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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 1587 by gezelter, Fri Jul 8 20:25:32 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, SHIFTED_POTENTIAL)
90	>	*      If cutoffMethod was explicitly set, use that choice.
91	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
92	>	*
93	>	* cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
94	>	*      If cutoffPolicy was explicitly set, use that choice.
95	>	*      If cutoffPolicy was not explicitly set, use TRADITIONAL
96	>	*
97	>	* switchingRadius : realType
98	>	*  If the cutoffMethod was set to SWITCHED:
99	>	*      If the switchingRadius was explicitly set, use that value
100	>	*          (but do a sanity check first).
101	>	*      If the switchingRadius was not explicitly set: use 0.85 *
102	>	*      cutoffRadius_
103	>	*  If the cutoffMethod was not set to SWITCHED:
104	>	*      Set switchingRadius equal to cutoffRadius for safety.
105	>	*/
106	>	void ForceManager::setupCutoffs() {
107	>
108	>	Globals* simParams_ = info_->getSimParams();
109	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
110	>
111	>	if (simParams_->haveCutoffRadius()) {
112	>	rCut_ = simParams_->getCutoffRadius();
113	>	} else {
114	>	if (info_->usesElectrostaticAtoms()) {
115	>	sprintf(painCave.errMsg,
116	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
117	>	"\tOpenMD will use a default value of 12.0 angstroms"
118	>	"\tfor the cutoffRadius.\n");
119	>	painCave.isFatal = 0;
120	>	painCave.severity = OPENMD_INFO;
121	>	simError();
122	>	rCut_ = 12.0;
123	>	} else {
124	>	RealType thisCut;
125	>	set<AtomType*>::iterator i;
126	>	set<AtomType*> atomTypes;
127	>	atomTypes = info_->getSimulatedAtomTypes();
128	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
129	>	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
130	>	rCut_ = max(thisCut, rCut_);
131	>	}
132	>	sprintf(painCave.errMsg,
133	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
134	>	"\tOpenMD will use %lf angstroms.\n",
135	>	rCut_);
136	>	painCave.isFatal = 0;
137	>	painCave.severity = OPENMD_INFO;
138	>	simError();
139	>	}
140	>	}
141
142	<	if (!info_->isFortranInitialized()) {
143	<	info_->update();
142	>	fDecomp_->setUserCutoff(rCut_);
143	>	interactionMan_->setCutoffRadius(rCut_);
144	>
145	>	map<string, CutoffMethod> stringToCutoffMethod;
146	>	stringToCutoffMethod["HARD"] = HARD;
147	>	stringToCutoffMethod["SWITCHED"] = SWITCHED;
148	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
149	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
150	>
151	>	if (simParams_->haveCutoffMethod()) {
152	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
153	>	map<string, CutoffMethod>::iterator i;
154	>	i = stringToCutoffMethod.find(cutMeth);
155	>	if (i == stringToCutoffMethod.end()) {
156	>	sprintf(painCave.errMsg,
157	>	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
158	>	"\tShould be one of: "
159	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
160	>	cutMeth.c_str());
161	>	painCave.isFatal = 1;
162	>	painCave.severity = OPENMD_ERROR;
163	>	simError();
164	>	} else {
165	>	cutoffMethod_ = i->second;
166	>	}
167	>	} else {
168	>	sprintf(painCave.errMsg,
169	>	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
170	>	"\tOpenMD will use SHIFTED_FORCE.\n");
171	>	painCave.isFatal = 0;
172	>	painCave.severity = OPENMD_INFO;
173	>	simError();
174	>	cutoffMethod_ = SHIFTED_FORCE;
175		}
176
177	<	preCalculation();
178	<
179	<	calcShortRangeInteraction();
177	>	map<string, CutoffPolicy> stringToCutoffPolicy;
178	>	stringToCutoffPolicy["MIX"] = MIX;
179	>	stringToCutoffPolicy["MAX"] = MAX;
180	>	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
181
182	<	calcLongRangeInteraction(needPotential, needStress);
182	>	std::string cutPolicy;
