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root/OpenMD/branches/development/src/brains/ForceManager.cpp

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trunk/src/brains/ForceManager.cpp (file contents), Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
branches/development/src/brains/ForceManager.cpp (file contents), Revision 1613 by gezelter, Thu Aug 18 20:18:19 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) {
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
119	<	if (!info_->isFortranInitialized()) {
120	<	info_->update();
119	>	if (simParams_->haveCutoffRadius()) {
120	>	rCut_ = simParams_->getCutoffRadius();
121	>	} else {
122	>	if (info_->usesElectrostaticAtoms()) {
123	>	sprintf(painCave.errMsg,
124	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
125	>	"\tOpenMD will use a default value of 12.0 angstroms"
126	>	"\tfor the cutoffRadius.\n");
127	>	painCave.isFatal = 0;
128	>	painCave.severity = OPENMD_INFO;
129	>	simError();
130	>	rCut_ = 12.0;
131	>	} else {
132	>	RealType thisCut;
133	>	set<AtomType*>::iterator i;
134	>	set<AtomType*> atomTypes;
135	>	atomTypes = info_->getSimulatedAtomTypes();
136	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
137	>	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
138	>	rCut_ = max(thisCut, rCut_);
139	>	}
140	>	sprintf(painCave.errMsg,
141	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
142	>	"\tOpenMD will use %lf angstroms.\n",
143	>	rCut_);
144	>	painCave.isFatal = 0;
145	>	painCave.severity = OPENMD_INFO;
146	>	simError();
147	>	}
148		}
149
150	<	preCalculation();
151	<
86	<	calcShortRangeInteraction();
150	>	fDecomp_->setUserCutoff(rCut_);
151	>	interactionMan_->setCutoffRadius(rCut_);
152
153	<	calcLongRangeInteraction(needPotential, needStress);
153	>	map<string, CutoffMethod> stringToCutoffMethod;
154	>	stringToCutoffMethod["HARD"] = HARD;
155	>	stringToCutoffMethod["SWITCHED"] = SWITCHED;
156	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
157	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
158	>
159	>	if (simParams_->haveCutoffMethod()) {
160	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
161	>	map<string, CutoffMethod>::iterator i;
162	>	i = stringToCutoffMethod.find(cutMeth);
163	>	if (i == stringToCutoffMethod.end()) {
164	>	sprintf(painCave.errMsg,
165	>	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
166	>	"\tShould be one of: "
167	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
168	>	cutMeth.c_str());
169	>	painCave.isFatal = 1;
170	>	painCave.severity = OPENMD_ERROR;
171	>	simError();
172	>	} else {
173	>	cutoffMethod_ = i->second;
174	>	}
175	>	} else {
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	>	}
184
185	<	postCalculation();
185	>	map<string, CutoffPolicy> stringToCutoffPolicy;
186	>	stringToCutoffPolicy["MIX"] = MIX;
187	>	stringToCutoffPolicy["MAX"] = MAX;
188	>	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
189
190	<	/*
191	<	std::vector<BendOrderStruct> bendOrderStruct;
192	<	for(std::map<Bend*, BendDataSet>::iterator i = bendDataSets.begin(); i != bendDataSets.end(); ++i) {
193	<	BendOrderStruct tmp;
194	<	tmp.bend= const_cast<Bend*>(i->first);
97	<	tmp.dataSet = i->second;
98	<	bendOrderStruct.push_back(tmp);
190	>	std::string cutPolicy;
191	>	if (forceFieldOptions_.haveCutoffPolicy()){
192	>	cutPolicy = forceFieldOptions_.getCutoffPolicy();
193	>	}else if (simParams_->haveCutoffPolicy()) {
194	>	cutPolicy = simParams_->getCutoffPolicy();
195		}
196
197	<	std::vector<TorsionOrderStruct> torsionOrderStruct;
198	<	for(std::map<Torsion*, TorsionDataSet>::iterator j = torsionDataSets.begin(); j != torsionDataSets.end(); ++j) {
199	<	TorsionOrderStruct tmp;
200	<	tmp.torsion = const_cast<Torsion*>(j->first);
