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root/OpenMD/branches/development/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.
branches/development/src/brains/ForceManager.cpp (file contents), Revision 1616 by gezelter, Tue Aug 30 15:45:35 2011 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 47 | Line 47
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 "parallel/ForceMatrixDecomposition.hpp"
61
62	<	/*
63	<	struct BendOrderStruct {
64	<	Bend* bend;
63	<	BendDataSet dataSet;
64	<	};
65	<	struct TorsionOrderStruct {
66	<	Torsion* torsion;
67	<	TorsionDataSet dataSet;
68	<	};
62	>	#include <cstdio>
63	>	#include <iostream>
64	>	#include <iomanip>
65
66	<	bool  BendSortFunctor(const BendOrderStruct& b1, const BendOrderStruct& b2) {
67	<	return b1.dataSet.deltaV < b2.dataSet.deltaV;
66	>	using namespace std;
67	>	namespace OpenMD {
68	>
69	>	ForceManager::ForceManager(SimInfo * info) : info_(info) {
70	>	forceField_ = info_->getForceField();
71	>	interactionMan_ = new InteractionManager();
72	>	fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
73		}
74
75	<	bool  TorsionSortFunctor(const TorsionOrderStruct& t1, const TorsionOrderStruct& t2) {
76	<	return t1.dataSet.deltaV < t2.dataSet.deltaV;
77	<	}
78	<	*/
79	<	void ForceManager::calcForces(bool needPotential, bool needStress) {
80	<
81	<	if (!info_->isFortranInitialized()) {
82	<	info_->update();
75	>	/**
76	>	* setupCutoffs
77	>	*
78	>	* Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
79	>	* and cutoffPolicy
80	>	*
81	>	* cutoffRadius : realType
82	>	*  If the cutoffRadius was explicitly set, use that value.
83	>	*  If the cutoffRadius was not explicitly set:
84	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
85	>	*      No electrostatic atoms?  Poll the atom types present in the
86	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
87	>	*      Use the maximum suggested value that was found.
88	>	*
89	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
90	>	*                        or SHIFTED_POTENTIAL)
91	>	*      If cutoffMethod was explicitly set, use that choice.
92	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
93	>	*
94	>	* cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
95	>	*      If cutoffPolicy was explicitly set, use that choice.
96	>	*      If cutoffPolicy was not explicitly set, use TRADITIONAL
97	>	*
98	>	* switchingRadius : realType
99	>	*  If the cutoffMethod was set to SWITCHED:
100	>	*      If the switchingRadius was explicitly set, use that value
101	>	*          (but do a sanity check first).
102	>	*      If the switchingRadius was not explicitly set: use 0.85 *
103	>	*      cutoffRadius_
104	>	*  If the cutoffMethod was not set to SWITCHED:
105	>	*      Set switchingRadius equal to cutoffRadius for safety.
106	>	*/
107	>	void ForceManager::setupCutoffs() {
108	>
109	>	Globals* simParams_ = info_->getSimParams();
110	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
111	>	int mdFileVersion;
112	>
113	>	if (simParams_->haveMDfileVersion())
114	>	mdFileVersion = simParams_->getMDfileVersion();
115	>	else
116	>	mdFileVersion = 0;
117	>
118	>	if (simParams_->haveCutoffRadius()) {
119	>	rCut_ = simParams_->getCutoffRadius();
120	>	} else {
121	>	if (info_->usesElectrostaticAtoms()) {
122	>	sprintf(painCave.errMsg,
123	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
124	>	"\tOpenMD will use a default value of 12.0 angstroms"
125	>	"\tfor the cutoffRadius.\n");
126	>	painCave.isFatal = 0;
127	>	painCave.severity = OPENMD_INFO;
128	>	simError();
129	>	rCut_ = 12.0;
130	>	} else {
131	>	RealType thisCut;
132	>	set<AtomType*>::iterator i;
133	>	set<AtomType*> atomTypes;
134	>	atomTypes = info_->getSimulatedAtomTypes();
135	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
136	>	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
137	>	rCut_ = max(thisCut, rCut_);
138	>	}
139	>	sprintf(painCave.errMsg,
140	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
141	>	"\tOpenMD will use %lf angstroms.\n",
142	>	rCut_);
143	>	painCave.isFatal = 0;
144	>	painCave.severity = OPENMD_INFO;
