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

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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 1597 by gezelter, Tue Jul 26 15:49:24 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	>
112	>	if (simParams_->haveCutoffRadius()) {
113	>	rCut_ = simParams_->getCutoffRadius();
114	>	} else {
115	>	if (info_->usesElectrostaticAtoms()) {
116	>	sprintf(painCave.errMsg,
117	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
118	>	"\tOpenMD will use a default value of 12.0 angstroms"
119	>	"\tfor the cutoffRadius.\n");
120	>	painCave.isFatal = 0;
121	>	painCave.severity = OPENMD_INFO;
122	>	simError();
123	>	rCut_ = 12.0;
124	>	} else {
125	>	RealType thisCut;
126	>	set<AtomType*>::iterator i;
127	>	set<AtomType*> atomTypes;
128	>	atomTypes = info_->getSimulatedAtomTypes();
129	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
130	>	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
131	>	rCut_ = max(thisCut, rCut_);
132	>	}
133	>	sprintf(painCave.errMsg,
134	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
135	>	"\tOpenMD will use %lf angstroms.\n",
136	>	rCut_);
137	>	painCave.isFatal = 0;
138	>	painCave.severity = OPENMD_INFO;
139	>	simError();
140	>	}
141	>	}
142
143	<	if (!info_->isFortranInitialized()) {
144	<	info_->update();
143	>	fDecomp_->setUserCutoff(rCut_);
144	>	interactionMan_->setCutoffRadius(rCut_);
145	>
146	>	map<string, CutoffMethod> stringToCutoffMethod;
147	>	stringToCutoffMethod["HARD"] = HARD;
148	>	stringToCutoffMethod["SWITCHED"] = SWITCHED;
149	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
150	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
151	>
152	>	if (simParams_->haveCutoffMethod()) {
153	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
154	>	map<string, CutoffMethod>::iterator i;
155	>	i = stringToCutoffMethod.find(cutMeth);
156	>	if (i == stringToCutoffMethod.end()) {
157	>	sprintf(painCave.errMsg,
158	>	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
159	>	"\tShould be one of: "
160	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
161	>	cutMeth.c_str());
162	>	painCave.isFatal = 1;
163	>	painCave.severity = OPENMD_ERROR;
164	>	simError();
165	>	} else {
166	>	cutoffMethod_ = i->second;
167	>	}
168	>	} else {
169	>	sprintf(painCave.errMsg,
170	>	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
171	>	"\tOpenMD will use SHIFTED_FORCE.\n");
172	>	painCave.isFatal = 0;
173	>	painCave.severity = OPENMD_INFO;
174	>	simError();
175	>	cutoffMethod_ = SHIFTED_FORCE;
176		}
177
178	<	preCalculation();
179	<
180	<	calcShortRangeInteraction();
178	>	map<string, CutoffPolicy> stringToCutoffPolicy;
179	>	stringToCutoffPolicy["MIX"] = MIX;
180	>	stringToCutoffPolicy["MAX"] = MAX;
181	>	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
182
183	<	calcLongRangeInteraction(needPotential, needStress);
183	>	std::string cutPolicy;
184	>	if (forceFieldOptions_.haveCutoffPolicy()){
185	>	cutPolicy = forceFieldOptions_.getCutoffPolicy();
186	>	}else if (simParams_->haveCutoffPolicy()) {
187	>	cutPolicy = simParams_->getCutoffPolicy();
188	>	}
189
190	<	postCalculation();
190	>	if (!cutPolicy.empty()){
191	>	toUpper(cutPolicy);
192	>	map<string, CutoffPolicy>::iterator i;
193	>	i = stringToCutoffPolicy.find(cutPolicy);
194
195	<	/*
196	<	std::vector<BendOrderStruct> bendOrderStruct;
