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

Comparing:
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 1583 by gezelter, Thu Jun 16 22:00:08 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, cutoffMethod, and cutoffPolicy
79	>	*
80	>	* cutoffRadius : realType
81	>	*  If the cutoffRadius was explicitly set, use that value.
82	>	*  If the cutoffRadius was not explicitly set:
83	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
84	>	*      No electrostatic atoms?  Poll the atom types present in the
85	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
86	>	*      Use the maximum suggested value that was found.
87	>	*
88	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
89	>	*      If cutoffMethod was explicitly set, use that choice.
90	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
91	>	*
92	>	* cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
93	>	*      If cutoffPolicy was explicitly set, use that choice.
94	>	*      If cutoffPolicy was not explicitly set, use TRADITIONAL
95	>	*/
96	>	void ForceManager::setupCutoffs() {
97	>
98	>	Globals* simParams_ = info_->getSimParams();
99	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
100	>
101	>	if (simParams_->haveCutoffRadius()) {
102	>	rCut_ = simParams_->getCutoffRadius();
103	>	} else {
104	>	if (info_->usesElectrostaticAtoms()) {
105	>	sprintf(painCave.errMsg,
106	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
107	>	"\tOpenMD will use a default value of 12.0 angstroms"
108	>	"\tfor the cutoffRadius.\n");
109	>	painCave.isFatal = 0;
110	>	painCave.severity = OPENMD_INFO;
111	>	simError();
112	>	rCut_ = 12.0;
113	>	} else {
114	>	RealType thisCut;
115	>	set<AtomType*>::iterator i;
116	>	set<AtomType*> atomTypes;
117	>	atomTypes = info_->getSimulatedAtomTypes();
118	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
119	>	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
120	>	rCut_ = max(thisCut, rCut_);
121	>	}
122	>	sprintf(painCave.errMsg,
123	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
124	>	"\tOpenMD will use %lf angstroms.\n",
125	>	rCut_);
126	>	painCave.isFatal = 0;
127	>	painCave.severity = OPENMD_INFO;
128	>	simError();
129	>	}
130	>	}
131
132	<	if (!info_->isFortranInitialized()) {
133	<	info_->update();
132	>	fDecomp_->setUserCutoff(rCut_);
133	>
134	>	map<string, CutoffMethod> stringToCutoffMethod;
135	>	stringToCutoffMethod["HARD"] = HARD;
136	>	stringToCutoffMethod["SWITCHED"] = SWITCHED;
137	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
138	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
139	>
140	>	if (simParams_->haveCutoffMethod()) {
141	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
142	>	map<string, CutoffMethod>::iterator i;
143	>	i = stringToCutoffMethod.find(cutMeth);
144	>	if (i == stringToCutoffMethod.end()) {
145	>	sprintf(painCave.errMsg,
146	>	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
147	>	"\tShould be one of: "
148	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
149	>	cutMeth.c_str());
150	>	painCave.isFatal = 1;
151	>	painCave.severity = OPENMD_ERROR;
152	>	simError();
153	>	} else {
154	>	cutoffMethod_ = i->second;
155	>	}
156	>	} else {
157	>	sprintf(painCave.errMsg,
158	>	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
159	>	"\tOpenMD will use SHIFTED_FORCE.\n");
160	>	painCave.isFatal = 0;
161	>	painCave.severity = OPENMD_INFO;
162	>	simError();
163	>	cutoffMethod_ = SHIFTED_FORCE;
164		}
165
166	<	preCalculation();
167	<
168	<	calcShortRangeInteraction();
166	>	map<string, CutoffPolicy> stringToCutoffPolicy;
167	>	stringToCutoffPolicy["MIX"] = MIX;
168	>	stringToCutoffPolicy["MAX"] = MAX;
169	>	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
