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root/OpenMD/branches/devel_omp/src/brains/ForceManager.cpp
Revision: 1614
Committed: Tue Aug 23 20:55:51 2011 UTC (13 years, 8 months ago) by mciznick
File size: 44345 byte(s)
Log Message: 
Updated scalability of OpenMP threads.

File Contents

# User Rev Content
1 gezelter 507 /*
2 gezelter 246 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3     *
4     * The University of Notre Dame grants you ("Licensee") a
5     * non-exclusive, royalty free, license to use, modify and
6     * redistribute this software in source and binary code form, provided
7     * that the following conditions are met:
8     *
9 gezelter 1390 * 1. Redistributions of source code must retain the above copyright
10 gezelter 246 * notice, this list of conditions and the following disclaimer.
11     *
12 gezelter 1390 * 2. Redistributions in binary form must reproduce the above copyright
13 gezelter 246 * notice, this list of conditions and the following disclaimer in the
14     * documentation and/or other materials provided with the
15     * distribution.
16     *
17     * This software is provided "AS IS," without a warranty of any
18     * kind. All express or implied conditions, representations and
19     * warranties, including any implied warranty of merchantability,
20     * fitness for a particular purpose or non-infringement, are hereby
21     * excluded. The University of Notre Dame and its licensors shall not
22     * be liable for any damages suffered by licensee as a result of
23     * using, modifying or distributing the software or its
24     * derivatives. In no event will the University of Notre Dame or its
25     * licensors be liable for any lost revenue, profit or data, or for
26     * direct, indirect, special, consequential, incidental or punitive
27     * damages, however caused and regardless of the theory of liability,
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 gezelter 1390 *
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 gezelter 246 */
41 mciznick 1598
42 gezelter 507 /**
43     * @file ForceManager.cpp
44     * @author tlin
45     * @date 11/09/2004
46     * @time 10:39am
47     * @version 1.0
48     */
49 gezelter 246
50     #include "brains/ForceManager.hpp"
51     #include "primitives/Molecule.hpp"
52 gezelter 1390 #define __OPENMD_C
53 gezelter 246 #include "utils/simError.h"
54 xsun 1215 #include "primitives/Bond.hpp"
55 tim 749 #include "primitives/Bend.hpp"
56 cli2 1275 #include "primitives/Torsion.hpp"
57     #include "primitives/Inversion.hpp"
58 gezelter 1551 #include "nonbonded/NonBondedInteraction.hpp"
59 gezelter 1549 #include "parallel/ForceMatrixDecomposition.hpp"
60 gezelter 1467
61 gezelter 1583 #include <cstdio>
62     #include <iostream>
63     #include <iomanip>
64    
65 mciznick 1598 #include <omp.h>
66 mciznick 1614 //#include <time.h>
67     #include <sys/time.h>
68 mciznick 1598
69 gezelter 1545 using namespace std;
70 gezelter 1390 namespace OpenMD {
71 gezelter 1576
72 mciznick 1614 //long int elapsedTime = 0;
73    
74 mciznick 1598 ForceManager::ForceManager(SimInfo * info) :
75     info_(info) {
76     forceField_ = info_->getForceField();
77     interactionMan_ = new InteractionManager();
78     fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
79     }
80 gezelter 1576
81 mciznick 1598 /**
82     * setupCutoffs
83     *
84     * Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
85     * and cutoffPolicy
86     *
87     * cutoffRadius : realType
88     * If the cutoffRadius was explicitly set, use that value.
89     * If the cutoffRadius was not explicitly set:
90     * Are there electrostatic atoms? Use 12.0 Angstroms.
91     * No electrostatic atoms? Poll the atom types present in the
92     * simulation for suggested cutoff values (e.g. 2.5 * sigma).
93     * Use the maximum suggested value that was found.
94     *
95     * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
96     * or SHIFTED_POTENTIAL)
97     * If cutoffMethod was explicitly set, use that choice.
98     * If cutoffMethod was not explicitly set, use SHIFTED_FORCE
99     *
100     * cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
101     * If cutoffPolicy was explicitly set, use that choice.
102     * If cutoffPolicy was not explicitly set, use TRADITIONAL
103     *
104     * switchingRadius : realType
105     * If the cutoffMethod was set to SWITCHED:
106     * If the switchingRadius was explicitly set, use that value
107     * (but do a sanity check first).
108     * If the switchingRadius was not explicitly set: use 0.85 *
109     * cutoffRadius_
110     * If the cutoffMethod was not set to SWITCHED:
111     * Set switchingRadius equal to cutoffRadius for safety.
112     */
113     void ForceManager::setupCutoffs() {
114 gezelter 1583
115 mciznick 1598 Globals* simParams_ = info_->getSimParams();
116     ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
117 gezelter 1576
118 mciznick 1598 if (simParams_->haveCutoffRadius())
119     {
120     rCut_ = simParams_->getCutoffRadius();
121     } else
122     {
123     if (info_->usesElectrostaticAtoms())
124     {
125     sprintf(painCave.errMsg, "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
126     "\tOpenMD will use a default value of 12.0 angstroms"
127     "\tfor the cutoffRadius.\n");
128     painCave.isFatal = 0;
129     painCave.severity = OPENMD_INFO;
130     simError();
131     rCut_ = 12.0;
132     } else
133     {
134     RealType thisCut;
135     set<AtomType*>::iterator i;
136     set<AtomType*> atomTypes;
137     atomTypes = info_->getSimulatedAtomTypes();
138     for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
139     {
140     thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
141     rCut_ = max(thisCut, rCut_);
142     }
143     sprintf(painCave.errMsg, "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
144     "\tOpenMD will use %lf angstroms.\n", rCut_);
145     painCave.isFatal = 0;
146     painCave.severity = OPENMD_INFO;
147     simError();
148     }
149     }
150 gezelter 1576
151 mciznick 1598 fDecomp_->setUserCutoff(rCut_);
152     interactionMan_->setCutoffRadius(rCut_);
153 gezelter 1576
154 mciznick 1598 map<string, CutoffMethod> stringToCutoffMethod;
155     stringToCutoffMethod["HARD"] = HARD;
156     stringToCutoffMethod["SWITCHED"] = SWITCHED;
157     stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
158     stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
159 gezelter 1576
160 mciznick 1598 if (simParams_->haveCutoffMethod())
161     {
162     string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
163     map<string, CutoffMethod>::iterator i;
164     i = stringToCutoffMethod.find(cutMeth);
165     if (i == stringToCutoffMethod.end())
166     {
167     sprintf(painCave.errMsg, "ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
168     "\tShould be one of: "
169     "HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n", cutMeth.c_str());
170     painCave.isFatal = 1;
171     painCave.severity = OPENMD_ERROR;
172     simError();
173     } else
174     {
175     cutoffMethod_ = i->second;
176     }
177     } else
178     {
179     sprintf(painCave.errMsg, "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
