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Revision 1570 by gezelter, Thu May 26 21:56:04 2011 UTC vs.
Revision 1808 by gezelter, Mon Oct 22 20:42:10 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   /**
44   * @file ForceManager.cpp
45   * @author tlin
46   * @date 11/09/2004
46 – * @time 10:39am
47   * @version 1.0
48   */
49  
50 +
51   #include "brains/ForceManager.hpp"
52   #include "primitives/Molecule.hpp"
53   #define __OPENMD_C
# Line 56 | Line 57
57   #include "primitives/Torsion.hpp"
58   #include "primitives/Inversion.hpp"
59   #include "nonbonded/NonBondedInteraction.hpp"
60 + #include "perturbations/ElectricField.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 <
72 < #ifdef IS_MPI
73 <    fDecomp_ = new ForceMatrixDecomposition(info_);
68 < #else
69 <    // fDecomp_ = new ForceSerialDecomposition(info);
70 < #endif
71 >    forceField_ = info_->getForceField();
72 >    interactionMan_ = new InteractionManager();
73 >    fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
74    }
75 +
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 +    Globals* simParams_ = info_->getSimParams();
111 +    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
112 +    int mdFileVersion;
113 +    rCut_ = 0.0; //Needs a value for a later max() call;  
114 +    
115 +    if (simParams_->haveMDfileVersion())
116 +      mdFileVersion = simParams_->getMDfileVersion();
117 +    else
118 +      mdFileVersion = 0;
119 +  
120 +    if (simParams_->haveCutoffRadius()) {
121 +      rCut_ = simParams_->getCutoffRadius();
122 +    } else {      
123 +      if (info_->usesElectrostaticAtoms()) {
124 +        sprintf(painCave.errMsg,
125 +                "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 +        RealType thisCut;
134 +        set<AtomType*>::iterator i;
135 +        set<AtomType*> atomTypes;
136 +        atomTypes = info_->getSimulatedAtomTypes();        
137 +        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
138 +          thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
139 +          rCut_ = max(thisCut, rCut_);
140 +        }
141 +        sprintf(painCave.errMsg,
142 +                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
143 +                "\tOpenMD will use %lf angstroms.\n",
144 +                rCut_);
145 +        painCave.isFatal = 0;
146 +        painCave.severity = OPENMD_INFO;
147 +        simError();
148 +      }
149 +    }
150 +
151 +    fDecomp_->setUserCutoff(rCut_);
152 +    interactionMan_->setCutoffRadius(rCut_);
153 +
154 +    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    
160 <  void ForceManager::calcForces() {
160 >    if (simParams_->haveCutoffMethod()) {
161 >      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
162 >      map<string, CutoffMethod>::iterator i;
163 >      i = stringToCutoffMethod.find(cutMeth);
164 >      if (i == stringToCutoffMethod.end()) {
165 >        sprintf(painCave.errMsg,
166 >                "ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
167 >                "\tShould be one of: "
168 >                "HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
169 >                cutMeth.c_str());
170 >        painCave.isFatal = 1;
171 >        painCave.severity = OPENMD_ERROR;
172 >        simError();
173 >      } else {
174 >        cutoffMethod_ = i->second;
175 >      }
176 >    } else {
177 >      if (mdFileVersion > 1) {
178 >        sprintf(painCave.errMsg,
179 >                "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 >      } else {
186 >        // handle the case where the old file version was in play
187 >        // (there should be no cutoffMethod, so we have to deduce it
188 >        // from other data).        
189 >
190 >        sprintf(painCave.errMsg,
191 >                "ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
192 >                "\tOpenMD found a file which does not set a cutoffMethod.\n"
193 >                "\tOpenMD will attempt to deduce a cutoffMethod using the\n"
194 >                "\tbehavior of the older (version 1) code.  To remove this\n"
195 >                "\twarning, add an explicit cutoffMethod and change the top\n"
196 >                "\tof the file so that it begins with <OpenMD version=2>\n");
197 >        painCave.isFatal = 0;
198 >        painCave.severity = OPENMD_WARNING;
199 >        simError();            
200 >                
201 >        // The old file version tethered the shifting behavior to the
202 >        // electrostaticSummationMethod keyword.