170
171	<	calcLongRangeInteraction(needPotential, needStress);
171	>	std::string cutPolicy;
172	>	if (forceFieldOptions_.haveCutoffPolicy()){
173	>	cutPolicy = forceFieldOptions_.getCutoffPolicy();
174	>	}else if (simParams_->haveCutoffPolicy()) {
175	>	cutPolicy = simParams_->getCutoffPolicy();
176	>	}
177
178	<	postCalculation();
178	>	if (!cutPolicy.empty()){
179	>	toUpper(cutPolicy);
180	>	map<string, CutoffPolicy>::iterator i;
181	>	i = stringToCutoffPolicy.find(cutPolicy);
182
183	<	/*
184	<	std::vector<BendOrderStruct> bendOrderStruct;
185	<	for(std::map<Bend*, BendDataSet>::iterator i = bendDataSets.begin(); i != bendDataSets.end(); ++i) {
186	<	BendOrderStruct tmp;
187	<	tmp.bend= const_cast<Bend*>(i->first);
188	<	tmp.dataSet = i->second;
189	<	bendOrderStruct.push_back(tmp);
183	>	if (i == stringToCutoffPolicy.end()) {
184	>	sprintf(painCave.errMsg,
185	>	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
186	>	"\tShould be one of: "
187	>	"MIX, MAX, or TRADITIONAL\n",
188	>	cutPolicy.c_str());
189	>	painCave.isFatal = 1;
190	>	painCave.severity = OPENMD_ERROR;
191	>	simError();
192	>	} else {
193	>	cutoffPolicy_ = i->second;
194	>	}
195	>	} else {
196	>	sprintf(painCave.errMsg,
197	>	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
198	>	"\tOpenMD will use TRADITIONAL.\n");
199	>	painCave.isFatal = 0;
200	>	painCave.severity = OPENMD_INFO;
201	>	simError();
202	>	cutoffPolicy_ = TRADITIONAL;
203		}
204	+	fDecomp_->setCutoffPolicy(cutoffPolicy_);
205	+	}
206
207	<	std::vector<TorsionOrderStruct> torsionOrderStruct;
208	<	for(std::map<Torsion*, TorsionDataSet>::iterator j = torsionDataSets.begin(); j != torsionDataSets.end(); ++j) {
209	<	TorsionOrderStruct tmp;
210	<	tmp.torsion = const_cast<Torsion*>(j->first);
211	<	tmp.dataSet = j->second;
212	<	torsionOrderStruct.push_back(tmp);
213	<	}
207	>	/**
208	>	* setupSwitching
209	>	*
210	>	* Sets the values of switchingRadius and
211	>	*  If the switchingRadius was explicitly set, use that value (but check it)
212	>	*  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
213	>	*/
214	>	void ForceManager::setupSwitching() {
215	>	Globals* simParams_ = info_->getSimParams();
216	>
217	>	// create the switching function object:
218	>	switcher_ = new SwitchingFunction();
219
220	<	std::sort(bendOrderStruct.begin(), bendOrderStruct.end(), std::ptr_fun(BendSortFunctor));
221	<	std::sort(torsionOrderStruct.begin(), torsionOrderStruct.end(), std::ptr_fun(TorsionSortFunctor));
222	<	std::cout << "bend" << std::endl;
223	<	for (std::vector<BendOrderStruct>::iterator k = bendOrderStruct.begin(); k != bendOrderStruct.end(); ++k) {
224	<	Bend* bend = k->bend;
225	<	std::cout << "atom1=" <<bend->getAtomA()->getGlobalIndex() << ",atom2 = "<< bend->getAtomB()->getGlobalIndex() << ",atom3="<<bend->getAtomC()->getGlobalIndex() << " ";
226	<	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;
220	>	if (simParams_->haveSwitchingRadius()) {
221	>	rSwitch_ = simParams_->getSwitchingRadius();
222	>	if (rSwitch_ > rCut_) {
223	>	sprintf(painCave.errMsg,
224	>	"ForceManager::setupSwitching: switchingRadius (%f) is larger "
225	>	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
226	>	painCave.isFatal = 1;
227	>	painCave.severity = OPENMD_ERROR;
228	>	simError();
229	>	}
230	>	} else {
231	>	rSwitch_ = 0.85 * rCut_;
232	>	sprintf(painCave.errMsg,
233	>	"ForceManager::setupSwitching: No value was set for the switchingRadius.\n"
234	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
235	>	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
236	>	painCave.isFatal = 0;
237	>	painCave.severity = OPENMD_WARNING;
238	>	simError();
239	>	}
240	>
241	>	// Default to cubic switching function.