145	>	simError();
146	>	}
147		}
148
149	<	preCalculation();
150	<
86	<	calcShortRangeInteraction();
149	>	fDecomp_->setUserCutoff(rCut_);
150	>	interactionMan_->setCutoffRadius(rCut_);
151
152	<	calcLongRangeInteraction(needPotential, needStress);
152	>	map<string, CutoffMethod> stringToCutoffMethod;
153	>	stringToCutoffMethod["HARD"] = HARD;
154	>	stringToCutoffMethod["SWITCHED"] = SWITCHED;
155	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
156	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
157	>
158	>	if (simParams_->haveCutoffMethod()) {
159	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
160	>	map<string, CutoffMethod>::iterator i;
161	>	i = stringToCutoffMethod.find(cutMeth);
162	>	if (i == stringToCutoffMethod.end()) {
163	>	sprintf(painCave.errMsg,
164	>	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
165	>	"\tShould be one of: "
166	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
167	>	cutMeth.c_str());
168	>	painCave.isFatal = 1;
169	>	painCave.severity = OPENMD_ERROR;
170	>	simError();
171	>	} else {
172	>	cutoffMethod_ = i->second;
173	>	}
174	>	} else {
175	>	if (mdFileVersion > 1) {
176	>	sprintf(painCave.errMsg,
177	>	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
178	>	"\tOpenMD will use SHIFTED_FORCE.\n");
179	>	painCave.isFatal = 0;
180	>	painCave.severity = OPENMD_INFO;
181	>	simError();
182	>	cutoffMethod_ = SHIFTED_FORCE;
183	>	} else {
184	>	// handle the case where the old file version was in play
185	>	// (there should be no cutoffMethod, so we have to deduce it
186	>	// from other data).
187
188	<	postCalculation();
188	>	sprintf(painCave.errMsg,
189	>	"ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
190	>	"\tOpenMD found a file which does not set a cutoffMethod.\n"
191	>	"\tOpenMD will attempt to deduce a cutoffMethod using the\n"
192	>	"\tbehavior of the older (version 1) code.  To remove this\n"
193	>	"\twarning, add an explicit cutoffMethod and change the top\n"
194	>	"\tof the file so that it begins with <OpenMD version=2>\n");
195	>	painCave.isFatal = 0;
196	>	painCave.severity = OPENMD_WARNING;
197	>	simError();
198	>
199	>	// The old file version tethered the shifting behavior to the
200	>	// electrostaticSummationMethod keyword.
201	>
202	>	if (simParams_->haveElectrostaticSummationMethod()) {
203	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
204	>	toUpper(myMethod);
205	>
206	>	if (myMethod == "SHIFTED_POTENTIAL") {
207	>	cutoffMethod_ = SHIFTED_POTENTIAL;
208	>	} else if (myMethod == "SHIFTED_FORCE") {
209	>	cutoffMethod_ = SHIFTED_FORCE;
210	>	}
211	>
212	>	if (simParams_->haveSwitchingRadius())
213	>	rSwitch_ = simParams_->getSwitchingRadius();
214
215	<	/*
216	<	std::vector<BendOrderStruct> bendOrderStruct;
217	<	for(std::map<Bend*, BendDataSet>::iterator i = bendDataSets.begin(); i != bendDataSets.end(); ++i) {
218	<	BendOrderStruct tmp;
219	<	tmp.bend= const_cast<Bend*>(i->first);
220	<	tmp.dataSet = i->second;
221	<	bendOrderStruct.push_back(tmp);
215	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
216	>	if (simParams_->haveSwitchingRadius()){
217	>	sprintf(painCave.errMsg,
218	>	"ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
219	>	"\tA value was set for the switchingRadius\n"
220	>	"\teven though the electrostaticSummationMethod was\n"
221	>	"\tset to %s\n", myMethod.c_str());
222	>	painCave.severity = OPENMD_WARNING;
223	>	painCave.isFatal = 1;
224	>	simError();
225	>	}
226	>	}
227	>	if (abs(rCut_ - rSwitch_) < 0.0001) {
228	>	if (cutoffMethod_ == SHIFTED_FORCE) {
229	>	sprintf(painCave.errMsg,
230	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
231	>	"\tcutoffRadius and switchingRadius are set to the\n"
232	>	"\tsame value.  OpenMD will use shifted force\n"
233	>	"\tpotentials instead of switching functions.\n");
234	>	painCave.isFatal = 0;
235	>	painCave.severity = OPENMD_WARNING;
236	>	simError();
237	>	} else {
238	>	cutoffMethod_ = SHIFTED_POTENTIAL;
239	>	sprintf(painCave.errMsg,
240	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
241	>	"\tcutoffRadius and switchingRadius are set to the\n"