197	<	for(std::map<Bend*, BendDataSet>::iterator i = bendDataSets.begin(); i != bendDataSets.end(); ++i) {
198	<	BendOrderStruct tmp;
199	<	tmp.bend= const_cast<Bend*>(i->first);
200	<	tmp.dataSet = i->second;
201	<	bendOrderStruct.push_back(tmp);
195	>	if (i == stringToCutoffPolicy.end()) {
196	>	sprintf(painCave.errMsg,
197	>	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
198	>	"\tShould be one of: "
199	>	"MIX, MAX, or TRADITIONAL\n",
200	>	cutPolicy.c_str());
201	>	painCave.isFatal = 1;
202	>	painCave.severity = OPENMD_ERROR;
203	>	simError();
204	>	} else {
205	>	cutoffPolicy_ = i->second;
206	>	}
207	>	} else {
208	>	sprintf(painCave.errMsg,
209	>	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
210	>	"\tOpenMD will use TRADITIONAL.\n");
211	>	painCave.isFatal = 0;
212	>	painCave.severity = OPENMD_INFO;
213	>	simError();
214	>	cutoffPolicy_ = TRADITIONAL;
215		}
216
217	<	std::vector<TorsionOrderStruct> torsionOrderStruct;
218	<	for(std::map<Torsion*, TorsionDataSet>::iterator j = torsionDataSets.begin(); j != torsionDataSets.end(); ++j) {
219	<	TorsionOrderStruct tmp;
220	<	tmp.torsion = const_cast<Torsion*>(j->first);
221	<	tmp.dataSet = j->second;
222	<	torsionOrderStruct.push_back(tmp);
217	>	fDecomp_->setCutoffPolicy(cutoffPolicy_);
218	>
219	>	// create the switching function object:
220	>
221	>	switcher_ = new SwitchingFunction();
222	>
223	>	if (cutoffMethod_ == SWITCHED) {
224	>	if (simParams_->haveSwitchingRadius()) {
225	>	rSwitch_ = simParams_->getSwitchingRadius();
226	>	if (rSwitch_ > rCut_) {
227	>	sprintf(painCave.errMsg,
228	>	"ForceManager::setupCutoffs: switchingRadius (%f) is larger "
229	>	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
230	>	painCave.isFatal = 1;
231	>	painCave.severity = OPENMD_ERROR;
232	>	simError();
233	>	}
234	>	} else {
235	>	rSwitch_ = 0.85 * rCut_;
236	>	sprintf(painCave.errMsg,
237	>	"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
238	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
239	>	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
240	>	painCave.isFatal = 0;
241	>	painCave.severity = OPENMD_WARNING;
242	>	simError();
243	>	}
244	>	} else {
245	>	if (simParams_->haveSwitchingRadius()) {
246	>	map<string, CutoffMethod>::const_iterator it;
247	>	string theMeth;
248	>	for (it = stringToCutoffMethod.begin();
249	>	it != stringToCutoffMethod.end(); ++it) {
250	>	if (it->second == cutoffMethod_) {
251	>	theMeth = it->first;
252	>	break;
253	>	}
254	>	}
255	>	sprintf(painCave.errMsg,
256	>	"ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
257	>	"\tis not set to SWITCHED, so switchingRadius value\n"
258	>	"\twill be ignored for this simulation\n", theMeth.c_str());
259	>	painCave.isFatal = 0;
260	>	painCave.severity = OPENMD_WARNING;
261	>	simError();
262	>	}
263	>
264	>	rSwitch_ = rCut_;
265		}
266
267	<	std::sort(bendOrderStruct.begin(), bendOrderStruct.end(), std::ptr_fun(BendSortFunctor));
268	<	std::sort(torsionOrderStruct.begin(), torsionOrderStruct.end(), std::ptr_fun(TorsionSortFunctor));
269	<	for (std::vector<BendOrderStruct>::iterator k = bendOrderStruct.begin(); k != bendOrderStruct.end(); ++k) {
270	<	Bend* bend = k->bend;
271	<	std::cout << "Bend: atom1=" <<bend->getAtomA()->getGlobalIndex() << ",atom2 = "<< bend->getAtomB()->getGlobalIndex() << ",atom3="<<bend->getAtomC()->getGlobalIndex() << " ";
272	<	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;
267	>	// Default to cubic switching function.
