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root/OpenMD/trunk/src/brains/ForceManager.cpp
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Comparing trunk/src/brains/ForceManager.cpp (file contents):
Revision 1448 by gezelter, Thu Jun 17 14:58:49 2010 UTC vs.
Revision 1788 by gezelter, Wed Aug 29 20:17:07 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 "perturbations/ElectricField.hpp"
62 + #include "parallel/ForceMatrixDecomposition.hpp"
63 +
64 + #include <cstdio>
65 + #include <iostream>
66 + #include <iomanip>
67 +
68 + using namespace std;
69   namespace OpenMD {
70 +  
71 +  ForceManager::ForceManager(SimInfo * info) : info_(info) {
72 +    forceField_ = info_->getForceField();
73 +    interactionMan_ = new InteractionManager();
74 +    fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
75 +  }
76  
77 <  void ForceManager::calcForces(bool needPotential, bool needStress) {
77 >  /**
78 >   * setupCutoffs
79 >   *
80 >   * Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
81 >   * and cutoffPolicy
82 >   *
83 >   * cutoffRadius : realType
84 >   *  If the cutoffRadius was explicitly set, use that value.
85 >   *  If the cutoffRadius was not explicitly set:
86 >   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
87 >   *      No electrostatic atoms?  Poll the atom types present in the
88 >   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
89 >   *      Use the maximum suggested value that was found.
90 >   *
91 >   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
92 >   *                        or SHIFTED_POTENTIAL)
93 >   *      If cutoffMethod was explicitly set, use that choice.
94 >   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
95 >   *
96 >   * cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
97 >   *      If cutoffPolicy was explicitly set, use that choice.
98 >   *      If cutoffPolicy was not explicitly set, use TRADITIONAL
99 >   *
100 >   * switchingRadius : realType
101 >   *  If the cutoffMethod was set to SWITCHED:
102 >   *      If the switchingRadius was explicitly set, use that value
103 >   *          (but do a sanity check first).
104 >   *      If the switchingRadius was not explicitly set: use 0.85 *
105 >   *      cutoffRadius_
106 >   *  If the cutoffMethod was not set to SWITCHED:
107 >   *      Set switchingRadius equal to cutoffRadius for safety.
108 >   */
109 >  void ForceManager::setupCutoffs() {
110      
111 <    if (!info_->isFortranInitialized()) {
112 <      info_->update();
113 <    }
111 >    Globals* simParams_ = info_->getSimParams();
112 >    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
113 >    int mdFileVersion;
114 >    rCut_ = 0.0; //Needs a value for a later max() call;  
115      
116 <    preCalculation();
117 <    
118 <    calcShortRangeInteraction();
116 >    if (simParams_->haveMDfileVersion())
117 >      mdFileVersion = simParams_->getMDfileVersion();
118 >    else
119 >      mdFileVersion = 0;
120 >  
121 >    if (simParams_->haveCutoffRadius()) {
122 >      rCut_ = simParams_->getCutoffRadius();
123 >    } else {      
124 >      if (info_->usesElectrostaticAtoms()) {
125 >        sprintf(painCave.errMsg,
126 >                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
127 >                "\tOpenMD will use a default value of 12.0 angstroms"
128 >                "\tfor the cutoffRadius.\n");
129 >        painCave.isFatal = 0;
130 >        painCave.severity = OPENMD_INFO;
131 >        simError();
132 >        rCut_ = 12.0;
133 >      } else {
134 >        RealType thisCut;
135 >        set<AtomType*>::iterator i;
136 >        set<AtomType*> atomTypes;
137 >        atomTypes = info_->getSimulatedAtomTypes();        
138 >        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
139 >          thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
140 >          rCut_ = max(thisCut, rCut_);
141 >        }
142 >        sprintf(painCave.errMsg,
143 >                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
144 >                "\tOpenMD will use %lf angstroms.\n",
145 >                rCut_);
