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root/OpenMD/branches/development/src/brains/ForceManager.cpp
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trunk/src/brains/ForceManager.cpp (file contents), Revision 1448 by gezelter, Thu Jun 17 14:58:49 2010 UTC vs.
branches/development/src/brains/ForceManager.cpp (file contents), Revision 1710 by gezelter, Fri May 18 21:44:02 2012 UTC

# Line 36 | Line 36
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).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   /**
# Line 47 | Line 48
48   * @version 1.0
49   */
50  
51 +
52   #include "brains/ForceManager.hpp"
53   #include "primitives/Molecule.hpp"
52 – #include "UseTheForce/doForces_interface.h"
54   #define __OPENMD_C
54 – #include "UseTheForce/DarkSide/fInteractionMap.h"
55   #include "utils/simError.h"
56   #include "primitives/Bond.hpp"
57   #include "primitives/Bend.hpp"
58   #include "primitives/Torsion.hpp"
59   #include "primitives/Inversion.hpp"
60 + #include "nonbonded/NonBondedInteraction.hpp"
61 + #include "parallel/ForceMatrixDecomposition.hpp"
62 +
63 + #include <cstdio>
64 + #include <iostream>
65 + #include <iomanip>
66 +
67 + using namespace std;
68   namespace OpenMD {
69 +  
70 +  ForceManager::ForceManager(SimInfo * info) : info_(info) {
71 +    forceField_ = info_->getForceField();
72 +    interactionMan_ = new InteractionManager();
73 +    fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
74 +  }
75  
76 <  void ForceManager::calcForces(bool needPotential, bool needStress) {
76 >  /**
77 >   * setupCutoffs
78 >   *
79 >   * Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
80 >   * and cutoffPolicy
81 >   *
82 >   * cutoffRadius : realType
83 >   *  If the cutoffRadius was explicitly set, use that value.
84 >   *  If the cutoffRadius was not explicitly set:
85 >   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
86 >   *      No electrostatic atoms?  Poll the atom types present in the
87 >   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
88 >   *      Use the maximum suggested value that was found.
89 >   *
90 >   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
91 >   *                        or SHIFTED_POTENTIAL)
92 >   *      If cutoffMethod was explicitly set, use that choice.
93 >   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
94 >   *
95 >   * cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
96 >   *      If cutoffPolicy was explicitly set, use that choice.
97 >   *      If cutoffPolicy was not explicitly set, use TRADITIONAL
98 >   *
99 >   * switchingRadius : realType
100 >   *  If the cutoffMethod was set to SWITCHED:
101 >   *      If the switchingRadius was explicitly set, use that value
102 >   *          (but do a sanity check first).
103 >   *      If the switchingRadius was not explicitly set: use 0.85 *
104 >   *      cutoffRadius_
105 >   *  If the cutoffMethod was not set to SWITCHED:
106 >   *      Set switchingRadius equal to cutoffRadius for safety.
