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Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1549 by gezelter, Wed Apr 27 18:38:15 2011 UTC vs.
Revision 1733 by jmichalk, Tue Jun 5 17:48:40 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"
61 – //#include "parallel/ForceSerialDecomposition.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_);
70 < #else
71 <    // fDecomp_ = new ForceSerialDecomposition(info);
72 < #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 +    
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 <  void ForceManager::calcForces() {
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 <    if (!info_->isFortranInitialized()) {
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 <      swfun_ = interactionMan_->getSwitchingFunction();
385 <      fDecomp_->distributeInitialData();
386 <      info_->setupFortran();
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      }
397 +
398 +    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
399      
400 +    // Force fields can set options on how to scale van der Waals and
401 +    // electrostatic interactions for atoms connected via bonds, bends
402 +    // and torsions in this case the topological distance between
403 +    // atoms is:
404 +    // 0 = topologically unconnected
405 +    // 1 = bonded together
406 +    // 2 = connected via a bend
407 +    // 3 = connected via a torsion
408 +    
409 +    vdwScale_.reserve(4);
410 +    fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
411 +
412 +    electrostaticScale_.reserve(4);
413 +    fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
414 +
415 +    vdwScale_[0] = 1.0;
416 +    vdwScale_[1] = fopts.getvdw12scale();
417 +    vdwScale_[2] = fopts.getvdw13scale();
418 +    vdwScale_[3] = fopts.getvdw14scale();
419 +    
420 +    electrostaticScale_[0] = 1.0;
421 +    electrostaticScale_[1] = fopts.getelectrostatic12scale();
422 +    electrostaticScale_[2] = fopts.getelectrostatic13scale();
423 +    electrostaticScale_[3] = fopts.getelectrostatic14scale();    
424 +    
425 +    fDecomp_->distributeInitialData();
426 +
427 +    initialized_ = true;
428 +
429 +  }
430 +
431 +  void ForceManager::calcForces() {
432 +    
433 +    if (!initialized_) initialize();
434 +
435      preCalculation();  
436      shortRangeInteractions();
437      longRangeInteractions();
438 <    postCalculation();
90 <    
438 >    postCalculation();    
439    }
440    
441    void ForceManager::preCalculation() {
# Line 104 | Line 452 | namespace OpenMD {
452      
453      for (mol = info_->beginMolecule(mi); mol != NULL;
454           mol = info_->nextMolecule(mi)) {
455 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
455 >      for(atom = mol->beginAtom(ai); atom != NULL;
456 >          atom = mol->nextAtom(ai)) {
457          atom->zeroForcesAndTorques();
458        }
459 <          
459 >      
460        //change the positions of atoms which belong to the rigidbodies
461        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
462             rb = mol->nextRigidBody(rbIter)) {
463          rb->zeroForcesAndTorques();
464        }        
465 <
465 >      
466        if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
467          for(cg = mol->beginCutoffGroup(ci); cg != NULL;
468              cg = mol->nextCutoffGroup(ci)) {
# Line 122 | Line 471 | namespace OpenMD {
471          }
472        }      
473      }
125 –  
126 –    // Zero out the stress tensor
127 –    tau *= 0.0;
474      
475 +    // Zero out the stress tensor
476 +    stressTensor *= 0.0;
477 +    // Zero out the heatFlux
478 +    fDecomp_->setHeatFlux( V3Zero );    
479    }
480    
481    void ForceManager::shortRangeInteractions() {
# Line 158 | Line 508 | namespace OpenMD {
508  
509        for (bond = mol->beginBond(bondIter); bond != NULL;
510             bond = mol->nextBond(bondIter)) {
511 <        bond->calcForce();
511 >        bond->calcForce(doParticlePot_);
512          bondPotential += bond->getPotential();
513        }
514  
# Line 166 | Line 516 | namespace OpenMD {
516             bend = mol->nextBend(bendIter)) {
517          
518          RealType angle;
519 <        bend->calcForce(angle);
519 >        bend->calcForce(angle, doParticlePot_);
520          RealType currBendPot = bend->getPotential();          
