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Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC vs.
Revision 1764 by gezelter, Tue Jul 3 18:32:27 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() {
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()) {
111 <      info_->update();
112 <    }
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 <    preCalculation();
116 <    
117 <    calcShortRangeInteraction();
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 <    calcLongRangeInteraction();
151 >    fDecomp_->setUserCutoff(rCut_);
152 >    interactionMan_->setCutoffRadius(rCut_);
153  
154 <    postCalculation();
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 >    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 +    interactionMan_->setSwitchingRadius(rSwitch_);
373    }
374 +
375 +
376 +
377    
378 +  void ForceManager::initialize() {
379 +
380 +    if (!info_->isTopologyDone()) {
381 +
382 +      info_->update();
383 +      interactionMan_->setSimInfo(info_);
384 +      interactionMan_->initialize();
385 +
386 +      // We want to delay the cutoffs until after the interaction
387 +      // manager has set up the atom-atom interactions so that we can
388 +      // query them for suggested cutoff values
389 +      setupCutoffs();
390 +
391 +      info_->prepareTopology();      
392 +
393 +      doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
394 +      doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
395 +      if (doHeatFlux_) doParticlePot_ = true;
396 +  
397 +    }
398 +
399 +    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
400 +    
401 +    // Force fields can set options on how to scale van der Waals and
402 +    // electrostatic interactions for atoms connected via bonds, bends
403 +    // and torsions in this case the topological distance between
404 +    // atoms is:
405 +    // 0 = topologically unconnected
406 +    // 1 = bonded together
407 +    // 2 = connected via a bend
408 +    // 3 = connected via a torsion
409 +    
410 +    vdwScale_.reserve(4);
411 +    fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
412 +
413 +    electrostaticScale_.reserve(4);
414 +    fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
415 +
416 +    vdwScale_[0] = 1.0;
417 +    vdwScale_[1] = fopts.getvdw12scale();
418 +    vdwScale_[2] = fopts.getvdw13scale();
419 +    vdwScale_[3] = fopts.getvdw14scale();
420 +    
421 +    electrostaticScale_[0] = 1.0;
422 +    electrostaticScale_[1] = fopts.getelectrostatic12scale();
423 +    electrostaticScale_[2] = fopts.getelectrostatic13scale();
424 +    electrostaticScale_[3] = fopts.getelectrostatic14scale();    
425 +    
426 +    fDecomp_->distributeInitialData();
427 +
428 +    initialized_ = true;
429 +
430 +  }
431 +
432 +  void ForceManager::calcForces() {
433 +    
434 +    if (!initialized_) initialize();
435 +
436 +    preCalculation();  
437 +    shortRangeInteractions();
438 +    longRangeInteractions();
439 +    postCalculation();    
440 +  }
441 +  
442    void ForceManager::preCalculation() {
443      SimInfo::MoleculeIterator mi;
444      Molecule* mol;
# Line 82 | Line 446 | namespace OpenMD {
446      Atom* atom;
447      Molecule::RigidBodyIterator rbIter;
448      RigidBody* rb;
449 +    Molecule::CutoffGroupIterator ci;
450 +    CutoffGroup* cg;
451      
452 <    // forces are zeroed here, before any are accumulated.
453 <    // NOTE: do not rezero the forces in Fortran.
452 >    // forces and potentials are zeroed here, before any are
453 >    // accumulated.
