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Comparing branches/development/src/nonbonded/InteractionManager.cpp (file contents):
Revision 1545 by gezelter, Fri Apr 8 21:25:19 2011 UTC vs.
Revision 1576 by gezelter, Wed Jun 8 16:05:07 2011 UTC

# Line 40 | Line 40
40   */
41  
42   #include "nonbonded/InteractionManager.hpp"
43 – #include "UseTheForce/doForces_interface.h"
43  
44   namespace OpenMD {
45  
46 <  InteractionManager* InteractionManager::_instance = NULL;
48 <  SimInfo* InteractionManager::info_ = NULL;
49 <  bool InteractionManager::initialized_ = false;
46 >  InteractionManager::InteractionManager() {
47  
48 <  RealType InteractionManager::rCut_ = 0.0;
49 <  RealType InteractionManager::rSwitch_ = 0.0;
50 <  RealType InteractionManager::skinThickness_ = 0.0;
51 <  RealType InteractionManager::listRadius_ = 0.0;
52 <  CutoffMethod InteractionManager::cutoffMethod_ = SHIFTED_FORCE;
53 <  SwitchingFunctionType InteractionManager::sft_ = cubic;
54 <  RealType InteractionManager::vdwScale_[4] = {1.0, 0.0, 0.0, 0.0};
55 <  RealType InteractionManager::electrostaticScale_[4] = {1.0, 0.0, 0.0, 0.0};
56 <
57 <  map<int, AtomType*> InteractionManager::typeMap_;
61 <  map<pair<AtomType*, AtomType*>, set<NonBondedInteraction*> > InteractionManager::interactions_;
62 <
63 <  LJ* InteractionManager::lj_ = new LJ();
64 <  GB* InteractionManager::gb_ = new GB();
65 <  Sticky* InteractionManager::sticky_ = new Sticky();
66 <  Morse* InteractionManager::morse_ = new Morse();
67 <  EAM* InteractionManager::eam_ = new EAM();
68 <  SC* InteractionManager::sc_ = new SC();
69 <  Electrostatic* InteractionManager::electrostatic_ = new Electrostatic();
70 <  MAW* InteractionManager::maw_ = new MAW();
71 <  SwitchingFunction* InteractionManager::switcher_ = new SwitchingFunction();
72 <
73 <  InteractionManager* InteractionManager::Instance() {
74 <    if (!_instance) {
75 <      _instance = new InteractionManager();
76 <    }
77 <    return _instance;
48 >    initialized_ = false;
49 >        
50 >    lj_ = new LJ();
51 >    gb_ = new GB();
52 >    sticky_ = new Sticky();
53 >    morse_ = new Morse();
54 >    eam_ = new EAM();
55 >    sc_ = new SC();
56 >    electrostatic_ = new Electrostatic();
57 >    maw_ = new MAW();
58    }
59  
60    void InteractionManager::initialize() {
# Line 90 | Line 70 | namespace OpenMD {
70      electrostatic_->setForceField(forceField_);
71      maw_->setForceField(forceField_);
72  
93 –    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
94 –
95 –    // Force fields can set options on how to scale van der Waals and electrostatic
96 –    // interactions for atoms connected via bonds, bends and torsions
97 –    // in this case the topological distance between atoms is:
98 –    // 0 = topologically unconnected
99 –    // 1 = bonded together
100 –    // 2 = connected via a bend
101 –    // 3 = connected via a torsion
102 –
103 –    vdwScale_[0] = 1.0;
104 –    vdwScale_[1] = fopts.getvdw12scale();
105 –    vdwScale_[2] = fopts.getvdw13scale();
106 –    vdwScale_[3] = fopts.getvdw14scale();
107 –
108 –    electrostaticScale_[0] = 1.0;
109 –    electrostaticScale_[1] = fopts.getelectrostatic12scale();
110 –    electrostaticScale_[2] = fopts.getelectrostatic13scale();
111 –    electrostaticScale_[3] = fopts.getelectrostatic14scale();    
112 –
73      ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
74      ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
75      AtomType* atype1;
# Line 303 | Line 263 | namespace OpenMD {
263          }
264        }
265      }
306 –
307 –    setupCutoffs();
308 –    setupSwitching();
309 –    setupNeighborlists();
266  
311 –    //int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0;
312 –    //int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0;
313 –    //notifyFortranCutoffs(&rCut_, &rSwitch_, &ljsp, &ljsf);
314 –    //notifyFortranSkinThickness(&skinThickness_);
315 –
267      initialized_ = true;
268    }
269    
319 –  /**
320 –   * setupCutoffs
321 –   *
322 –   * Sets the values of cutoffRadius and cutoffMethod
323 –   *
324 –   * cutoffRadius : realType
325 –   *  If the cutoffRadius was explicitly set, use that value.