521          
522          bendPotential += bend->getPotential();
# Line 176 | Line 526 | namespace OpenMD {
526            dataSet.prev.angle = dataSet.curr.angle = angle;
527            dataSet.prev.potential = dataSet.curr.potential = currBendPot;
528            dataSet.deltaV = 0.0;
529 <          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
529 >          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
530 >                                                                  dataSet));
531          }else {
532            i->second.prev.angle = i->second.curr.angle;
533            i->second.prev.potential = i->second.curr.potential;
# Line 190 | Line 541 | namespace OpenMD {
541        for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
542             torsion = mol->nextTorsion(torsionIter)) {
543          RealType angle;
544 <        torsion->calcForce(angle);
544 >        torsion->calcForce(angle, doParticlePot_);
545          RealType currTorsionPot = torsion->getPotential();
546          torsionPotential += torsion->getPotential();
547          map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
# Line 214 | Line 565 | namespace OpenMD {
565             inversion != NULL;
566             inversion = mol->nextInversion(inversionIter)) {
567          RealType angle;
568 <        inversion->calcForce(angle);
568 >        inversion->calcForce(angle, doParticlePot_);
569          RealType currInversionPot = inversion->getPotential();
570          inversionPotential += inversion->getPotential();
571          map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
# Line 247 | Line 598 | namespace OpenMD {
598    
599    void ForceManager::longRangeInteractions() {
600  
601 <    // some of this initial stuff will go away:
601 >
602      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
603      DataStorage* config = &(curSnapshot->atomData);
604      DataStorage* cgConfig = &(curSnapshot->cgData);
254 –    RealType* frc = config->getArrayPointer(DataStorage::dslForce);
255 –    RealType* pos = config->getArrayPointer(DataStorage::dslPosition);
256 –    RealType* trq = config->getArrayPointer(DataStorage::dslTorque);
257 –    RealType* A = config->getArrayPointer(DataStorage::dslAmat);
258 –    RealType* electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
259 –    RealType* particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
260 –    RealType* rc;    
605  
606 <    if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
607 <      rc = cgConfig->getArrayPointer(DataStorage::dslPosition);
606 >    //calculate the center of mass of cutoff group
607 >
608 >    SimInfo::MoleculeIterator mi;
609 >    Molecule* mol;
610 >    Molecule::CutoffGroupIterator ci;
611 >    CutoffGroup* cg;
612 >
613 >    if(info_->getNCutoffGroups() > 0){      
614 >      for (mol = info_->beginMolecule(mi); mol != NULL;
615 >           mol = info_->nextMolecule(mi)) {
616 >        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
617 >            cg = mol->nextCutoffGroup(ci)) {
618 >          cg->updateCOM();
619 >        }
620 >      }      
621      } else {
622        // center of mass of the group is the same as position of the atom  
623        // if cutoff group does not exist
624 <      rc = pos;
624 >      cgConfig->position = config->position;
625 >      cgConfig->velocity = config->velocity;
626      }
269 –    
270 –    //initialize data before passing to fortran
271 –    RealType longRangePotential[LR_POT_TYPES];
272 –    RealType lrPot = 0.0;
273 –    int isError = 0;
627  
628 <    for (int i=0; i<LR_POT_TYPES;i++){
276 <      longRangePotential[i]=0.0; //Initialize array
277 <    }
278 <
279 <    // new stuff starts here:
280 <
628 >    fDecomp_->zeroWorkArrays();
629      fDecomp_->distributeData();
630 <
631 <    int cg1, cg2, atom1, atom2;
632 <    Vector3d d_grp, dag;
633 <    RealType rgrpsq, rgrp;
630 >    
631 >    int cg1, cg2, atom1, atom2, topoDist;
632 >    Vector3d d_grp, dag, d, gvel2, vel2;
633 >    RealType rgrpsq, rgrp, r2, r;
634 >    RealType electroMult, vdwMult;
635      RealType vij;
636 <    Vector3d fij, fg;
637 <    pair<int, int> gtypes;
636 >    Vector3d fij, fg, f1;
637 >    tuple3<RealType, RealType, RealType> cuts;
638      RealType rCutSq;