454      
455 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
456 +
457 +    snap->setBondPotential(0.0);
458 +    snap->setBendPotential(0.0);
459 +    snap->setTorsionPotential(0.0);
460 +    snap->setInversionPotential(0.0);
461 +
462 +    potVec zeroPot(0.0);
463 +    snap->setLongRangePotential(zeroPot);
464 +    snap->setExcludedPotentials(zeroPot);
465 +
466 +    snap->setRestraintPotential(0.0);
467 +    snap->setRawPotential(0.0);
468 +
469      for (mol = info_->beginMolecule(mi); mol != NULL;
470           mol = info_->nextMolecule(mi)) {
471 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
471 >      for(atom = mol->beginAtom(ai); atom != NULL;
472 >          atom = mol->nextAtom(ai)) {
473          atom->zeroForcesAndTorques();
474        }
475 <          
475 >      
476        //change the positions of atoms which belong to the rigidbodies
477        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
478             rb = mol->nextRigidBody(rbIter)) {
479          rb->zeroForcesAndTorques();
480        }        
481 <          
481 >      
482 >      if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
483 >        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
484 >            cg = mol->nextCutoffGroup(ci)) {
485 >          //calculate the center of mass of cutoff group
486 >          cg->updateCOM();
487 >        }
488 >      }      
489      }
490      
491      // Zero out the stress tensor
492 <    tau *= 0.0;
493 <    
492 >    stressTensor *= 0.0;
493 >    // Zero out the heatFlux
494 >    fDecomp_->setHeatFlux( Vector3d(0.0) );    
495    }
496    
497 <  void ForceManager::calcShortRangeInteraction() {
497 >  void ForceManager::shortRangeInteractions() {
498      Molecule* mol;
499      RigidBody* rb;
500      Bond* bond;
# Line 135 | Line 524 | namespace OpenMD {
524  
525        for (bond = mol->beginBond(bondIter); bond != NULL;
526             bond = mol->nextBond(bondIter)) {
527 <        bond->calcForce();
527 >        bond->calcForce(doParticlePot_);
528          bondPotential += bond->getPotential();
529        }
530  
# Line 143 | Line 532 | namespace OpenMD {
532             bend = mol->nextBend(bendIter)) {
533          
534          RealType angle;
535 <        bend->calcForce(angle);
535 >        bend->calcForce(angle, doParticlePot_);
536          RealType currBendPot = bend->getPotential();          
537          
538          bendPotential += bend->getPotential();
539 <        std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
539 >        map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
540          if (i == bendDataSets.end()) {
541            BendDataSet dataSet;
542            dataSet.prev.angle = dataSet.curr.angle = angle;
543            dataSet.prev.potential = dataSet.curr.potential = currBendPot;
544            dataSet.deltaV = 0.0;
545 <          bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
545 >          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
546 >                                                                  dataSet));
547          }else {
548            i->second.prev.angle = i->second.curr.angle;
549            i->second.prev.potential = i->second.curr.potential;
# Line 167 | Line 557 | namespace OpenMD {
557        for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
558             torsion = mol->nextTorsion(torsionIter)) {
559          RealType angle;
560 <        torsion->calcForce(angle);
560 >        torsion->calcForce(angle, doParticlePot_);
561          RealType currTorsionPot = torsion->getPotential();
562          torsionPotential += torsion->getPotential();
563 <        std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
563 >        map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
564          if (i == torsionDataSets.end()) {
565            TorsionDataSet dataSet;
566            dataSet.prev.angle = dataSet.curr.angle = angle;
567            dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
568            dataSet.deltaV = 0.0;
569 <          torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
569 >          torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
570          }else {
571            i->second.prev.angle = i->second.curr.angle;
572            i->second.prev.potential = i->second.curr.potential;
# Line 186 | Line 576 | namespace OpenMD {
576                                     i->second.prev.potential);
577          }      
578        }      
579 <
579 >      
580        for (inversion = mol->beginInversion(inversionIter);
581             inversion != NULL;
582             inversion = mol->nextInversion(inversionIter)) {
583          RealType angle;
584 <        inversion->calcForce(angle);
584 >        inversion->calcForce(angle, doParticlePot_);
585          RealType currInversionPot = inversion->getPotential();
586          inversionPotential += inversion->getPotential();
587 <        std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
587 >        map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
588          if (i == inversionDataSets.end()) {
589            InversionDataSet dataSet;
590            dataSet.prev.angle = dataSet.curr.angle = angle;
591            dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
592            dataSet.deltaV = 0.0;
593 <          inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
593 >          inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
594          }else {
595            i->second.prev.angle = i->second.curr.angle;
596            i->second.prev.potential = i->second.curr.potential;
# Line 211 | Line 601 | namespace OpenMD {
601          }      
602        }      
603      }
604 <    
605 <    RealType  shortRangePotential = bondPotential + bendPotential +
606 <      torsionPotential +  inversionPotential;    
604 >
605 > #ifdef IS_MPI
606 >    // Collect from all nodes.  This should eventually be moved into a
607 >    // SystemDecomposition, but this is a better place than in
608 >    // Thermo to do the collection.