180     "\tOpenMD will use SHIFTED_FORCE.\n");
181     painCave.isFatal = 0;
182     painCave.severity = OPENMD_INFO;
183     simError();
184     cutoffMethod_ = SHIFTED_FORCE;
185     }
186 gezelter 1587
187 mciznick 1598 map<string, CutoffPolicy> stringToCutoffPolicy;
188     stringToCutoffPolicy["MIX"] = MIX;
189     stringToCutoffPolicy["MAX"] = MAX;
190     stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
191 gezelter 1576
192 mciznick 1598 std::string cutPolicy;
193     if (forceFieldOptions_.haveCutoffPolicy())
194     {
195     cutPolicy = forceFieldOptions_.getCutoffPolicy();
196     } else if (simParams_->haveCutoffPolicy())
197     {
198     cutPolicy = simParams_->getCutoffPolicy();
199     }
200 gezelter 1587
201 mciznick 1598 if (!cutPolicy.empty())
202     {
203     toUpper(cutPolicy);
204     map<string, CutoffPolicy>::iterator i;
205     i = stringToCutoffPolicy.find(cutPolicy);
206 gezelter 1576
207 mciznick 1598 if (i == stringToCutoffPolicy.end())
208     {
209     sprintf(painCave.errMsg, "ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
210     "\tShould be one of: "
211     "MIX, MAX, or TRADITIONAL\n", cutPolicy.c_str());
212     painCave.isFatal = 1;
213     painCave.severity = OPENMD_ERROR;
214     simError();
215     } else
216     {
217     cutoffPolicy_ = i->second;
218     }
219     } else
220     {
221     sprintf(painCave.errMsg, "ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
222     "\tOpenMD will use TRADITIONAL.\n");
223     painCave.isFatal = 0;
224     painCave.severity = OPENMD_INFO;
225     simError();
226     cutoffPolicy_ = TRADITIONAL;
227     }
228 gezelter 1590
229 mciznick 1598 fDecomp_->setCutoffPolicy(cutoffPolicy_);
230 gezelter 1576
231 mciznick 1598 // create the switching function object:
232 gezelter 1576
233 mciznick 1598 switcher_ = new SwitchingFunction();
234 gezelter 1576
235 mciznick 1598 if (cutoffMethod_ == SWITCHED)
236     {
237     if (simParams_->haveSwitchingRadius())
238     {
239     rSwitch_ = simParams_->getSwitchingRadius();
240     if (rSwitch_ > rCut_)
241     {
242     sprintf(painCave.errMsg, "ForceManager::setupCutoffs: switchingRadius (%f) is larger "
243     "than the cutoffRadius(%f)\n", rSwitch_, rCut_);
244     painCave.isFatal = 1;
245     painCave.severity = OPENMD_ERROR;
246     simError();
247     }
248     } else
249     {
250     rSwitch_ = 0.85 * rCut_;
251     sprintf(painCave.errMsg, "ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
252     "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
253     "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
254     painCave.isFatal = 0;
255     painCave.severity = OPENMD_WARNING;
256     simError();
257     }
258     } else
259     {
260     if (simParams_->haveSwitchingRadius())
261     {
262     map<string, CutoffMethod>::const_iterator it;
263     string theMeth;
264     for (it = stringToCutoffMethod.begin(); it != stringToCutoffMethod.end(); ++it)
265     {
266     if (it->second == cutoffMethod_)
267     {
268     theMeth = it->first;
269     break;
270     }
271     }
272     sprintf(painCave.errMsg, "ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
273     "\tis not set to SWITCHED, so switchingRadius value\n"
274     "\twill be ignored for this simulation\n", theMeth.c_str());
275     painCave.isFatal = 0;
276     painCave.severity = OPENMD_WARNING;
277     simError();
278     }
279 gezelter 1576
280 mciznick 1598 rSwitch_ = rCut_;
281     }
282 gezelter 1576
283 mciznick 1598 // Default to cubic switching function.
284     sft_ = cubic;
285     if (simParams_->haveSwitchingFunctionType())
286     {
287     string funcType = simParams_->getSwitchingFunctionType();
288     toUpper(funcType);
289     if (funcType == "CUBIC")
290     {
291     sft_ = cubic;
292     } else
293     {
294     if (funcType == "FIFTH_ORDER_POLYNOMIAL")
295     {
296     sft_ = fifth_order_poly;
297     } else
298     {
299     // throw error
300     sprintf(painCave.errMsg,
301     "ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
302     "\tswitchingFunctionType must be one of: "
303     "\"cubic\" or \"fifth_order_polynomial\".", funcType.c_str());
304     painCave.isFatal = 1;
305     painCave.severity = OPENMD_ERROR;
306     simError();
307     }
308     }
309     }
310     switcher_->setSwitchType(sft_);
311     switcher_->setSwitch(rSwitch_, rCut_);
312     interactionMan_->setSwitchingRadius(rSwitch_);
313     }
314 gezelter 1576
315 mciznick 1598 void ForceManager::initialize() {
316 gezelter 1576
317 mciznick 1598 if (!info_->isTopologyDone())
318     {
319 gezelter 1576
320 mciznick 1598 info_->update();
321     interactionMan_->setSimInfo(info_);
322     interactionMan_->initialize();
323 gezelter 246
324 mciznick 1598 // We want to delay the cutoffs until after the interaction
325     // manager has set up the atom-atom interactions so that we can
326     // query them for suggested cutoff values
327     setupCutoffs();
328 gezelter 246
329 mciznick 1598 info_->prepareTopology();
330     }
331 gezelter 246
332 mciznick 1598 ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
333 gezelter 246
334 mciznick 1598 // Force fields can set options on how to scale van der Waals and
335     // electrostatic interactions for atoms connected via bonds, bends
336     // and torsions in this case the topological distance between
337     // atoms is:
338     // 0 = topologically unconnected
339     // 1 = bonded together
340     // 2 = connected via a bend
341     // 3 = connected via a torsion
342 chuckv 1595
343 mciznick 1598 vdwScale_.reserve(4);
344     fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
345 chuckv 1595
346 mciznick 1598 electrostaticScale_.reserve(4);
347     fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
348 chuckv 1595
349 mciznick 1598 vdwScale_[0] = 1.0;
350     vdwScale_[1] = fopts.getvdw12scale();
351     vdwScale_[2] = fopts.getvdw13scale();
352     vdwScale_[3] = fopts.getvdw14scale();
353 chuckv 1595
354 mciznick 1598 electrostaticScale_[0] = 1.0;
355     electrostaticScale_[1] = fopts.getelectrostatic12scale();
356     electrostaticScale_[2] = fopts.getelectrostatic13scale();
357     electrostaticScale_[3] = fopts.getelectrostatic14scale();
358 chuckv 1595
359 mciznick 1598 fDecomp_->distributeInitialData();
360 chuckv 1595
361 mciznick 1598 initialized_ = true;
362 chuckv 1595
363 mciznick 1598 }
364 chuckv 1595
365 mciznick 1598 void ForceManager::calcForces() {
366 chuckv 1595
367 mciznick 1598 if (!initialized_)
368     initialize();
369 chuckv 1595
370 mciznick 1598 preCalculation();
371     shortRangeInteractions();
372     // longRangeInteractions();
373 mciznick 1608 // longRangeInteractionsRapaport();
374     longRangeInteractionsParallel();
375 mciznick 1598 postCalculation();
376     }
377 chuckv 1595
378 mciznick 1598 void ForceManager::preCalculation() {
379     SimInfo::MoleculeIterator mi;
380     Molecule* mol;
381     Molecule::AtomIterator ai;
382     Atom* atom;
383     Molecule::RigidBodyIterator rbIter;
384     RigidBody* rb;
385     Molecule::CutoffGroupIterator ci;
386     CutoffGroup* cg;
387 chuckv 1595
388 mciznick 1598 // forces are zeroed here, before any are accumulated.