639      bool in_switching_region;
640      RealType sw, dswdr, swderiv;
# Line 293 | Line 642 | namespace OpenMD {
642      InteractionData idat;
643      SelfData sdat;
644      RealType mf;
645 +    RealType lrPot;
646 +    RealType vpair;
647 +    RealType dVdFQ1(0.0);
648 +    RealType dVdFQ2(0.0);
649 +    potVec longRangePotential(0.0);
650 +    potVec workPot(0.0);
651 +    vector<int>::iterator ia, jb;
652  
653      int loopStart, loopEnd;
654  
655 +    idat.vdwMult = &vdwMult;
656 +    idat.electroMult = &electroMult;
657 +    idat.pot = &workPot;
658 +    sdat.pot = fDecomp_->getEmbeddingPotential();
659 +    idat.vpair = &vpair;
660 +    idat.dVdFQ1 = &dVdFQ1;
661 +    idat.dVdFQ2 = &dVdFQ2;
662 +    idat.f1 = &f1;
663 +    idat.sw = &sw;
664 +    idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
665 +    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
666 +    idat.doParticlePot = doParticlePot_;
667 +    sdat.doParticlePot = doParticlePot_;
668 +    
669      loopEnd = PAIR_LOOP;
670      if (info_->requiresPrepair() ) {
671        loopStart = PREPAIR_LOOP;
672      } else {
673        loopStart = PAIR_LOOP;
674      }
675 <
676 <    for (int iLoop = loopStart; iLoop < loopEnd; iLoop++) {
677 <      
675 >  
676 >    for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
677 >    
678        if (iLoop == loopStart) {
679          bool update_nlist = fDecomp_->checkNeighborList();
680          if (update_nlist)
681            neighborList = fDecomp_->buildNeighborList();
682 <      }
682 >      }            
683  
684        for (vector<pair<int, int> >::iterator it = neighborList.begin();
685               it != neighborList.end(); ++it) {
686 <        
686 >                
687          cg1 = (*it).first;
688          cg2 = (*it).second;
689 +        
690 +        cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
691  
320 –        gtypes = fDecomp_->getGroupTypes(cg1, cg2);
692          d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
693 +
694          curSnapshot->wrapVector(d_grp);        
695          rgrpsq = d_grp.lengthSquare();
696 <        rCutSq = groupCutoffMap[gtypes].first;
696 >        rCutSq = cuts.second;
697  
698          if (rgrpsq < rCutSq) {
699 <          idat.rcut = groupCutoffMap[gtypes].second;
699 >          idat.rcut = &cuts.first;
700            if (iLoop == PAIR_LOOP) {
701 <            vij *= 0.0;
701 >            vij = 0.0;
702              fij = V3Zero;
703            }
704            
705 <          in_switching_region = swfun_->getSwitch(rgrpsq, idat.sw, dswdr, rgrp);              
705 >          in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
706 >                                                     rgrp);
707 >          
708            atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
709            atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
710  
711 <          for (vector<int>::iterator ia = atomListRow.begin();
711 >          if (doHeatFlux_)
712 >            gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
713 >        
714 >          for (ia = atomListRow.begin();
715                 ia != atomListRow.end(); ++ia) {            
716              atom1 = (*ia);
717              
718 <            for (vector<int>::iterator jb = atomListColumn.begin();
718 >            for (jb = atomListColumn.begin();
719                   jb != atomListColumn.end(); ++jb) {              
720                atom2 = (*jb);
721 <              
721 >
722                if (!fDecomp_->skipAtomPair(atom1, atom2)) {
723 +                vpair = 0.0;
724 +                workPot = 0.0;
725 +                f1 = V3Zero;
726 +                dVdFQ1 = 0.0;
727 +                dVdFQ2 = 0.0;
728 +
729 +                fDecomp_->fillInteractionData(idat, atom1, atom2);
730                  
731 <                idat = fDecomp_->fillInteractionData(atom1, atom2);
731 >                topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
732 >                vdwMult = vdwScale_[topoDist];
733 >                electroMult = electrostaticScale_[topoDist];
734  
735                  if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
736 <                  idat.d = d_grp;
737 <                  idat.r2 = rgrpsq;
736 >                  idat.d = &d_grp;