183	>	if (forceFieldOptions_.haveCutoffPolicy()){
184	>	cutPolicy = forceFieldOptions_.getCutoffPolicy();
185	>	}else if (simParams_->haveCutoffPolicy()) {
186	>	cutPolicy = simParams_->getCutoffPolicy();
187	>	}
188
189	<	postCalculation();
189	>	if (!cutPolicy.empty()){
190	>	toUpper(cutPolicy);
191	>	map<string, CutoffPolicy>::iterator i;
192	>	i = stringToCutoffPolicy.find(cutPolicy);
193
194	<	/*
195	<	std::vector<BendOrderStruct> bendOrderStruct;
196	<	for(std::map<Bend*, BendDataSet>::iterator i = bendDataSets.begin(); i != bendDataSets.end(); ++i) {
197	<	BendOrderStruct tmp;
198	<	tmp.bend= const_cast<Bend*>(i->first);
199	<	tmp.dataSet = i->second;
200	<	bendOrderStruct.push_back(tmp);
194	>	if (i == stringToCutoffPolicy.end()) {
195	>	sprintf(painCave.errMsg,
196	>	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
197	>	"\tShould be one of: "
198	>	"MIX, MAX, or TRADITIONAL\n",
199	>	cutPolicy.c_str());
200	>	painCave.isFatal = 1;
201	>	painCave.severity = OPENMD_ERROR;
202	>	simError();
203	>	} else {
204	>	cutoffPolicy_ = i->second;
205	>	}
206	>	} else {
207	>	sprintf(painCave.errMsg,
208	>	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
209	>	"\tOpenMD will use TRADITIONAL.\n");
210	>	painCave.isFatal = 0;
211	>	painCave.severity = OPENMD_INFO;
212	>	simError();
213	>	cutoffPolicy_ = TRADITIONAL;
214		}
215
216	<	std::vector<TorsionOrderStruct> torsionOrderStruct;
217	<	for(std::map<Torsion*, TorsionDataSet>::iterator j = torsionDataSets.begin(); j != torsionDataSets.end(); ++j) {
218	<	TorsionOrderStruct tmp;
219	<	tmp.torsion = const_cast<Torsion*>(j->first);
220	<	tmp.dataSet = j->second;
221	<	torsionOrderStruct.push_back(tmp);
216	>	fDecomp_->setCutoffPolicy(cutoffPolicy_);
217	>
218	>	// create the switching function object:
219	>
220	>	switcher_ = new SwitchingFunction();
221	>
222	>	if (cutoffMethod_ == SWITCHED) {
223	>	if (simParams_->haveSwitchingRadius()) {
224	>	rSwitch_ = simParams_->getSwitchingRadius();
225	>	if (rSwitch_ > rCut_) {
226	>	sprintf(painCave.errMsg,
227	>	"ForceManager::setupCutoffs: switchingRadius (%f) is larger "
228	>	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
229	>	painCave.isFatal = 1;
230	>	painCave.severity = OPENMD_ERROR;
231	>	simError();
232	>	}
233	>	} else {
234	>	rSwitch_ = 0.85 * rCut_;
235	>	sprintf(painCave.errMsg,
236	>	"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
237	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
238	>	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
239	>	painCave.isFatal = 0;
240	>	painCave.severity = OPENMD_WARNING;
241	>	simError();
242	>	}
243	>	} else {
244	>	if (simParams_->haveSwitchingRadius()) {
245	>	map<string, CutoffMethod>::const_iterator it;
246	>	string theMeth;
247	>	for (it = stringToCutoffMethod.begin();
248	>	it != stringToCutoffMethod.end(); ++it) {
249	>	if (it->second == cutoffMethod_) {
250	>	theMeth = it->first;
251	>	break;
252	>	}
253	>	}
254	>	sprintf(painCave.errMsg,
255	>	"ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
256	>	"\tis not set to SWITCHED, so switchingRadius value\n"
257	>	"\twill be ignored for this simulation\n", theMeth.c_str());
258	>	painCave.isFatal = 0;
259	>	painCave.severity = OPENMD_WARNING;
260	>	simError();
261	>	}
262	>
263	>	rSwitch_ = rCut_;
264		}
265
266	<	std::sort(bendOrderStruct.begin(), bendOrderStruct.end(), std::ptr_fun(BendSortFunctor));
267	<	std::sort(torsionOrderStruct.begin(), torsionOrderStruct.end(), std::ptr_fun(TorsionSortFunctor));
268	<	std::cout << "bend" << std::endl;
269	<	for (std::vector<BendOrderStruct>::iterator k = bendOrderStruct.begin(); k != bendOrderStruct.end(); ++k) {
270	<	Bend* bend = k->bend;
271	<	std::cout << "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;
266	>	// Default to cubic switching function.