326 –   *  If the cutoffRadius was not explicitly set:
327 –   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
328 –   *      No electrostatic atoms?  Poll the atom types present in the
329 –   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
330 –   *      Use the maximum suggested value that was found.
331 –   *
332 –   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
333 –   *      If cutoffMethod was explicitly set, use that choice.
334 –   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
335 –   */
336 –  void InteractionManager::setupCutoffs() {
337 –    
338 –    Globals* simParams_ = info_->getSimParams();
339 –    
340 –    if (simParams_->haveCutoffRadius()) {
341 –      rCut_ = simParams_->getCutoffRadius();
342 –    } else {      
343 –      if (info_->usesElectrostaticAtoms()) {
344 –        sprintf(painCave.errMsg,
345 –                "InteractionManager::setupCutoffs: No value was set for the cutoffRadius.\n"
346 –                "\tOpenMD will use a default value of 12.0 angstroms"
347 –                "\tfor the cutoffRadius.\n");
348 –        painCave.isFatal = 0;
349 –        painCave.severity = OPENMD_INFO;
350 –        simError();
351 –        rCut_ = 12.0;
352 –      } else {
353 –        RealType thisCut;
354 –        set<AtomType*>::iterator i;
355 –        set<AtomType*> atomTypes;
356 –        atomTypes = info_->getSimulatedAtomTypes();        
357 –        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
358 –          thisCut = getSuggestedCutoffRadius((*i));
359 –          rCut_ = max(thisCut, rCut_);
360 –        }
361 –        sprintf(painCave.errMsg,
362 –                "InteractionManager::setupCutoffs: No value was set for the cutoffRadius.\n"
363 –                "\tOpenMD will use %lf angstroms.\n",
364 –                rCut_);
365 –        painCave.isFatal = 0;
366 –        painCave.severity = OPENMD_INFO;
367 –        simError();
368 –      }            
369 –    }
370 –
371 –    map<string, CutoffMethod> stringToCutoffMethod;
372 –    stringToCutoffMethod["HARD"] = HARD;
373 –    stringToCutoffMethod["SWITCHED"] = SWITCHED;
374 –    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
375 –    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
376 –  
377 –    if (simParams_->haveCutoffMethod()) {
378 –      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
379 –      map<string, CutoffMethod>::iterator i;
380 –      i = stringToCutoffMethod.find(cutMeth);
381 –      if (i == stringToCutoffMethod.end()) {
382 –        sprintf(painCave.errMsg,
383 –                "InteractionManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
384 –                "\tShould be one of: "
385 –                "HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
386 –                cutMeth.c_str());
387 –        painCave.isFatal = 1;
388 –        painCave.severity = OPENMD_ERROR;
389 –        simError();
390 –      } else {
391 –        cutoffMethod_ = i->second;
392 –      }
393 –    } else {
394 –      sprintf(painCave.errMsg,
395 –              "InteractionManager::setupCutoffs: No value was set for the cutoffMethod.\n"
396 –              "\tOpenMD will use SHIFTED_FORCE.\n");
397 –        painCave.isFatal = 0;
398 –        painCave.severity = OPENMD_INFO;
399 –        simError();
400 –        cutoffMethod_ = SHIFTED_FORCE;        
401 –    }
402 –  }
403 –
404 –
405 –  /**
406 –   * setupSwitching
407 –   *
408 –   * Sets the values of switchingRadius and
409 –   *  If the switchingRadius was explicitly set, use that value (but check it)
410 –   *  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
411 –   */
412 –  void InteractionManager::setupSwitching() {
413 –    Globals* simParams_ = info_->getSimParams();
414 –
415 –    if (simParams_->haveSwitchingRadius()) {
416 –      rSwitch_ = simParams_->getSwitchingRadius();
417 –      if (rSwitch_ > rCut_) {        
418 –        sprintf(painCave.errMsg,
419 –                "InteractionManager::setupSwitching: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
420 –                rSwitch_, rCut_);