737 >                  idat.r2 = &rgrpsq;
738 >                  if (doHeatFlux_)
739 >                    vel2 = gvel2;
740                  } else {
741 <                  idat.d = fDecomp_->getInteratomicVector(atom1, atom2);
742 <                  curSnapshot->wrapVector(idat.d);
743 <                  idat.r2 = idat.d.lengthSquare();
741 >                  d = fDecomp_->getInteratomicVector(atom1, atom2);
742 >                  curSnapshot->wrapVector( d );
743 >                  r2 = d.lengthSquare();
744 >                  idat.d = &d;
745 >                  idat.r2 = &r2;
746 >                  if (doHeatFlux_)
747 >                    vel2 = fDecomp_->getAtomVelocityColumn(atom2);
748                  }
357 –                
358 –                idat.rij = sqrt(idat.r2);
749                
750 +                r = sqrt( *(idat.r2) );
751 +                idat.rij = &r;
752 +              
753                  if (iLoop == PREPAIR_LOOP) {
754                    interactionMan_->doPrePair(idat);
755                  } else {
756                    interactionMan_->doPair(idat);
757 <                  vij += idat.vpair;
758 <                  fij += idat.f1;
759 <                  tau -= outProduct(idat.d, idat.f1);
757 >                  fDecomp_->unpackInteractionData(idat, atom1, atom2);
758 >                  vij += vpair;
759 >                  fij += f1;
760 >                  stressTensor -= outProduct( *(idat.d), f1);
761 >                  if (doHeatFlux_)
762 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
763                  }
764                }
765              }
# Line 373 | Line 769 | namespace OpenMD {
769              if (in_switching_region) {
770                swderiv = vij * dswdr / rgrp;
771                fg = swderiv * d_grp;
376 –
772                fij += fg;
773  
774                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
775 <                tau -= outProduct(idat.d, fg);
775 >                stressTensor -= outProduct( *(idat.d), fg);
776 >                if (doHeatFlux_)
777 >                  fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
778 >                
779                }
780            
781 <              for (vector<int>::iterator ia = atomListRow.begin();
781 >              for (ia = atomListRow.begin();
782                     ia != atomListRow.end(); ++ia) {            
783                  atom1 = (*ia);                
784 <                mf = fDecomp_->getMfactRow(atom1);
784 >                mf = fDecomp_->getMassFactorRow(atom1);
785                  // fg is the force on atom ia due to cutoff group's
786                  // presence in switching region
787                  fg = swderiv * d_grp * mf;
788                  fDecomp_->addForceToAtomRow(atom1, fg);
391 –
789                  if (atomListRow.size() > 1) {
790                    if (info_->usesAtomicVirial()) {
791                      // find the distance between the atom
792                      // and the center of the cutoff group:
793                      dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
794 <                    tau -= outProduct(dag, fg);
794 >                    stressTensor -= outProduct(dag, fg);
795 >                    if (doHeatFlux_)
796 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
797                    }
798                  }
799                }
800 <              for (vector<int>::iterator jb = atomListColumn.begin();
800 >              for (jb = atomListColumn.begin();
801                     jb != atomListColumn.end(); ++jb) {              
802                  atom2 = (*jb);
803 <                mf = fDecomp_->getMfactColumn(atom2);
803 >                mf = fDecomp_->getMassFactorColumn(atom2);
804                  // fg is the force on atom jb due to cutoff group's
805                  // presence in switching region
806                  fg = -swderiv * d_grp * mf;
# Line 412 | Line 811 | namespace OpenMD {
811                      // find the distance between the atom
812                      // and the center of the cutoff group:
813                      dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
814 <                    tau -= outProduct(dag, fg);
814 >                    stressTensor -= outProduct(dag, fg);
815 >                    if (doHeatFlux_)