107 >   */
108 >  void ForceManager::setupCutoffs() {
109      
110 <    if (!info_->isFortranInitialized()) {
110 >    Globals* simParams_ = info_->getSimParams();
111 >    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
112 >    int mdFileVersion;
113 >    
114 >    if (simParams_->haveMDfileVersion())
115 >      mdFileVersion = simParams_->getMDfileVersion();
116 >    else
117 >      mdFileVersion = 0;
118 >  
119 >    if (simParams_->haveCutoffRadius()) {
120 >      rCut_ = simParams_->getCutoffRadius();
121 >    } else {      
122 >      if (info_->usesElectrostaticAtoms()) {
123 >        sprintf(painCave.errMsg,
124 >                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
125 >                "\tOpenMD will use a default value of 12.0 angstroms"
126 >                "\tfor the cutoffRadius.\n");
127 >        painCave.isFatal = 0;
128 >        painCave.severity = OPENMD_INFO;
129 >        simError();
130 >        rCut_ = 12.0;
131 >      } else {
132 >        RealType thisCut;
133 >        set<AtomType*>::iterator i;
134 >        set<AtomType*> atomTypes;
135 >        atomTypes = info_->getSimulatedAtomTypes();        
136 >        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
137 >          thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
138 >          rCut_ = max(thisCut, rCut_);
139 >        }
140 >        sprintf(painCave.errMsg,
141 >                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
142 >                "\tOpenMD will use %lf angstroms.\n",
143 >                rCut_);
144 >        painCave.isFatal = 0;
145 >        painCave.severity = OPENMD_INFO;
146 >        simError();
147 >      }
148 >    }
149 >
150 >    fDecomp_->setUserCutoff(rCut_);
151 >    interactionMan_->setCutoffRadius(rCut_);
152 >
153 >    map<string, CutoffMethod> stringToCutoffMethod;
154 >    stringToCutoffMethod["HARD"] = HARD;
155 >    stringToCutoffMethod["SWITCHED"] = SWITCHED;
156 >    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
157 >    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
158 >  
159 >    if (simParams_->haveCutoffMethod()) {
160 >      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
161 >      map<string, CutoffMethod>::iterator i;
162 >      i = stringToCutoffMethod.find(cutMeth);
163 >      if (i == stringToCutoffMethod.end()) {
164 >        sprintf(painCave.errMsg,
165 >                "ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
166 >                "\tShould be one of: "
167 >                "HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
168 >                cutMeth.c_str());
169 >        painCave.isFatal = 1;
170 >        painCave.severity = OPENMD_ERROR;
171 >        simError();
172 >      } else {
173 >        cutoffMethod_ = i->second;
174 >      }
175 >    } else {
176 >      if (mdFileVersion > 1) {
177 >        sprintf(painCave.errMsg,
178 >                "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
179 >                "\tOpenMD will use SHIFTED_FORCE.\n");
180 >        painCave.isFatal = 0;
181 >        painCave.severity = OPENMD_INFO;
182 >        simError();
183 >        cutoffMethod_ = SHIFTED_FORCE;        
184 >      } else {
185 >        // handle the case where the old file version was in play
186 >        // (there should be no cutoffMethod, so we have to deduce it
187 >        // from other data).        
188 >
189 >        sprintf(painCave.errMsg,
190 >                "ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
191 >                "\tOpenMD found a file which does not set a cutoffMethod.\n"
192 >                "\tOpenMD will attempt to deduce a cutoffMethod using the\n"
193 >                "\tbehavior of the older (version 1) code.  To remove this\n"
194 >                "\twarning, add an explicit cutoffMethod and change the top\n"
195 >                "\tof the file so that it begins with <OpenMD version=2>\n");
196 >        painCave.isFatal = 0;
197 >        painCave.severity = OPENMD_WARNING;
198 >        simError();            
199 >                
200 >        // The old file version tethered the shifting behavior to the
201 >        // electrostaticSummationMethod keyword.
202 >        
203 >        if (simParams_->haveElectrostaticSummationMethod()) {
204 >          string myMethod = simParams_->getElectrostaticSummationMethod();
205 >          toUpper(myMethod);
206 >        
207 >          if (myMethod == "SHIFTED_POTENTIAL") {
208 >            cutoffMethod_ = SHIFTED_POTENTIAL;
209 >          } else if (myMethod == "SHIFTED_FORCE") {
210 >            cutoffMethod_ = SHIFTED_FORCE;
211 >          }
212 >        
213 >          if (simParams_->haveSwitchingRadius())