203 >        
204 >        if (simParams_->haveElectrostaticSummationMethod()) {
205 >          string myMethod = simParams_->getElectrostaticSummationMethod();
206 >          toUpper(myMethod);
207 >        
208 >          if (myMethod == "SHIFTED_POTENTIAL") {
209 >            cutoffMethod_ = SHIFTED_POTENTIAL;
210 >          } else if (myMethod == "SHIFTED_FORCE") {
211 >            cutoffMethod_ = SHIFTED_FORCE;
212 >          }
213 >        
214 >          if (simParams_->haveSwitchingRadius())
215 >            rSwitch_ = simParams_->getSwitchingRadius();
216 >
217 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
218 >            if (simParams_->haveSwitchingRadius()){
219 >              sprintf(painCave.errMsg,
220 >                      "ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
221 >                      "\tA value was set for the switchingRadius\n"
222 >                      "\teven though the electrostaticSummationMethod was\n"
223 >                      "\tset to %s\n", myMethod.c_str());
224 >              painCave.severity = OPENMD_WARNING;
225 >              painCave.isFatal = 1;
226 >              simError();            
227 >            }
228 >          }
229 >          if (abs(rCut_ - rSwitch_) < 0.0001) {
230 >            if (cutoffMethod_ == SHIFTED_FORCE) {              
231 >              sprintf(painCave.errMsg,
232 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
233 >                      "\tcutoffRadius and switchingRadius are set to the\n"
234 >                      "\tsame value.  OpenMD will use shifted force\n"
235 >                      "\tpotentials instead of switching functions.\n");
236 >              painCave.isFatal = 0;
237 >              painCave.severity = OPENMD_WARNING;
238 >              simError();            
239 >            } else {
240 >              cutoffMethod_ = SHIFTED_POTENTIAL;
241 >              sprintf(painCave.errMsg,
242 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
243 >                      "\tcutoffRadius and switchingRadius are set to the\n"
244 >                      "\tsame value.  OpenMD will use shifted potentials\n"
245 >                      "\tinstead of switching functions.\n");
246 >              painCave.isFatal = 0;
247 >              painCave.severity = OPENMD_WARNING;
248 >              simError();            
249 >            }
250 >          }
251 >        }
252 >      }
253 >    }
254 >
255 >    map<string, CutoffPolicy> stringToCutoffPolicy;
256 >    stringToCutoffPolicy["MIX"] = MIX;
257 >    stringToCutoffPolicy["MAX"] = MAX;
258 >    stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;    
259 >
260 >    string cutPolicy;
261 >    if (forceFieldOptions_.haveCutoffPolicy()){
262 >      cutPolicy = forceFieldOptions_.getCutoffPolicy();
263 >    }else if (simParams_->haveCutoffPolicy()) {
264 >      cutPolicy = simParams_->getCutoffPolicy();
265 >    }
266 >
267 >    if (!cutPolicy.empty()){
268 >      toUpper(cutPolicy);
269 >      map<string, CutoffPolicy>::iterator i;
270 >      i = stringToCutoffPolicy.find(cutPolicy);
271 >
272 >      if (i == stringToCutoffPolicy.end()) {
273 >        sprintf(painCave.errMsg,
274 >                "ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
275 >                "\tShould be one of: "
276 >                "MIX, MAX, or TRADITIONAL\n",
277 >                cutPolicy.c_str());
278 >        painCave.isFatal = 1;
279 >        painCave.severity = OPENMD_ERROR;
280 >        simError();
281 >      } else {
282 >        cutoffPolicy_ = i->second;
283 >      }
284 >    } else {
285 >      sprintf(painCave.errMsg,
286 >              "ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
287 >              "\tOpenMD will use TRADITIONAL.\n");
288 >      painCave.isFatal = 0;
289 >      painCave.severity = OPENMD_INFO;
290 >      simError();
291 >      cutoffPolicy_ = TRADITIONAL;        
292 >    }
293 >
294 >    fDecomp_->setCutoffPolicy(cutoffPolicy_);
295 >        
296 >    // create the switching function object:
297 >
298 >    switcher_ = new SwitchingFunction();
299 >  
300 >    if (cutoffMethod_ == SWITCHED) {
301 >      if (simParams_->haveSwitchingRadius()) {
302 >        rSwitch_ = simParams_->getSwitchingRadius();
303 >        if (rSwitch_ > rCut_) {        
304 >          sprintf(painCave.errMsg,
305 >                  "ForceManager::setupCutoffs: switchingRadius (%f) is larger "
306 >                  "than the cutoffRadius(%f)\n", rSwitch_, rCut_);
307 >          painCave.isFatal = 1;
308 >          painCave.severity = OPENMD_ERROR;
309 >          simError();
310 >        }
311 >      } else {      
312 >        rSwitch_ = 0.85 * rCut_;
313 >        sprintf(painCave.errMsg,
314 >                "ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
315 >                "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
316 >                "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
317 >        painCave.isFatal = 0;
318 >        painCave.severity = OPENMD_WARNING;
319 >        simError();
320 >      }
321 >    } else {
322 >      if (mdFileVersion > 1) {
323 >        // throw an error if we define a switching radius and don't need one.