242	>	"\tsame value.  OpenMD will use shifted potentials\n"
243	>	"\tinstead of switching functions.\n");
244	>	painCave.isFatal = 0;
245	>	painCave.severity = OPENMD_WARNING;
246	>	simError();
247	>	}
248	>	}
249	>	}
250	>	}
251		}
252
253	<	std::vector<TorsionOrderStruct> torsionOrderStruct;
254	<	for(std::map<Torsion*, TorsionDataSet>::iterator j = torsionDataSets.begin(); j != torsionDataSets.end(); ++j) {
255	<	TorsionOrderStruct tmp;
256	<	tmp.torsion = const_cast<Torsion*>(j->first);
257	<	tmp.dataSet = j->second;
258	<	torsionOrderStruct.push_back(tmp);
253	>	map<string, CutoffPolicy> stringToCutoffPolicy;
254	>	stringToCutoffPolicy["MIX"] = MIX;
255	>	stringToCutoffPolicy["MAX"] = MAX;
256	>	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
257	>
258	>	std::string cutPolicy;
259	>	if (forceFieldOptions_.haveCutoffPolicy()){
260	>	cutPolicy = forceFieldOptions_.getCutoffPolicy();
261	>	}else if (simParams_->haveCutoffPolicy()) {
262	>	cutPolicy = simParams_->getCutoffPolicy();
263		}
264	+
265	+	if (!cutPolicy.empty()){
266	+	toUpper(cutPolicy);
267	+	map<string, CutoffPolicy>::iterator i;
268	+	i = stringToCutoffPolicy.find(cutPolicy);
269	+
270	+	if (i == stringToCutoffPolicy.end()) {
271	+	sprintf(painCave.errMsg,
272	+	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
273	+	"\tShould be one of: "
274	+	"MIX, MAX, or TRADITIONAL\n",
275	+	cutPolicy.c_str());
276	+	painCave.isFatal = 1;
277	+	painCave.severity = OPENMD_ERROR;
278	+	simError();
279	+	} else {
280	+	cutoffPolicy_ = i->second;
281	+	}
282	+	} else {
283	+	sprintf(painCave.errMsg,
284	+	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
285	+	"\tOpenMD will use TRADITIONAL.\n");
286	+	painCave.isFatal = 0;
287	+	painCave.severity = OPENMD_INFO;
288	+	simError();
289	+	cutoffPolicy_ = TRADITIONAL;
290	+	}
291	+
292	+	fDecomp_->setCutoffPolicy(cutoffPolicy_);
293	+
294	+	// create the switching function object:
295	+
296	+	switcher_ = new SwitchingFunction();
297	+
298	+	if (cutoffMethod_ == SWITCHED) {
299	+	if (simParams_->haveSwitchingRadius()) {
300	+	rSwitch_ = simParams_->getSwitchingRadius();
301	+	if (rSwitch_ > rCut_) {
302	+	sprintf(painCave.errMsg,
303	+	"ForceManager::setupCutoffs: switchingRadius (%f) is larger "
304	+	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
305	+	painCave.isFatal = 1;
306	+	painCave.severity = OPENMD_ERROR;
307	+	simError();
308	+	}
309	+	} else {
310	+	rSwitch_ = 0.85 * rCut_;
311	+	sprintf(painCave.errMsg,
312	+	"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
313	+	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
314	+	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
315	+	painCave.isFatal = 0;
316	+	painCave.severity = OPENMD_WARNING;
317	+	simError();
318	+	}
319	+	} else {
320	+	if (simParams_->haveSwitchingRadius()) {
321	+	map<string, CutoffMethod>::const_iterator it;
322	+	string theMeth;
323	+	for (it = stringToCutoffMethod.begin();
324	+	it != stringToCutoffMethod.end(); ++it) {
325	+	if (it->second == cutoffMethod_) {
326	+	theMeth = it->first;
327	+	break;
328	+	}
329	+	}
330	+	sprintf(painCave.errMsg,
331	+	"ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
332	+	"\tis not set to SWITCHED, so switchingRadius value\n"
333	+	"\twill be ignored for this simulation\n", theMeth.c_str());
334	+	painCave.isFatal = 0;
335	+	painCave.severity = OPENMD_WARNING;
336	+	simError();
337	+	}
338	+
339	+	rSwitch_ = rCut_;
340	+	}
341
342	<	std::sort(bendOrderStruct.begin(), bendOrderStruct.end(), std::ptr_fun(BendSortFunctor));
343	<	std::sort(torsionOrderStruct.begin(), torsionOrderStruct.end(), std::ptr_fun(TorsionSortFunctor));
344	<	for (std::vector<BendOrderStruct>::iterator k = bendOrderStruct.begin(); k != bendOrderStruct.end(); ++k) {
345	<	Bend* bend = k->bend;
346	<	std::cout << "Bend: atom1=" <<bend->getAtomA()->getGlobalIndex() << ",atom2 = "<< bend->getAtomB()->getGlobalIndex() << ",atom3="<<bend->getAtomC()->getGlobalIndex() << " ";
347	<	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;
342	>	// Default to cubic switching function.