201	<	tmp.dataSet = j->second;
202	<	torsionOrderStruct.push_back(tmp);
203	<	}
204	<
205	<	std::sort(bendOrderStruct.begin(), bendOrderStruct.end(), std::ptr_fun(BendSortFunctor));
206	<	std::sort(torsionOrderStruct.begin(), torsionOrderStruct.end(), std::ptr_fun(TorsionSortFunctor));
207	<	std::cout << "bend" << std::endl;
208	<	for (std::vector<BendOrderStruct>::iterator k = bendOrderStruct.begin(); k != bendOrderStruct.end(); ++k) {
209	<	Bend* bend = k->bend;
210	<	std::cout << "atom1=" <<bend->getAtomA()->getGlobalIndex() << ",atom2 = "<< bend->getAtomB()->getGlobalIndex() << ",atom3="<<bend->getAtomC()->getGlobalIndex() << " ";
211	<	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;
212	<	}
213	<	std::cout << "torsio" << std::endl;
214	<	for (std::vector<TorsionOrderStruct>::iterator l = torsionOrderStruct.begin(); l != torsionOrderStruct.end(); ++l) {
215	<	Torsion* torsion = l->torsion;
216	<	std::cout << "atom1=" <<torsion->getAtomA()->getGlobalIndex() << ",atom2 = "<< torsion->getAtomB()->getGlobalIndex() << ",atom3="<<torsion->getAtomC()->getGlobalIndex() << ",atom4="<<torsion->getAtomD()->getGlobalIndex()<< " ";
217	<	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;
218	<	}
219	<	*/
197	>	if (!cutPolicy.empty()){
198	>	toUpper(cutPolicy);
199	>	map<string, CutoffPolicy>::iterator i;
200	>	i = stringToCutoffPolicy.find(cutPolicy);
201	>
202	>	if (i == stringToCutoffPolicy.end()) {
203	>	sprintf(painCave.errMsg,
204	>	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
205	>	"\tShould be one of: "
206	>	"MIX, MAX, or TRADITIONAL\n",
207	>	cutPolicy.c_str());
208	>	painCave.isFatal = 1;
209	>	painCave.severity = OPENMD_ERROR;
210	>	simError();
211	>	} else {
212	>	cutoffPolicy_ = i->second;
213	>	}
214	>	} else {
215	>	sprintf(painCave.errMsg,
216	>	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
217	>	"\tOpenMD will use TRADITIONAL.\n");
218	>	painCave.isFatal = 0;
219	>	painCave.severity = OPENMD_INFO;
220	>	simError();
221	>	cutoffPolicy_ = TRADITIONAL;
222	>	}
223	>
224	>	fDecomp_->setCutoffPolicy(cutoffPolicy_);
225	>
226	>	// create the switching function object:
227	>
228	>	switcher_ = new SwitchingFunction();
229	>
230	>	if (cutoffMethod_ == SWITCHED) {
231	>	if (simParams_->haveSwitchingRadius()) {
232	>	rSwitch_ = simParams_->getSwitchingRadius();
233	>	if (rSwitch_ > rCut_) {
234	>	sprintf(painCave.errMsg,
235	>	"ForceManager::setupCutoffs: switchingRadius (%f) is larger "
236	>	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
237	>	painCave.isFatal = 1;
238	>	painCave.severity = OPENMD_ERROR;
239	>	simError();
240	>	}
241	>	} else {
242	>	rSwitch_ = 0.85 * rCut_;
243	>	sprintf(painCave.errMsg,
244	>	"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
245	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
246	>	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
247	>	painCave.isFatal = 0;
248	>	painCave.severity = OPENMD_WARNING;
249	>	simError();
250	>	}
251	>	} else {
252	>	if (simParams_->haveSwitchingRadius()) {
253	>	map<string, CutoffMethod>::const_iterator it;
254	>	string theMeth;
255	>	for (it = stringToCutoffMethod.begin();
256	>	it != stringToCutoffMethod.end(); ++it) {
257	>	if (it->second == cutoffMethod_) {
258	>	theMeth = it->first;
259	>	break;
260	>	}
261	>	}
262	>	sprintf(painCave.errMsg,
263	>	"ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
264	>	"\tis not set to SWITCHED, so switchingRadius value\n"
265	>	"\twill be ignored for this simulation\n", theMeth.c_str());
266	>	painCave.isFatal = 0;
267	>	painCave.severity = OPENMD_WARNING;
268	>	simError();
269	>	}
270	>
271	>	rSwitch_ = rCut_;
272	>	}
273	>
274	>	// Default to cubic switching function.