268	>	sft_ = cubic;
269	>	if (simParams_->haveSwitchingFunctionType()) {
270	>	string funcType = simParams_->getSwitchingFunctionType();
271	>	toUpper(funcType);
272	>	if (funcType == "CUBIC") {
273	>	sft_ = cubic;
274	>	} else {
275	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
276	>	sft_ = fifth_order_poly;
277	>	} else {
278	>	// throw error
279	>	sprintf( painCave.errMsg,
280	>	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
281	>	"\tswitchingFunctionType must be one of: "
282	>	"\"cubic\" or \"fifth_order_polynomial\".",
283	>	funcType.c_str() );
284	>	painCave.isFatal = 1;
285	>	painCave.severity = OPENMD_ERROR;
286	>	simError();
287	>	}
288	>	}
289		}
290	<	for (std::vector<TorsionOrderStruct>::iterator l = torsionOrderStruct.begin(); l != torsionOrderStruct.end(); ++l) {
291	<	Torsion* torsion = l->torsion;
292	<	std::cout << "Torsion: atom1=" <<torsion->getAtomA()->getGlobalIndex() << ",atom2 = "<< torsion->getAtomB()->getGlobalIndex() << ",atom3="<<torsion->getAtomC()->getGlobalIndex() << ",atom4="<<torsion->getAtomD()->getGlobalIndex()<< " ";
293	<	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;
290	>	switcher_->setSwitchType(sft_);
291	>	switcher_->setSwitch(rSwitch_, rCut_);
292	>	interactionMan_->setSwitchingRadius(rSwitch_);
293	>	}
294	>
295	>	void ForceManager::initialize() {
296	>
297	>	if (!info_->isTopologyDone()) {
298	>
299	>	info_->update();
300	>	interactionMan_->setSimInfo(info_);
301	>	interactionMan_->initialize();
302	>
303	>	// We want to delay the cutoffs until after the interaction
304	>	// manager has set up the atom-atom interactions so that we can
305	>	// query them for suggested cutoff values
306	>	setupCutoffs();
307	>
308	>	info_->prepareTopology();
309		}
310	<	*/
310	>
311	>	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
312	>
313	>	// Force fields can set options on how to scale van der Waals and
314	>	// electrostatic interactions for atoms connected via bonds, bends
315	>	// and torsions in this case the topological distance between
316	>	// atoms is:
317	>	// 0 = topologically unconnected
318	>	// 1 = bonded together
319	>	// 2 = connected via a bend
320	>	// 3 = connected via a torsion
321	>
322	>	vdwScale_.reserve(4);
323	>	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
324	>
325	>	electrostaticScale_.reserve(4);
326	>	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
327	>
328	>	vdwScale_[0] = 1.0;
329	>	vdwScale_[1] = fopts.getvdw12scale();
330	>	vdwScale_[2] = fopts.getvdw13scale();
331	>	vdwScale_[3] = fopts.getvdw14scale();
332	>
333	>	electrostaticScale_[0] = 1.0;
334	>	electrostaticScale_[1] = fopts.getelectrostatic12scale();
335	>	electrostaticScale_[2] = fopts.getelectrostatic13scale();
336	>	electrostaticScale_[3] = fopts.getelectrostatic14scale();
337	>
338	>	fDecomp_->distributeInitialData();
339	>
340	>	initialized_ = true;
341	>
342		}
343
344	+	void ForceManager::calcForces() {
345	+
346	+	if (!initialized_) initialize();
347	+
348	+	preCalculation();
349	+	shortRangeInteractions();
350	+	longRangeInteractions();
351	+	postCalculation();
352	+	}
353	+
354		void ForceManager::preCalculation() {
355		SimInfo::MoleculeIterator mi;
356		Molecule* mol;
#	Line 128 | Line 358 | namespace oopse {
358		Atom* atom;
359		Molecule::RigidBodyIterator rbIter;
360		RigidBody* rb;
361	+	Molecule::CutoffGroupIterator ci;
362	+	CutoffGroup* cg;
363
364		// forces are zeroed here, before any are accumulated.
365	<	// NOTE: do not rezero the forces in Fortran.