609 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
610 >                              MPI::SUM);
611 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
612 >                              MPI::SUM);
613 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
614 >                              MPI::REALTYPE, MPI::SUM);
615 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
616 >                              MPI::REALTYPE, MPI::SUM);
617 > #endif
618 >
619      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
620 <    curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
621 <    curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
622 <    curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
623 <    curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
624 <    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
620 >
621 >    curSnapshot->setBondPotential(bondPotential);
622 >    curSnapshot->setBendPotential(bendPotential);
623 >    curSnapshot->setTorsionPotential(torsionPotential);
624 >    curSnapshot->setInversionPotential(inversionPotential);
625      
626 +    // RealType shortRangePotential = bondPotential + bendPotential +
627 +    //   torsionPotential +  inversionPotential;    
628 +
629 +    // curSnapshot->setShortRangePotential(shortRangePotential);
630    }
631    
632 <  void ForceManager::calcLongRangeInteraction() {
227 <    Snapshot* curSnapshot;
228 <    DataStorage* config;
229 <    RealType* frc;
230 <    RealType* pos;
231 <    RealType* trq;
232 <    RealType* A;
233 <    RealType* electroFrame;
234 <    RealType* rc;
235 <    RealType* particlePot;
236 <    
237 <    //get current snapshot from SimInfo
238 <    curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
239 <    
240 <    //get array pointers
241 <    config = &(curSnapshot->atomData);
242 <    frc = config->getArrayPointer(DataStorage::dslForce);
243 <    pos = config->getArrayPointer(DataStorage::dslPosition);
244 <    trq = config->getArrayPointer(DataStorage::dslTorque);
245 <    A   = config->getArrayPointer(DataStorage::dslAmat);
246 <    electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
247 <    particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
632 >  void ForceManager::longRangeInteractions() {
633  
634 +
635 +    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
636 +    DataStorage* config = &(curSnapshot->atomData);
637 +    DataStorage* cgConfig = &(curSnapshot->cgData);
638 +
639      //calculate the center of mass of cutoff group
640 +
641      SimInfo::MoleculeIterator mi;
642      Molecule* mol;
643      Molecule::CutoffGroupIterator ci;
644      CutoffGroup* cg;
645 <    Vector3d com;
646 <    std::vector<Vector3d> rcGroup;
256 <    
257 <    if(info_->getNCutoffGroups() > 0){
258 <      
645 >
646 >    if(info_->getNCutoffGroups() > 0){      
647        for (mol = info_->beginMolecule(mi); mol != NULL;
648             mol = info_->nextMolecule(mi)) {
649          for(cg = mol->beginCutoffGroup(ci); cg != NULL;
650              cg = mol->nextCutoffGroup(ci)) {
651 <          cg->getCOM(com);
264 <          rcGroup.push_back(com);
651 >          cg->updateCOM();
652          }
653 <      }// end for (mol)
267 <      
268 <      rc = rcGroup[0].getArrayPointer();
653 >      }      
654      } else {
655        // center of mass of the group is the same as position of the atom  
656        // if cutoff group does not exist
657 <      rc = pos;
657 >      cgConfig->position = config->position;
658 >      cgConfig->velocity = config->velocity;
659      }
660 +
661 +    fDecomp_->zeroWorkArrays();
662 +    fDecomp_->distributeData();
663      
664 <    //initialize data before passing to fortran
665 <    RealType longRangePotential[LR_POT_TYPES];
666 <    RealType lrPot = 0.0;
667 <    Vector3d totalDipole;
668 <    int isError = 0;
664 >    int cg1, cg2, atom1, atom2, topoDist;
665 >    Vector3d d_grp, dag, d, gvel2, vel2;
666 >    RealType rgrpsq, rgrp, r2, r;
667 >    RealType electroMult, vdwMult;
668 >    RealType vij;
669 >    Vector3d fij, fg, f1;
670 >    tuple3<RealType, RealType, RealType> cuts;
671 >    RealType rCutSq;
672 >    bool in_switching_region;
673 >    RealType sw, dswdr, swderiv;
674 >    vector<int> atomListColumn, atomListRow, atomListLocal;
675 >    InteractionData idat;
676 >    SelfData sdat;
677 >    RealType mf;
678 >    RealType lrPot;
679 >    RealType vpair;
680 >    RealType dVdFQ1(0.0);
681 >    RealType dVdFQ2(0.0);
682 >    potVec longRangePotential(0.0);
683 >    potVec workPot(0.0);
684 >    potVec exPot(0.0);
685 >    vector<int>::iterator ia, jb;
686  
687 <    for (int i=0; i<LR_POT_TYPES;i++){
688 <      longRangePotential[i]=0.0; //Initialize array
689 <    }
687 >    int loopStart, loopEnd;
688 >
689 >    idat.vdwMult = &vdwMult;
690 >    idat.electroMult = &electroMult;
691 >    idat.pot = &workPot;
692 >    idat.excludedPot = &exPot;
693 >    sdat.pot = fDecomp_->getEmbeddingPotential();
694 >    sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
695 >    idat.vpair = &vpair;
696 >    idat.dVdFQ1 = &dVdFQ1;
697 >    idat.dVdFQ2 = &dVdFQ2;
698 >    idat.f1 = &f1;
699 >    idat.sw = &sw;
700 >    idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
701 >    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