275	>	sft_ = cubic;
276	>	if (simParams_->haveSwitchingFunctionType()) {
277	>	string funcType = simParams_->getSwitchingFunctionType();
278	>	toUpper(funcType);
279	>	if (funcType == "CUBIC") {
280	>	sft_ = cubic;
281	>	} else {
282	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
283	>	sft_ = fifth_order_poly;
284	>	} else {
285	>	// throw error
286	>	sprintf( painCave.errMsg,
287	>	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
288	>	"\tswitchingFunctionType must be one of: "
289	>	"\"cubic\" or \"fifth_order_polynomial\".",
290	>	funcType.c_str() );
291	>	painCave.isFatal = 1;
292	>	painCave.severity = OPENMD_ERROR;
293	>	simError();
294	>	}
295	>	}
296	>	}
297	>	switcher_->setSwitchType(sft_);
298	>	switcher_->setSwitch(rSwitch_, rCut_);
299	>	interactionMan_->setSwitchingRadius(rSwitch_);
300		}
301	+
302	+	void ForceManager::initialize() {
303
304	+	if (!info_->isTopologyDone()) {
305	+
306	+	info_->update();
307	+	interactionMan_->setSimInfo(info_);
308	+	interactionMan_->initialize();
309	+
310	+	// We want to delay the cutoffs until after the interaction
311	+	// manager has set up the atom-atom interactions so that we can
312	+	// query them for suggested cutoff values
313	+	setupCutoffs();
314	+
315	+	info_->prepareTopology();
316	+	}
317	+
318	+	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
319	+
320	+	// Force fields can set options on how to scale van der Waals and
321	+	// electrostatic interactions for atoms connected via bonds, bends
322	+	// and torsions in this case the topological distance between
323	+	// atoms is:
324	+	// 0 = topologically unconnected
325	+	// 1 = bonded together
326	+	// 2 = connected via a bend
327	+	// 3 = connected via a torsion
328	+
329	+	vdwScale_.reserve(4);
330	+	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
331	+
332	+	electrostaticScale_.reserve(4);
333	+	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
334	+
335	+	vdwScale_[0] = 1.0;
336	+	vdwScale_[1] = fopts.getvdw12scale();
337	+	vdwScale_[2] = fopts.getvdw13scale();
338	+	vdwScale_[3] = fopts.getvdw14scale();
339	+
340	+	electrostaticScale_[0] = 1.0;
341	+	electrostaticScale_[1] = fopts.getelectrostatic12scale();
342	+	electrostaticScale_[2] = fopts.getelectrostatic13scale();
343	+	electrostaticScale_[3] = fopts.getelectrostatic14scale();
344	+
345	+	fDecomp_->distributeInitialData();
346	+
347	+	initialized_ = true;
348	+
349	+	}
350	+
351	+	void ForceManager::calcForces() {
352	+
353	+	if (!initialized_) initialize();
354	+
355	+	preCalculation();
356	+	shortRangeInteractions();
357	+	longRangeInteractions();
358	+	postCalculation();
359	+	}
360	+
361		void ForceManager::preCalculation() {
362		SimInfo::MoleculeIterator mi;
363		Molecule* mol;
#	Line 130 | Line 365 | namespace oopse {
365		Atom* atom;
366		Molecule::RigidBodyIterator rbIter;
367		RigidBody* rb;
368	+	Molecule::CutoffGroupIterator ci;
369	+	CutoffGroup* cg;
370
371		// forces are zeroed here, before any are accumulated.
372	<	// NOTE: do not rezero the forces in Fortran.