242	>	sft_ = cubic;
243	>	if (simParams_->haveSwitchingFunctionType()) {
244	>	string funcType = simParams_->getSwitchingFunctionType();
245	>	toUpper(funcType);
246	>	if (funcType == "CUBIC") {
247	>	sft_ = cubic;
248	>	} else {
249	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
250	>	sft_ = fifth_order_poly;
251	>	} else {
252	>	// throw error
253	>	sprintf( painCave.errMsg,
254	>	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
255	>	"\tswitchingFunctionType must be one of: "
256	>	"\"cubic\" or \"fifth_order_polynomial\".",
257	>	funcType.c_str() );
258	>	painCave.isFatal = 1;
259	>	painCave.severity = OPENMD_ERROR;
260	>	simError();
261	>	}
262	>	}
263		}
264	<	std::cout << "torsio" << std::endl;
265	<	for (std::vector<TorsionOrderStruct>::iterator l = torsionOrderStruct.begin(); l != torsionOrderStruct.end(); ++l) {
266	<	Torsion* torsion = l->torsion;
267	<	std::cout << "atom1=" <<torsion->getAtomA()->getGlobalIndex() << ",atom2 = "<< torsion->getAtomB()->getGlobalIndex() << ",atom3="<<torsion->getAtomC()->getGlobalIndex() << ",atom4="<<torsion->getAtomD()->getGlobalIndex()<< " ";
268	<	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;
264	>	switcher_->setSwitchType(sft_);
265	>	switcher_->setSwitch(rSwitch_, rCut_);
266	>	}
267	>
268	>	void ForceManager::initialize() {
269	>
270	>	if (!info_->isTopologyDone()) {
271	>	info_->update();
272	>	interactionMan_->setSimInfo(info_);
273	>	interactionMan_->initialize();
274	>
275	>	// We want to delay the cutoffs until after the interaction
276	>	// manager has set up the atom-atom interactions so that we can
277	>	// query them for suggested cutoff values
278	>
279	>	setupCutoffs();
280	>	setupSwitching();
281	>
282	>	info_->prepareTopology();
283		}
284	<	*/
284	>
285	>	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
286	>
287	>	// Force fields can set options on how to scale van der Waals and electrostatic
288	>	// interactions for atoms connected via bonds, bends and torsions
289	>	// in this case the topological distance between atoms is:
290	>	// 0 = topologically unconnected
291	>	// 1 = bonded together
292	>	// 2 = connected via a bend
293	>	// 3 = connected via a torsion
294	>
295	>	vdwScale_.reserve(4);
296	>	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
297	>
298	>	electrostaticScale_.reserve(4);
299	>	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
300	>
301	>	vdwScale_[0] = 1.0;
302	>	vdwScale_[1] = fopts.getvdw12scale();
303	>	vdwScale_[2] = fopts.getvdw13scale();
304	>	vdwScale_[3] = fopts.getvdw14scale();
305	>
306	>	electrostaticScale_[0] = 1.0;
307	>	electrostaticScale_[1] = fopts.getelectrostatic12scale();
308	>	electrostaticScale_[2] = fopts.getelectrostatic13scale();
309	>	electrostaticScale_[3] = fopts.getelectrostatic14scale();
310	>
311	>	fDecomp_->distributeInitialData();
312	>
313	>	initialized_ = true;
314	>
315		}
316
317	+	void ForceManager::calcForces() {
318	+
319	+	if (!initialized_) initialize();
320	+
321	+	preCalculation();
322	+	shortRangeInteractions();
323	+	longRangeInteractions();
324	+	postCalculation();
325	+	}
326	+
327		void ForceManager::preCalculation() {
328		SimInfo::MoleculeIterator mi;
329		Molecule* mol;
#	Line 130 | Line 331 | namespace oopse {
331		Atom* atom;
332		Molecule::RigidBodyIterator rbIter;
333		RigidBody* rb;
334	+	Molecule::CutoffGroupIterator ci;
335	+	CutoffGroup* cg;
336
337		// forces are zeroed here, before any are accumulated.
338	<	// NOTE: do not rezero the forces in Fortran.