702 >    idat.doParticlePot = doParticlePot_;
703 >    sdat.doParticlePot = doParticlePot_;
704      
705 <    doForceLoop(pos,
706 <                rc,
707 <                A,
708 <                electroFrame,
709 <                frc,
290 <                trq,
291 <                tau.getArrayPointer(),
292 <                longRangePotential,
293 <                particlePot,
294 <                &isError );
295 <    
296 <    if( isError ){
297 <      sprintf( painCave.errMsg,
298 <               "Error returned from the fortran force calculation.\n" );
299 <      painCave.isFatal = 1;
300 <      simError();
705 >    loopEnd = PAIR_LOOP;
706 >    if (info_->requiresPrepair() ) {
707 >      loopStart = PREPAIR_LOOP;
708 >    } else {
709 >      loopStart = PAIR_LOOP;
710      }
711 <    for (int i=0; i<LR_POT_TYPES;i++){
712 <      lrPot += longRangePotential[i]; //Quick hack
711 >    for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
712 >    
713 >      if (iLoop == loopStart) {
714 >        bool update_nlist = fDecomp_->checkNeighborList();
715 >        if (update_nlist)
716 >          neighborList = fDecomp_->buildNeighborList();
717 >      }            
718 >
719 >      for (vector<pair<int, int> >::iterator it = neighborList.begin();
720 >             it != neighborList.end(); ++it) {
721 >                
722 >        cg1 = (*it).first;
723 >        cg2 = (*it).second;
724 >        
725 >        cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
726 >
727 >        d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
728 >
729 >        curSnapshot->wrapVector(d_grp);        
730 >        rgrpsq = d_grp.lengthSquare();
731 >        rCutSq = cuts.second;
732 >
733 >        if (rgrpsq < rCutSq) {
734 >          idat.rcut = &cuts.first;
735 >          if (iLoop == PAIR_LOOP) {
736 >            vij = 0.0;
737 >            fij = V3Zero;
738 >          }
739 >          
740 >          in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
741 >                                                     rgrp);
742 >
743 >          atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
744 >          atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
745 >
746 >          if (doHeatFlux_)
747 >            gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
748 >
749 >          for (ia = atomListRow.begin();
750 >               ia != atomListRow.end(); ++ia) {            
751 >            atom1 = (*ia);
752 >
753 >            for (jb = atomListColumn.begin();
754 >                 jb != atomListColumn.end(); ++jb) {              
755 >              atom2 = (*jb);
756 >
757 >              if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
758 >
759 >                vpair = 0.0;
760 >                workPot = 0.0;
761 >                exPot = 0.0;
762 >                f1 = V3Zero;
763 >                dVdFQ1 = 0.0;
764 >                dVdFQ2 = 0.0;
765 >
766 >                fDecomp_->fillInteractionData(idat, atom1, atom2);
767 >
768 >                topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
769 >                vdwMult = vdwScale_[topoDist];
770 >                electroMult = electrostaticScale_[topoDist];
771 >
772 >                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
773 >                  idat.d = &d_grp;
774 >                  idat.r2 = &rgrpsq;
775 >                  if (doHeatFlux_)
776 >                    vel2 = gvel2;
777 >                } else {
778 >                  d = fDecomp_->getInteratomicVector(atom1, atom2);
779 >                  curSnapshot->wrapVector( d );
780 >                  r2 = d.lengthSquare();
781 >                  idat.d = &d;
782 >                  idat.r2 = &r2;
783 >                  if (doHeatFlux_)
784 >                    vel2 = fDecomp_->getAtomVelocityColumn(atom2);
785 >                }
786 >              
787 >                r = sqrt( *(idat.r2) );
788 >                idat.rij = &r;
789 >              
790 >                if (iLoop == PREPAIR_LOOP) {
791 >                  interactionMan_->doPrePair(idat);
792 >                } else {
793 >                  interactionMan_->doPair(idat);
794 >                  fDecomp_->unpackInteractionData(idat, atom1, atom2);
795 >                  vij += vpair;
796 >                  fij += f1;
797 >                  stressTensor -= outProduct( *(idat.d), f1);
798 >                  if (doHeatFlux_)
799 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
800 >                }
801 >              }
802 >            }
803 >          }
804 >
805 >          if (iLoop == PAIR_LOOP) {
806 >            if (in_switching_region) {
807 >              swderiv = vij * dswdr / rgrp;
808 >              fg = swderiv * d_grp;
809 >              fij += fg;
810 >
811 >              if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
812 >                stressTensor -= outProduct( *(idat.d), fg);
813 >                if (doHeatFlux_)
814 >                  fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
815 >                
816 >              }
817 >          
818 >              for (ia = atomListRow.begin();
819 >                   ia != atomListRow.end(); ++ia) {            
820 >                atom1 = (*ia);                
821 >                mf = fDecomp_->getMassFactorRow(atom1);