373	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
374	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
372	>
373	>	for (mol = info_->beginMolecule(mi); mol != NULL;
374	>	mol = info_->nextMolecule(mi)) {
375	>	for(atom = mol->beginAtom(ai); atom != NULL;
376	>	atom = mol->nextAtom(ai)) {
377		atom->zeroForcesAndTorques();
378		}
379	<
379	>
380		//change the positions of atoms which belong to the rigidbodies
381	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
381	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
382	>	rb = mol->nextRigidBody(rbIter)) {
383		rb->zeroForcesAndTorques();
384		}
385	+
386	+	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
387	+	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
388	+	cg = mol->nextCutoffGroup(ci)) {
389	+	//calculate the center of mass of cutoff group
390	+	cg->updateCOM();
391	+	}
392	+	}
393		}
394
395	+	// Zero out the stress tensor
396	+	tau *= 0.0;
397	+
398		}
399	<
400	<	void ForceManager::calcShortRangeInteraction() {
399	>
400	>	void ForceManager::shortRangeInteractions() {
401		Molecule* mol;
402		RigidBody* rb;
403		Bond* bond;
404		Bend* bend;
405		Torsion* torsion;
406	+	Inversion* inversion;
407		SimInfo::MoleculeIterator mi;
408		Molecule::RigidBodyIterator rbIter;
409		Molecule::BondIterator bondIter;;
410		Molecule::BendIterator  bendIter;
411		Molecule::TorsionIterator  torsionIter;
412	<	double bondPotential = 0.0;
413	<	double bendPotential = 0.0;
414	<	double torsionPotential = 0.0;
412	>	Molecule::InversionIterator  inversionIter;
413	>	RealType bondPotential = 0.0;
414	>	RealType bendPotential = 0.0;
415	>	RealType torsionPotential = 0.0;
416	>	RealType inversionPotential = 0.0;
417
418		//calculate short range interactions
419	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
419	>	for (mol = info_->beginMolecule(mi); mol != NULL;
420	>	mol = info_->nextMolecule(mi)) {
421
422		//change the positions of atoms which belong to the rigidbodies
423	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
424	<	rb->updateAtoms();
423	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
424	>	rb = mol->nextRigidBody(rbIter)) {
425	>	rb->updateAtoms();
426		}
427
428	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
428	>	for (bond = mol->beginBond(bondIter); bond != NULL;
429	>	bond = mol->nextBond(bondIter)) {
430		bond->calcForce();
431		bondPotential += bond->getPotential();
432		}
433
434	<
435	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
436	<
437	<	double angle;
438	<	bend->calcForce(angle);
439	<	double currBendPot = bend->getPotential();
440	<	bendPotential += bend->getPotential();
441	<	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
442	<	if (i == bendDataSets.end()) {
443	<	BendDataSet dataSet;
444	<	dataSet.prev.angle = dataSet.curr.angle = angle;
445	<	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
446	<	dataSet.deltaV = 0.0;
447	<	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
448	<	}else {
449	<	i->second.prev.angle = i->second.curr.angle;
450	<	i->second.prev.potential = i->second.curr.potential;
451	<	i->second.curr.angle = angle;
452	<	i->second.curr.potential = currBendPot;
453	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
454	<	}
434	>	for (bend = mol->beginBend(bendIter); bend != NULL;
435	>	bend = mol->nextBend(bendIter)) {
436	>
437	>	RealType angle;
438	>	bend->calcForce(angle);
439	>	RealType currBendPot = bend->getPotential();
440	>
441	>	bendPotential += bend->getPotential();
442	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
443	>	if (i == bendDataSets.end()) {
444	>	BendDataSet dataSet;
445	>	dataSet.prev.angle = dataSet.curr.angle = angle;
446	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
447	>	dataSet.deltaV = 0.0;
448	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
449	>	dataSet));
450	>	}else {
451	>	i->second.prev.angle = i->second.curr.angle;
452	>	i->second.prev.potential = i->second.curr.potential;
453	>	i->second.curr.angle = angle;
454	>	i->second.curr.potential = currBendPot;
455	>	i->second.deltaV =  fabs(i->second.curr.potential -
456	>	i->second.prev.potential);
457	>	}
458		}
459	<
460	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
461	<	double angle;
462	<	torsion->calcForce(angle);
463	<	double currTorsionPot = torsion->getPotential();
464	<	torsionPotential += torsion->getPotential();