366	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
367	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
365	>
366	>	for (mol = info_->beginMolecule(mi); mol != NULL;
367	>	mol = info_->nextMolecule(mi)) {
368	>	for(atom = mol->beginAtom(ai); atom != NULL;
369	>	atom = mol->nextAtom(ai)) {
370		atom->zeroForcesAndTorques();
371	+	cerr << "apos = " << atom->getPos() << "\n";
372		}
373	<
373	>
374		//change the positions of atoms which belong to the rigidbodies
375	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
375	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
376	>	rb = mol->nextRigidBody(rbIter)) {
377		rb->zeroForcesAndTorques();
378		}
379	+
380	+	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
381	+	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
382	+	cg = mol->nextCutoffGroup(ci)) {
383	+	//calculate the center of mass of cutoff group
384	+	cg->updateCOM();
385	+	cerr << "cgpos = " << cg->getPos() << "\n";
386	+	}
387	+	}
388		}
389
390	+	// Zero out the stress tensor
391	+	tau *= 0.0;
392	+
393		}
394	<
395	<	void ForceManager::calcShortRangeInteraction() {
394	>
395	>	void ForceManager::shortRangeInteractions() {
396		Molecule* mol;
397		RigidBody* rb;
398		Bond* bond;
399		Bend* bend;
400		Torsion* torsion;
401	+	Inversion* inversion;
402		SimInfo::MoleculeIterator mi;
403		Molecule::RigidBodyIterator rbIter;
404		Molecule::BondIterator bondIter;;
405		Molecule::BendIterator  bendIter;
406		Molecule::TorsionIterator  torsionIter;
407	+	Molecule::InversionIterator  inversionIter;
408		RealType bondPotential = 0.0;
409		RealType bendPotential = 0.0;
410		RealType torsionPotential = 0.0;
411	+	RealType inversionPotential = 0.0;
412
413		//calculate short range interactions
414	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
414	>	for (mol = info_->beginMolecule(mi); mol != NULL;
415	>	mol = info_->nextMolecule(mi)) {
416
417		//change the positions of atoms which belong to the rigidbodies
418	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
419	<	rb->updateAtoms();
418	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
419	>	rb = mol->nextRigidBody(rbIter)) {
420	>	rb->updateAtoms();
421		}
422
423	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
423	>	for (bond = mol->beginBond(bondIter); bond != NULL;
424	>	bond = mol->nextBond(bondIter)) {
425		bond->calcForce();
426		bondPotential += bond->getPotential();
427		}
428
429	<
430	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
431	<
432	<	RealType angle;
433	<	bend->calcForce(angle);
434	<	RealType currBendPot = bend->getPotential();
435	<	bendPotential += bend->getPotential();
436	<	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
437	<	if (i == bendDataSets.end()) {
438	<	BendDataSet dataSet;
439	<	dataSet.prev.angle = dataSet.curr.angle = angle;
440	<	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
441	<	dataSet.deltaV = 0.0;
442	<	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
443	<	}else {
444	<	i->second.prev.angle = i->second.curr.angle;
445	<	i->second.prev.potential = i->second.curr.potential;
446	<	i->second.curr.angle = angle;
447	<	i->second.curr.potential = currBendPot;
448	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
449	<	}
450	<	}
451	<
452	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
199	<	RealType angle;
200	<	torsion->calcForce(angle);
201	<	RealType currTorsionPot = torsion->getPotential();
202	<	torsionPotential += torsion->getPotential();
203	<	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
204	<	if (i == torsionDataSets.end()) {
205	<	TorsionDataSet dataSet;
206	<	dataSet.prev.angle = dataSet.curr.angle = angle;
207	<	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
208	<	dataSet.deltaV = 0.0;
209	<	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
210	<	}else {
211	<	i->second.prev.angle = i->second.curr.angle;
212	<	i->second.prev.potential = i->second.curr.potential;
213	<	i->second.curr.angle = angle;
214	<	i->second.curr.potential = currTorsionPot;
215	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
216	<	}
429	>	for (bend = mol->beginBend(bendIter); bend != NULL;
430	>	bend = mol->nextBend(bendIter)) {
431	>
432	>	RealType angle;
433	>	bend->calcForce(angle);
434	>	RealType currBendPot = bend->getPotential();
435	>
436	>	bendPotential += bend->getPotential();