214 >            rSwitch_ = simParams_->getSwitchingRadius();
215 >
216 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
217 >            if (simParams_->haveSwitchingRadius()){
218 >              sprintf(painCave.errMsg,
219 >                      "ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
220 >                      "\tA value was set for the switchingRadius\n"
221 >                      "\teven though the electrostaticSummationMethod was\n"
222 >                      "\tset to %s\n", myMethod.c_str());
223 >              painCave.severity = OPENMD_WARNING;
224 >              painCave.isFatal = 1;
225 >              simError();            
226 >            }
227 >          }
228 >          if (abs(rCut_ - rSwitch_) < 0.0001) {
229 >            if (cutoffMethod_ == SHIFTED_FORCE) {              
230 >              sprintf(painCave.errMsg,
231 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
232 >                      "\tcutoffRadius and switchingRadius are set to the\n"
233 >                      "\tsame value.  OpenMD will use shifted force\n"
234 >                      "\tpotentials instead of switching functions.\n");
235 >              painCave.isFatal = 0;
236 >              painCave.severity = OPENMD_WARNING;
237 >              simError();            
238 >            } else {
239 >              cutoffMethod_ = SHIFTED_POTENTIAL;
240 >              sprintf(painCave.errMsg,
241 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
242 >                      "\tcutoffRadius and switchingRadius are set to the\n"
243 >                      "\tsame value.  OpenMD will use shifted potentials\n"
244 >                      "\tinstead of switching functions.\n");
245 >              painCave.isFatal = 0;
246 >              painCave.severity = OPENMD_WARNING;
247 >              simError();            
248 >            }
249 >          }
250 >        }
251 >      }
252 >    }
253 >
254 >    map<string, CutoffPolicy> stringToCutoffPolicy;
255 >    stringToCutoffPolicy["MIX"] = MIX;
256 >    stringToCutoffPolicy["MAX"] = MAX;
257 >    stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;    
258 >
259 >    string cutPolicy;
260 >    if (forceFieldOptions_.haveCutoffPolicy()){
261 >      cutPolicy = forceFieldOptions_.getCutoffPolicy();
262 >    }else if (simParams_->haveCutoffPolicy()) {
263 >      cutPolicy = simParams_->getCutoffPolicy();
264 >    }
265 >
266 >    if (!cutPolicy.empty()){
267 >      toUpper(cutPolicy);
268 >      map<string, CutoffPolicy>::iterator i;
269 >      i = stringToCutoffPolicy.find(cutPolicy);
270 >
271 >      if (i == stringToCutoffPolicy.end()) {
272 >        sprintf(painCave.errMsg,
273 >                "ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
274 >                "\tShould be one of: "
275 >                "MIX, MAX, or TRADITIONAL\n",
276 >                cutPolicy.c_str());
277 >        painCave.isFatal = 1;
278 >        painCave.severity = OPENMD_ERROR;
279 >        simError();
280 >      } else {
281 >        cutoffPolicy_ = i->second;
282 >      }
283 >    } else {
284 >      sprintf(painCave.errMsg,
285 >              "ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
286 >              "\tOpenMD will use TRADITIONAL.\n");
287 >      painCave.isFatal = 0;
288 >      painCave.severity = OPENMD_INFO;
289 >      simError();
290 >      cutoffPolicy_ = TRADITIONAL;        
291 >    }
292 >
293 >    fDecomp_->setCutoffPolicy(cutoffPolicy_);
294 >        
295 >    // create the switching function object:
296 >
297 >    switcher_ = new SwitchingFunction();
298 >  
299 >    if (cutoffMethod_ == SWITCHED) {
300 >      if (simParams_->haveSwitchingRadius()) {
301 >        rSwitch_ = simParams_->getSwitchingRadius();
302 >        if (rSwitch_ > rCut_) {        
303 >          sprintf(painCave.errMsg,
304 >                  "ForceManager::setupCutoffs: switchingRadius (%f) is larger "
305 >                  "than the cutoffRadius(%f)\n", rSwitch_, rCut_);
306 >          painCave.isFatal = 1;
307 >          painCave.severity = OPENMD_ERROR;
308 >          simError();
309 >        }
310 >      } else {      
311 >        rSwitch_ = 0.85 * rCut_;
312 >        sprintf(painCave.errMsg,
313 >                "ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
314 >                "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
315 >                "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
316 >        painCave.isFatal = 0;
317 >        painCave.severity = OPENMD_WARNING;
318 >        simError();
319 >      }
320 >    } else {
321 >      if (mdFileVersion > 1) {
322 >        // throw an error if we define a switching radius and don't need one.
323 >        // older file versions should not do this.