421 –        painCave.isFatal = 1;
422 –        painCave.severity = OPENMD_ERROR;
423 –        simError();
424 –      }
425 –    } else {      
426 –      rSwitch_ = 0.85 * rCut_;
427 –      sprintf(painCave.errMsg,
428 –              "InteractionManager::setupSwitching: No value was set for the switchingRadius.\n"
429 –              "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
430 –              "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
431 –      painCave.isFatal = 0;
432 –      painCave.severity = OPENMD_WARNING;
433 –      simError();
434 –    }          
435 –    
436 –    if (simParams_->haveSwitchingFunctionType()) {
437 –      string funcType = simParams_->getSwitchingFunctionType();
438 –      toUpper(funcType);
439 –      if (funcType == "CUBIC") {
440 –        sft_ = cubic;
441 –      } else {
442 –        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
443 –          sft_ = fifth_order_poly;
444 –        } else {
445 –          // throw error        
446 –          sprintf( painCave.errMsg,
447 –                   "InteractionManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
448 –                   "\tswitchingFunctionType must be one of: "
449 –                   "\"cubic\" or \"fifth_order_polynomial\".",
450 –                   funcType.c_str() );
451 –          painCave.isFatal = 1;
452 –          painCave.severity = OPENMD_ERROR;
453 –          simError();
454 –        }          
455 –      }
456 –    }
457 –
458 –    switcher_->setSwitchType(sft_);
459 –    switcher_->setSwitch(rSwitch_, rCut_);
460 –  }
461 –
462 –  /**
463 –   * setupNeighborlists
464 –   *
465 –   *  If the skinThickness was explicitly set, use that value (but check it)
466 –   *  If the skinThickness was not explicitly set: use 1.0 angstroms
467 –   */
468 –  void InteractionManager::setupNeighborlists() {  
469 –
470 –    Globals* simParams_ = info_->getSimParams();    
471 –  
472 –    if (simParams_->haveSkinThickness()) {
473 –      skinThickness_ = simParams_->getSkinThickness();
474 –    } else {      
475 –      skinThickness_ = 1.0;
476 –      sprintf(painCave.errMsg,
477 –              "InteractionManager::setupNeighborlists: No value was set for the skinThickness.\n"
478 –              "\tOpenMD will use a default value of %f Angstroms\n"
479 –              "\tfor this simulation\n", skinThickness_);
480 –      painCave.severity = OPENMD_INFO;
481 –      painCave.isFatal = 0;
482 –      simError();
483 –    }            
484 –
485 –    listRadius_ = rCut_ + skinThickness_;
486 –  }
487 –
488 –
270    void InteractionManager::doPrePair(InteractionData idat){
271      
272      if (!initialized_) initialize();
273          
274      set<NonBondedInteraction*>::iterator it;
275  
276 <    for (it = interactions_[idat.atypes].begin();
277 <         it != interactions_[idat.atypes].end(); ++it){
276 >    for (it = interactions_[ idat.atypes ].begin();
277 >         it != interactions_[ idat.atypes ].end(); ++it){
278        if ((*it)->getFamily() == METALLIC_FAMILY) {
279          dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
280        }
# Line 524 | Line 305 | namespace OpenMD {
305    
306      set<NonBondedInteraction*>::iterator it;
307  
308 <    for (it = interactions_[idat.atypes].begin();
309 <         it != interactions_[idat.atypes].end(); ++it)
308 >    for (it = interactions_[ idat.atypes ].begin();
309 >         it != interactions_[ idat.atypes ].end(); ++it)
310        (*it)->calcForce(idat);
311      
312      return;    
# Line 537 | Line 318 | namespace OpenMD {
318      
319      set<NonBondedInteraction*>::iterator it;
320  
321 <    for (it = interactions_[idat.atypes].begin();
322 <         it != interactions_[idat.atypes].end(); ++it){
321 >    for (it = interactions_[ idat.atypes ].begin();
322 >         it != interactions_[ idat.atypes ].end(); ++it){
323        if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
324          dynamic_cast<ElectrostaticInteraction*>(*it)->calcSkipCorrection(idat);
325        }

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