437	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
438	>	if (i == bendDataSets.end()) {
439	>	BendDataSet dataSet;
440	>	dataSet.prev.angle = dataSet.curr.angle = angle;
441	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
442	>	dataSet.deltaV = 0.0;
443	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
444	>	dataSet));
445	>	}else {
446	>	i->second.prev.angle = i->second.curr.angle;
447	>	i->second.prev.potential = i->second.curr.potential;
448	>	i->second.curr.angle = angle;
449	>	i->second.curr.potential = currBendPot;
450	>	i->second.deltaV =  fabs(i->second.curr.potential -
451	>	i->second.prev.potential);
452	>	}
453		}
454	<
454	>
455	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
456	>	torsion = mol->nextTorsion(torsionIter)) {
457	>	RealType angle;
458	>	torsion->calcForce(angle);
459	>	RealType currTorsionPot = torsion->getPotential();
460	>	torsionPotential += torsion->getPotential();
461	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
462	>	if (i == torsionDataSets.end()) {
463	>	TorsionDataSet dataSet;
464	>	dataSet.prev.angle = dataSet.curr.angle = angle;
465	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
466	>	dataSet.deltaV = 0.0;
467	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
468	>	}else {
469	>	i->second.prev.angle = i->second.curr.angle;
470	>	i->second.prev.potential = i->second.curr.potential;
471	>	i->second.curr.angle = angle;
472	>	i->second.curr.potential = currTorsionPot;
473	>	i->second.deltaV =  fabs(i->second.curr.potential -
474	>	i->second.prev.potential);
475	>	}
476	>	}
477	>
478	>	for (inversion = mol->beginInversion(inversionIter);
479	>	inversion != NULL;
480	>	inversion = mol->nextInversion(inversionIter)) {
481	>	RealType angle;
482	>	inversion->calcForce(angle);
483	>	RealType currInversionPot = inversion->getPotential();
484	>	inversionPotential += inversion->getPotential();
485	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
486	>	if (i == inversionDataSets.end()) {
487	>	InversionDataSet dataSet;
488	>	dataSet.prev.angle = dataSet.curr.angle = angle;
489	>	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
490	>	dataSet.deltaV = 0.0;
491	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
492	>	}else {
493	>	i->second.prev.angle = i->second.curr.angle;
494	>	i->second.prev.potential = i->second.curr.potential;
495	>	i->second.curr.angle = angle;
496	>	i->second.curr.potential = currInversionPot;
497	>	i->second.deltaV =  fabs(i->second.curr.potential -
498	>	i->second.prev.potential);
499	>	}
500	>	}
501		}
502
503	<	RealType  shortRangePotential = bondPotential + bendPotential + torsionPotential;
503	>	RealType  shortRangePotential = bondPotential + bendPotential +
504	>	torsionPotential +  inversionPotential;
505		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
506		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
507		curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
508		curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
509		curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
510	<
510	>	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
511		}
512	+
513	+	void ForceManager::longRangeInteractions() {
514
515	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
516	<	Snapshot* curSnapshot;
517	<	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();
515	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
516	>	DataStorage* config = &(curSnapshot->atomData);
517	>	DataStorage* cgConfig = &(curSnapshot->cgData);
518
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	–
519		//calculate the center of mass of cutoff group
520	+
521		SimInfo::MoleculeIterator mi;
522		Molecule* mol;
523		Molecule::CutoffGroupIterator ci;
524		CutoffGroup* cg;
256	–	Vector3d com;
257	–	std::vector<Vector3d> rcGroup;
525
526	<	if(info_->getNCutoffGroups() > 0){
527	<
528	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
529	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
530	<	cg->getCOM(com);
531	<	rcGroup.push_back(com);
526	>	if(info_->getNCutoffGroups() > 0){
527	>	for (mol = info_->beginMolecule(mi); mol != NULL;
528	>	mol = info_->nextMolecule(mi)) {
529	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
530	>	cg = mol->nextCutoffGroup(ci)) {
531	>	cerr << "branch1\n";
532	>	cerr << "globind = " << cg->getGlobalIndex() << "\n";