465	<	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
466	<	if (i == torsionDataSets.end()) {
467	<	TorsionDataSet dataSet;
468	<	dataSet.prev.angle = dataSet.curr.angle = angle;
469	<	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
470	<	dataSet.deltaV = 0.0;
471	<	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
472	<	}else {
473	<	i->second.prev.angle = i->second.curr.angle;
474	<	i->second.prev.potential = i->second.curr.potential;
475	<	i->second.curr.angle = angle;
476	<	i->second.curr.potential = currTorsionPot;
477	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
478	<	}
479	<	}
480	<
459	>
460	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
461	>	torsion = mol->nextTorsion(torsionIter)) {
462	>	RealType angle;
463	>	torsion->calcForce(angle);
464	>	RealType currTorsionPot = torsion->getPotential();
465	>	torsionPotential += torsion->getPotential();
466	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
467	>	if (i == torsionDataSets.end()) {
468	>	TorsionDataSet dataSet;
469	>	dataSet.prev.angle = dataSet.curr.angle = angle;
470	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
471	>	dataSet.deltaV = 0.0;
472	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
473	>	}else {
474	>	i->second.prev.angle = i->second.curr.angle;
475	>	i->second.prev.potential = i->second.curr.potential;
476	>	i->second.curr.angle = angle;
477	>	i->second.curr.potential = currTorsionPot;
478	>	i->second.deltaV =  fabs(i->second.curr.potential -
479	>	i->second.prev.potential);
480	>	}
481	>	}
482	>
483	>	for (inversion = mol->beginInversion(inversionIter);
484	>	inversion != NULL;
485	>	inversion = mol->nextInversion(inversionIter)) {
486	>	RealType angle;
487	>	inversion->calcForce(angle);
488	>	RealType currInversionPot = inversion->getPotential();
489	>	inversionPotential += inversion->getPotential();
490	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
491	>	if (i == inversionDataSets.end()) {
492	>	InversionDataSet dataSet;
493	>	dataSet.prev.angle = dataSet.curr.angle = angle;
494	>	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
495	>	dataSet.deltaV = 0.0;
496	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
497	>	}else {
498	>	i->second.prev.angle = i->second.curr.angle;
499	>	i->second.prev.potential = i->second.curr.potential;
500	>	i->second.curr.angle = angle;
501	>	i->second.curr.potential = currInversionPot;
502	>	i->second.deltaV =  fabs(i->second.curr.potential -
503	>	i->second.prev.potential);
504	>	}
505	>	}
506		}
507
508	<	double  shortRangePotential = bondPotential + bendPotential + torsionPotential;
508	>	RealType  shortRangePotential = bondPotential + bendPotential +
509	>	torsionPotential +  inversionPotential;
510		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
511		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
512		curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
513		curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
514		curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
515	<
515	>	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
516		}
517	+
518	+	void ForceManager::longRangeInteractions() {
519
520	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
521	<	Snapshot* curSnapshot;
522	<	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();
520	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
521	>	DataStorage* config = &(curSnapshot->atomData);
522	>	DataStorage* cgConfig = &(curSnapshot->cgData);
523
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);
252	–
524		//calculate the center of mass of cutoff group
525	+
526		SimInfo::MoleculeIterator mi;
527		Molecule* mol;
528		Molecule::CutoffGroupIterator ci;
529		CutoffGroup* cg;
258	–	Vector3d com;
259	–	std::vector<Vector3d> rcGroup;
530
531	<	if(info_->getNCutoffGroups() > 0){
532	<
533	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
534	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
535	<	cg->getCOM(com);
536	<	rcGroup.push_back(com);
531	>	if(info_->getNCutoffGroups() > 0){
532	>	for (mol = info_->beginMolecule(mi); mol != NULL;
533	>	mol = info_->nextMolecule(mi)) {
534	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
535	>	cg = mol->nextCutoffGroup(ci)) {
536	>	cg->updateCOM();
537		}
538	<	}// end for (mol)
269	<
270	<	rc = rcGroup[0].getArrayPointer();
538	>	}