822 >                // fg is the force on atom ia due to cutoff group's
823 >                // presence in switching region
824 >                fg = swderiv * d_grp * mf;
825 >                fDecomp_->addForceToAtomRow(atom1, fg);
826 >                if (atomListRow.size() > 1) {
827 >                  if (info_->usesAtomicVirial()) {
828 >                    // find the distance between the atom
829 >                    // and the center of the cutoff group:
830 >                    dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
831 >                    stressTensor -= outProduct(dag, fg);
832 >                    if (doHeatFlux_)
833 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
834 >                  }
835 >                }
836 >              }
837 >              for (jb = atomListColumn.begin();
838 >                   jb != atomListColumn.end(); ++jb) {              
839 >                atom2 = (*jb);
840 >                mf = fDecomp_->getMassFactorColumn(atom2);
841 >                // fg is the force on atom jb due to cutoff group's
842 >                // presence in switching region
843 >                fg = -swderiv * d_grp * mf;
844 >                fDecomp_->addForceToAtomColumn(atom2, fg);
845 >
846 >                if (atomListColumn.size() > 1) {
847 >                  if (info_->usesAtomicVirial()) {
848 >                    // find the distance between the atom
849 >                    // and the center of the cutoff group:
850 >                    dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
851 >                    stressTensor -= outProduct(dag, fg);
852 >                    if (doHeatFlux_)
853 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
854 >                  }
855 >                }
856 >              }
857 >            }
858 >            //if (!info_->usesAtomicVirial()) {
859 >            //  stressTensor -= outProduct(d_grp, fij);
860 >            //  if (doHeatFlux_)
861 >            //     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
862 >            //}
863 >          }
864 >        }
865 >      }
866 >
867 >      if (iLoop == PREPAIR_LOOP) {
868 >        if (info_->requiresPrepair()) {
869 >
870 >          fDecomp_->collectIntermediateData();
871 >
872 >          for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
873 >            fDecomp_->fillSelfData(sdat, atom1);
874 >            interactionMan_->doPreForce(sdat);
875 >          }
876 >
877 >          fDecomp_->distributeIntermediateData();
878 >
879 >        }
880 >      }
881      }
882      
883 <    // grab the simulation box dipole moment if specified
884 <    if (info_->getCalcBoxDipole()){
885 <      getAccumulatedBoxDipole(totalDipole.getArrayPointer());
886 <      
887 <      curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
888 <      curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
889 <      curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
883 >    // collects pairwise information
884 >    fDecomp_->collectData();
885 >        
886 >    if (info_->requiresSelfCorrection()) {
887 >      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
888 >        fDecomp_->fillSelfData(sdat, atom1);
889 >        interactionMan_->doSelfCorrection(sdat);
890 >      }
891      }
892 +
893 +    // collects single-atom information
894 +    fDecomp_->collectSelfData();
895 +
896 +    longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
897 +      *(fDecomp_->getPairwisePotential());
898 +
899 +    curSnapshot->setLongRangePotential(longRangePotential);
900 +
901 +    // lrPot = longRangePotential.sum();
902 +
903 +    // //store the long range potential  
904 +    // curSnapshot->setLongRangePotential(lrPot);
905      
906 <    //store the tau and long range potential    
907 <    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
908 <    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
318 <    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
906 >    curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
907 >                                         *(fDecomp_->getExcludedPotential()));
908 >
909    }
910  
911    
# Line 325 | Line 915 | namespace OpenMD {
915      Molecule::RigidBodyIterator rbIter;
916      RigidBody* rb;
917      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
918 <    
918 >  
919      // collect the atomic forces onto rigid bodies
920      
921      for (mol = info_->beginMolecule(mi); mol != NULL;
# Line 333 | Line 923 | namespace OpenMD {
923        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
924             rb = mol->nextRigidBody(rbIter)) {
925          Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
926 <        tau += rbTau;
926 >        stressTensor += rbTau;
927        }
928      }
929      
930   #ifdef IS_MPI
931 <    Mat3x3d tmpTau(tau);
932 <    MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
343 <                  9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
931 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
932 >                              MPI::REALTYPE, MPI::SUM);
933   #endif
934 <    curSnapshot->statData.setTau(tau);
934 >    curSnapshot->setStressTensor(stressTensor);
935 >    
936    }
937  
938   } //end namespace OpenMD

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