324 >        if (simParams_->haveSwitchingRadius()) {
325 >          map<string, CutoffMethod>::const_iterator it;
326 >          string theMeth;
327 >          for (it = stringToCutoffMethod.begin();
328 >               it != stringToCutoffMethod.end(); ++it) {
329 >            if (it->second == cutoffMethod_) {
330 >              theMeth = it->first;
331 >              break;
332 >            }
333 >          }
334 >          sprintf(painCave.errMsg,
335 >                  "ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
336 >                  "\tis not set to SWITCHED, so switchingRadius value\n"
337 >                  "\twill be ignored for this simulation\n", theMeth.c_str());
338 >          painCave.isFatal = 0;
339 >          painCave.severity = OPENMD_WARNING;
340 >          simError();
341 >        }
342 >      }
343 >      rSwitch_ = rCut_;
344 >    }
345 >    
346 >    // Default to cubic switching function.
347 >    sft_ = cubic;
348 >    if (simParams_->haveSwitchingFunctionType()) {
349 >      string funcType = simParams_->getSwitchingFunctionType();
350 >      toUpper(funcType);
351 >      if (funcType == "CUBIC") {
352 >        sft_ = cubic;
353 >      } else {
354 >        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
355 >          sft_ = fifth_order_poly;
356 >        } else {
357 >          // throw error        
358 >          sprintf( painCave.errMsg,
359 >                   "ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
360 >                   "\tswitchingFunctionType must be one of: "
361 >                   "\"cubic\" or \"fifth_order_polynomial\".",
362 >                   funcType.c_str() );
363 >          painCave.isFatal = 1;
364 >          painCave.severity = OPENMD_ERROR;
365 >          simError();
366 >        }          
367 >      }
368 >    }
369 >    switcher_->setSwitchType(sft_);
370 >    switcher_->setSwitch(rSwitch_, rCut_);
371 >    interactionMan_->setSwitchingRadius(rSwitch_);
372 >  }
373 >
374 >
375 >
376 >  
377 >  void ForceManager::initialize() {
378 >
379 >    if (!info_->isTopologyDone()) {
380 >
381        info_->update();
382 +      interactionMan_->setSimInfo(info_);
383 +      interactionMan_->initialize();
384 +
385 +      // We want to delay the cutoffs until after the interaction
386 +      // manager has set up the atom-atom interactions so that we can
387 +      // query them for suggested cutoff values
388 +      setupCutoffs();
389 +
390 +      info_->prepareTopology();      
391      }
392 +
393 +    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
394      
395 <    preCalculation();
395 >    // Force fields can set options on how to scale van der Waals and
396 >    // electrostatic interactions for atoms connected via bonds, bends
397 >    // and torsions in this case the topological distance between
398 >    // atoms is:
399 >    // 0 = topologically unconnected
400 >    // 1 = bonded together
401 >    // 2 = connected via a bend
402 >    // 3 = connected via a torsion
403      
404 <    calcShortRangeInteraction();
404 >    vdwScale_.reserve(4);
405 >    fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
406  
407 <    calcLongRangeInteraction(needPotential, needStress);
407 >    electrostaticScale_.reserve(4);
408 >    fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
409  
410 <    postCalculation(needStress);
410 >    vdwScale_[0] = 1.0;
411 >    vdwScale_[1] = fopts.getvdw12scale();
412 >    vdwScale_[2] = fopts.getvdw13scale();
413 >    vdwScale_[3] = fopts.getvdw14scale();
414      
415 +    electrostaticScale_[0] = 1.0;
416 +    electrostaticScale_[1] = fopts.getelectrostatic12scale();
417 +    electrostaticScale_[2] = fopts.getelectrostatic13scale();
418 +    electrostaticScale_[3] = fopts.getelectrostatic14scale();    
419 +    
420 +    fDecomp_->distributeInitialData();
421 +
422 +    initialized_ = true;
423 +
424    }
425 +
426 +  void ForceManager::calcForces() {
427 +    
428 +    if (!initialized_) initialize();
429 +
430 +    preCalculation();  
431 +    shortRangeInteractions();
432 +    longRangeInteractions();
433 +    postCalculation();    
434 +  }
435    
436    void ForceManager::preCalculation() {
437      SimInfo::MoleculeIterator mi;
# Line 82 | Line 440 | namespace OpenMD {
440      Atom* atom;
441      Molecule::RigidBodyIterator rbIter;
442      RigidBody* rb;
443 +    Molecule::CutoffGroupIterator ci;
444 +    CutoffGroup* cg;
445      
446      // forces are zeroed here, before any are accumulated.