339	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
338	>
339	>	for (mol = info_->beginMolecule(mi); mol != NULL;
340	>	mol = info_->nextMolecule(mi)) {
341		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
342		atom->zeroForcesAndTorques();
343		}
344	<
344	>
345		//change the positions of atoms which belong to the rigidbodies
346	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
346	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
347	>	rb = mol->nextRigidBody(rbIter)) {
348		rb->zeroForcesAndTorques();
349		}
350	+
351	+	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
352	+	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
353	+	cg = mol->nextCutoffGroup(ci)) {
354	+	//calculate the center of mass of cutoff group
355	+	cg->updateCOM();
356	+	}
357	+	}
358		}
359	+
360	+	// Zero out the stress tensor
361	+	tau *= 0.0;
362
363		}
364	<
365	<	void ForceManager::calcShortRangeInteraction() {
364	>
365	>	void ForceManager::shortRangeInteractions() {
366		Molecule* mol;
367		RigidBody* rb;
368		Bond* bond;
369		Bend* bend;
370		Torsion* torsion;
371	+	Inversion* inversion;
372		SimInfo::MoleculeIterator mi;
373		Molecule::RigidBodyIterator rbIter;
374		Molecule::BondIterator bondIter;;
375		Molecule::BendIterator  bendIter;
376		Molecule::TorsionIterator  torsionIter;
377	<	double bondPotential = 0.0;
378	<	double bendPotential = 0.0;
379	<	double torsionPotential = 0.0;
377	>	Molecule::InversionIterator  inversionIter;
378	>	RealType bondPotential = 0.0;
379	>	RealType bendPotential = 0.0;
380	>	RealType torsionPotential = 0.0;
381	>	RealType inversionPotential = 0.0;
382
383		//calculate short range interactions
384	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
384	>	for (mol = info_->beginMolecule(mi); mol != NULL;
385	>	mol = info_->nextMolecule(mi)) {
386
387		//change the positions of atoms which belong to the rigidbodies
388	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
389	<	rb->updateAtoms();
388	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
389	>	rb = mol->nextRigidBody(rbIter)) {
390	>	rb->updateAtoms();
391		}
392
393	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
393	>	for (bond = mol->beginBond(bondIter); bond != NULL;
394	>	bond = mol->nextBond(bondIter)) {
395		bond->calcForce();
396		bondPotential += bond->getPotential();
397		}
398
399	<
400	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
401	<
402	<	double angle;
403	<	bend->calcForce(angle);
404	<	double currBendPot = bend->getPotential();
405	<	bendPotential += bend->getPotential();
406	<	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
407	<	if (i == bendDataSets.end()) {
408	<	BendDataSet dataSet;
409	<	dataSet.prev.angle = dataSet.curr.angle = angle;
410	<	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
411	<	dataSet.deltaV = 0.0;
412	<	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
413	<	}else {
414	<	i->second.prev.angle = i->second.curr.angle;
415	<	i->second.prev.potential = i->second.curr.potential;
416	<	i->second.curr.angle = angle;
417	<	i->second.curr.potential = currBendPot;
418	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
419	<	}
399	>	for (bend = mol->beginBend(bendIter); bend != NULL;
400	>	bend = mol->nextBend(bendIter)) {
401	>
402	>	RealType angle;
403	>	bend->calcForce(angle);
404	>	RealType currBendPot = bend->getPotential();
405	>
406	>	bendPotential += bend->getPotential();
407	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
408	>	if (i == bendDataSets.end()) {
409	>	BendDataSet dataSet;
410	>	dataSet.prev.angle = dataSet.curr.angle = angle;
411	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
412	>	dataSet.deltaV = 0.0;
413	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
414	>	}else {
415	>	i->second.prev.angle = i->second.curr.angle;
416	>	i->second.prev.potential = i->second.curr.potential;
417	>	i->second.curr.angle = angle;
418	>	i->second.curr.potential = currBendPot;
419	>	i->second.deltaV =  fabs(i->second.curr.potential -
420	>	i->second.prev.potential);
421	>	}
422		}
423	<
424	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
425	<	double angle;
426	<	torsion->calcForce(angle);
427	<	double currTorsionPot = torsion->getPotential();
428	<	torsionPotential += torsion->getPotential();
429	<	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
430	<	if (i == torsionDataSets.end()) {