324 >        // older file versions should not do this.
325 >        if (simParams_->haveSwitchingRadius()) {
326 >          map<string, CutoffMethod>::const_iterator it;
327 >          string theMeth;
328 >          for (it = stringToCutoffMethod.begin();
329 >               it != stringToCutoffMethod.end(); ++it) {
330 >            if (it->second == cutoffMethod_) {
331 >              theMeth = it->first;
332 >              break;
333 >            }
334 >          }
335 >          sprintf(painCave.errMsg,
336 >                  "ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
337 >                  "\tis not set to SWITCHED, so switchingRadius value\n"
338 >                  "\twill be ignored for this simulation\n", theMeth.c_str());
339 >          painCave.isFatal = 0;
340 >          painCave.severity = OPENMD_WARNING;
341 >          simError();
342 >        }
343 >      }
344 >      rSwitch_ = rCut_;
345 >    }
346      
347 +    // Default to cubic switching function.
348 +    sft_ = cubic;
349 +    if (simParams_->haveSwitchingFunctionType()) {
350 +      string funcType = simParams_->getSwitchingFunctionType();
351 +      toUpper(funcType);
352 +      if (funcType == "CUBIC") {
353 +        sft_ = cubic;
354 +      } else {
355 +        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
356 +          sft_ = fifth_order_poly;
357 +        } else {
358 +          // throw error        
359 +          sprintf( painCave.errMsg,
360 +                   "ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
361 +                   "\tswitchingFunctionType must be one of: "
362 +                   "\"cubic\" or \"fifth_order_polynomial\".",
363 +                   funcType.c_str() );
364 +          painCave.isFatal = 1;
365 +          painCave.severity = OPENMD_ERROR;
366 +          simError();
367 +        }          
368 +      }
369 +    }
370 +    switcher_->setSwitchType(sft_);
371 +    switcher_->setSwitch(rSwitch_, rCut_);
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 <      swfun_ = interactionMan_->getSwitchingFunction();
385 <      fDecomp_->distributeInitialData();
386 <      info_->prepareTopology();
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 >      doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
393 >      doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
394 >      if (doHeatFlux_) doParticlePot_ = true;
395 >
396 >      doElectricField_ = info_->getSimParams()->getOutputElectricField();
397 >  
398      }
399 +
400 +    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
401 +    
402 +    // Force fields can set options on how to scale van der Waals and
403 +    // electrostatic interactions for atoms connected via bonds, bends
404 +    // and torsions in this case the topological distance between
405 +    // atoms is:
406 +    // 0 = topologically unconnected
407 +    // 1 = bonded together
408 +    // 2 = connected via a bend
409 +    // 3 = connected via a torsion
410 +    
411 +    vdwScale_.reserve(4);
412 +    fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
413 +
414 +    electrostaticScale_.reserve(4);
415 +    fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
416 +
417 +    vdwScale_[0] = 1.0;
418 +    vdwScale_[1] = fopts.getvdw12scale();
419 +    vdwScale_[2] = fopts.getvdw13scale();
420 +    vdwScale_[3] = fopts.getvdw14scale();
421 +    
422 +    electrostaticScale_[0] = 1.0;
423 +    electrostaticScale_[1] = fopts.getelectrostatic12scale();
424 +    electrostaticScale_[2] = fopts.getelectrostatic13scale();
425 +    electrostaticScale_[3] = fopts.getelectrostatic14scale();    
426 +    
427 +    if (info_->getSimParams()->haveElectricField()) {
428 +      ElectricField* eField = new ElectricField(info_);
429 +      perturbations_.push_back(eField);
430 +    }
431 +
432 +    fDecomp_->distributeInitialData();
433 +
434 +    initialized_ = true;
435 +
436 +  }
437 +
438 +  void ForceManager::calcForces() {
439      
440 +    if (!initialized_) initialize();
441 +
442      preCalculation();  
443      shortRangeInteractions();
444      longRangeInteractions();
445 <    postCalculation();
88 <    
445 >    postCalculation();    
446    }
447    
448    void ForceManager::preCalculation() {
# Line 98 | Line 455 | namespace OpenMD {
455      Molecule::CutoffGroupIterator ci;
456      CutoffGroup* cg;
457      
458 <    // forces are zeroed here, before any are accumulated.
