	>	fij += f1;
853	>	stressTensor -= outProduct( *(idat.d), f1);
854	>	if (doHeatFlux_)
855	>	fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
856	>	}
857	>	}
858	>	}
859	>	}
860	>
861	>	if (iLoop == PAIR_LOOP) {
862	>	if (in_switching_region) {
863	>	swderiv = vij * dswdr / rgrp;
864	>	fg = swderiv * d_grp;
865	>	fij += fg;
866	>
867	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
868	>	if (!fDecomp_->skipAtomPair(atomListRow[0],
869	>	atomListColumn[0],
870	>	cg1, cg2)) {
871	>	stressTensor -= outProduct( *(idat.d), fg);
872	>	if (doHeatFlux_)
873	>	fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
874	>	}
875	>	}
876	>
877	>	for (ia = atomListRow.begin();
878	>	ia != atomListRow.end(); ++ia) {
879	>	atom1 = (*ia);
880	>	mf = fDecomp_->getMassFactorRow(atom1);
881	>	// fg is the force on atom ia due to cutoff group's
882	>	// presence in switching region
883	>	fg = swderiv * d_grp * mf;
884	>	fDecomp_->addForceToAtomRow(atom1, fg);
885	>	if (atomListRow.size() > 1) {
886	>	if (info_->usesAtomicVirial()) {
887	>	// find the distance between the atom
888	>	// and the center of the cutoff group:
889	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
890	>	stressTensor -= outProduct(dag, fg);
891	>	if (doHeatFlux_)
892	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
893	>	}
894	>	}
895	>	}
896	>	for (jb = atomListColumn.begin();
897	>	jb != atomListColumn.end(); ++jb) {
898	>	atom2 = (*jb);
899	>	mf = fDecomp_->getMassFactorColumn(atom2);
900	>	// fg is the force on atom jb due to cutoff group's
901	>	// presence in switching region
902	>	fg = -swderiv * d_grp * mf;
903	>	fDecomp_->addForceToAtomColumn(atom2, fg);
904	>
905	>	if (atomListColumn.size() > 1) {
906	>	if (info_->usesAtomicVirial()) {
907	>	// find the distance between the atom
908	>	// and the center of the cutoff group:
909	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
910	>	stressTensor -= outProduct(dag, fg);
911	>	if (doHeatFlux_)
912	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
913	>	}
914	>	}
915	>	}
916	>	}
917	>	//if (!info_->usesAtomicVirial()) {
918	>	//  stressTensor -= outProduct(d_grp, fij);
919	>	//  if (doHeatFlux_)
920	>	//     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
921	>	//}
922	>	}
923	>	}
924	>	}
925	>
926	>	if (iLoop == PREPAIR_LOOP) {
927	>	if (info_->requiresPrepair()) {
928	>
929	>	fDecomp_->collectIntermediateData();
930	>
931	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
932	>	fDecomp_->fillSelfData(sdat, atom1);
933	>	interactionMan_->doPreForce(sdat);
934	>	}
935	>
936	>	fDecomp_->distributeIntermediateData();
937	>
938	>	}
939	>	}
940		}
941	<	for (int i=0; i<LR_POT_TYPES;i++){
942	<	lrPot += longRangePotential[i]; //Quick hack
941	>
942	>	// collects pairwise information
943	>	fDecomp_->collectData();
944	>	if (cutoffMethod_ == EWALD_FULL) {
945	>	interactionMan_->doReciprocalSpaceSum(reciprocalPotential);
946	>
947	>	curSnapshot->setReciprocalPotential(reciprocalPotential);
948		}
949	+
950	+	if (info_->requiresSelfCorrection()) {
951	+	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
952	+	fDecomp_->fillSelfData(sdat, atom1);
953	+	interactionMan_->doSelfCorrection(sdat);
954	+	}
955	+	}
956
957	<	//store the tau and long range potential
958	<	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];
957	>	// collects single-atom information
958	>	fDecomp_->collectSelfData();
959
960	<	curSnapshot->statData.setTau(tau);
961	<	}
960	>	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
961	>	*(fDecomp_->getPairwisePotential());
962
963	+	curSnapshot->setLongRangePotential(longRangePotential);
964	+
965	+	curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
966	+	*(fDecomp_->getExcludedPotential()));
967
968	+	}
969	+
970		void ForceManager::postCalculation() {
971	+
972	+	vector<Perturbation*>::iterator pi;
973	+	for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
974	+	(*pi)->applyPerturbation();
975	+	}
976	+
977		SimInfo::MoleculeIterator mi;
978		Molecule* mol;
979		Molecule::RigidBodyIterator rbIter;
980		RigidBody* rb;
981	<
981	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
982	>
983		// collect the atomic forces onto rigid bodies
984	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
985	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
986	<	rb->calcForcesAndTorques();
984	>
985	>	for (mol = info_->beginMolecule(mi); mol != NULL;
986	>	mol = info_->nextMolecule(mi)) {
987	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
988	>	rb = mol->nextRigidBody(rbIter)) {
989	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
990	>	stressTensor += rbTau;
991		}
992		}
993	+
994	+	#ifdef IS_MPI
995	+	MPI_Allreduce(MPI_IN_PLACE, stressTensor.getArrayPointer(), 9,
996	+	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
997	+	#endif
998	+	curSnapshot->setStressTensor(stressTensor);
999	+
1000	+	if (info_->getSimParams()->getUseLongRangeCorrections()) {
1001	+	/*
1002	+	RealType vol = curSnapshot->getVolume();
1003	+	RealType Elrc(0.0);
1004	+	RealType Wlrc(0.0);
1005
1006	<	}
1006	>	set<AtomType*>::iterator i;
1007	>	set<AtomType*>::iterator j;
1008	>
1009	>	RealType n_i, n_j;
1010	>	RealType rho_i, rho_j;
1011	>	pair<RealType, RealType> LRI;
1012	>
1013	>	for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
1014	>	n_i = RealType(info_->getGlobalCountOfType(*i));
1015	>	rho_i = n_i /  vol;
1016	>	for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) {
1017	>	n_j = RealType(info_->getGlobalCountOfType(*j));
1018	>	rho_j = n_j / vol;
1019	>
1020	>	LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) );
1021
1022	<	} //end namespace oopse
1022	>	Elrc += n_i   * rho_j * LRI.first;
1023	>	Wlrc -= rho_i * rho_j * LRI.second;
1024	>	}
1025	>	}
1026	>	Elrc *= 2.0 * NumericConstant::PI;
1027	>	Wlrc *= 2.0 * NumericConstant::PI;
1028	>
1029	>	RealType lrp = curSnapshot->getLongRangePotential();
1030	>	curSnapshot->setLongRangePotential(lrp + Elrc);
1031	>	stressTensor += Wlrc * SquareMatrix3<RealType>::identity();
1032	>	curSnapshot->setStressTensor(stressTensor);
1033	>	*/
1034	>
1035	>	}
1036	>	}
1037	>	}

Comparing trunk/src/brains/ForceManager.cpp (property svn:keywords):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 2047 by gezelter, Thu Dec 11 16:16:43 2014 UTC

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