146 >        painCave.isFatal = 0;
147 >        painCave.severity = OPENMD_INFO;
148 >        simError();
149 >      }
150 >    }
151  
152 <    calcLongRangeInteraction(needPotential, needStress);
152 >    fDecomp_->setUserCutoff(rCut_);
153 >    interactionMan_->setCutoffRadius(rCut_);
154  
155 <    postCalculation(needStress);
155 >    map<string, CutoffMethod> stringToCutoffMethod;
156 >    stringToCutoffMethod["HARD"] = HARD;
157 >    stringToCutoffMethod["SWITCHED"] = SWITCHED;
158 >    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
159 >    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
160 >  
161 >    if (simParams_->haveCutoffMethod()) {
162 >      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
163 >      map<string, CutoffMethod>::iterator i;
164 >      i = stringToCutoffMethod.find(cutMeth);
165 >      if (i == stringToCutoffMethod.end()) {
166 >        sprintf(painCave.errMsg,
167 >                "ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
168 >                "\tShould be one of: "
169 >                "HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
170 >                cutMeth.c_str());
171 >        painCave.isFatal = 1;
172 >        painCave.severity = OPENMD_ERROR;
173 >        simError();
174 >      } else {
175 >        cutoffMethod_ = i->second;
176 >      }
177 >    } else {
178 >      if (mdFileVersion > 1) {
179 >        sprintf(painCave.errMsg,
180 >                "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
181 >                "\tOpenMD will use SHIFTED_FORCE.\n");
182 >        painCave.isFatal = 0;
183 >        painCave.severity = OPENMD_INFO;
184 >        simError();
185 >        cutoffMethod_ = SHIFTED_FORCE;        
186 >      } else {
187 >        // handle the case where the old file version was in play
188 >        // (there should be no cutoffMethod, so we have to deduce it
189 >        // from other data).        
190 >
191 >        sprintf(painCave.errMsg,
192 >                "ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
193 >                "\tOpenMD found a file which does not set a cutoffMethod.\n"
194 >                "\tOpenMD will attempt to deduce a cutoffMethod using the\n"
195 >                "\tbehavior of the older (version 1) code.  To remove this\n"
196 >                "\twarning, add an explicit cutoffMethod and change the top\n"
197 >                "\tof the file so that it begins with <OpenMD version=2>\n");
198 >        painCave.isFatal = 0;
199 >        painCave.severity = OPENMD_WARNING;
200 >        simError();            
201 >                
202 >        // The old file version tethered the shifting behavior to the
203 >        // electrostaticSummationMethod keyword.
204 >        
205 >        if (simParams_->haveElectrostaticSummationMethod()) {
206 >          string myMethod = simParams_->getElectrostaticSummationMethod();
207 >          toUpper(myMethod);
208 >        
209 >          if (myMethod == "SHIFTED_POTENTIAL") {
210 >            cutoffMethod_ = SHIFTED_POTENTIAL;
211 >          } else if (myMethod == "SHIFTED_FORCE") {
212 >            cutoffMethod_ = SHIFTED_FORCE;
213 >          }
214 >        
215 >          if (simParams_->haveSwitchingRadius())
216 >            rSwitch_ = simParams_->getSwitchingRadius();
217 >
218 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
219 >            if (simParams_->haveSwitchingRadius()){
220 >              sprintf(painCave.errMsg,
221 >                      "ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
222 >                      "\tA value was set for the switchingRadius\n"
223 >                      "\teven though the electrostaticSummationMethod was\n"
224 >                      "\tset to %s\n", myMethod.c_str());
225 >              painCave.severity = OPENMD_WARNING;
226 >              painCave.isFatal = 1;
227 >              simError();            
228 >            }
229 >          }
230 >          if (abs(rCut_ - rSwitch_) < 0.0001) {
231 >            if (cutoffMethod_ == SHIFTED_FORCE) {              
232 >              sprintf(painCave.errMsg,