458 >    // forces and potentials are zeroed here, before any are
459 >    // accumulated.
460      
461 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
462 +
463 +    snap->setBondPotential(0.0);
464 +    snap->setBendPotential(0.0);
465 +    snap->setTorsionPotential(0.0);
466 +    snap->setInversionPotential(0.0);
467 +
468 +    potVec zeroPot(0.0);
469 +    snap->setLongRangePotential(zeroPot);
470 +    snap->setExcludedPotentials(zeroPot);
471 +
472 +    snap->setRestraintPotential(0.0);
473 +    snap->setRawPotential(0.0);
474 +
475      for (mol = info_->beginMolecule(mi); mol != NULL;
476           mol = info_->nextMolecule(mi)) {
477 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
477 >      for(atom = mol->beginAtom(ai); atom != NULL;
478 >          atom = mol->nextAtom(ai)) {
479          atom->zeroForcesAndTorques();
480        }
481 <          
481 >      
482        //change the positions of atoms which belong to the rigidbodies
483        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
484             rb = mol->nextRigidBody(rbIter)) {
485          rb->zeroForcesAndTorques();
486        }        
487 <
487 >      
488        if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
489          for(cg = mol->beginCutoffGroup(ci); cg != NULL;
490              cg = mol->nextCutoffGroup(ci)) {
# Line 120 | Line 493 | namespace OpenMD {
493          }
494        }      
495      }
123 –  
124 –    // Zero out the stress tensor
125 –    tau *= 0.0;
496      
497 +    // Zero out the stress tensor
498 +    stressTensor *= 0.0;
499 +    // Zero out the heatFlux
500 +    fDecomp_->setHeatFlux( Vector3d(0.0) );    
501    }
502    
503    void ForceManager::shortRangeInteractions() {
# Line 156 | Line 530 | namespace OpenMD {
530  
531        for (bond = mol->beginBond(bondIter); bond != NULL;
532             bond = mol->nextBond(bondIter)) {
533 <        bond->calcForce();
533 >        bond->calcForce(doParticlePot_);
534          bondPotential += bond->getPotential();
535        }
536  
# Line 164 | Line 538 | namespace OpenMD {
538             bend = mol->nextBend(bendIter)) {
539          
540          RealType angle;
541 <        bend->calcForce(angle);
541 >        bend->calcForce(angle, doParticlePot_);
542          RealType currBendPot = bend->getPotential();          
543          
544          bendPotential += bend->getPotential();
# Line 174 | Line 548 | namespace OpenMD {
548            dataSet.prev.angle = dataSet.curr.angle = angle;
549            dataSet.prev.potential = dataSet.curr.potential = currBendPot;
550            dataSet.deltaV = 0.0;
551 <          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
551 >          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
552 >                                                                  dataSet));
553          }else {
554            i->second.prev.angle = i->second.curr.angle;
555            i->second.prev.potential = i->second.curr.potential;
# Line 188 | Line 563 | namespace OpenMD {
563        for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
564             torsion = mol->nextTorsion(torsionIter)) {
565          RealType angle;
566 <        torsion->calcForce(angle);
566 >        torsion->calcForce(angle, doParticlePot_);
567          RealType currTorsionPot = torsion->getPotential();
568          torsionPotential += torsion->getPotential();
569          map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
# Line 212 | Line 587 | namespace OpenMD {
587             inversion != NULL;
588             inversion = mol->nextInversion(inversionIter)) {
589          RealType angle;
590 <        inversion->calcForce(angle);
590 >        inversion->calcForce(angle, doParticlePot_);
591          RealType currInversionPot = inversion->getPotential();
592          inversionPotential += inversion->getPotential();
593          map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
# Line 232 | Line 607 | namespace OpenMD {
607          }      
608        }      
609      }
610 <    
611 <    RealType  shortRangePotential = bondPotential + bendPotential +
612 <      torsionPotential +  inversionPotential;    
610 >
611 > #ifdef IS_MPI
612 >    // Collect from all nodes.  This should eventually be moved into a
613 >    // SystemDecomposition, but this is a better place than in
614 >    // Thermo to do the collection.