533	>	cg->updateCOM();
534		}
535	<	}// end for (mol)
267	<
268	<	rc = rcGroup[0].getArrayPointer();
535	>	}
536		} else {
537	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
538	<	rc = pos;
537	>	// center of mass of the group is the same as position of the atom
538	>	// if cutoff group does not exist
539	>	cerr << "branch2\n";
540	>	cgConfig->position = config->position;
541		}
542	<
543	<	//initialize data before passing to fortran
544	<	RealType longRangePotential[LR_POT_TYPES];
276	<	RealType lrPot = 0.0;
542	>
543	>	fDecomp_->zeroWorkArrays();
544	>	fDecomp_->distributeData();
545
546	<	Mat3x3d tau;
547	<	short int passedCalcPot = needPotential;
548	<	short int passedCalcStress = needStress;
549	<	int isError = 0;
546	>	int cg1, cg2, atom1, atom2, topoDist;
547	>	Vector3d d_grp, dag, d;
548	>	RealType rgrpsq, rgrp, r2, r;
549	>	RealType electroMult, vdwMult;
550	>	RealType vij;
551	>	Vector3d fij, fg, f1;
552	>	tuple3<RealType, RealType, RealType> cuts;
553	>	RealType rCutSq;
554	>	bool in_switching_region;
555	>	RealType sw, dswdr, swderiv;
556	>	vector<int> atomListColumn, atomListRow, atomListLocal;
557	>	InteractionData idat;
558	>	SelfData sdat;
559	>	RealType mf;
560	>	RealType lrPot;
561	>	RealType vpair;
562	>	potVec longRangePotential(0.0);
563	>	potVec workPot(0.0);
564
565	<	for (int i=0; i<LR_POT_TYPES;i++){
566	<	longRangePotential[i]=0.0; //Initialize array
565	>	int loopStart, loopEnd;
566	>
567	>	idat.vdwMult = &vdwMult;
568	>	idat.electroMult = &electroMult;
569	>	idat.pot = &workPot;
570	>	sdat.pot = fDecomp_->getEmbeddingPotential();
571	>	idat.vpair = &vpair;
572	>	idat.f1 = &f1;
573	>	idat.sw = &sw;
574	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
575	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
576	>
577	>	loopEnd = PAIR_LOOP;
578	>	if (info_->requiresPrepair() ) {
579	>	loopStart = PREPAIR_LOOP;
580	>	} else {
581	>	loopStart = PAIR_LOOP;
582		}
583	+
584	+	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
585	+
586	+	if (iLoop == loopStart) {
587	+	bool update_nlist = fDecomp_->checkNeighborList();
588	+	if (update_nlist)
589	+	neighborList = fDecomp_->buildNeighborList();
590	+	}
591	+
592	+	for (vector<pair<int, int> >::iterator it = neighborList.begin();
593	+	it != neighborList.end(); ++it) {
594	+
595	+	cg1 = (*it).first;
596	+	cg2 = (*it).second;
597	+
598	+	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
599
600	<	doForceLoop( pos,
601	<	rc,
602	<	A,
290	<	electroFrame,
291	<	frc,
292	<	trq,
293	<	tau.getArrayPointer(),
294	<	longRangePotential,
295	<	&passedCalcPot,
296	<	&passedCalcStress,
297	<	&isError );
600	>	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
601	>	curSnapshot->wrapVector(d_grp);
602	>	rgrpsq = d_grp.lengthSquare();
603
604	<	if( isError ){
605	<	sprintf( painCave.errMsg,
606	<	"Error returned from the fortran force calculation.\n" );
607	<	painCave.isFatal = 1;
608	<	simError();
604	>	rCutSq = cuts.second;
605	>
606	>	if (rgrpsq < rCutSq) {
607	>	idat.rcut = &cuts.first;
608	>	if (iLoop == PAIR_LOOP) {
609	>	vij = 0.0;
610	>	fij = V3Zero;
611	>	}
612	>
613	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
614	>	rgrp);
615	>
616	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
617	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
618	>
619	>	for (vector<int>::iterator ia = atomListRow.begin();
620	>	ia != atomListRow.end(); ++ia) {
621	>	atom1 = (*ia);
622	>
623	>	for (vector<int>::iterator jb = atomListColumn.begin();
624	>	jb != atomListColumn.end(); ++jb) {
625	>	atom2 = (*jb);
626	>
627	>	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
628	>	vpair = 0.0;
629	>	workPot = 0.0;
630	>	f1 = V3Zero;
631	>
632	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
633	>
634	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
635	>	vdwMult = vdwScale_[topoDist];
636	>	electroMult = electrostaticScale_[topoDist];
637	>
638	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
639	>	idat.d = &d_grp;
640	>	idat.r2 = &rgrpsq;
641	>	cerr << "dgrp = " << d_grp << "\n";
642	>	} else {
643	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
644	>	curSnapshot->wrapVector( d );
645	>	r2 = d.lengthSquare();
646	>	cerr << "datm = " << d<< "\n";
647	>	idat.d = &d;
648	>	idat.r2 = &r2;
649	>	}
650	>
651	>	cerr << "idat.d = " << *(idat.d) << "\n";