389 chuckv 1595
390 mciznick 1598 for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
391     {
392     for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai))
393     {
394     atom->zeroForcesAndTorques();
395     }
396 chuckv 1595
397 mciznick 1598 //change the positions of atoms which belong to the rigidbodies
398     for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter))
399     {
400     rb->zeroForcesAndTorques();
401     }
402 chuckv 1595
403 mciznick 1598 if (info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms())
404     {
405     for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
406     {
407     //calculate the center of mass of cutoff group
408     cg->updateCOM();
409     }
410     }
411     }
412 chuckv 1595
413 mciznick 1598 // Zero out the stress tensor
414     tau *= 0.0;
415 chuckv 1595
416 mciznick 1598 }
417 chuckv 1595
418 mciznick 1598 void ForceManager::shortRangeInteractions() {
419     Molecule* mol;
420     RigidBody* rb;
421     Bond* bond;
422     Bend* bend;
423     Torsion* torsion;
424     Inversion* inversion;
425     SimInfo::MoleculeIterator mi;
426     Molecule::RigidBodyIterator rbIter;
427     Molecule::BondIterator bondIter;
428     ;
429     Molecule::BendIterator bendIter;
430     Molecule::TorsionIterator torsionIter;
431     Molecule::InversionIterator inversionIter;
432     RealType bondPotential = 0.0;
433     RealType bendPotential = 0.0;
434     RealType torsionPotential = 0.0;
435     RealType inversionPotential = 0.0;
436 chuckv 1595
437 mciznick 1598 //calculate short range interactions
438     for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
439     {
440 chuckv 1595
441 mciznick 1598 //change the positions of atoms which belong to the rigidbodies
442     for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter))
443     {
444     rb->updateAtoms();
445     }
446 chuckv 1595
447 mciznick 1598 for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter))
448     {
449     bond->calcForce();
450     bondPotential += bond->getPotential();
451     }
452 chuckv 1595
453 mciznick 1598 for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter))
454     {
455 chuckv 1595
456 mciznick 1598 RealType angle;
457     bend->calcForce(angle);
458     RealType currBendPot = bend->getPotential();
459 chuckv 1595
460 mciznick 1598 bendPotential += bend->getPotential();
461     map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
462     if (i == bendDataSets.end())
463     {
464     BendDataSet dataSet;
465     dataSet.prev.angle = dataSet.curr.angle = angle;
466     dataSet.prev.potential = dataSet.curr.potential = currBendPot;
467     dataSet.deltaV = 0.0;
468     bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
469     } else
470     {
471     i->second.prev.angle = i->second.curr.angle;
472     i->second.prev.potential = i->second.curr.potential;
473     i->second.curr.angle = angle;
474     i->second.curr.potential = currBendPot;
475     i->second.deltaV = fabs(i->second.curr.potential - i->second.prev.potential);
476     }
477     }
478 chuckv 1595
479 mciznick 1598 for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter))
480     {
481     RealType angle;
482     torsion->calcForce(angle);
483     RealType currTorsionPot = torsion->getPotential();
484     torsionPotential += torsion->getPotential();
485     map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
486     if (i == torsionDataSets.end())
487     {
488     TorsionDataSet dataSet;
489     dataSet.prev.angle = dataSet.curr.angle = angle;
490     dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
491     dataSet.deltaV = 0.0;
492     torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
493     } else
494     {
495     i->second.prev.angle = i->second.curr.angle;
496     i->second.prev.potential = i->second.curr.potential;
497     i->second.curr.angle = angle;
498     i->second.curr.potential = currTorsionPot;
499     i->second.deltaV = fabs(i->second.curr.potential - i->second.prev.potential);
500     }
501     }
502 chuckv 1595
503 mciznick 1598 for (inversion = mol->beginInversion(inversionIter); inversion != NULL; inversion = mol->nextInversion(
504     inversionIter))
505     {
506     RealType angle;
507     inversion->calcForce(angle);
508     RealType currInversionPot = inversion->getPotential();
509     inversionPotential += inversion->getPotential();
510     map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
511     if (i == inversionDataSets.end())
512     {
513     InversionDataSet dataSet;
514     dataSet.prev.angle = dataSet.curr.angle = angle;
515     dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
516     dataSet.deltaV = 0.0;
517     inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
518     } else
519     {
520     i->second.prev.angle = i->second.curr.angle;
521     i->second.prev.potential = i->second.curr.potential;
522     i->second.curr.angle = angle;
523     i->second.curr.potential = currInversionPot;
524     i->second.deltaV = fabs(i->second.curr.potential - i->second.prev.potential);
525     }
526     }
527     }
528 chuckv 1595
529 mciznick 1598 RealType shortRangePotential = bondPotential + bendPotential + torsionPotential + inversionPotential;
530     Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
531     curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
532     curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
533     curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
534     curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
535     curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
536     }
537 chuckv 1595
538 mciznick 1608 void ForceManager::longRangeInteractionsParallel() {
539    
540     Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
541     DataStorage* config = &(curSnapshot->atomData);
542     DataStorage* cgConfig = &(curSnapshot->cgData);
543    
544     //calculate the center of mass of cutoff group
545    
546     SimInfo::MoleculeIterator mi;
547     Molecule* mol;
548     Molecule::CutoffGroupIterator ci;
549     CutoffGroup* cg;
550    
551     if (info_->getNCutoffGroups() > 0)
552     {
553     for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
554     {
555     for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
556     {
557     // cerr << "branch1\n";