267	>	sft_ = cubic;
268	>	if (simParams_->haveSwitchingFunctionType()) {
269	>	string funcType = simParams_->getSwitchingFunctionType();
270	>	toUpper(funcType);
271	>	if (funcType == "CUBIC") {
272	>	sft_ = cubic;
273	>	} else {
274	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
275	>	sft_ = fifth_order_poly;
276	>	} else {
277	>	// throw error
278	>	sprintf( painCave.errMsg,
279	>	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
280	>	"\tswitchingFunctionType must be one of: "
281	>	"\"cubic\" or \"fifth_order_polynomial\".",
282	>	funcType.c_str() );
283	>	painCave.isFatal = 1;
284	>	painCave.severity = OPENMD_ERROR;
285	>	simError();
286	>	}
287	>	}
288		}
289	<	std::cout << "torsio" << std::endl;
290	<	for (std::vector<TorsionOrderStruct>::iterator l = torsionOrderStruct.begin(); l != torsionOrderStruct.end(); ++l) {
291	<	Torsion* torsion = l->torsion;
292	<	std::cout << "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;
289	>	switcher_->setSwitchType(sft_);
290	>	switcher_->setSwitch(rSwitch_, rCut_);
291	>	interactionMan_->setSwitchingRadius(rSwitch_);
292	>	}
293	>
294	>	void ForceManager::initialize() {
295	>
296	>	if (!info_->isTopologyDone()) {
297	>	info_->update();
298	>	interactionMan_->setSimInfo(info_);
299	>	interactionMan_->initialize();
300	>
301	>	// We want to delay the cutoffs until after the interaction
302	>	// manager has set up the atom-atom interactions so that we can
303	>	// query them for suggested cutoff values
304	>
305	>	setupCutoffs();
306	>
307	>	info_->prepareTopology();
308		}
309	<	*/
309	>
310	>	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
311	>
312	>	// Force fields can set options on how to scale van der Waals and electrostatic
313	>	// interactions for atoms connected via bonds, bends and torsions
314	>	// in this case the topological distance between atoms is:
315	>	// 0 = topologically unconnected
316	>	// 1 = bonded together
317	>	// 2 = connected via a bend
318	>	// 3 = connected via a torsion
319	>
320	>	vdwScale_.reserve(4);
321	>	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
322	>
323	>	electrostaticScale_.reserve(4);
324	>	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
325	>
326	>	vdwScale_[0] = 1.0;
327	>	vdwScale_[1] = fopts.getvdw12scale();
328	>	vdwScale_[2] = fopts.getvdw13scale();
329	>	vdwScale_[3] = fopts.getvdw14scale();
330	>
331	>	electrostaticScale_[0] = 1.0;
332	>	electrostaticScale_[1] = fopts.getelectrostatic12scale();
333	>	electrostaticScale_[2] = fopts.getelectrostatic13scale();
334	>	electrostaticScale_[3] = fopts.getelectrostatic14scale();
335	>
336	>	fDecomp_->distributeInitialData();
337	>
338	>	initialized_ = true;
339	>
340		}
341
342	+	void ForceManager::calcForces() {
343	+
344	+	if (!initialized_) initialize();
345	+
346	+	preCalculation();
347	+	shortRangeInteractions();
348	+	longRangeInteractions();
349	+	postCalculation();
350	+	}
351	+
352		void ForceManager::preCalculation() {
353		SimInfo::MoleculeIterator mi;
354		Molecule* mol;
#	Line 130 | Line 356 | namespace oopse {
356		Atom* atom;
357		Molecule::RigidBodyIterator rbIter;
358		RigidBody* rb;
359	+	Molecule::CutoffGroupIterator ci;
360	+	CutoffGroup* cg;
361
362		// forces are zeroed here, before any are accumulated.
363	<	// NOTE: do not rezero the forces in Fortran.