343	>	sft_ = cubic;
344	>	if (simParams_->haveSwitchingFunctionType()) {
345	>	string funcType = simParams_->getSwitchingFunctionType();
346	>	toUpper(funcType);
347	>	if (funcType == "CUBIC") {
348	>	sft_ = cubic;
349	>	} else {
350	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
351	>	sft_ = fifth_order_poly;
352	>	} else {
353	>	// throw error
354	>	sprintf( painCave.errMsg,
355	>	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
356	>	"\tswitchingFunctionType must be one of: "
357	>	"\"cubic\" or \"fifth_order_polynomial\".",
358	>	funcType.c_str() );
359	>	painCave.isFatal = 1;
360	>	painCave.severity = OPENMD_ERROR;
361	>	simError();
362	>	}
363	>	}
364		}
365	<	for (std::vector<TorsionOrderStruct>::iterator l = torsionOrderStruct.begin(); l != torsionOrderStruct.end(); ++l) {
366	<	Torsion* torsion = l->torsion;
367	<	std::cout << "Torsion: atom1=" <<torsion->getAtomA()->getGlobalIndex() << ",atom2 = "<< torsion->getAtomB()->getGlobalIndex() << ",atom3="<<torsion->getAtomC()->getGlobalIndex() << ",atom4="<<torsion->getAtomD()->getGlobalIndex()<< " ";
368	<	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;
365	>	switcher_->setSwitchType(sft_);
366	>	switcher_->setSwitch(rSwitch_, rCut_);
367	>	interactionMan_->setSwitchingRadius(rSwitch_);
368	>	}
369	>
370	>
371	>
372	>
373	>	void ForceManager::initialize() {
374	>
375	>	if (!info_->isTopologyDone()) {
376	>
377	>	info_->update();
378	>	interactionMan_->setSimInfo(info_);
379	>	interactionMan_->initialize();
380	>
381	>	// We want to delay the cutoffs until after the interaction
382	>	// manager has set up the atom-atom interactions so that we can
383	>	// query them for suggested cutoff values
384	>	setupCutoffs();
385	>
386	>	info_->prepareTopology();
387		}
388	<	*/
388	>
389	>	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
390	>
391	>	// Force fields can set options on how to scale van der Waals and
392	>	// electrostatic interactions for atoms connected via bonds, bends
393	>	// and torsions in this case the topological distance between
394	>	// atoms is:
395	>	// 0 = topologically unconnected
396	>	// 1 = bonded together
397	>	// 2 = connected via a bend
398	>	// 3 = connected via a torsion
399	>
400	>	vdwScale_.reserve(4);
401	>	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
402	>
403	>	electrostaticScale_.reserve(4);
404	>	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
405	>
406	>	vdwScale_[0] = 1.0;
407	>	vdwScale_[1] = fopts.getvdw12scale();
408	>	vdwScale_[2] = fopts.getvdw13scale();
409	>	vdwScale_[3] = fopts.getvdw14scale();
410	>
411	>	electrostaticScale_[0] = 1.0;
412	>	electrostaticScale_[1] = fopts.getelectrostatic12scale();
413	>	electrostaticScale_[2] = fopts.getelectrostatic13scale();
414	>	electrostaticScale_[3] = fopts.getelectrostatic14scale();
415	>
416	>	fDecomp_->distributeInitialData();
417	>
418	>	initialized_ = true;
419	>
420		}
421
422	+	void ForceManager::calcForces() {
423	+
424	+	if (!initialized_) initialize();
425	+
426	+	preCalculation();
427	+	shortRangeInteractions();
428	+	longRangeInteractions();
429	+	postCalculation();
430	+	}
431	+
432		void ForceManager::preCalculation() {
433		SimInfo::MoleculeIterator mi;
434		Molecule* mol;
#	Line 128 | Line 436 | namespace oopse {
436		Atom* atom;
437		Molecule::RigidBodyIterator rbIter;
438		RigidBody* rb;
439	+	Molecule::CutoffGroupIterator ci;
440	+	CutoffGroup* cg;
441
442		// forces are zeroed here, before any are accumulated.
