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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 1584 by gezelter, Fri Jun 17 20:16:35 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 87 | Line 67 | namespace OpenMD {
67      eam_->setForceField(forceField_);
68      sc_->setForceField(forceField_);
69      morse_->setForceField(forceField_);
70 +    electrostatic_->setSimInfo(info_);
71      electrostatic_->setForceField(forceField_);
72      maw_->setForceField(forceField_);
73  
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 –
74      ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
75      ForceField::AtomTypeContainer::MapTypeIterator i1, i2;
76      AtomType* atype1;
# Line 281 | Line 242 | namespace OpenMD {
242      }
243      
244      
245 <    // make sure every pair of atom types in this simulation has a
246 <    // non-bonded interaction:
245 >    // Make sure every pair of atom types in this simulation has a
246 >    // non-bonded interaction.  If not, just inform the user.
247  
248      set<AtomType*> simTypes = info_->getSimulatedAtomTypes();
249      set<AtomType*>::iterator it, jt;
250 +
251      for (it = simTypes.begin(); it != simTypes.end(); ++it) {
252        atype1 = (*it);
253 <      for (jt = simTypes.begin(); jt != simTypes.end(); ++jt) {
253 >      for (jt = it; jt != simTypes.end(); ++jt) {
254          atype2 = (*jt);
255          key = make_pair(atype1, atype2);
256          
257          if (interactions_[key].size() == 0) {
258            sprintf( painCave.errMsg,
259 <                   "InteractionManager unable to find an appropriate non-bonded\n"
260 <                   "\tinteraction for atom types %s - %s\n",
259 >                   "InteractionManager could not find a matching non-bonded\n"
260 >                   "\tinteraction for atom types %s - %s\n"
261 >                   "\tProceeding without this interaction.\n",
262                     atype1->getName().c_str(), atype2->getName().c_str());
263            painCave.severity = OPENMD_INFO;
264 <          painCave.isFatal = 1;
264 >          painCave.isFatal = 0;
265            simError();
266          }
267        }
268      }
269  
307 –    setupCutoffs();
308 –    setupSwitching();
309 –    setupNeighborlists();
310 –
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 –
270      initialized_ = true;
271    }
272 <  
273 <  /**
274 <   * 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 <    }
272 >
273 >  void InteractionManager::setCutoffRadius(RealType rcut) {
274 >    electrostatic_->setCutoffRadius(rcut);
275    }
276  
277 <
278 <  /**
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_);
277 >  void InteractionManager::setSwitchingRadius(RealType rswitch) {
278 >    electrostatic_->setSwitchingRadius(rswitch);
279    }
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();    
280    
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 –
281    void InteractionManager::doPrePair(InteractionData idat){
282      
283      if (!initialized_) initialize();
284          
285      set<NonBondedInteraction*>::iterator it;
286  
287 <    for (it = interactions_[idat.atypes].begin();
288 <         it != interactions_[idat.atypes].end(); ++it){
287 >    for (it = interactions_[ idat.atypes ].begin();
288 >         it != interactions_[ idat.atypes ].end(); ++it){
289        if ((*it)->getFamily() == METALLIC_FAMILY) {
290          dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat);
291        }
# Line 524 | Line 316 | namespace OpenMD {
316    
317      set<NonBondedInteraction*>::iterator it;
318  
319 <    for (it = interactions_[idat.atypes].begin();
320 <         it != interactions_[idat.atypes].end(); ++it)
319 >    for (it = interactions_[ idat.atypes ].begin();
320 >         it != interactions_[ idat.atypes ].end(); ++it)
321        (*it)->calcForce(idat);
322      
323      return;    
# Line 537 | Line 329 | namespace OpenMD {
329      
330      set<NonBondedInteraction*>::iterator it;
331  
332 <    for (it = interactions_[idat.atypes].begin();
333 <         it != interactions_[idat.atypes].end(); ++it){
332 >    for (it = interactions_[ idat.atypes ].begin();
333 >         it != interactions_[ idat.atypes ].end(); ++it){
334        if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) {
335          dynamic_cast<ElectrostaticInteraction*>(*it)->calcSkipCorrection(idat);
336        }

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