364	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
363	>
364	>	for (mol = info_->beginMolecule(mi); mol != NULL;
365	>	mol = info_->nextMolecule(mi)) {
366		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
367		atom->zeroForcesAndTorques();
368		}
369	<
369	>
370		//change the positions of atoms which belong to the rigidbodies
371	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
371	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
372	>	rb = mol->nextRigidBody(rbIter)) {
373		rb->zeroForcesAndTorques();
374		}
375	+
376	+	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
377	+	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
378	+	cg = mol->nextCutoffGroup(ci)) {
379	+	//calculate the center of mass of cutoff group
380	+	cg->updateCOM();
381	+	}
382	+	}
383		}
384	+
385	+	// Zero out the stress tensor
386	+	tau *= 0.0;
387
388		}
389	<
390	<	void ForceManager::calcShortRangeInteraction() {
389	>
390	>	void ForceManager::shortRangeInteractions() {
391		Molecule* mol;
392		RigidBody* rb;
393		Bond* bond;
394		Bend* bend;
395		Torsion* torsion;
396	+	Inversion* inversion;
397		SimInfo::MoleculeIterator mi;
398		Molecule::RigidBodyIterator rbIter;
399		Molecule::BondIterator bondIter;;
400		Molecule::BendIterator  bendIter;
401		Molecule::TorsionIterator  torsionIter;
402	<	double bondPotential = 0.0;
403	<	double bendPotential = 0.0;
404	<	double torsionPotential = 0.0;
402	>	Molecule::InversionIterator  inversionIter;
403	>	RealType bondPotential = 0.0;
404	>	RealType bendPotential = 0.0;
405	>	RealType torsionPotential = 0.0;
406	>	RealType inversionPotential = 0.0;
407
408		//calculate short range interactions
409	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
409	>	for (mol = info_->beginMolecule(mi); mol != NULL;
410	>	mol = info_->nextMolecule(mi)) {
411
412		//change the positions of atoms which belong to the rigidbodies
413	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
414	<	rb->updateAtoms();
413	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
414	>	rb = mol->nextRigidBody(rbIter)) {
415	>	rb->updateAtoms();
416		}
417
418	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
418	>	for (bond = mol->beginBond(bondIter); bond != NULL;
419	>	bond = mol->nextBond(bondIter)) {
420		bond->calcForce();
421		bondPotential += bond->getPotential();
422		}
423
424	<
425	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
426	<
427	<	double angle;
428	<	bend->calcForce(angle);
429	<	double currBendPot = bend->getPotential();
430	<	bendPotential += bend->getPotential();
431	<	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
432	<	if (i == bendDataSets.end()) {
433	<	BendDataSet dataSet;
434	<	dataSet.prev.angle = dataSet.curr.angle = angle;
435	<	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
436	<	dataSet.deltaV = 0.0;
437	<	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
438	<	}else {
439	<	i->second.prev.angle = i->second.curr.angle;
440	<	i->second.prev.potential = i->second.curr.potential;
441	<	i->second.curr.angle = angle;
442	<	i->second.curr.potential = currBendPot;
443	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
444	<	}
424	>	for (bend = mol->beginBend(bendIter); bend != NULL;
425	>	bend = mol->nextBend(bendIter)) {
426	>
427	>	RealType angle;
428	>	bend->calcForce(angle);
429	>	RealType currBendPot = bend->getPotential();
430	>
431	>	bendPotential += bend->getPotential();
432	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
433	>	if (i == bendDataSets.end()) {
434	>	BendDataSet dataSet;
435	>	dataSet.prev.angle = dataSet.curr.angle = angle;
436	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
437	>	dataSet.deltaV = 0.0;
438	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
439	>	}else {
440	>	i->second.prev.angle = i->second.curr.angle;
441	>	i->second.prev.potential = i->second.curr.potential;
442	>	i->second.curr.angle = angle;
443	>	i->second.curr.potential = currBendPot;
444	>	i->second.deltaV =  fabs(i->second.curr.potential -
445	>	i->second.prev.potential);
446	>	}
447		}
448	<
449	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
450	<	double angle;
451	<	torsion->calcForce(angle);
452	<	double currTorsionPot = torsion->getPotential();
453	<	torsionPotential += torsion->getPotential();