87 –    // NOTE: do not rezero the forces in Fortran.
447      
448      for (mol = info_->beginMolecule(mi); mol != NULL;
449           mol = info_->nextMolecule(mi)) {
450 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
450 >      for(atom = mol->beginAtom(ai); atom != NULL;
451 >          atom = mol->nextAtom(ai)) {
452          atom->zeroForcesAndTorques();
453        }
454 <          
454 >      
455        //change the positions of atoms which belong to the rigidbodies
456        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
457             rb = mol->nextRigidBody(rbIter)) {
458          rb->zeroForcesAndTorques();
459        }        
460 <          
460 >      
461 >      if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
462 >        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
463 >            cg = mol->nextCutoffGroup(ci)) {
464 >          //calculate the center of mass of cutoff group
465 >          cg->updateCOM();
466 >        }
467 >      }      
468      }
469      
470      // Zero out the stress tensor
# Line 105 | Line 472 | namespace OpenMD {
472      
473    }
474    
475 <  void ForceManager::calcShortRangeInteraction() {
475 >  void ForceManager::shortRangeInteractions() {
476      Molecule* mol;
477      RigidBody* rb;
478      Bond* bond;
# Line 147 | Line 514 | namespace OpenMD {
514          RealType currBendPot = bend->getPotential();          
515          
516          bendPotential += bend->getPotential();
517 <        std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
517 >        map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
518          if (i == bendDataSets.end()) {
519            BendDataSet dataSet;
520            dataSet.prev.angle = dataSet.curr.angle = angle;
521            dataSet.prev.potential = dataSet.curr.potential = currBendPot;
522            dataSet.deltaV = 0.0;
523 <          bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
523 >          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
524 >                                                                  dataSet));
525          }else {
526            i->second.prev.angle = i->second.curr.angle;
527            i->second.prev.potential = i->second.curr.potential;
# Line 170 | Line 538 | namespace OpenMD {
538          torsion->calcForce(angle);
539          RealType currTorsionPot = torsion->getPotential();
540          torsionPotential += torsion->getPotential();
541 <        std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
541 >        map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
542          if (i == torsionDataSets.end()) {
543            TorsionDataSet dataSet;
544            dataSet.prev.angle = dataSet.curr.angle = angle;
545            dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
546            dataSet.deltaV = 0.0;
547 <          torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
547 >          torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
548          }else {
549            i->second.prev.angle = i->second.curr.angle;
550            i->second.prev.potential = i->second.curr.potential;
# Line 186 | Line 554 | namespace OpenMD {
554                                     i->second.prev.potential);
555          }      
556        }      
557 <
557 >      
558        for (inversion = mol->beginInversion(inversionIter);
559             inversion != NULL;
560             inversion = mol->nextInversion(inversionIter)) {
# Line 194 | Line 562 | namespace OpenMD {
562          inversion->calcForce(angle);
563          RealType currInversionPot = inversion->getPotential();
564          inversionPotential += inversion->getPotential();
565 <        std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
565 >        map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
566          if (i == inversionDataSets.end()) {
567            InversionDataSet dataSet;
568            dataSet.prev.angle = dataSet.curr.angle = angle;
569            dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
570            dataSet.deltaV = 0.0;
571 <          inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
571 >          inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
572          }else {
573            i->second.prev.angle = i->second.curr.angle;
574            i->second.prev.potential = i->second.curr.potential;
# Line 219 | Line 587 | namespace OpenMD {
587      curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
588      curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