431	<	TorsionDataSet dataSet;
432	<	dataSet.prev.angle = dataSet.curr.angle = angle;
433	<	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
434	<	dataSet.deltaV = 0.0;
435	<	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
436	<	}else {
437	<	i->second.prev.angle = i->second.curr.angle;
438	<	i->second.prev.potential = i->second.curr.potential;
439	<	i->second.curr.angle = angle;
440	<	i->second.curr.potential = currTorsionPot;
441	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
442	<	}
443	<	}
444	<
423	>
424	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
425	>	torsion = mol->nextTorsion(torsionIter)) {
426	>	RealType angle;
427	>	torsion->calcForce(angle);
428	>	RealType currTorsionPot = torsion->getPotential();
429	>	torsionPotential += torsion->getPotential();
430	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
431	>	if (i == torsionDataSets.end()) {
432	>	TorsionDataSet dataSet;
433	>	dataSet.prev.angle = dataSet.curr.angle = angle;
434	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
435	>	dataSet.deltaV = 0.0;
436	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
437	>	}else {
438	>	i->second.prev.angle = i->second.curr.angle;
439	>	i->second.prev.potential = i->second.curr.potential;
440	>	i->second.curr.angle = angle;
441	>	i->second.curr.potential = currTorsionPot;
442	>	i->second.deltaV =  fabs(i->second.curr.potential -
443	>	i->second.prev.potential);
444	>	}
445	>	}
446	>
447	>	for (inversion = mol->beginInversion(inversionIter);
448	>	inversion != NULL;
449	>	inversion = mol->nextInversion(inversionIter)) {
450	>	RealType angle;
451	>	inversion->calcForce(angle);
452	>	RealType currInversionPot = inversion->getPotential();
453	>	inversionPotential += inversion->getPotential();
454	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
455	>	if (i == inversionDataSets.end()) {
456	>	InversionDataSet dataSet;
457	>	dataSet.prev.angle = dataSet.curr.angle = angle;
458	>	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
459	>	dataSet.deltaV = 0.0;
460	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, 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 = currInversionPot;
466	>	i->second.deltaV =  fabs(i->second.curr.potential -
467	>	i->second.prev.potential);
468	>	}
469	>	}
470		}
471
472	<	double  shortRangePotential = bondPotential + bendPotential + torsionPotential;
472	>	RealType  shortRangePotential = bondPotential + bendPotential +
473	>	torsionPotential +  inversionPotential;
474		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
475		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
476		curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
477		curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
478		curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
479	<
479	>	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
480		}
481	+
482	+	void ForceManager::longRangeInteractions() {
483
484	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
485	<	Snapshot* curSnapshot;
486	<	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();
484	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
485	>	DataStorage* config = &(curSnapshot->atomData);
486	>	DataStorage* cgConfig = &(curSnapshot->cgData);
487
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	–
488		//calculate the center of mass of cutoff group
489	+
490		SimInfo::MoleculeIterator mi;
491		Molecule* mol;
492		Molecule::CutoffGroupIterator ci;
493		CutoffGroup* cg;
258	–	Vector3d com;
259	–	std::vector<Vector3d> rcGroup;
494
495	<	if(info_->getNCutoffGroups() > 0){
496	<
497	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
498	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
499	<	cg->getCOM(com);
500	<	rcGroup.push_back(com);
495	>	if(info_->getNCutoffGroups() > 0){
496	>	for (mol = info_->beginMolecule(mi); mol != NULL;
497	>	mol = info_->nextMolecule(mi)) {
498	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
499	>	cg = mol->nextCutoffGroup(ci)) {
500	>	cg->updateCOM();
501		}
502	<	}// end for (mol)
269	<
270	<	rc = rcGroup[0].getArrayPointer();
502	>	}
503		} else {
504	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
505	<	rc = pos;
504	>	// center of mass of the group is the same as position of the atom
505	>	// if cutoff group does not exist
506	>	cgConfig->position = config->position;
507		}
508	<