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	>	cerr << "d = " << *(idat.d) << "\tv=" << vpair << "\tf=" << f1 << "\n";
662	>	vij += vpair;
663	>	fij += f1;
664	>	tau -= outProduct( *(idat.d), f1);
665	>	}
666	>	}
667	>	}
668	>	}
669	>
670	>	if (iLoop == PAIR_LOOP) {
671	>	if (in_switching_region) {
672	>	swderiv = vij * dswdr / rgrp;
673	>	fg = swderiv * d_grp;
674	>	fij += fg;
675	>
676	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
677	>	tau -= outProduct( *(idat.d), fg);
678	>	}
679	>
680	>	for (vector<int>::iterator ia = atomListRow.begin();
681	>	ia != atomListRow.end(); ++ia) {
682	>	atom1 = (*ia);
683	>	mf = fDecomp_->getMassFactorRow(atom1);
684	>	// fg is the force on atom ia due to cutoff group's
685	>	// presence in switching region
686	>	fg = swderiv * d_grp * mf;
687	>	fDecomp_->addForceToAtomRow(atom1, fg);
688	>
689	>	if (atomListRow.size() > 1) {
690	>	if (info_->usesAtomicVirial()) {
691	>	// find the distance between the atom
692	>	// and the center of the cutoff group:
693	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
694	>	tau -= outProduct(dag, fg);
695	>	}
696	>	}
697	>	}
698	>	for (vector<int>::iterator jb = atomListColumn.begin();
699	>	jb != atomListColumn.end(); ++jb) {
700	>	atom2 = (*jb);
701	>	mf = fDecomp_->getMassFactorColumn(atom2);
702	>	// fg is the force on atom jb due to cutoff group's
703	>	// presence in switching region
704	>	fg = -swderiv * d_grp * mf;
705	>	fDecomp_->addForceToAtomColumn(atom2, fg);
706	>
707	>	if (atomListColumn.size() > 1) {
708	>	if (info_->usesAtomicVirial()) {
709	>	// find the distance between the atom
710	>	// and the center of the cutoff group:
711	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
712	>	tau -= outProduct(dag, fg);
713	>	}
714	>	}
715	>	}
716	>	}
717	>	//if (!SIM_uses_AtomicVirial) {
718	>	//  tau -= outProduct(d_grp, fij);
719	>	//}
720	>	}
721	>	}
722	>	}
723	>
724	>	if (iLoop == PREPAIR_LOOP) {
725	>	if (info_->requiresPrepair()) {
726	>
727	>	fDecomp_->collectIntermediateData();
728	>
729	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
730	>	fDecomp_->fillSelfData(sdat, atom1);
731	>	interactionMan_->doPreForce(sdat);
732	>	}
733	>
734	>	fDecomp_->distributeIntermediateData();
735	>
736	>	}
737	>	}
738	>
739		}
740	<	for (int i=0; i<LR_POT_TYPES;i++){
741	<	lrPot += longRangePotential[i]; //Quick hack
740	>
741	>	fDecomp_->collectData();
742	>
743	>	if (info_->requiresSelfCorrection()) {
744	>
745	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
746	>	fDecomp_->fillSelfData(sdat, atom1);
747	>	interactionMan_->doSelfCorrection(sdat);
748	>	}
749	>
750		}
751
752	+	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
753	+	*(fDecomp_->getPairwisePotential());
754	+
755	+	lrPot = longRangePotential.sum();
756	+
757		//store the tau and long range potential
758		curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
759	<	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
760	<	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
313	<
314	<	curSnapshot->statData.setTau(tau);
759	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
760	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
761		}
762
763	<
763	>
764		void ForceManager::postCalculation() {
765		SimInfo::MoleculeIterator mi;
766		Molecule* mol;
767		Molecule::RigidBodyIterator rbIter;
768		RigidBody* rb;
769	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
770
771		// collect the atomic forces onto rigid bodies
772	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
773	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
774	<	rb->calcForcesAndTorques();
772	>
773	>	for (mol = info_->beginMolecule(mi); mol != NULL;
774	>	mol = info_->nextMolecule(mi)) {
775	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
776	>	rb = mol->nextRigidBody(rbIter)) {
777	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
778	>	tau += rbTau;
779		}
780		}
781	<
781	>
782	>	#ifdef IS_MPI
783	>	Mat3x3d tmpTau(tau);
784	>	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
785	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
786	>	#endif
787	>	curSnapshot->statData.setTau(tau);
788		}
789
790	<	} //end namespace oopse
790	>	} //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 1597 by gezelter, Tue Jul 26 15:49:24 2011 UTC

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