589      curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
590 <    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
223 <    
590 >    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;    
591    }
592    
593 <  void ForceManager::calcLongRangeInteraction(bool needPotential,
227 <                                              bool needStress) {
228 <    Snapshot* curSnapshot;
229 <    DataStorage* config;
230 <    RealType* frc;
231 <    RealType* pos;
232 <    RealType* trq;
233 <    RealType* A;
234 <    RealType* electroFrame;
235 <    RealType* rc;
236 <    RealType* particlePot;
237 <    
238 <    //get current snapshot from SimInfo
239 <    curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
240 <    
241 <    //get array pointers
242 <    config = &(curSnapshot->atomData);
243 <    frc = config->getArrayPointer(DataStorage::dslForce);
244 <    pos = config->getArrayPointer(DataStorage::dslPosition);
245 <    trq = config->getArrayPointer(DataStorage::dslTorque);
246 <    A   = config->getArrayPointer(DataStorage::dslAmat);
247 <    electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
248 <    particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
593 >  void ForceManager::longRangeInteractions() {
594  
595 +    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
596 +    DataStorage* config = &(curSnapshot->atomData);
597 +    DataStorage* cgConfig = &(curSnapshot->cgData);
598 +
599      //calculate the center of mass of cutoff group
600 +
601      SimInfo::MoleculeIterator mi;
602      Molecule* mol;
603      Molecule::CutoffGroupIterator ci;
604      CutoffGroup* cg;
605 <    Vector3d com;
606 <    std::vector<Vector3d> rcGroup;
257 <    
258 <    if(info_->getNCutoffGroups() > 0){
259 <      
605 >
606 >    if(info_->getNCutoffGroups() > 0){      
607        for (mol = info_->beginMolecule(mi); mol != NULL;
608             mol = info_->nextMolecule(mi)) {
609          for(cg = mol->beginCutoffGroup(ci); cg != NULL;
610              cg = mol->nextCutoffGroup(ci)) {
611 <          cg->getCOM(com);
265 <          rcGroup.push_back(com);
611 >          cg->updateCOM();
612          }
613 <      }// end for (mol)
268 <      
269 <      rc = rcGroup[0].getArrayPointer();
613 >      }      
614      } else {
615        // center of mass of the group is the same as position of the atom  
616        // if cutoff group does not exist
617 <      rc = pos;
617 >      cgConfig->position = config->position;
618      }
619 +
620 +    fDecomp_->zeroWorkArrays();
621 +    fDecomp_->distributeData();
622      
623 <    //initialize data before passing to fortran
624 <    RealType longRangePotential[LR_POT_TYPES];
625 <    RealType lrPot = 0.0;
626 <    Vector3d totalDipole;
627 <    short int passedCalcPot = needPotential;
628 <    short int passedCalcStress = needStress;
629 <    int isError = 0;
623 >    int cg1, cg2, atom1, atom2, topoDist;
624 >    Vector3d d_grp, dag, d;
625 >    RealType rgrpsq, rgrp, r2, r;
626 >    RealType electroMult, vdwMult;
627 >    RealType vij;
628 >    Vector3d fij, fg, f1;
629 >    tuple3<RealType, RealType, RealType> cuts;
630 >    RealType rCutSq;
631 >    bool in_switching_region;
632 >    RealType sw, dswdr, swderiv;
633 >    vector<int> atomListColumn, atomListRow, atomListLocal;
634 >    InteractionData idat;
635 >    SelfData sdat;
636 >    RealType mf;
637 >    RealType lrPot;
638 >    RealType vpair;
639 >    potVec longRangePotential(0.0);
640 >    potVec workPot(0.0);
641  
642 <    for (int i=0; i<LR_POT_TYPES;i++){
643 <      longRangePotential[i]=0.0; //Initialize array
644 <    }
642 >    int loopStart, loopEnd;
643 >
644 >    idat.vdwMult = &vdwMult;
645 >    idat.electroMult = &electroMult;
646 >    idat.pot = &workPot;
647 >    sdat.pot = fDecomp_->getEmbeddingPotential();
648 >    idat.vpair = &vpair;
649 >    idat.f1 = &f1;
650 >    idat.sw = &sw;
651 >    idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
652 >    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
653      
654 <    doForceLoop(pos,
655 <                rc,
656 <                A,
657 <                electroFrame,
658 <                frc,
293 <                trq,
294 <                tau.getArrayPointer(),
295 <                longRangePotential,
296 <                particlePot,
297 <                &passedCalcPot,
298 <                &passedCalcStress,
299 <                &isError );
300 <    
301 <    if( isError ){
302 <      sprintf( painCave.errMsg,
303 <               "Error returned from the fortran force calculation.\n" );