558     // cerr << "globind = " << cg->getGlobalIndex() << ":" << __LINE__ << "\n";
559     cg->updateCOM();
560    
561     // cerr << "gbI: " << cg->getGlobalIndex() << " locI: " << cg->getLocalIndex() << " x: "
562     // << cgConfig->position[cg->getLocalIndex()].x() << " y: " << cgConfig->position[cg->getLocalIndex()].y()
563     // << " z: " << cgConfig->position[cg->getLocalIndex()].z() << "\n";
564     }
565     }
566     } else
567     {
568     // center of mass of the group is the same as position of the atom
569     // if cutoff group does not exist
570     // cerr << ":" << __LINE__ << "branch2\n";
571     cgConfig->position = config->position;
572     }
573    
574     fDecomp_->zeroWorkArrays();
575     fDecomp_->distributeData();
576    
577     int atom1, atom2, topoDist;
578     Vector3d d_grp, dag, d;
579     RealType rgrpsq, rgrp, r2, r;
580     RealType electroMult, vdwMult;
581     RealType vij;
582     Vector3d fij, fg, f1;
583     tuple3<RealType, RealType, RealType> cuts;
584     RealType rCutSq;
585     bool in_switching_region;
586     RealType sw, dswdr, swderiv;
587     vector<int> atomListColumn, atomListRow, atomListLocal;
588    
589 mciznick 1614 /* Defines local interaction data to each thread */
590 mciznick 1608 InteractionDataPrv idatPrv;
591    
592     SelfData sdat;
593     RealType mf;
594     RealType lrPot;
595     RealType vpair;
596     potVec longRangePotential(0.0);
597     potVec workPot(0.0);
598    
599     int loopStart, loopEnd;
600     sdat.pot = fDecomp_->getEmbeddingPotential();
601    
602     vector<CutoffGroup *> cgs;
603    
604     for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
605     {
606     for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
607     {
608     cgs.push_back(cg);
609     }
610     }
611    
612     loopEnd = PAIR_LOOP;
613     if (info_->requiresPrepair())
614     {
615     loopStart = PREPAIR_LOOP;
616     } else
617     {
618     loopStart = PAIR_LOOP;
619     }
620    
621     for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++)
622     {
623    
624     if (iLoop == loopStart)
625     {
626     bool update_nlist = fDecomp_->checkNeighborList();
627     if (update_nlist)
628     neighborMatW = fDecomp_->buildLayerBasedNeighborList();
629     }
630    
631 mciznick 1614 /* Eager initialization */
632     /* Initializes InteractionManager before force calculations */
633     interactionMan_->initializeOMP();
634     /* Initializes forces used in simulation before force calculations */
635     interactionMan_->initNonbondedForces();
636    
637 mciznick 1608 vector<CutoffGroup *>::iterator cg1;
638     vector<CutoffGroup *>::iterator cg2;
639    
640 mciznick 1614 /* Defines local accumulators for each thread */
641     vector<Vector3d> forceLcl;
642     Vector3d fatom1Lcl;
643     Mat3x3d tauLcl;
644     potVec potLcl;
645 mciznick 1608
646 mciznick 1614 /* Defines the size of chunks into which the loop iterations will be split */
647     int chunkSize = cgs.size() / (omp_get_max_threads() * 5);
648    
649     /*struct timeval tv, tv2;
650    
651     gettimeofday(&tv, NULL);*/
652    
653     /* Defines the parallel region and the list of variables that should be shared and private to each thread */
654     #pragma omp parallel default(none) shared(curSnapshot, iLoop, cgs, chunkSize, config) \
655     private(cg1, cg2, cuts, d_grp, rgrpsq, rCutSq, idatPrv, vij, fij, in_switching_region, \
656     dswdr, rgrp, atomListRow, atomListColumn, atom1, atom2, topoDist, d, r2, swderiv, fg, mf, \
657     dag, tauLcl, forceLcl, fatom1Lcl, potLcl)
658 mciznick 1608 {
659     idatPrv.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
660     idatPrv.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
661 mciznick 1614 forceLcl = vector<Vector3d>(config->force.size());
662     tauLcl *= 0;
663 mciznick 1608
664 mciznick 1614 /* Spreads force calculations between threads. Each thread receives chunkSize portion of the CutoffGroups. */
665     #pragma omp for schedule(dynamic, chunkSize)
666 mciznick 1608 for (cg1 = cgs.begin(); cg1 < cgs.end(); ++cg1)
667     {
668 mciznick 1614 /* Iterates between neighbors of the CutoffGroup */
669 mciznick 1608 for (cg2 = neighborMatW[(*cg1)->getGlobalIndex()].begin(); cg2 < neighborMatW[(*cg1)->getGlobalIndex()].end(); ++cg2)
670     {
671    
672     cuts = fDecomp_->getGroupCutoffs((*cg1)->getGlobalIndex(), (*cg2)->getGlobalIndex());
673    
674     d_grp = fDecomp_->getIntergroupVector((*cg1), (*cg2));
675     curSnapshot->wrapVector(d_grp);
676     rgrpsq = d_grp.lengthSquare();
677    
678     rCutSq = cuts.second;
679    
680     // printf("Thread %d\tcg1:%d\tcg2:%d d_grp\tx:%f\ty:%f\tz:%f\trgrpsq:%f\n", omp_get_thread_num(), (*cg1)->getGlobalIndex(), (*cg2)->getGlobalIndex(), d_grp.x(), d_grp.y(), d_grp.z(), rgrpsq);
681    
682     if (rgrpsq < rCutSq)
683     {
684     idatPrv.rcut = cuts.first;
685     if (iLoop == PAIR_LOOP)
686     {
687     vij = 0.0;
688     fij = V3Zero;
689     }
690    
691 mciznick 1614 in_switching_region = switcher_->getSwitch(rgrpsq, idatPrv.sw, dswdr, rgrp);
692 mciznick 1608
693     // printf("in_switching_region:%d\trgrpsq:%f\t*idatPrv.sw:%f\tdswdr:%f\trgrp:%f\n", (in_switching_region == false ? 0 : 1), rgrpsq, idatPrv.sw, dswdr, rgrp);
694    
695     atomListRow = fDecomp_->getAtomsInGroupRow((*cg1)->getGlobalIndex());
696     atomListColumn = fDecomp_->getAtomsInGroupColumn((*cg2)->getGlobalIndex());
697    
698     for (vector<int>::iterator ia = atomListRow.begin(); ia != atomListRow.end(); ++ia)
699     {
700     atom1 = (*ia);
701 mciznick 1614 fatom1Lcl = V3Zero;
702 mciznick 1608
703     for (vector<int>::iterator jb = atomListColumn.begin(); jb != atomListColumn.end(); ++jb)
704     {
705     atom2 = (*jb);
706    
707     if (!fDecomp_->skipAtomPair(atom1, atom2))
708     {
709     idatPrv.vpair = 0.0;
710     idatPrv.pot = 0.0;
711     idatPrv.f1 = V3Zero;
712    
713     fDecomp_->fillInteractionDataOMP(idatPrv, atom1, atom2);
714    
715     topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
716     idatPrv.vdwMult = vdwScale_[topoDist];
717     idatPrv.electroMult = electrostaticScale_[topoDist];
718    
719     // printf("topoDist:%d\tidatPrv.vdwMult:%f\tidatPrv.electroMult:%f\n", topoDist, idatPrv.vdwMult, idatPrv.electroMult);
720    
721     if (atomListRow.size() == 1 && atomListColumn.size() == 1)
722     {