443	<	// NOTE: do not rezero the forces in Fortran.
444	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
445	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
443	>
444	>	for (mol = info_->beginMolecule(mi); mol != NULL;
445	>	mol = info_->nextMolecule(mi)) {
446	>	for(atom = mol->beginAtom(ai); atom != NULL;
447	>	atom = mol->nextAtom(ai)) {
448		atom->zeroForcesAndTorques();
449		}
450	<
450	>
451		//change the positions of atoms which belong to the rigidbodies
452	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
452	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
453	>	rb = mol->nextRigidBody(rbIter)) {
454		rb->zeroForcesAndTorques();
455		}
456	+
457	+	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
458	+	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
459	+	cg = mol->nextCutoffGroup(ci)) {
460	+	//calculate the center of mass of cutoff group
461	+	cg->updateCOM();
462	+	}
463	+	}
464		}
465
466	+	// Zero out the stress tensor
467	+	tau *= 0.0;
468	+
469		}
470	<
471	<	void ForceManager::calcShortRangeInteraction() {
470	>
471	>	void ForceManager::shortRangeInteractions() {
472		Molecule* mol;
473		RigidBody* rb;
474		Bond* bond;
475		Bend* bend;
476		Torsion* torsion;
477	+	Inversion* inversion;
478		SimInfo::MoleculeIterator mi;
479		Molecule::RigidBodyIterator rbIter;
480		Molecule::BondIterator bondIter;;
481		Molecule::BendIterator  bendIter;
482		Molecule::TorsionIterator  torsionIter;
483	+	Molecule::InversionIterator  inversionIter;
484		RealType bondPotential = 0.0;
485		RealType bendPotential = 0.0;
486		RealType torsionPotential = 0.0;
487	+	RealType inversionPotential = 0.0;
488
489		//calculate short range interactions
490	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
490	>	for (mol = info_->beginMolecule(mi); mol != NULL;
491	>	mol = info_->nextMolecule(mi)) {
492
493		//change the positions of atoms which belong to the rigidbodies
494	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
495	<	rb->updateAtoms();
494	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
495	>	rb = mol->nextRigidBody(rbIter)) {
496	>	rb->updateAtoms();
497		}
498
499	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
499	>	for (bond = mol->beginBond(bondIter); bond != NULL;
500	>	bond = mol->nextBond(bondIter)) {
501		bond->calcForce();
502		bondPotential += bond->getPotential();
503		}
504
505	<
506	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
507	<
508	<	RealType angle;
509	<	bend->calcForce(angle);
510	<	RealType currBendPot = bend->getPotential();
511	<	bendPotential += bend->getPotential();
512	<	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
513	<	if (i == bendDataSets.end()) {
514	<	BendDataSet dataSet;
515	<	dataSet.prev.angle = dataSet.curr.angle = angle;
516	<	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
517	<	dataSet.deltaV = 0.0;
518	<	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
519	<	}else {
520	<	i->second.prev.angle = i->second.curr.angle;
521	<	i->second.prev.potential = i->second.curr.potential;
522	<	i->second.curr.angle = angle;
523	<	i->second.curr.potential = currBendPot;
524	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
525	<	}
505	>	for (bend = mol->beginBend(bendIter); bend != NULL;
506	>	bend = mol->nextBend(bendIter)) {
507	>
508	>	RealType angle;
509	>	bend->calcForce(angle);
510	>	RealType currBendPot = bend->getPotential();
511	>
512	>	bendPotential += bend->getPotential();
513	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
514	>	if (i == bendDataSets.end()) {
515	>	BendDataSet dataSet;
516	>	dataSet.prev.angle = dataSet.curr.angle = angle;
517	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
518	>	dataSet.deltaV = 0.0;
519	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
520	>	dataSet));
521	>	}else {
522	>	i->second.prev.angle = i->second.curr.angle;
523	>	i->second.prev.potential = i->second.curr.potential;
524	>	i->second.curr.angle = angle;
525	>	i->second.curr.potential = currBendPot;
526	>	i->second.deltaV =  fabs(i->second.curr.potential -
527	>	i->second.prev.potential);
528	>	}
529		}
530	<
531	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
530	>
531	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
532	>	torsion = mol->nextTorsion(torsionIter)) {
533		RealType angle;