615 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
616 >                              MPI::SUM);
617 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
618 >                              MPI::SUM);
619 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
620 >                              MPI::REALTYPE, MPI::SUM);
621 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
622 >                              MPI::REALTYPE, MPI::SUM);
623 > #endif
624 >
625      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
626 <    curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
627 <    curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
628 <    curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
629 <    curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
630 <    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;    
626 >
627 >    curSnapshot->setBondPotential(bondPotential);
628 >    curSnapshot->setBendPotential(bendPotential);
629 >    curSnapshot->setTorsionPotential(torsionPotential);
630 >    curSnapshot->setInversionPotential(inversionPotential);
631 >    
632 >    // RealType shortRangePotential = bondPotential + bendPotential +
633 >    //   torsionPotential +  inversionPotential;    
634 >
635 >    // curSnapshot->setShortRangePotential(shortRangePotential);
636    }
637    
638    void ForceManager::longRangeInteractions() {
639  
640 <    // some of this initial stuff will go away:
640 >
641      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
642      DataStorage* config = &(curSnapshot->atomData);
643      DataStorage* cgConfig = &(curSnapshot->cgData);
252 –    RealType* frc = config->getArrayPointer(DataStorage::dslForce);
253 –    RealType* pos = config->getArrayPointer(DataStorage::dslPosition);
254 –    RealType* trq = config->getArrayPointer(DataStorage::dslTorque);
255 –    RealType* A = config->getArrayPointer(DataStorage::dslAmat);
256 –    RealType* electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
257 –    RealType* particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
258 –    RealType* rc;    
644  
645 <    if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
646 <      rc = cgConfig->getArrayPointer(DataStorage::dslPosition);
645 >    //calculate the center of mass of cutoff group
646 >
647 >    SimInfo::MoleculeIterator mi;
648 >    Molecule* mol;
649 >    Molecule::CutoffGroupIterator ci;
650 >    CutoffGroup* cg;
651 >
652 >    if(info_->getNCutoffGroups() > 0){      
653 >      for (mol = info_->beginMolecule(mi); mol != NULL;
654 >           mol = info_->nextMolecule(mi)) {
655 >        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
656 >            cg = mol->nextCutoffGroup(ci)) {
657 >          cg->updateCOM();
658 >        }
659 >      }      
660      } else {
661        // center of mass of the group is the same as position of the atom  
662        // if cutoff group does not exist
663 <      rc = pos;
663 >      cgConfig->position = config->position;
664 >      cgConfig->velocity = config->velocity;
665      }
267 –    
268 –    //initialize data before passing to fortran
269 –    RealType longRangePotential[N_INTERACTION_FAMILIES];
270 –    RealType lrPot = 0.0;
271 –    int isError = 0;
666  
667 <    // dangerous to iterate over enums, but we'll live on the edge:
274 <    for (int i = NO_FAMILY; i != N_INTERACTION_FAMILIES; ++i){
275 <      longRangePotential[i]=0.0; //Initialize array
276 <    }
277 <
278 <    // new stuff starts here:
279 <
667 >    fDecomp_->zeroWorkArrays();
668      fDecomp_->distributeData();
669 <
670 <    int cg1, cg2, atom1, atom2;
671 <    Vector3d d_grp, dag;
672 <    RealType rgrpsq, rgrp;
669 >    
670 >    int cg1, cg2, atom1, atom2, topoDist;
671 >    Vector3d d_grp, dag, d, gvel2, vel2;
672 >    RealType rgrpsq, rgrp, r2, r;
673 >    RealType electroMult, vdwMult;
674      RealType vij;
675 <    Vector3d fij, fg;
676 <    pair<int, int> gtypes;
675 >    Vector3d fij, fg, f1;
676 >    tuple3<RealType, RealType, RealType> cuts;
677      RealType rCutSq;
678      bool in_switching_region;
679      RealType sw, dswdr, swderiv;
# Line 292 | Line 681 | namespace OpenMD {
681      InteractionData idat;
682      SelfData sdat;
683      RealType mf;
684 +    RealType vpair;
685 +    RealType dVdFQ1(0.0);
686 +    RealType dVdFQ2(0.0);
687 +    potVec longRangePotential(0.0);
688 +    potVec workPot(0.0);
689 +    potVec exPot(0.0);