454	<	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
455	<	if (i == torsionDataSets.end()) {
456	<	TorsionDataSet dataSet;
457	<	dataSet.prev.angle = dataSet.curr.angle = angle;
458	<	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
459	<	dataSet.deltaV = 0.0;
460	<	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
461	<	}else {
462	<	i->second.prev.angle = i->second.curr.angle;
463	<	i->second.prev.potential = i->second.curr.potential;
464	<	i->second.curr.angle = angle;
465	<	i->second.curr.potential = currTorsionPot;
466	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
467	<	}
468	<	}
469	<
448	>
449	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
450	>	torsion = mol->nextTorsion(torsionIter)) {
451	>	RealType angle;
452	>	torsion->calcForce(angle);
453	>	RealType currTorsionPot = torsion->getPotential();
454	>	torsionPotential += torsion->getPotential();
455	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
456	>	if (i == torsionDataSets.end()) {
457	>	TorsionDataSet dataSet;
458	>	dataSet.prev.angle = dataSet.curr.angle = angle;
459	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
460	>	dataSet.deltaV = 0.0;
461	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
462	>	}else {
463	>	i->second.prev.angle = i->second.curr.angle;
464	>	i->second.prev.potential = i->second.curr.potential;
465	>	i->second.curr.angle = angle;
466	>	i->second.curr.potential = currTorsionPot;
467	>	i->second.deltaV =  fabs(i->second.curr.potential -
468	>	i->second.prev.potential);
469	>	}
470	>	}
471	>
472	>	for (inversion = mol->beginInversion(inversionIter);
473	>	inversion != NULL;
474	>	inversion = mol->nextInversion(inversionIter)) {
475	>	RealType angle;
476	>	inversion->calcForce(angle);
477	>	RealType currInversionPot = inversion->getPotential();
478	>	inversionPotential += inversion->getPotential();
479	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
480	>	if (i == inversionDataSets.end()) {
481	>	InversionDataSet dataSet;
482	>	dataSet.prev.angle = dataSet.curr.angle = angle;
483	>	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
484	>	dataSet.deltaV = 0.0;
485	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
486	>	}else {
487	>	i->second.prev.angle = i->second.curr.angle;
488	>	i->second.prev.potential = i->second.curr.potential;
489	>	i->second.curr.angle = angle;
490	>	i->second.curr.potential = currInversionPot;
491	>	i->second.deltaV =  fabs(i->second.curr.potential -
492	>	i->second.prev.potential);
493	>	}
494	>	}
495		}
496
497	<	double  shortRangePotential = bondPotential + bendPotential + torsionPotential;
497	>	RealType  shortRangePotential = bondPotential + bendPotential +
498	>	torsionPotential +  inversionPotential;
499		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
500		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
501		curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
502		curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
503		curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
504	<
504	>	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
505		}
506	+
507	+	void ForceManager::longRangeInteractions() {
508
509	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
510	<	Snapshot* curSnapshot;
511	<	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();
509	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
510	>	DataStorage* config = &(curSnapshot->atomData);
511	>	DataStorage* cgConfig = &(curSnapshot->cgData);
512
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	–
513		//calculate the center of mass of cutoff group
514	+
515		SimInfo::MoleculeIterator mi;
516		Molecule* mol;
517		Molecule::CutoffGroupIterator ci;
518		CutoffGroup* cg;
258	–	Vector3d com;
259	–	std::vector<Vector3d> rcGroup;
519
520	<	if(info_->getNCutoffGroups() > 0){
521	<
522	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
523	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
524	<	cg->getCOM(com);
525	<	rcGroup.push_back(com);
520	>	if(info_->getNCutoffGroups() > 0){
521	>	for (mol = info_->beginMolecule(mi); mol != NULL;
522	>	mol = info_->nextMolecule(mi)) {
523	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
524	>	cg = mol->nextCutoffGroup(ci)) {
525	>	cg->updateCOM();
526		}
527	<	}// end for (mol)
269	<