534	<	torsion->calcForce(angle);
534	>	torsion->calcForce(angle);
535		RealType currTorsionPot = torsion->getPotential();
536	<	torsionPotential += torsion->getPotential();
537	<	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
538	<	if (i == torsionDataSets.end()) {
539	<	TorsionDataSet dataSet;
540	<	dataSet.prev.angle = dataSet.curr.angle = angle;
541	<	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
542	<	dataSet.deltaV = 0.0;
543	<	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
544	<	}else {
545	<	i->second.prev.angle = i->second.curr.angle;
546	<	i->second.prev.potential = i->second.curr.potential;
547	<	i->second.curr.angle = angle;
548	<	i->second.curr.potential = currTorsionPot;
549	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
550	<	}
551	<	}
552	<
536	>	torsionPotential += torsion->getPotential();
537	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
538	>	if (i == torsionDataSets.end()) {
539	>	TorsionDataSet dataSet;
540	>	dataSet.prev.angle = dataSet.curr.angle = angle;
541	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
542	>	dataSet.deltaV = 0.0;
543	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
544	>	}else {
545	>	i->second.prev.angle = i->second.curr.angle;
546	>	i->second.prev.potential = i->second.curr.potential;
547	>	i->second.curr.angle = angle;
548	>	i->second.curr.potential = currTorsionPot;
549	>	i->second.deltaV =  fabs(i->second.curr.potential -
550	>	i->second.prev.potential);
551	>	}
552	>	}
553	>
554	>	for (inversion = mol->beginInversion(inversionIter);
555	>	inversion != NULL;
556	>	inversion = mol->nextInversion(inversionIter)) {
557	>	RealType angle;
558	>	inversion->calcForce(angle);
559	>	RealType currInversionPot = inversion->getPotential();
560	>	inversionPotential += inversion->getPotential();
561	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
562	>	if (i == inversionDataSets.end()) {
563	>	InversionDataSet dataSet;
564	>	dataSet.prev.angle = dataSet.curr.angle = angle;
565	>	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
566	>	dataSet.deltaV = 0.0;
567	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
568	>	}else {
569	>	i->second.prev.angle = i->second.curr.angle;
570	>	i->second.prev.potential = i->second.curr.potential;
571	>	i->second.curr.angle = angle;
572	>	i->second.curr.potential = currInversionPot;
573	>	i->second.deltaV =  fabs(i->second.curr.potential -
574	>	i->second.prev.potential);
575	>	}
576	>	}
577		}
578
579	<	RealType  shortRangePotential = bondPotential + bendPotential + torsionPotential;
579	>	RealType  shortRangePotential = bondPotential + bendPotential +
580	>	torsionPotential +  inversionPotential;
581		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
582		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
583		curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
584		curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
585		curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
586	<
586	>	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
587		}
588	+
589	+	void ForceManager::longRangeInteractions() {
590
591	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
592	<	Snapshot* curSnapshot;
593	<	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();
591	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
592	>	DataStorage* config = &(curSnapshot->atomData);
593	>	DataStorage* cgConfig = &(curSnapshot->cgData);
594
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);
250	–
595		//calculate the center of mass of cutoff group
596	+
597		SimInfo::MoleculeIterator mi;
598		Molecule* mol;
599		Molecule::CutoffGroupIterator ci;
600		CutoffGroup* cg;
256	–	Vector3d com;
257	–	std::vector<Vector3d> rcGroup;
601
602	<	if(info_->getNCutoffGroups() > 0){
603	<
604	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
605	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
606	<	cg->getCOM(com);
607	<	rcGroup.push_back(com);
602	>	if(info_->getNCutoffGroups() > 0){
603	>	for (mol = info_->beginMolecule(mi); mol != NULL;
604	>	mol = info_->nextMolecule(mi)) {
605	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
606	>	cg = mol->nextCutoffGroup(ci)) {
607	>	cg->updateCOM();
608		}
609	<	}// end for (mol)
267	<
268	<	rc = rcGroup[0].getArrayPointer();
609	>	}
610		} else {