690 +    Vector3d eField1(0.0);
691 +    Vector3d eField2(0.0);
692 +    vector<int>::iterator ia, jb;
693  
694      int loopStart, loopEnd;
695  
696 +    idat.vdwMult = &vdwMult;
697 +    idat.electroMult = &electroMult;
698 +    idat.pot = &workPot;
699 +    idat.excludedPot = &exPot;
700 +    sdat.pot = fDecomp_->getEmbeddingPotential();
701 +    sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
702 +    idat.vpair = &vpair;
703 +    idat.dVdFQ1 = &dVdFQ1;
704 +    idat.dVdFQ2 = &dVdFQ2;
705 +    idat.eField1 = &eField1;
706 +    idat.eField2 = &eField2;  
707 +    idat.f1 = &f1;
708 +    idat.sw = &sw;
709 +    idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
710 +    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
711 +    idat.doParticlePot = doParticlePot_;
712 +    idat.doElectricField = doElectricField_;
713 +    sdat.doParticlePot = doParticlePot_;
714 +    
715      loopEnd = PAIR_LOOP;
716      if (info_->requiresPrepair() ) {
717        loopStart = PREPAIR_LOOP;
718      } else {
719        loopStart = PAIR_LOOP;
720      }
721 <
722 <    for (int iLoop = loopStart; iLoop < loopEnd; iLoop++) {
306 <      
721 >    for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
722 >    
723        if (iLoop == loopStart) {
724          bool update_nlist = fDecomp_->checkNeighborList();
725          if (update_nlist)
726            neighborList = fDecomp_->buildNeighborList();
727 <      }
727 >      }            
728  
729        for (vector<pair<int, int> >::iterator it = neighborList.begin();
730               it != neighborList.end(); ++it) {
731 <        
731 >                
732          cg1 = (*it).first;
733          cg2 = (*it).second;
734 +        
735 +        cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
736  
319 –        gtypes = fDecomp_->getGroupTypes(cg1, cg2);
737          d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
738 +
739          curSnapshot->wrapVector(d_grp);        
740          rgrpsq = d_grp.lengthSquare();
741 <        rCutSq = groupCutoffMap[gtypes].first;
741 >        rCutSq = cuts.second;
742  
743          if (rgrpsq < rCutSq) {
744 <          *(idat.rcut) = groupCutoffMap[gtypes].second;
744 >          idat.rcut = &cuts.first;
745            if (iLoop == PAIR_LOOP) {
746 <            vij *= 0.0;
746 >            vij = 0.0;
747              fij = V3Zero;
748            }
749            
750 <          in_switching_region = swfun_->getSwitch(rgrpsq, *(idat.sw), dswdr,
751 <                                                  rgrp);              
750 >          in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
751 >                                                     rgrp);
752 >
753            atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
754            atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
755  
756 <          for (vector<int>::iterator ia = atomListRow.begin();
756 >          if (doHeatFlux_)
757 >            gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
758 >
759 >          for (ia = atomListRow.begin();
760                 ia != atomListRow.end(); ++ia) {            
761              atom1 = (*ia);
762 <            
763 <            for (vector<int>::iterator jb = atomListColumn.begin();
762 >
763 >            for (jb = atomListColumn.begin();
764                   jb != atomListColumn.end(); ++jb) {              
765                atom2 = (*jb);
344 –              
345 –              if (!fDecomp_->skipAtomPair(atom1, atom2)) {
346 –                
347 –                idat = fDecomp_->fillInteractionData(atom1, atom2);
766  
767 +              if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
768 +
769 +                vpair = 0.0;
770 +                workPot = 0.0;
771 +                exPot = 0.0;
772 +                f1 = V3Zero;
773 +                dVdFQ1 = 0.0;
774 +                dVdFQ2 = 0.0;
775 +
776 +                fDecomp_->fillInteractionData(idat, atom1, atom2);
777 +
778 +                topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
779 +                vdwMult = vdwScale_[topoDist];
780 +                electroMult = electrostaticScale_[topoDist];
781 +
782                  if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
783 <                  *(idat.d) = d_grp;
784 <                  *(idat.r2) = rgrpsq;
783 >                  idat.d = &d_grp;
784 >                  idat.r2 = &rgrpsq;
785 >                  if (doHeatFlux_)