723     idatPrv.d = d_grp;
724     idatPrv.r2 = rgrpsq;
725 mciznick 1614 //cerr << "dgrp = " << d_grp << ":" << __LINE__ << "\n";
726 mciznick 1608 } else
727     {
728     d = fDecomp_->getInteratomicVector(atom1, atom2);
729     curSnapshot->wrapVector(d);
730     r2 = d.lengthSquare();
731 mciznick 1614 //cerr << "datm = " << d << ":" << __LINE__ << "\n";
732 mciznick 1608 idatPrv.d = d;
733     idatPrv.r2 = r2;
734     }
735    
736 mciznick 1614 //printf("idatPrv.d x:%f\ty:%f\tz:%f\tidatPrv.r2:%f\n", (idatPrv.d).x(), (idatPrv.d).y(), (idatPrv.d).z(), idatPrv.r2);
737     //cerr << "idat.d = " << *(idat.d) << ":" << __LINE__ << "\n";
738 mciznick 1608 idatPrv.rij = sqrt((idatPrv.r2));
739 mciznick 1614 //cerr << "idat.rij = " << *(idat.rij) << "\n";
740 mciznick 1608
741     if (iLoop == PREPAIR_LOOP)
742     {
743     interactionMan_->doPrePairOMP(idatPrv);
744     } else
745     {
746     interactionMan_->doPairOMP(idatPrv);
747    
748 mciznick 1614 /* Accumulates potential and forces in local arrays */
749     potLcl += idatPrv.pot;
750     fatom1Lcl += idatPrv.f1;
751     forceLcl[atom2] -= idatPrv.f1;
752     //cerr << "d = " << *(idat.d) << "\tv=" << vpair << "\tf=" << f1 << ":" << __LINE__ << "\n";
753     //printf("d x:%f y:%f z:%f vpair:%f f1 x:%f y:%f z:%f\n", idatPrv.d.x(), idatPrv.d.y(), idatPrv.d.z(), idatPrv.vpair, idatPrv.f1.x(), idatPrv.f1.y(), idatPrv.f1.z());
754     vij += idatPrv.vpair;
755     fij += idatPrv.f1;
756     tauLcl -= outProduct(idatPrv.d, idatPrv.f1);
757     //printf("vij:%f fij x:%f y:%f z:%f\n", vij, fij.x(), fij.y(), fij.z());
758 mciznick 1608 }
759     }
760     }
761 mciznick 1614 /* We can accumulate force for current CutoffGroup in shared memory without worring about read after write bugs*/
762     config->force[atom1] += fatom1Lcl;
763 mciznick 1608 }
764    
765     if (iLoop == PAIR_LOOP)
766     {
767     if (in_switching_region)
768     {
769     swderiv = vij * dswdr / rgrp;
770     fg = swderiv * d_grp;
771     fij += fg;
772    
773     if (atomListRow.size() == 1 && atomListColumn.size() == 1)
774     {
775 mciznick 1614 tauLcl -= outProduct(idatPrv.d, fg);
776 mciznick 1608 }
777    
778     for (vector<int>::iterator ia = atomListRow.begin(); ia != atomListRow.end(); ++ia)
779     {
780     atom1 = (*ia);
781     mf = fDecomp_->getMassFactorRow(atom1);
782     // fg is the force on atom ia due to cutoff group's
783     // presence in switching region
784     fg = swderiv * d_grp * mf;
785 mciznick 1614 #pragma omp critical (forceLck)
786     {
787     fDecomp_->addForceToAtomRow(atom1, fg);
788     }
789 mciznick 1608
790     if (atomListRow.size() > 1)
791     {
792     if (info_->usesAtomicVirial())
793     {
794     // find the distance between the atom
795     // and the center of the cutoff group:
796     dag = fDecomp_->getAtomToGroupVectorRow(atom1, (*cg1)->getGlobalIndex());
797 mciznick 1614 tauLcl -= outProduct(dag, fg);
798 mciznick 1608 }
799     }
800     }
801     for (vector<int>::iterator jb = atomListColumn.begin(); jb != atomListColumn.end(); ++jb)
802     {
803     atom2 = (*jb);
804     mf = fDecomp_->getMassFactorColumn(atom2);
805     // fg is the force on atom jb due to cutoff group's
806     // presence in switching region
807     fg = -swderiv * d_grp * mf;
808 mciznick 1614 #pragma omp critical (forceLck)
809     {
810     fDecomp_->addForceToAtomColumn(atom2, fg);
811     }
812 mciznick 1608
813     if (atomListColumn.size() > 1)
814     {
815     if (info_->usesAtomicVirial())
816     {
817     // find the distance between the atom
818     // and the center of the cutoff group:
819     dag = fDecomp_->getAtomToGroupVectorColumn(atom2, (*cg2)->getGlobalIndex());
820 mciznick 1614 tauLcl -= outProduct(dag, fg);
821 mciznick 1608 }
822     }
823     }
824     }
825     //if (!SIM_uses_AtomicVirial) {
826     // tau -= outProduct(d_grp, fij);
827     //}
828     }
829     }
830     }
831     }// END: omp for loop
832 mciznick 1614 /* Critical region which accumulates forces from local to shared arrays */
833     #pragma omp critical (forceAdd)
834     {
835     for (int currAtom = 0; currAtom < config->force.size(); ++currAtom)
836     {
837     config->force[currAtom] += forceLcl[currAtom];
838     }
839 mciznick 1608
840 mciznick 1614 tau -= tauLcl;
841     *(fDecomp_->getPairwisePotential()) += potLcl;
842     }
843     }// END: omp parallel region
844    
845     /*gettimeofday(&tv2, NULL);
846    
847     elapsedTime += 1000000 * (tv2.tv_sec - tv.tv_sec)
848     + (tv2.tv_usec - tv.tv_usec);
849    
850     Globals *simParams_ = info_->getSimParams();
851    
852     if(curSnapshot->getTime() >= simParams_->getRunTime() - 1)
853     {
854     printf("Force calculation time: %ld [us]\n", elapsedTime);
855     }*/
856    
857 mciznick 1608 if (iLoop == PREPAIR_LOOP)
858     {
859     if (info_->requiresPrepair())
860     {
861    
862     fDecomp_->collectIntermediateData();
863    
864     for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++)
865     {
866     fDecomp_->fillSelfData(sdat, atom1);
867     interactionMan_->doPreForce(sdat);
868     }
869    
870     fDecomp_->distributeIntermediateData();
871    
872     }
873     }
874     }
875    
876     fDecomp_->collectData();
877    
878     if (info_->requiresSelfCorrection())
879     {
880    
881     for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++)
882     {
883     fDecomp_->fillSelfData(sdat, atom1);
884     interactionMan_->doSelfCorrection(sdat);
885     }
886    
887     }
888    
889     longRangePotential = *(fDecomp_->getEmbeddingPotential()) + *(fDecomp_->getPairwisePotential());
890    
891     lrPot = longRangePotential.sum();
892    
893     //store the tau and long range potential
894     curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
895     curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
896     curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
897     }
898    
899 mciznick 1598 void ForceManager::longRangeInteractionsRapaport() {
900 chuckv 1595
901 mciznick 1598 Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
902     DataStorage* config = &(curSnapshot->atomData);
903     DataStorage* cgConfig = &(curSnapshot->cgData);
904 chuckv 1595
905 mciznick 1598 //calculate the center of mass of cutoff group
906 chuckv 1595
907 mciznick 1598 SimInfo::MoleculeIterator mi;