509	<	//initialize data before passing to fortran
510	<	double longRangePotential[LR_POT_TYPES];
278	<	double lrPot = 0.0;
508	>
509	>	fDecomp_->zeroWorkArrays();
510	>	fDecomp_->distributeData();
511
512	<	Mat3x3d tau;
513	<	short int passedCalcPot = needPotential;
514	<	short int passedCalcStress = needStress;
515	<	int isError = 0;
512	>	int cg1, cg2, atom1, atom2, topoDist;
513	>	Vector3d d_grp, dag, d;
514	>	RealType rgrpsq, rgrp, r2, r;
515	>	RealType electroMult, vdwMult;
516	>	RealType vij;
517	>	Vector3d fij, fg, f1;
518	>	tuple3<RealType, RealType, RealType> cuts;
519	>	RealType rCutSq;
520	>	bool in_switching_region;
521	>	RealType sw, dswdr, swderiv;
522	>	vector<int> atomListColumn, atomListRow, atomListLocal;
523	>	InteractionData idat;
524	>	SelfData sdat;
525	>	RealType mf;
526	>	RealType lrPot;
527	>	RealType vpair;
528	>	potVec longRangePotential(0.0);
529	>	potVec workPot(0.0);
530
531	<	for (int i=0; i<LR_POT_TYPES;i++){
532	<	longRangePotential[i]=0.0; //Initialize array
531	>	int loopStart, loopEnd;
532	>
533	>	idat.vdwMult = &vdwMult;
534	>	idat.electroMult = &electroMult;
535	>	idat.pot = &workPot;
536	>	sdat.pot = fDecomp_->getEmbeddingPotential();
537	>	idat.vpair = &vpair;
538	>	idat.f1 = &f1;
539	>	idat.sw = &sw;
540	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
541	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
542	>
543	>	loopEnd = PAIR_LOOP;
544	>	if (info_->requiresPrepair() ) {
545	>	loopStart = PREPAIR_LOOP;
546	>	} else {
547	>	loopStart = PAIR_LOOP;
548		}
549	+
550	+	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
551	+
552	+	if (iLoop == loopStart) {
553	+	bool update_nlist = fDecomp_->checkNeighborList();
554	+	if (update_nlist)
555	+	neighborList = fDecomp_->buildNeighborList();
556	+	}
557	+
558	+	for (vector<pair<int, int> >::iterator it = neighborList.begin();
559	+	it != neighborList.end(); ++it) {
560	+
561	+	cg1 = (*it).first;
562	+	cg2 = (*it).second;
563	+
564	+	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
565
566	<	doForceLoop( pos,
567	<	rc,
568	<	A,
292	<	electroFrame,
293	<	frc,
294	<	trq,
295	<	tau.getArrayPointer(),
296	<	longRangePotential,
297	<	&passedCalcPot,
298	<	&passedCalcStress,
299	<	&isError );
566	>	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
567	>	curSnapshot->wrapVector(d_grp);
568	>	rgrpsq = d_grp.lengthSquare();
569
570	<	if( isError ){
571	<	sprintf( painCave.errMsg,
572	<	"Error returned from the fortran force calculation.\n" );
573	<	painCave.isFatal = 1;
574	<	simError();
570	>	rCutSq = cuts.second;
571	>
572	>	if (rgrpsq < rCutSq) {
573	>	idat.rcut = &cuts.first;
574	>	if (iLoop == PAIR_LOOP) {
575	>	vij *= 0.0;
576	>	fij = V3Zero;
577	>	}
578	>
579	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
580	>	rgrp);
581	>
582	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
583	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
584	>
585	>	for (vector<int>::iterator ia = atomListRow.begin();
586	>	ia != atomListRow.end(); ++ia) {
587	>	atom1 = (*ia);
588	>
589	>	for (vector<int>::iterator jb = atomListColumn.begin();
590	>	jb != atomListColumn.end(); ++jb) {
591	>	atom2 = (*jb);
592	>
593	>	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
594	>	vpair = 0.0;
595	>	workPot = 0.0;
596	>	f1 = V3Zero;
597	>
598	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
599	>
600	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
601	>	vdwMult = vdwScale_[topoDist];
602	>	electroMult = electrostaticScale_[topoDist];
603	>
604	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
605	>	idat.d = &d_grp;
606	>	idat.r2 = &rgrpsq;
607	>	} else {
608	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
609	>	curSnapshot->wrapVector( d );
610	>	r2 = d.lengthSquare();
611	>	idat.d = &d;
612	>	idat.r2 = &r2;
613	>	}
614	>
615	>	r = sqrt( *(idat.r2) );
616	>	idat.rij = &r;
617	>
618	>	if (iLoop == PREPAIR_LOOP) {
619	>	interactionMan_->doPrePair(idat);
620	>	} else {
621	>	interactionMan_->doPair(idat);
622	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
623	>	vij += vpair;
624	>	fij += f1;
625	>	tau -= outProduct( *(idat.d), f1);
626	>	}
627	>	}
628	>	}
629	>	}
630	>
631	>	if (iLoop == PAIR_LOOP) {
632	>	if (in_switching_region) {
633	>	swderiv = vij * dswdr / rgrp;
634	>	fg = swderiv * d_grp;
635	>
636	>	fij += fg;
637	>
638	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
639	>	tau -= outProduct( *(idat.d), fg);