270	<	rc = rcGroup[0].getArrayPointer();
527	>	}
528		} else {
529	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
530	<	rc = pos;
529	>	// center of mass of the group is the same as position of the atom
530	>	// if cutoff group does not exist
531	>	cgConfig->position = config->position;
532		}
533	<
534	<	//initialize data before passing to fortran
535	<	double longRangePotential[LR_POT_TYPES];
278	<	double lrPot = 0.0;
533	>
534	>	fDecomp_->zeroWorkArrays();
535	>	fDecomp_->distributeData();
536
537	<	Mat3x3d tau;
538	<	short int passedCalcPot = needPotential;
539	<	short int passedCalcStress = needStress;
540	<	int isError = 0;
537	>	int cg1, cg2, atom1, atom2, topoDist;
538	>	Vector3d d_grp, dag, d;
539	>	RealType rgrpsq, rgrp, r2, r;
540	>	RealType electroMult, vdwMult;
541	>	RealType vij;
542	>	Vector3d fij, fg, f1;
543	>	tuple3<RealType, RealType, RealType> cuts;
544	>	RealType rCutSq;
545	>	bool in_switching_region;
546	>	RealType sw, dswdr, swderiv;
547	>	vector<int> atomListColumn, atomListRow, atomListLocal;
548	>	InteractionData idat;
549	>	SelfData sdat;
550	>	RealType mf;
551	>	RealType lrPot;
552	>	RealType vpair;
553	>	potVec longRangePotential(0.0);
554	>	potVec workPot(0.0);
555
556	<	for (int i=0; i<LR_POT_TYPES;i++){
557	<	longRangePotential[i]=0.0; //Initialize array
556	>	int loopStart, loopEnd;
557	>
558	>	idat.vdwMult = &vdwMult;
559	>	idat.electroMult = &electroMult;
560	>	idat.pot = &workPot;
561	>	sdat.pot = fDecomp_->getEmbeddingPotential();
562	>	idat.vpair = &vpair;
563	>	idat.f1 = &f1;
564	>	idat.sw = &sw;
565	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
566	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
567	>
568	>	loopEnd = PAIR_LOOP;
569	>	if (info_->requiresPrepair() ) {
570	>	loopStart = PREPAIR_LOOP;
571	>	} else {
572	>	loopStart = PAIR_LOOP;
573		}
574	+
575	+	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
576	+
577	+	if (iLoop == loopStart) {
578	+	bool update_nlist = fDecomp_->checkNeighborList();
579	+	if (update_nlist)
580	+	neighborList = fDecomp_->buildNeighborList();
581	+	}
582	+
583	+	for (vector<pair<int, int> >::iterator it = neighborList.begin();
584	+	it != neighborList.end(); ++it) {
585	+
586	+	cg1 = (*it).first;
587	+	cg2 = (*it).second;
588	+
589	+	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
590
591	<	doForceLoop( pos,
592	<	rc,
593	<	A,
292	<	electroFrame,
293	<	frc,
294	<	trq,
295	<	tau.getArrayPointer(),
296	<	longRangePotential,
297	<	&passedCalcPot,
298	<	&passedCalcStress,
299	<	&isError );
591	>	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
592	>	curSnapshot->wrapVector(d_grp);
593	>	rgrpsq = d_grp.lengthSquare();
594
595	<	if( isError ){
596	<	sprintf( painCave.errMsg,
597	<	"Error returned from the fortran force calculation.\n" );
598	<	painCave.isFatal = 1;
599	<	simError();
595	>	rCutSq = cuts.second;
596	>
597	>	if (rgrpsq < rCutSq) {
598	>	idat.rcut = &cuts.first;
599	>	if (iLoop == PAIR_LOOP) {
600	>	vij = 0.0;
601	>	fij = V3Zero;
602	>	}
603	>
604	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
605	>	rgrp);
606	>
607	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
608	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
609	>
610	>	for (vector<int>::iterator ia = atomListRow.begin();
611	>	ia != atomListRow.end(); ++ia) {
612	>	atom1 = (*ia);
613	>
614	>	for (vector<int>::iterator jb = atomListColumn.begin();
615	>	jb != atomListColumn.end(); ++jb) {
616	>	atom2 = (*jb);
617	>
618	>	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
619	>	vpair = 0.0;
620	>	workPot = 0.0;
621	>	f1 = V3Zero;
622	>
623	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
624	>
625	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
626	>	vdwMult = vdwScale_[topoDist];
627	>	electroMult = electrostaticScale_[topoDist];
628	>
629	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
630	>	idat.d = &d_grp;
631	>	idat.r2 = &rgrpsq;
632	>	} else {
633	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
634	>	curSnapshot->wrapVector( d );
635	>	r2 = d.lengthSquare();
636	>	idat.d = &d;
637	>	idat.r2 = &r2;
638	>	}
639	>
640	>	r = sqrt( *(idat.r2) );
641	>	idat.rij = &r;
642	>
643	>	if (iLoop == PREPAIR_LOOP) {
644	>	interactionMan_->doPrePair(idat);
645	>	} else {
646	>	interactionMan_->doPair(idat);