908     Molecule* mol;
909     Molecule::CutoffGroupIterator ci;
910     CutoffGroup* cg;
911 chuckv 1595
912 mciznick 1598 if (info_->getNCutoffGroups() > 0)
913     {
914     for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
915     {
916     for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
917     {
918 mciznick 1608 // cerr << "branch1\n";
919     // cerr << "globind = " << cg->getGlobalIndex() << ":" << __LINE__ << "\n";
920 mciznick 1598 cg->updateCOM();
921    
922 mciznick 1608 // cerr << "gbI: " << cg->getGlobalIndex() << " locI: " << cg->getLocalIndex() << " x: "
923     // << cgConfig->position[cg->getLocalIndex()].x() << " y: " << cgConfig->position[cg->getLocalIndex()].y()
924     // << " z: " << cgConfig->position[cg->getLocalIndex()].z() << "\n";
925 mciznick 1598 }
926     }
927     } else
928     {
929     // center of mass of the group is the same as position of the atom
930     // if cutoff group does not exist
931 mciznick 1608 // cerr << ":" << __LINE__ << "branch2\n";
932 mciznick 1598 cgConfig->position = config->position;
933     }
934    
935     fDecomp_->zeroWorkArrays();
936     fDecomp_->distributeData();
937    
938     int atom1, atom2, topoDist;
939     CutoffGroup *cg1;
940     Vector3d d_grp, dag, d;
941     RealType rgrpsq, rgrp, r2, r;
942     RealType electroMult, vdwMult;
943     RealType vij;
944     Vector3d fij, fg, f1;
945     tuple3<RealType, RealType, RealType> cuts;
946     RealType rCutSq;
947     bool in_switching_region;
948     RealType sw, dswdr, swderiv;
949     vector<int> atomListColumn, atomListRow, atomListLocal;
950     InteractionData idat;
951     SelfData sdat;
952     RealType mf;
953     RealType lrPot;
954     RealType vpair;
955     potVec longRangePotential(0.0);
956     potVec workPot(0.0);
957    
958     int loopStart, loopEnd;
959    
960     idat.vdwMult = &vdwMult;
961     idat.electroMult = &electroMult;
962     idat.pot = &workPot;
963     sdat.pot = fDecomp_->getEmbeddingPotential();
964     idat.vpair = &vpair;
965     idat.f1 = &f1;
966     idat.sw = &sw;
967     idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
968     idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
969    
970     loopEnd = PAIR_LOOP;
971     if (info_->requiresPrepair())
972     {
973     loopStart = PREPAIR_LOOP;
974     } else
975     {
976     loopStart = PAIR_LOOP;
977     }
978    
979     for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++)
980     {
981    
982     if (iLoop == loopStart)
983     {
984     bool update_nlist = fDecomp_->checkNeighborList();
985     if (update_nlist)
986     neighborMatW = fDecomp_->buildLayerBasedNeighborList();
987     }
988    
989     for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
990     {
991     for (cg1 = mol->beginCutoffGroup(ci); cg1 != NULL; cg1 = mol->nextCutoffGroup(ci))
992     {
993     // printf("Thread %d executes loop iteration %d\n", omp_get_thread_num(), i);
994 mciznick 1608 for (vector<CutoffGroup *>::iterator cg2 = neighborMatW[cg1->getGlobalIndex()].begin(); cg2
995     != neighborMatW[cg1->getGlobalIndex()].end(); ++cg2)
996 mciznick 1598 {
997    
998     cuts = fDecomp_->getGroupCutoffs(cg1->getGlobalIndex(), (*cg2)->getGlobalIndex());
999    
1000     d_grp = fDecomp_->getIntergroupVector(cg1, (*cg2));
1001     curSnapshot->wrapVector(d_grp);
1002     rgrpsq = d_grp.lengthSquare();
1003    
1004     rCutSq = cuts.second;
1005    
1006     if (rgrpsq < rCutSq)
1007     {
1008     idat.rcut = &cuts.first;
1009     if (iLoop == PAIR_LOOP)
1010     {
1011     vij = 0.0;
1012     fij = V3Zero;
1013     }
1014    
1015     in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr, rgrp);
1016    
1017     atomListRow = fDecomp_->getAtomsInGroupRow(cg1->getGlobalIndex());
1018     atomListColumn = fDecomp_->getAtomsInGroupColumn((*cg2)->getGlobalIndex());
1019    
1020     for (vector<int>::iterator ia = atomListRow.begin(); ia != atomListRow.end(); ++ia)
1021     {
1022     atom1 = (*ia);
1023    
1024     for (vector<int>::iterator jb = atomListColumn.begin(); jb != atomListColumn.end(); ++jb)
1025     {
1026     atom2 = (*jb);
1027    
1028     if (!fDecomp_->skipAtomPair(atom1, atom2))
1029     {
1030     vpair = 0.0;
1031     workPot = 0.0;
1032     f1 = V3Zero;
1033    
1034     fDecomp_->fillInteractionData(idat, atom1, atom2);
1035    
1036     topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
1037     vdwMult = vdwScale_[topoDist];
1038     electroMult = electrostaticScale_[topoDist];
1039    
1040     if (atomListRow.size() == 1 && atomListColumn.size() == 1)
1041     {
1042     idat.d = &d_grp;
1043     idat.r2 = &rgrpsq;
1044 mciznick 1608 // cerr << "dgrp = " << d_grp << ":" << __LINE__ << "\n";
1045 mciznick 1598 } else
1046     {
1047     d = fDecomp_->getInteratomicVector(atom1, atom2);
1048     curSnapshot->wrapVector(d);
1049     r2 = d.lengthSquare();
1050 mciznick 1608 // cerr << "datm = " << d << ":" << __LINE__ << "\n";
1051 mciznick 1598 idat.d = &d;
1052     idat.r2 = &r2;
1053     }
1054    
1055 mciznick 1608 // cerr << "idat.d = " << *(idat.d) << ":" << __LINE__ << "\n";
1056 mciznick 1598 r = sqrt(*(idat.r2));
1057     idat.rij = &r;
1058 mciznick 1608 // cerr << "idat.rij = " << *(idat.rij) << "\n";
1059 mciznick 1598
1060     if (iLoop == PREPAIR_LOOP)
1061     {
1062     interactionMan_->doPrePair(idat);
1063     } else
1064     {
1065     interactionMan_->doPair(idat);
1066     fDecomp_->unpackInteractionData(idat, atom1, atom2);
1067    
1068 mciznick 1608 // cerr << "d = " << *(idat.d) << "\tv=" << vpair << "\tf=" << f1 << ":" << __LINE__ << "\n";
1069 mciznick 1598 vij += vpair;
1070     fij += f1;
1071     tau -= outProduct(*(idat.d), f1);
1072     }
1073     }
1074     }
1075     }
1076    
1077     if (iLoop == PAIR_LOOP)
1078     {
1079     if (in_switching_region)
1080     {
1081     swderiv = vij * dswdr / rgrp;
1082     fg = swderiv * d_grp;
1083     fij += fg;
1084    
1085     if (atomListRow.size() == 1 && atomListColumn.size() == 1)
1086     {
1087     tau -= outProduct(*(idat.d), fg);
1088     }
1089    
1090     for (vector<int>::iterator ia = atomListRow.begin(); ia != atomListRow.end(); ++ia)
1091     {
1092     atom1 = (*ia);
1093     mf = fDecomp_->getMassFactorRow(atom1);
1094     // fg is the force on atom ia due to cutoff group's
1095     // presence in switching region