539		} else {
540	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
541	<	rc = pos;
540	>	// center of mass of the group is the same as position of the atom
541	>	// if cutoff group does not exist
542	>	cgConfig->position = config->position;
543		}
544	<
545	<	//initialize data before passing to fortran
546	<	double longRangePotential[LR_POT_TYPES];
278	<	double lrPot = 0.0;
544	>
545	>	fDecomp_->zeroWorkArrays();
546	>	fDecomp_->distributeData();
547
548	<	Mat3x3d tau;
549	<	short int passedCalcPot = needPotential;
550	<	short int passedCalcStress = needStress;
551	<	int isError = 0;
548	>	int cg1, cg2, atom1, atom2, topoDist;
549	>	Vector3d d_grp, dag, d;
550	>	RealType rgrpsq, rgrp, r2, r;
551	>	RealType electroMult, vdwMult;
552	>	RealType vij;
553	>	Vector3d fij, fg, f1;
554	>	tuple3<RealType, RealType, RealType> cuts;
555	>	RealType rCutSq;
556	>	bool in_switching_region;
557	>	RealType sw, dswdr, swderiv;
558	>	vector<int> atomListColumn, atomListRow, atomListLocal;
559	>	InteractionData idat;
560	>	SelfData sdat;
561	>	RealType mf;
562	>	RealType lrPot;
563	>	RealType vpair;
564	>	potVec longRangePotential(0.0);
565	>	potVec workPot(0.0);
566
567	<	for (int i=0; i<LR_POT_TYPES;i++){
568	<	longRangePotential[i]=0.0; //Initialize array
567	>	int loopStart, loopEnd;
568	>
569	>	idat.vdwMult = &vdwMult;
570	>	idat.electroMult = &electroMult;
571	>	idat.pot = &workPot;
572	>	sdat.pot = fDecomp_->getEmbeddingPotential();
573	>	idat.vpair = &vpair;
574	>	idat.f1 = &f1;
575	>	idat.sw = &sw;
576	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
577	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
578	>
579	>	loopEnd = PAIR_LOOP;
580	>	if (info_->requiresPrepair() ) {
581	>	loopStart = PREPAIR_LOOP;
582	>	} else {
583	>	loopStart = PAIR_LOOP;
584		}
585	+
586	+	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
587	+
588	+	if (iLoop == loopStart) {
589	+	bool update_nlist = fDecomp_->checkNeighborList();
590	+	if (update_nlist)
591	+	neighborList = fDecomp_->buildNeighborList();
592	+	}
593
594	<	doForceLoop( pos,
595	<	rc,
596	<	A,
597	<	electroFrame,
598	<	frc,
599	<	trq,
600	<	tau.getArrayPointer(),
296	<	longRangePotential,
297	<	&passedCalcPot,
298	<	&passedCalcStress,
299	<	&isError );
594	>	for (vector<pair<int, int> >::iterator it = neighborList.begin();
595	>	it != neighborList.end(); ++it) {
596	>
597	>	cg1 = (*it).first;
598	>	cg2 = (*it).second;
599	>
600	>	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
601
602	<	if( isError ){
603	<	sprintf( painCave.errMsg,
604	<	"Error returned from the fortran force calculation.\n" );
605	<	painCave.isFatal = 1;
606	<	simError();
602	>	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
603	>
604	>	curSnapshot->wrapVector(d_grp);
605	>	rgrpsq = d_grp.lengthSquare();
606	>	rCutSq = cuts.second;
607	>
608	>	if (rgrpsq < rCutSq) {
609	>	idat.rcut = &cuts.first;
610	>	if (iLoop == PAIR_LOOP) {
611	>	vij = 0.0;
612	>	fij = V3Zero;
613	>	}
614	>
615	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
616	>	rgrp);
617	>
618	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
619	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
620	>
621	>
622	>	for (vector<int>::iterator ia = atomListRow.begin();
623	>	ia != atomListRow.end(); ++ia) {
624	>	atom1 = (*ia);
625	>
626	>	for (vector<int>::iterator jb = atomListColumn.begin();
627	>	jb != atomListColumn.end(); ++jb) {
628	>	atom2 = (*jb);
629	>
630	>	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
631	>	vpair = 0.0;
632	>	workPot = 0.0;
633	>	f1 = V3Zero;
634	>
635	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
636	>
637	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
638	>	vdwMult = vdwScale_[topoDist];
639	>	electroMult = electrostaticScale_[topoDist];
640	>
641	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
642	>	idat.d = &d_grp;
643	>	idat.r2 = &rgrpsq;
644	>	} else {
645	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
646	>	curSnapshot->wrapVector( d );
647	>	r2 = d.lengthSquare();
648	>	idat.d = &d;
649	>	idat.r2 = &r2;
650	>	}
651	>
652	>	r = sqrt( *(idat.r2) );
653	>	idat.rij = &r;
654	>
655	>	if (iLoop == PREPAIR_LOOP) {
656	>	interactionMan_->doPrePair(idat);
657	>	} else {
658	>	interactionMan_->doPair(idat);
659	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
660	>
661	>	vij += vpair;
662	>	fij += f1;