611	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
612	<	rc = pos;
611	>	// center of mass of the group is the same as position of the atom
612	>	// if cutoff group does not exist
613	>	cgConfig->position = config->position;
614		}
615	<
616	<	//initialize data before passing to fortran
617	<	RealType longRangePotential[LR_POT_TYPES];
276	<	RealType lrPot = 0.0;
615	>
616	>	fDecomp_->zeroWorkArrays();
617	>	fDecomp_->distributeData();
618
619	<	Mat3x3d tau;
620	<	short int passedCalcPot = needPotential;
621	<	short int passedCalcStress = needStress;
622	<	int isError = 0;
619	>	int cg1, cg2, atom1, atom2, topoDist;
620	>	Vector3d d_grp, dag, d;
621	>	RealType rgrpsq, rgrp, r2, r;
622	>	RealType electroMult, vdwMult;
623	>	RealType vij;
624	>	Vector3d fij, fg, f1;
625	>	tuple3<RealType, RealType, RealType> cuts;
626	>	RealType rCutSq;
627	>	bool in_switching_region;
628	>	RealType sw, dswdr, swderiv;
629	>	vector<int> atomListColumn, atomListRow, atomListLocal;
630	>	InteractionData idat;
631	>	SelfData sdat;
632	>	RealType mf;
633	>	RealType lrPot;
634	>	RealType vpair;
635	>	potVec longRangePotential(0.0);
636	>	potVec workPot(0.0);
637
638	<	for (int i=0; i<LR_POT_TYPES;i++){
639	<	longRangePotential[i]=0.0; //Initialize array
638	>	int loopStart, loopEnd;
639	>
640	>	idat.vdwMult = &vdwMult;
641	>	idat.electroMult = &electroMult;
642	>	idat.pot = &workPot;
643	>	sdat.pot = fDecomp_->getEmbeddingPotential();
644	>	idat.vpair = &vpair;
645	>	idat.f1 = &f1;
646	>	idat.sw = &sw;
647	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
648	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
649	>
650	>	loopEnd = PAIR_LOOP;
651	>	if (info_->requiresPrepair() ) {
652	>	loopStart = PREPAIR_LOOP;
653	>	} else {
654	>	loopStart = PAIR_LOOP;
655		}
656	+
657	+	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
658	+
659	+	if (iLoop == loopStart) {
660	+	bool update_nlist = fDecomp_->checkNeighborList();
661	+	if (update_nlist)
662	+	neighborList = fDecomp_->buildNeighborList();
663	+	}
664
665	<	doForceLoop( pos,
666	<	rc,
667	<	A,
668	<	electroFrame,
669	<	frc,
670	<	trq,
671	<	tau.getArrayPointer(),
294	<	longRangePotential,
295	<	&passedCalcPot,
296	<	&passedCalcStress,
297	<	&isError );
665	>	for (vector<pair<int, int> >::iterator it = neighborList.begin();
666	>	it != neighborList.end(); ++it) {
667	>
668	>	cg1 = (*it).first;
669	>	cg2 = (*it).second;
670	>
671	>	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
672
673	<	if( isError ){
674	<	sprintf( painCave.errMsg,
675	<	"Error returned from the fortran force calculation.\n" );
676	<	painCave.isFatal = 1;
677	<	simError();
673	>	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
674	>
675	>	curSnapshot->wrapVector(d_grp);
676	>	rgrpsq = d_grp.lengthSquare();
677	>	rCutSq = cuts.second;
678	>
679	>	if (rgrpsq < rCutSq) {
680	>	idat.rcut = &cuts.first;
681	>	if (iLoop == PAIR_LOOP) {
682	>	vij = 0.0;
683	>	fij = V3Zero;
684	>	}
685	>
686	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
687	>	rgrp);
688	>
689	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
690	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
691	>
692	>	for (vector<int>::iterator ia = atomListRow.begin();
693	>	ia != atomListRow.end(); ++ia) {
694	>	atom1 = (*ia);
695	>
696	>	for (vector<int>::iterator jb = atomListColumn.begin();
697	>	jb != atomListColumn.end(); ++jb) {
698	>	atom2 = (*jb);
699	>
700	>	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
701	>	vpair = 0.0;
702	>	workPot = 0.0;
703	>	f1 = V3Zero;
704	>
705	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
706	>
707	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
708	>	vdwMult = vdwScale_[topoDist];
709	>	electroMult = electrostaticScale_[topoDist];
710	>
711	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
712	>	idat.d = &d_grp;
713	>	idat.r2 = &rgrpsq;
714	>	} else {
715	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
716	>	curSnapshot->wrapVector( d );
717	>	r2 = d.lengthSquare();
718	>	idat.d = &d;
719	>	idat.r2 = &r2;
720	>	}
721	>
722	>	r = sqrt( *(idat.r2) );
723	>	idat.rij = &r;
724	>
725	>	if (iLoop == PREPAIR_LOOP) {
726	>	interactionMan_->doPrePair(idat);
727	>	} else {
728	>	interactionMan_->doPair(idat);
729	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
730	>	vij += vpair;
731	>	fij += f1;