304 <      painCave.isFatal = 1;
305 <      simError();
654 >    loopEnd = PAIR_LOOP;
655 >    if (info_->requiresPrepair() ) {
656 >      loopStart = PREPAIR_LOOP;
657 >    } else {
658 >      loopStart = PAIR_LOOP;
659      }
660 <    for (int i=0; i<LR_POT_TYPES;i++){
661 <      lrPot += longRangePotential[i]; //Quick hack
309 <    }
660 >  
661 >    for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
662      
663 <    // grab the simulation box dipole moment if specified
664 <    if (info_->getCalcBoxDipole()){
665 <      getAccumulatedBoxDipole(totalDipole.getArrayPointer());
666 <      
667 <      curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
668 <      curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
669 <      curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
663 >      if (iLoop == loopStart) {
664 >        bool update_nlist = fDecomp_->checkNeighborList();
665 >        if (update_nlist)
666 >          neighborList = fDecomp_->buildNeighborList();
667 >      }            
668 >
669 >      for (vector<pair<int, int> >::iterator it = neighborList.begin();
670 >             it != neighborList.end(); ++it) {
671 >                
672 >        cg1 = (*it).first;
673 >        cg2 = (*it).second;
674 >        
675 >        cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
676 >
677 >        d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
678 >
679 >        curSnapshot->wrapVector(d_grp);        
680 >        rgrpsq = d_grp.lengthSquare();
681 >        rCutSq = cuts.second;
682 >
683 >        if (rgrpsq < rCutSq) {
684 >          idat.rcut = &cuts.first;
685 >          if (iLoop == PAIR_LOOP) {
686 >            vij = 0.0;
687 >            fij = V3Zero;
688 >          }
689 >          
690 >          in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
691 >                                                     rgrp);
692 >          
693 >          atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
694 >          atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
695 >
696 >          for (vector<int>::iterator ia = atomListRow.begin();
697 >               ia != atomListRow.end(); ++ia) {            
698 >            atom1 = (*ia);
699 >            
700 >            for (vector<int>::iterator jb = atomListColumn.begin();
701 >                 jb != atomListColumn.end(); ++jb) {              
702 >              atom2 = (*jb);
703 >
704 >              if (!fDecomp_->skipAtomPair(atom1, atom2)) {
705 >                vpair = 0.0;
706 >                workPot = 0.0;
707 >                f1 = V3Zero;
708 >
709 >                fDecomp_->fillInteractionData(idat, atom1, atom2);
710 >                
711 >                topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
712 >                vdwMult = vdwScale_[topoDist];
713 >                electroMult = electrostaticScale_[topoDist];
714 >
715 >                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
716 >                  idat.d = &d_grp;
717 >                  idat.r2 = &rgrpsq;
718 >                } else {
719 >                  d = fDecomp_->getInteratomicVector(atom1, atom2);
720 >                  curSnapshot->wrapVector( d );
721 >                  r2 = d.lengthSquare();
722 >                  idat.d = &d;
723 >                  idat.r2 = &r2;
724 >                }
725 >              
726 >                r = sqrt( *(idat.r2) );
727 >                idat.rij = &r;
728 >              
729 >                if (iLoop == PREPAIR_LOOP) {
730 >                  interactionMan_->doPrePair(idat);
731 >                } else {
732 >                  interactionMan_->doPair(idat);
733 >                  fDecomp_->unpackInteractionData(idat, atom1, atom2);
734 >                  vij += vpair;
735 >                  fij += f1;
736 >                  tau -= outProduct( *(idat.d), f1);
737 >                }
738 >              }
739 >            }
740 >          }
741 >
742 >          if (iLoop == PAIR_LOOP) {
743 >            if (in_switching_region) {
744 >              swderiv = vij * dswdr / rgrp;
745 >              fg = swderiv * d_grp;
746 >              fij += fg;
747 >
748 >              if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
749 >                tau -= outProduct( *(idat.d), fg);
750 >              }
751 >          
752 >              for (vector<int>::iterator ia = atomListRow.begin();
753 >                   ia != atomListRow.end(); ++ia) {            
754 >                atom1 = (*ia);                