786 >                    vel2 = gvel2;
787                  } else {
788 <                  *(idat.d) = fDecomp_->getInteratomicVector(atom1, atom2);
789 <                  curSnapshot->wrapVector( *(idat.d) );
790 <                  *(idat.r2) = idat.d->lengthSquare();
788 >                  d = fDecomp_->getInteratomicVector(atom1, atom2);
789 >                  curSnapshot->wrapVector( d );
790 >                  r2 = d.lengthSquare();
791 >                  idat.d = &d;
792 >                  idat.r2 = &r2;
793 >                  if (doHeatFlux_)
794 >                    vel2 = fDecomp_->getAtomVelocityColumn(atom2);
795                  }
357 –                
358 –                *(idat.rij) = sqrt( *(idat.r2) );
796                
797 +                r = sqrt( *(idat.r2) );
798 +                idat.rij = &r;
799 +              
800                  if (iLoop == PREPAIR_LOOP) {
801                    interactionMan_->doPrePair(idat);
802                  } else {
803                    interactionMan_->doPair(idat);
804 <                  vij += *(idat.vpair);
805 <                  fij += *(idat.f1);
806 <                  tau -= outProduct( *(idat.d), *(idat.f1));
804 >                  fDecomp_->unpackInteractionData(idat, atom1, atom2);
805 >                  vij += vpair;
806 >                  fij += f1;
807 >                  stressTensor -= outProduct( *(idat.d), f1);
808 >                  if (doHeatFlux_)
809 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
810                  }
811                }
812              }
# Line 373 | Line 816 | namespace OpenMD {
816              if (in_switching_region) {
817                swderiv = vij * dswdr / rgrp;
818                fg = swderiv * d_grp;
376 –
819                fij += fg;
820  
821                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
822 <                tau -= outProduct( *(idat.d), fg);
822 >                stressTensor -= outProduct( *(idat.d), fg);
823 >                if (doHeatFlux_)
824 >                  fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
825 >                
826                }
827            
828 <              for (vector<int>::iterator ia = atomListRow.begin();
828 >              for (ia = atomListRow.begin();
829                     ia != atomListRow.end(); ++ia) {            
830                  atom1 = (*ia);                
831                  mf = fDecomp_->getMassFactorRow(atom1);
# Line 388 | Line 833 | namespace OpenMD {
833                  // presence in switching region
834                  fg = swderiv * d_grp * mf;
835                  fDecomp_->addForceToAtomRow(atom1, fg);
391 –
836                  if (atomListRow.size() > 1) {
837                    if (info_->usesAtomicVirial()) {
838                      // find the distance between the atom
839                      // and the center of the cutoff group:
840                      dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
841 <                    tau -= outProduct(dag, fg);
841 >                    stressTensor -= outProduct(dag, fg);
842 >                    if (doHeatFlux_)
843 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
844                    }
845                  }
846                }
847 <              for (vector<int>::iterator jb = atomListColumn.begin();
847 >              for (jb = atomListColumn.begin();
848                     jb != atomListColumn.end(); ++jb) {              
849                  atom2 = (*jb);
850                  mf = fDecomp_->getMassFactorColumn(atom2);
# Line 412 | Line 858 | namespace OpenMD {
858                      // find the distance between the atom
859                      // and the center of the cutoff group:
860                      dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
861 <                    tau -= outProduct(dag, fg);
861 >                    stressTensor -= outProduct(dag, fg);
862 >                    if (doHeatFlux_)
863 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
864                    }
865                  }
866                }
867              }
868 <            //if (!SIM_uses_AtomicVirial) {
869 <            //  tau -= outProduct(d_grp, fij);
868 >            //if (!info_->usesAtomicVirial()) {
869 >            //  stressTensor -= outProduct(d_grp, fij);
870 >            //  if (doHeatFlux_)
871 >            //     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