1096     fg = swderiv * d_grp * mf;
1097     fDecomp_->addForceToAtomRow(atom1, fg);
1098    
1099     if (atomListRow.size() > 1)
1100     {
1101     if (info_->usesAtomicVirial())
1102     {
1103     // find the distance between the atom
1104     // and the center of the cutoff group:
1105     dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1->getGlobalIndex());
1106     tau -= outProduct(dag, fg);
1107     }
1108     }
1109     }
1110     for (vector<int>::iterator jb = atomListColumn.begin(); jb != atomListColumn.end(); ++jb)
1111     {
1112     atom2 = (*jb);
1113     mf = fDecomp_->getMassFactorColumn(atom2);
1114     // fg is the force on atom jb due to cutoff group's
1115     // presence in switching region
1116     fg = -swderiv * d_grp * mf;
1117     fDecomp_->addForceToAtomColumn(atom2, fg);
1118    
1119     if (atomListColumn.size() > 1)
1120     {
1121     if (info_->usesAtomicVirial())
1122     {
1123     // find the distance between the atom
1124     // and the center of the cutoff group:
1125     dag = fDecomp_->getAtomToGroupVectorColumn(atom2, (*cg2)->getGlobalIndex());
1126     tau -= outProduct(dag, fg);
1127     }
1128     }
1129     }
1130     }
1131     //if (!SIM_uses_AtomicVirial) {
1132     // tau -= outProduct(d_grp, fij);
1133     //}
1134     }
1135 chuckv 1595 }
1136     }
1137     }
1138 mciznick 1608 }
1139 chuckv 1595
1140 mciznick 1598 if (iLoop == PREPAIR_LOOP)
1141     {
1142     if (info_->requiresPrepair())
1143     {
1144 chuckv 1595
1145 mciznick 1598 fDecomp_->collectIntermediateData();
1146 chuckv 1595
1147 mciznick 1598 for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++)
1148     {
1149     fDecomp_->fillSelfData(sdat, atom1);
1150     interactionMan_->doPreForce(sdat);
1151     }
1152 chuckv 1595
1153 mciznick 1598 fDecomp_->distributeIntermediateData();
1154 chuckv 1595
1155 mciznick 1598 }
1156     }
1157     }
1158 chuckv 1595
1159 mciznick 1598 fDecomp_->collectData();
1160 chuckv 1595
1161 mciznick 1598 if (info_->requiresSelfCorrection())
1162     {
1163 chuckv 1595
1164 mciznick 1598 for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++)
1165     {
1166     fDecomp_->fillSelfData(sdat, atom1);
1167     interactionMan_->doSelfCorrection(sdat);
1168     }
1169 chuckv 1595
1170 mciznick 1598 }
1171 chuckv 1595
1172 mciznick 1598 longRangePotential = *(fDecomp_->getEmbeddingPotential()) + *(fDecomp_->getPairwisePotential());
1173 chuckv 1595
1174 mciznick 1598 lrPot = longRangePotential.sum();
1175 chuckv 1595
1176 mciznick 1598 //store the tau and long range potential
1177     curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
1178     curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
1179     curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
1180     }
1181 chuckv 1595
1182 mciznick 1598 void ForceManager::longRangeInteractions() {
1183 chuckv 1595
1184 mciznick 1598 Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
1185     DataStorage* config = &(curSnapshot->atomData);
1186     DataStorage* cgConfig = &(curSnapshot->cgData);
1187 gezelter 1581
1188 mciznick 1598 //calculate the center of mass of cutoff group
1189 gezelter 1545
1190 mciznick 1598 SimInfo::MoleculeIterator mi;
1191     Molecule* mol;
1192     Molecule::CutoffGroupIterator ci;
1193     CutoffGroup* cg;
1194 gezelter 1581
1195 mciznick 1598 if (info_->getNCutoffGroups() > 0)
1196     {
1197     for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
1198     {
1199     for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
1200     {
1201     cerr << "branch1\n";
1202     cerr << "globind = " << cg->getGlobalIndex() << "\n";
1203     cg->updateCOM();
1204     }
1205     }
1206     } else
1207     {
1208     // center of mass of the group is the same as position of the atom
1209     // if cutoff group does not exist
1210     cerr << "branch2\n";
1211     cgConfig->position = config->position;
1212     }
1213 gezelter 1581
1214 mciznick 1598 fDecomp_->zeroWorkArrays();
1215     fDecomp_->distributeData();
1216 gezelter 1581
1217 mciznick 1598 int cg1, cg2, atom1, atom2, topoDist;
1218     Vector3d d_grp, dag, d;
1219     RealType rgrpsq, rgrp, r2, r;
1220     RealType electroMult, vdwMult;
1221     RealType vij;
1222     Vector3d fij, fg, f1;
1223     tuple3<RealType, RealType, RealType> cuts;
1224     RealType rCutSq;
1225     bool in_switching_region;
1226     RealType sw, dswdr, swderiv;
1227     vector<int> atomListColumn, atomListRow, atomListLocal;
1228     InteractionData idat;
1229     SelfData sdat;
1230     RealType mf;
1231     RealType lrPot;
1232     RealType vpair;
1233     potVec longRangePotential(0.0);
1234     potVec workPot(0.0);
1235 gezelter 1544
1236 mciznick 1598 int loopStart, loopEnd;
1237 gezelter 1544
1238 mciznick 1598 idat.vdwMult = &vdwMult;
1239     idat.electroMult = &electroMult;
1240     idat.pot = &workPot;
1241     sdat.pot = fDecomp_->getEmbeddingPotential();
1242     idat.vpair = &vpair;
1243     idat.f1 = &f1;
1244     idat.sw = &sw;
1245     idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
1246     idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
1247 chuckv 1595
1248 mciznick 1598 loopEnd = PAIR_LOOP;
1249     if (info_->requiresPrepair())
1250     {
1251     loopStart = PREPAIR_LOOP;
1252     } else
1253     {
1254     loopStart = PAIR_LOOP;
1255     }
1256 gezelter 1545
1257 mciznick 1598 for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++)
1258     {
1259 gezelter 1545
1260 mciznick 1598 if (iLoop == loopStart)
1261     {
1262     bool update_nlist = fDecomp_->checkNeighborList();
1263     if (update_nlist)
1264     neighborList = fDecomp_->buildNeighborList();
1265 gezelter 1576
1266 mciznick 1598 }
1267 gezelter 1545
1268 mciznick 1598 for (vector<pair<int, int> >::iterator it = neighborList.begin(); it != neighborList.end(); ++it)
1269     {
1270     cg1 = (*it).first;
1271     cg2 = (*it).second;
1272 gezelter 1593
1273 mciznick 1598 cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
1274 gezelter 1575
1275 mciznick 1598 d_grp = fDecomp_->getIntergroupVector(cg1, cg2);
1276     curSnapshot->wrapVector(d_grp);
1277     rgrpsq = d_grp.lengthSquare();
1278 gezelter 1546
1279 mciznick 1598 rCutSq = cuts.second;
1280 gezelter 1593
1281 mciznick 1598 if (rgrpsq < rCutSq)
1282     {
1283     idat.rcut = &cuts.first;
1284     if (iLoop == PAIR_LOOP)