816 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
817                    }
818                  }
819                }
820              }
821 <            //if (!SIM_uses_AtomicVirial) {
822 <            //  tau -= outProduct(d_grp, fij);
821 >            //if (!info_->usesAtomicVirial()) {
822 >            //  stressTensor -= outProduct(d_grp, fij);
823 >            //  if (doHeatFlux_)
824 >            //     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
825              //}
826            }
827          }
828        }
829  
830        if (iLoop == PREPAIR_LOOP) {
831 <        if (info_->requiresPrepair()) {            
831 >        if (info_->requiresPrepair()) {
832 >
833            fDecomp_->collectIntermediateData();
834 <          atomListLocal = fDecomp_->getAtomList();
835 <          for (vector<int>::iterator ia = atomListLocal.begin();
836 <               ia != atomListLocal.end(); ++ia) {              
433 <            atom1 = (*ia);            
434 <            sdat = fDecomp_->fillSelfData(atom1);
834 >
835 >          for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
836 >            fDecomp_->fillSelfData(sdat, atom1);
837              interactionMan_->doPreForce(sdat);
838            }
839 <          fDecomp_->distributeIntermediateData();        
839 >
840 >          fDecomp_->distributeIntermediateData();
841 >
842          }
843        }
440 –
844      }
845      
846      fDecomp_->collectData();
847 <    
848 <    if (info_->requiresSkipCorrection() || info_->requiresSelfCorrection()) {
446 <      atomListLocal = fDecomp_->getAtomList();
447 <      for (vector<int>::iterator ia = atomListLocal.begin();
448 <           ia != atomListLocal.end(); ++ia) {              
449 <        atom1 = (*ia);    
847 >        
848 >    if (info_->requiresSelfCorrection()) {
849  
850 <        if (info_->requiresSkipCorrection()) {
851 <          vector<int> skipList = fDecomp_->getSkipsForAtom(atom1);
852 <          for (vector<int>::iterator jb = skipList.begin();
454 <               jb != skipList.end(); ++jb) {              
455 <            atom2 = (*jb);
456 <            idat = fDecomp_->fillSkipData(atom1, atom2);
457 <            interactionMan_->doSkipCorrection(idat);
458 <          }
459 <        }
460 <          
461 <        if (info_->requiresSelfCorrection()) {
462 <          sdat = fDecomp_->fillSelfData(atom1);
463 <          interactionMan_->doSelfCorrection(sdat);
464 <        }
850 >      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {          
851 >        fDecomp_->fillSelfData(sdat, atom1);
852 >        interactionMan_->doSelfCorrection(sdat);
853        }
466 –    }
854  
468 –    for (int i=0; i<LR_POT_TYPES;i++){
469 –      lrPot += longRangePotential[i]; //Quick hack
855      }
856 <        
857 <    //store the tau and long range potential    
856 >
857 >    longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
858 >      *(fDecomp_->getPairwisePotential());
859 >
860 >    lrPot = longRangePotential.sum();
861 >
862 >    //store the stressTensor and long range potential    
863      curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
864 <    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
865 <    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
864 >    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
865 >    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
866    }
867  
868    
# Line 490 | Line 880 | namespace OpenMD {
880        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
881             rb = mol->nextRigidBody(rbIter)) {
882          Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
883 <        tau += rbTau;
883 >        stressTensor += rbTau;
884        }
885      }
886      
887   #ifdef IS_MPI
888 <    Mat3x3d tmpTau(tau);
889 <    MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
890 <                  9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
888 >
889 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
890 >                              MPI::REALTYPE, MPI::SUM);
891   #endif
892 <    curSnapshot->statData.setTau(tau);
892 >    curSnapshot->setStressTensor(stressTensor);
893 >    
894    }
895  
896   } //end namespace OpenMD

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