872              //}
873            }
874          }
875        }
876  
877        if (iLoop == PREPAIR_LOOP) {
878 <        if (info_->requiresPrepair()) {            
878 >        if (info_->requiresPrepair()) {
879 >
880            fDecomp_->collectIntermediateData();
881  
882 <          for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
883 <            sdat = fDecomp_->fillSelfData(atom1);
882 >          for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
883 >            fDecomp_->fillSelfData(sdat, atom1);
884              interactionMan_->doPreForce(sdat);
885            }
886  
887 <          fDecomp_->distributeIntermediateData();        
887 >          fDecomp_->distributeIntermediateData();
888 >
889          }
890        }
439 –
891      }
892      
893 +    // collects pairwise information
894      fDecomp_->collectData();
443 –    
444 –    if ( info_->requiresSkipCorrection() ) {
445 –      
446 –      for (int atom1 = 0; atom1 < fDecomp_->getNAtomsInRow(); atom1++) {
447 –
448 –        vector<int> skipList = fDecomp_->getSkipsForRowAtom( atom1 );
895          
450 –        for (vector<int>::iterator jb = skipList.begin();
451 –             jb != skipList.end(); ++jb) {        
452 –    
453 –          atom2 = (*jb);
454 –          idat = fDecomp_->fillSkipData(atom1, atom2);
455 –          interactionMan_->doSkipCorrection(idat);
456 –
457 –        }
458 –      }
459 –    }
460 –    
896      if (info_->requiresSelfCorrection()) {
897 <
898 <      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {          
464 <        sdat = fDecomp_->fillSelfData(atom1);
897 >      for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
898 >        fDecomp_->fillSelfData(sdat, atom1);
899          interactionMan_->doSelfCorrection(sdat);
900        }
467 –
901      }
902  
903 <    // dangerous to iterate over enums, but we'll live on the edge:
904 <    for (int i = NO_FAMILY; i != N_INTERACTION_FAMILIES; ++i){
905 <      lrPot += longRangePotential[i]; //Quick hack
906 <    }
907 <        
908 <    //store the tau and long range potential    
909 <    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
910 <    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
911 <    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
903 >    // collects single-atom information
904 >    fDecomp_->collectSelfData();
905 >
906 >    longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
907 >      *(fDecomp_->getPairwisePotential());
908 >
909 >    curSnapshot->setLongRangePotential(longRangePotential);
910 >
911 >    // collects single-atom information
912 >    fDecomp_->collectSelfData();
913 >
914 >    longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
915 >      *(fDecomp_->getPairwisePotential());
916 >
917 >    curSnapshot->setLongRangePotential(longRangePotential);
918 >    
919 >    curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
920 >                                         *(fDecomp_->getExcludedPotential()));
921 >
922    }
923  
924    
925    void ForceManager::postCalculation() {
926 +
927 +    vector<Perturbation*>::iterator pi;
928 +    for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
929 +      (*pi)->applyPerturbation();
930 +    }
931 +
932      SimInfo::MoleculeIterator mi;
933      Molecule* mol;
934      Molecule::RigidBodyIterator rbIter;
935      RigidBody* rb;
936      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
937 <    
937 >  
938      // collect the atomic forces onto rigid bodies
939      
940      for (mol = info_->beginMolecule(mi); mol != NULL;
# Line 493 | Line 942 | namespace OpenMD {
942        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
943             rb = mol->nextRigidBody(rbIter)) {
944          Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
945 <        tau += rbTau;
945 >        stressTensor += rbTau;
946        }
947      }
948      
949   #ifdef IS_MPI
950 <    Mat3x3d tmpTau(tau);
951 <    MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
503 <                  9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
950 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
951 >                              MPI::REALTYPE, MPI::SUM);
952   #endif
953 <    curSnapshot->statData.setTau(tau);
953 >    curSnapshot->setStressTensor(stressTensor);
954 >    
955    }
507 –
956   } //end namespace OpenMD

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