1285     {
1286     vij = 0.0;
1287     fij = V3Zero;
1288     }
1289 gezelter 1545
1290 mciznick 1598 in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr, rgrp);
1291 gezelter 1545
1292 mciznick 1598 atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
1293     atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
1294 gezelter 1545
1295 mciznick 1598 for (vector<int>::iterator ia = atomListRow.begin(); ia != atomListRow.end(); ++ia)
1296     {
1297     atom1 = (*ia);
1298 gezelter 1545
1299 mciznick 1598 for (vector<int>::iterator jb = atomListColumn.begin(); jb != atomListColumn.end(); ++jb)
1300     {
1301     atom2 = (*jb);
1302 gezelter 1545
1303 mciznick 1598 if (!fDecomp_->skipAtomPair(atom1, atom2))
1304     {
1305     vpair = 0.0;
1306     workPot = 0.0;
1307     f1 = V3Zero;
1308 gezelter 1590
1309 mciznick 1598 fDecomp_->fillInteractionData(idat, atom1, atom2);
1310 gezelter 1570
1311 mciznick 1598 topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
1312     vdwMult = vdwScale_[topoDist];
1313     electroMult = electrostaticScale_[topoDist];
1314 gezelter 1590
1315 mciznick 1598 if (atomListRow.size() == 1 && atomListColumn.size() == 1)
1316     {
1317     idat.d = &d_grp;
1318     idat.r2 = &rgrpsq;
1319     cerr << "dgrp = " << d_grp << "\n";
1320     } else
1321     {
1322     d = fDecomp_->getInteratomicVector(atom1, atom2);
1323     curSnapshot->wrapVector(d);
1324     r2 = d.lengthSquare();
1325     cerr << "datm = " << d << "\n";
1326     idat.d = &d;
1327     idat.r2 = &r2;
1328     }
1329 gezelter 1590
1330 mciznick 1598 cerr << "idat.d = " << *(idat.d) << "\n";
1331     r = sqrt(*(idat.r2));
1332     idat.rij = &r;
1333 gezelter 1545
1334 mciznick 1598 if (iLoop == PREPAIR_LOOP)
1335     {
1336     interactionMan_->doPrePair(idat);
1337     } else
1338     {
1339     interactionMan_->doPair(idat);
1340     fDecomp_->unpackInteractionData(idat, atom1, atom2);
1341 gezelter 1545
1342 mciznick 1598 cerr << "d = " << *(idat.d) << "\tv=" << vpair << "\tf=" << f1 << "\n";
1343     vij += vpair;
1344     fij += f1;
1345     tau -= outProduct(*(idat.d), f1);
1346     }
1347     }
1348     }
1349     }
1350 gezelter 1570
1351 mciznick 1598 if (iLoop == PAIR_LOOP)
1352     {
1353     if (in_switching_region)
1354     {
1355     swderiv = vij * dswdr / rgrp;
1356     fg = swderiv * d_grp;
1357     fij += fg;
1358 gezelter 1570
1359 mciznick 1598 if (atomListRow.size() == 1 && atomListColumn.size() == 1)
1360     {
1361     tau -= outProduct(*(idat.d), fg);
1362     }
1363 gezelter 1583
1364 mciznick 1598 for (vector<int>::iterator ia = atomListRow.begin(); ia != atomListRow.end(); ++ia)
1365     {
1366     atom1 = (*ia);
1367     mf = fDecomp_->getMassFactorRow(atom1);
1368     // fg is the force on atom ia due to cutoff group's
1369     // presence in switching region
1370     fg = swderiv * d_grp * mf;
1371     fDecomp_->addForceToAtomRow(atom1, fg);
1372 gezelter 1575
1373 mciznick 1598 if (atomListRow.size() > 1)
1374     {
1375     if (info_->usesAtomicVirial())
1376     {
1377     // find the distance between the atom
1378     // and the center of the cutoff group:
1379     dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
1380     tau -= outProduct(dag, fg);
1381     }
1382     }
1383     }
1384     for (vector<int>::iterator jb = atomListColumn.begin(); jb != atomListColumn.end(); ++jb)
1385     {
1386     atom2 = (*jb);
1387     mf = fDecomp_->getMassFactorColumn(atom2);
1388     // fg is the force on atom jb due to cutoff group's
1389     // presence in switching region
1390     fg = -swderiv * d_grp * mf;
1391     fDecomp_->addForceToAtomColumn(atom2, fg);
1392 gezelter 246
1393 mciznick 1598 if (atomListColumn.size() > 1)
1394     {
1395     if (info_->usesAtomicVirial())
1396     {
1397     // find the distance between the atom
1398     // and the center of the cutoff group:
1399     dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
1400     tau -= outProduct(dag, fg);
1401     }
1402     }
1403     }
1404     }
1405     //if (!SIM_uses_AtomicVirial) {
1406     // tau -= outProduct(d_grp, fij);
1407     //}
1408     }
1409     }
1410     }
1411    
1412     if (iLoop == PREPAIR_LOOP)
1413     {
1414     if (info_->requiresPrepair())
1415     {
1416    
1417     fDecomp_->collectIntermediateData();
1418    
1419     for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++)
1420     {
1421     fDecomp_->fillSelfData(sdat, atom1);
1422     interactionMan_->doPreForce(sdat);
1423     }
1424    
1425     fDecomp_->distributeIntermediateData();
1426    
1427     }
1428     }
1429    
1430     }
1431    
1432     fDecomp_->collectData();
1433    
1434     if (info_->requiresSelfCorrection())
1435     {
1436    
1437     for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++)
1438     {
1439     fDecomp_->fillSelfData(sdat, atom1);
1440     interactionMan_->doSelfCorrection(sdat);
1441     }
1442    
1443     }
1444    
1445     longRangePotential = *(fDecomp_->getEmbeddingPotential()) + *(fDecomp_->getPairwisePotential());
1446    
1447     lrPot = longRangePotential.sum();
1448    
1449     //store the tau and long range potential
1450     curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
1451     curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
1452     curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
1453     }
1454    
1455     void ForceManager::postCalculation() {
1456     SimInfo::MoleculeIterator mi;
1457     Molecule* mol;
1458     Molecule::RigidBodyIterator rbIter;
1459     RigidBody* rb;
1460     Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
1461    
1462     // collect the atomic forces onto rigid bodies
1463    
1464     for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
1465     {
1466     for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter))
1467     {
1468     Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
1469     tau += rbTau;
1470     }
1471     }
1472    
1473 gezelter 1126 #ifdef IS_MPI
1474 mciznick 1598 Mat3x3d tmpTau(tau);
1475     MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
1476     9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1477 gezelter 1126 #endif
1478 mciznick 1598 curSnapshot->statData.setTau(tau);
1479     }
1480 gezelter 246
1481 gezelter 1390 } //end namespace OpenMD

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