663	>	tau -= outProduct( *(idat.d), f1);
664	>	}
665	>	}
666	>	}
667	>	}
668	>
669	>	if (iLoop == PAIR_LOOP) {
670	>	if (in_switching_region) {
671	>	swderiv = vij * dswdr / rgrp;
672	>	fg = swderiv * d_grp;
673	>	fij += fg;
674	>
675	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
676	>	tau -= outProduct( *(idat.d), fg);
677	>	}
678	>
679	>	for (vector<int>::iterator ia = atomListRow.begin();
680	>	ia != atomListRow.end(); ++ia) {
681	>	atom1 = (*ia);
682	>	mf = fDecomp_->getMassFactorRow(atom1);
683	>	// fg is the force on atom ia due to cutoff group's
684	>	// presence in switching region
685	>	fg = swderiv * d_grp * mf;
686	>	fDecomp_->addForceToAtomRow(atom1, fg);
687	>
688	>	if (atomListRow.size() > 1) {
689	>	if (info_->usesAtomicVirial()) {
690	>	// find the distance between the atom
691	>	// and the center of the cutoff group:
692	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
693	>	tau -= outProduct(dag, fg);
694	>	}
695	>	}
696	>	}
697	>	for (vector<int>::iterator jb = atomListColumn.begin();
698	>	jb != atomListColumn.end(); ++jb) {
699	>	atom2 = (*jb);
700	>	mf = fDecomp_->getMassFactorColumn(atom2);
701	>	// fg is the force on atom jb due to cutoff group's
702	>	// presence in switching region
703	>	fg = -swderiv * d_grp * mf;
704	>	fDecomp_->addForceToAtomColumn(atom2, fg);
705	>
706	>	if (atomListColumn.size() > 1) {
707	>	if (info_->usesAtomicVirial()) {
708	>	// find the distance between the atom
709	>	// and the center of the cutoff group:
710	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
711	>	tau -= outProduct(dag, fg);
712	>	}
713	>	}
714	>	}
715	>	}
716	>	//if (!info_->usesAtomicVirial()) {
717	>	//  tau -= outProduct(d_grp, fij);
718	>	//}
719	>	}
720	>	}
721	>	}
722	>
723	>	if (iLoop == PREPAIR_LOOP) {
724	>	if (info_->requiresPrepair()) {
725	>
726	>	fDecomp_->collectIntermediateData();
727	>
728	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
729	>	fDecomp_->fillSelfData(sdat, atom1);
730	>	interactionMan_->doPreForce(sdat);
731	>	}
732	>
733	>	fDecomp_->distributeIntermediateData();
734	>
735	>	}
736	>	}
737		}
738	<	for (int i=0; i<LR_POT_TYPES;i++){
739	<	lrPot += longRangePotential[i]; //Quick hack
738	>
739	>	fDecomp_->collectData();
740	>
741	>	if (info_->requiresSelfCorrection()) {
742	>
743	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
744	>	fDecomp_->fillSelfData(sdat, atom1);
745	>	interactionMan_->doSelfCorrection(sdat);
746	>	}
747	>
748		}
749
750	+	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
751	+	*(fDecomp_->getPairwisePotential());
752	+
753	+	lrPot = longRangePotential.sum();
754	+
755		//store the tau and long range potential
756		curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
757	<	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
758	<	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
315	<
316	<	curSnapshot->statData.setTau(tau);
757	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
758	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
759		}
760
761	<
761	>
762		void ForceManager::postCalculation() {
763		SimInfo::MoleculeIterator mi;
764		Molecule* mol;
765		Molecule::RigidBodyIterator rbIter;
766		RigidBody* rb;
767	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
768
769		// collect the atomic forces onto rigid bodies
770	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
771	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
772	<	rb->calcForcesAndTorques();
770	>
771	>	for (mol = info_->beginMolecule(mi); mol != NULL;
772	>	mol = info_->nextMolecule(mi)) {
773	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
774	>	rb = mol->nextRigidBody(rbIter)) {
775	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
776	>	tau += rbTau;
777		}
778		}
779	<
779	>
780	>	#ifdef IS_MPI
781	>	Mat3x3d tmpTau(tau);
782	>	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
783	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
784	>	#endif
785	>	curSnapshot->statData.setTau(tau);
786		}
787
788	<	} //end namespace oopse
788	>	} //end namespace OpenMD

Comparing:
trunk/src/brains/ForceManager.cpp (property svn:keywords), Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
branches/development/src/brains/ForceManager.cpp (property svn:keywords), Revision 1613 by gezelter, Thu Aug 18 20:18:19 2011 UTC

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