755 >                mf = fDecomp_->getMassFactorRow(atom1);
756 >                // fg is the force on atom ia due to cutoff group's
757 >                // presence in switching region
758 >                fg = swderiv * d_grp * mf;
759 >                fDecomp_->addForceToAtomRow(atom1, fg);
760 >                if (atomListRow.size() > 1) {
761 >                  if (info_->usesAtomicVirial()) {
762 >                    // find the distance between the atom
763 >                    // and the center of the cutoff group:
764 >                    dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
765 >                    tau -= outProduct(dag, fg);
766 >                  }
767 >                }
768 >              }
769 >              for (vector<int>::iterator jb = atomListColumn.begin();
770 >                   jb != atomListColumn.end(); ++jb) {              
771 >                atom2 = (*jb);
772 >                mf = fDecomp_->getMassFactorColumn(atom2);
773 >                // fg is the force on atom jb due to cutoff group's
774 >                // presence in switching region
775 >                fg = -swderiv * d_grp * mf;
776 >                fDecomp_->addForceToAtomColumn(atom2, fg);
777 >
778 >                if (atomListColumn.size() > 1) {
779 >                  if (info_->usesAtomicVirial()) {
780 >                    // find the distance between the atom
781 >                    // and the center of the cutoff group:
782 >                    dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
783 >                    tau -= outProduct(dag, fg);
784 >                  }
785 >                }
786 >              }
787 >            }
788 >            //if (!info_->usesAtomicVirial()) {
789 >            //  tau -= outProduct(d_grp, fij);
790 >            //}
791 >          }
792 >        }
793 >      }
794 >
795 >      if (iLoop == PREPAIR_LOOP) {
796 >        if (info_->requiresPrepair()) {
797 >
798 >          fDecomp_->collectIntermediateData();
799 >
800 >          for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
801 >            fDecomp_->fillSelfData(sdat, atom1);
802 >            interactionMan_->doPreForce(sdat);
803 >          }
804 >
805 >          fDecomp_->distributeIntermediateData();
806 >
807 >        }
808 >      }
809      }
810      
811 +    fDecomp_->collectData();
812 +        
813 +    if (info_->requiresSelfCorrection()) {
814 +
815 +      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {          
816 +        fDecomp_->fillSelfData(sdat, atom1);
817 +        interactionMan_->doSelfCorrection(sdat);
818 +      }
819 +
820 +    }
821 +
822 +    longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
823 +      *(fDecomp_->getPairwisePotential());
824 +
825 +    lrPot = longRangePotential.sum();
826 +
827      //store the tau and long range potential    
828      curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
829 <    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
830 <    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
829 >    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
830 >    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
831    }
832  
833    
834 <  void ForceManager::postCalculation(bool needStress) {
834 >  void ForceManager::postCalculation() {
835      SimInfo::MoleculeIterator mi;
836      Molecule* mol;
837      Molecule::RigidBodyIterator rbIter;
# Line 337 | Line 844 | namespace OpenMD {
844           mol = info_->nextMolecule(mi)) {
845        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
846             rb = mol->nextRigidBody(rbIter)) {
847 <        if (needStress) {          
848 <          Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
342 <          tau += rbTau;
343 <        } else{
344 <          rb->calcForcesAndTorques();
345 <        }
847 >        Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
848 >        tau += rbTau;
849        }
850      }
851 <
349 <    if (needStress) {
851 >    
852   #ifdef IS_MPI
853 <      Mat3x3d tmpTau(tau);
854 <      MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
855 <                    9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
853 >    Mat3x3d tmpTau(tau);
854 >    MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
855 >                  9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
856   #endif
857 <      curSnapshot->statData.setTau(tau);
356 <    }
857 >    curSnapshot->setTau(tau);
858    }
859  
860   } //end namespace OpenMD

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