732	>	tau -= outProduct( *(idat.d), f1);
733	>	}
734	>	}
735	>	}
736	>	}
737	>
738	>	if (iLoop == PAIR_LOOP) {
739	>	if (in_switching_region) {
740	>	swderiv = vij * dswdr / rgrp;
741	>	fg = swderiv * d_grp;
742	>	fij += fg;
743	>
744	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
745	>	tau -= outProduct( *(idat.d), fg);
746	>	}
747	>
748	>	for (vector<int>::iterator ia = atomListRow.begin();
749	>	ia != atomListRow.end(); ++ia) {
750	>	atom1 = (*ia);
751	>	mf = fDecomp_->getMassFactorRow(atom1);
752	>	// fg is the force on atom ia due to cutoff group's
753	>	// presence in switching region
754	>	fg = swderiv * d_grp * mf;
755	>	fDecomp_->addForceToAtomRow(atom1, fg);
756	>	if (atomListRow.size() > 1) {
757	>	if (info_->usesAtomicVirial()) {
758	>	// find the distance between the atom
759	>	// and the center of the cutoff group:
760	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
761	>	tau -= outProduct(dag, fg);
762	>	}
763	>	}
764	>	}
765	>	for (vector<int>::iterator jb = atomListColumn.begin();
766	>	jb != atomListColumn.end(); ++jb) {
767	>	atom2 = (*jb);
768	>	mf = fDecomp_->getMassFactorColumn(atom2);
769	>	// fg is the force on atom jb due to cutoff group's
770	>	// presence in switching region
771	>	fg = -swderiv * d_grp * mf;
772	>	fDecomp_->addForceToAtomColumn(atom2, fg);
773	>
774	>	if (atomListColumn.size() > 1) {
775	>	if (info_->usesAtomicVirial()) {
776	>	// find the distance between the atom
777	>	// and the center of the cutoff group:
778	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
779	>	tau -= outProduct(dag, fg);
780	>	}
781	>	}
782	>	}
783	>	}
784	>	//if (!info_->usesAtomicVirial()) {
785	>	//  tau -= outProduct(d_grp, fij);
786	>	//}
787	>	}
788	>	}
789	>	}
790	>
791	>	if (iLoop == PREPAIR_LOOP) {
792	>	if (info_->requiresPrepair()) {
793	>
794	>	fDecomp_->collectIntermediateData();
795	>
796	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
797	>	fDecomp_->fillSelfData(sdat, atom1);
798	>	interactionMan_->doPreForce(sdat);
799	>	}
800	>
801	>	fDecomp_->distributeIntermediateData();
802	>
803	>	}
804	>	}
805		}
806	<	for (int i=0; i<LR_POT_TYPES;i++){
807	<	lrPot += longRangePotential[i]; //Quick hack
806	>
807	>	fDecomp_->collectData();
808	>
809	>	if (info_->requiresSelfCorrection()) {
810	>
811	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
812	>	fDecomp_->fillSelfData(sdat, atom1);
813	>	interactionMan_->doSelfCorrection(sdat);
814	>	}
815	>
816		}
817
818	+	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
819	+	*(fDecomp_->getPairwisePotential());
820	+
821	+	lrPot = longRangePotential.sum();
822	+
823		//store the tau and long range potential
824		curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
825	<	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
826	<	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
313	<
314	<	curSnapshot->statData.setTau(tau);
825	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
826	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
827		}
828
829	<
829	>
830		void ForceManager::postCalculation() {
831		SimInfo::MoleculeIterator mi;
832		Molecule* mol;
833		Molecule::RigidBodyIterator rbIter;
834		RigidBody* rb;
835	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
836
837		// collect the atomic forces onto rigid bodies
838	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
839	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
840	<	rb->calcForcesAndTorques();
838	>
839	>	for (mol = info_->beginMolecule(mi); mol != NULL;
840	>	mol = info_->nextMolecule(mi)) {
841	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
842	>	rb = mol->nextRigidBody(rbIter)) {
843	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
844	>	tau += rbTau;
845		}
846		}
847	<
847	>
848	>	#ifdef IS_MPI
849	>	Mat3x3d tmpTau(tau);
850	>	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
851	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
852	>	#endif
853	>	curSnapshot->statData.setTau(tau);
854		}
855
856	<	} //end namespace oopse
856	>	} //end namespace OpenMD

Comparing:
trunk/src/brains/ForceManager.cpp (property svn:keywords), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/brains/ForceManager.cpp (property svn:keywords), Revision 1616 by gezelter, Tue Aug 30 15:45:35 2011 UTC

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