640	>	}
641	>
642	>	for (vector<int>::iterator ia = atomListRow.begin();
643	>	ia != atomListRow.end(); ++ia) {
644	>	atom1 = (*ia);
645	>	mf = fDecomp_->getMassFactorRow(atom1);
646	>	// fg is the force on atom ia due to cutoff group's
647	>	// presence in switching region
648	>	fg = swderiv * d_grp * mf;
649	>	fDecomp_->addForceToAtomRow(atom1, fg);
650	>
651	>	if (atomListRow.size() > 1) {
652	>	if (info_->usesAtomicVirial()) {
653	>	// find the distance between the atom
654	>	// and the center of the cutoff group:
655	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
656	>	tau -= outProduct(dag, fg);
657	>	}
658	>	}
659	>	}
660	>	for (vector<int>::iterator jb = atomListColumn.begin();
661	>	jb != atomListColumn.end(); ++jb) {
662	>	atom2 = (*jb);
663	>	mf = fDecomp_->getMassFactorColumn(atom2);
664	>	// fg is the force on atom jb due to cutoff group's
665	>	// presence in switching region
666	>	fg = -swderiv * d_grp * mf;
667	>	fDecomp_->addForceToAtomColumn(atom2, fg);
668	>
669	>	if (atomListColumn.size() > 1) {
670	>	if (info_->usesAtomicVirial()) {
671	>	// find the distance between the atom
672	>	// and the center of the cutoff group:
673	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
674	>	tau -= outProduct(dag, fg);
675	>	}
676	>	}
677	>	}
678	>	}
679	>	//if (!SIM_uses_AtomicVirial) {
680	>	//  tau -= outProduct(d_grp, fij);
681	>	//}
682	>	}
683	>	}
684	>	}
685	>
686	>	if (iLoop == PREPAIR_LOOP) {
687	>	if (info_->requiresPrepair()) {
688	>	fDecomp_->collectIntermediateData();
689	>
690	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
691	>	fDecomp_->fillSelfData(sdat, atom1);
692	>	interactionMan_->doPreForce(sdat);
693	>	}
694	>
695	>
696	>	fDecomp_->distributeIntermediateData();
697	>	}
698	>	}
699	>
700		}
701	<	for (int i=0; i<LR_POT_TYPES;i++){
702	<	lrPot += longRangePotential[i]; //Quick hack
701	>
702	>	fDecomp_->collectData();
703	>
704	>	if ( info_->requiresSkipCorrection() ) {
705	>
706	>	for (int atom1 = 0; atom1 < fDecomp_->getNAtomsInRow(); atom1++) {
707	>
708	>	vector<int> skipList = fDecomp_->getSkipsForAtom( atom1 );
709	>
710	>	for (vector<int>::iterator jb = skipList.begin();
711	>	jb != skipList.end(); ++jb) {
712	>
713	>	atom2 = (*jb);
714	>	fDecomp_->fillSkipData(idat, atom1, atom2);
715	>	interactionMan_->doSkipCorrection(idat);
716	>	fDecomp_->unpackSkipData(idat, atom1, atom2);
717	>
718	>	}
719	>	}
720		}
721	+
722	+	if (info_->requiresSelfCorrection()) {
723
724	+	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
725	+	fDecomp_->fillSelfData(sdat, atom1);
726	+	interactionMan_->doSelfCorrection(sdat);
727	+	}
728	+
729	+	}
730	+
731	+	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
732	+	*(fDecomp_->getPairwisePotential());
733	+
734	+	lrPot = longRangePotential.sum();
735	+
736		//store the tau and long range potential
737		curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
738	<	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
739	<	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
315	<
316	<	curSnapshot->statData.setTau(tau);
738	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
739	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
740		}
741
742	<
742	>
743		void ForceManager::postCalculation() {
744		SimInfo::MoleculeIterator mi;
745		Molecule* mol;
746		Molecule::RigidBodyIterator rbIter;
747		RigidBody* rb;
748	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
749
750		// collect the atomic forces onto rigid bodies
751	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
752	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
753	<	rb->calcForcesAndTorques();
751	>
752	>	for (mol = info_->beginMolecule(mi); mol != NULL;
753	>	mol = info_->nextMolecule(mi)) {
754	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
755	>	rb = mol->nextRigidBody(rbIter)) {
756	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
757	>	tau += rbTau;
758		}
759		}
760	<
760	>
761	>	#ifdef IS_MPI
762	>	Mat3x3d tmpTau(tau);
763	>	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
764	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
765	>	#endif
766	>	curSnapshot->statData.setTau(tau);
767		}
768
769	<	} //end namespace oopse
769	>	} //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 1583 by gezelter, Thu Jun 16 22:00:08 2011 UTC

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