647	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
648	>	vij += vpair;
649	>	fij += f1;
650	>	tau -= outProduct( *(idat.d), f1);
651	>	}
652	>	}
653	>	}
654	>	}
655	>
656	>	if (iLoop == PAIR_LOOP) {
657	>	if (in_switching_region) {
658	>	swderiv = vij * dswdr / rgrp;
659	>	fg = swderiv * d_grp;
660	>	fij += fg;
661	>
662	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
663	>	tau -= outProduct( *(idat.d), fg);
664	>	}
665	>
666	>	for (vector<int>::iterator ia = atomListRow.begin();
667	>	ia != atomListRow.end(); ++ia) {
668	>	atom1 = (*ia);
669	>	mf = fDecomp_->getMassFactorRow(atom1);
670	>	// fg is the force on atom ia due to cutoff group's
671	>	// presence in switching region
672	>	fg = swderiv * d_grp * mf;
673	>	fDecomp_->addForceToAtomRow(atom1, fg);
674	>
675	>	if (atomListRow.size() > 1) {
676	>	if (info_->usesAtomicVirial()) {
677	>	// find the distance between the atom
678	>	// and the center of the cutoff group:
679	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
680	>	tau -= outProduct(dag, fg);
681	>	}
682	>	}
683	>	}
684	>	for (vector<int>::iterator jb = atomListColumn.begin();
685	>	jb != atomListColumn.end(); ++jb) {
686	>	atom2 = (*jb);
687	>	mf = fDecomp_->getMassFactorColumn(atom2);
688	>	// fg is the force on atom jb due to cutoff group's
689	>	// presence in switching region
690	>	fg = -swderiv * d_grp * mf;
691	>	fDecomp_->addForceToAtomColumn(atom2, fg);
692	>
693	>	if (atomListColumn.size() > 1) {
694	>	if (info_->usesAtomicVirial()) {
695	>	// find the distance between the atom
696	>	// and the center of the cutoff group:
697	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
698	>	tau -= outProduct(dag, fg);
699	>	}
700	>	}
701	>	}
702	>	}
703	>	//if (!SIM_uses_AtomicVirial) {
704	>	//  tau -= outProduct(d_grp, fij);
705	>	//}
706	>	}
707	>	}
708	>	}
709	>
710	>	if (iLoop == PREPAIR_LOOP) {
711	>	if (info_->requiresPrepair()) {
712	>	fDecomp_->collectIntermediateData();
713	>
714	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
715	>	fDecomp_->fillSelfData(sdat, atom1);
716	>	interactionMan_->doPreForce(sdat);
717	>	}
718	>
719	>
720	>	fDecomp_->distributeIntermediateData();
721	>	}
722	>	}
723	>
724		}
725	<	for (int i=0; i<LR_POT_TYPES;i++){
726	<	lrPot += longRangePotential[i]; //Quick hack
725	>
726	>	fDecomp_->collectData();
727	>
728	>	if (info_->requiresSelfCorrection()) {
729	>
730	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
731	>	fDecomp_->fillSelfData(sdat, atom1);
732	>	interactionMan_->doSelfCorrection(sdat);
733	>	}
734	>
735		}
736
737	+	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
738	+	*(fDecomp_->getPairwisePotential());
739	+
740	+	lrPot = longRangePotential.sum();
741	+
742		//store the tau and long range potential
743		curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
744	<	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
745	<	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
315	<
316	<	curSnapshot->statData.setTau(tau);
744	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
745	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
746		}
747
748	<
748	>
749		void ForceManager::postCalculation() {
750		SimInfo::MoleculeIterator mi;
751		Molecule* mol;
752		Molecule::RigidBodyIterator rbIter;
753		RigidBody* rb;
754	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
755
756		// collect the atomic forces onto rigid bodies
757	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
758	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
759	<	rb->calcForcesAndTorques();
757	>
758	>	for (mol = info_->beginMolecule(mi); mol != NULL;
759	>	mol = info_->nextMolecule(mi)) {
760	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
761	>	rb = mol->nextRigidBody(rbIter)) {
762	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
763	>	tau += rbTau;
764		}
765		}
766	<
766	>
767	>	#ifdef IS_MPI
768	>	Mat3x3d tmpTau(tau);
769	>	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
770	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
771	>	#endif
772	>	curSnapshot->statData.setTau(tau);
773		}
774
775	<	} //end namespace oopse
775	>	} //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 1587 by gezelter, Fri Jul 8 20:25:32 2011 UTC

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