233 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
234 >                      "\tcutoffRadius and switchingRadius are set to the\n"
235 >                      "\tsame value.  OpenMD will use shifted force\n"
236 >                      "\tpotentials instead of switching functions.\n");
237 >              painCave.isFatal = 0;
238 >              painCave.severity = OPENMD_WARNING;
239 >              simError();            
240 >            } else {
241 >              cutoffMethod_ = SHIFTED_POTENTIAL;
242 >              sprintf(painCave.errMsg,
243 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
244 >                      "\tcutoffRadius and switchingRadius are set to the\n"
245 >                      "\tsame value.  OpenMD will use shifted potentials\n"
246 >                      "\tinstead of switching functions.\n");
247 >              painCave.isFatal = 0;
248 >              painCave.severity = OPENMD_WARNING;
249 >              simError();            
250 >            }
251 >          }
252 >        }
253 >      }
254 >    }
255 >
256 >    map<string, CutoffPolicy> stringToCutoffPolicy;
257 >    stringToCutoffPolicy["MIX"] = MIX;
258 >    stringToCutoffPolicy["MAX"] = MAX;
259 >    stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;    
260 >
261 >    string cutPolicy;
262 >    if (forceFieldOptions_.haveCutoffPolicy()){
263 >      cutPolicy = forceFieldOptions_.getCutoffPolicy();
264 >    }else if (simParams_->haveCutoffPolicy()) {
265 >      cutPolicy = simParams_->getCutoffPolicy();
266 >    }
267 >
268 >    if (!cutPolicy.empty()){
269 >      toUpper(cutPolicy);
270 >      map<string, CutoffPolicy>::iterator i;
271 >      i = stringToCutoffPolicy.find(cutPolicy);
272 >
273 >      if (i == stringToCutoffPolicy.end()) {
274 >        sprintf(painCave.errMsg,
275 >                "ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
276 >                "\tShould be one of: "
277 >                "MIX, MAX, or TRADITIONAL\n",
278 >                cutPolicy.c_str());
279 >        painCave.isFatal = 1;
280 >        painCave.severity = OPENMD_ERROR;
281 >        simError();
282 >      } else {
283 >        cutoffPolicy_ = i->second;
284 >      }
285 >    } else {
286 >      sprintf(painCave.errMsg,
287 >              "ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
288 >              "\tOpenMD will use TRADITIONAL.\n");
289 >      painCave.isFatal = 0;
290 >      painCave.severity = OPENMD_INFO;
291 >      simError();
292 >      cutoffPolicy_ = TRADITIONAL;        
293 >    }
294 >
295 >    fDecomp_->setCutoffPolicy(cutoffPolicy_);
296 >        
297 >    // create the switching function object:
298 >
299 >    switcher_ = new SwitchingFunction();
300 >  
301 >    if (cutoffMethod_ == SWITCHED) {
302 >      if (simParams_->haveSwitchingRadius()) {
303 >        rSwitch_ = simParams_->getSwitchingRadius();
304 >        if (rSwitch_ > rCut_) {        
305 >          sprintf(painCave.errMsg,
306 >                  "ForceManager::setupCutoffs: switchingRadius (%f) is larger "
307 >                  "than the cutoffRadius(%f)\n", rSwitch_, rCut_);
308 >          painCave.isFatal = 1;
309 >          painCave.severity = OPENMD_ERROR;
310 >          simError();
311 >        }
312 >      } else {      
313 >        rSwitch_ = 0.85 * rCut_;
314 >        sprintf(painCave.errMsg,
315 >                "ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
316 >                "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
317 >                "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
318 >        painCave.isFatal = 0;
319 >        painCave.severity = OPENMD_WARNING;
320 >        simError();
321 >      }
322 >    } else {
323 >      if (mdFileVersion > 1) {
324 >        // throw an error if we define a switching radius and don't need one.
325 >        // older file versions should not do this.
326 >        if (simParams_->haveSwitchingRadius()) {
327 >          map<string, CutoffMethod>::const_iterator it;
328 >          string theMeth;
329 >          for (it = stringToCutoffMethod.begin();
330 >               it != stringToCutoffMethod.end(); ++it) {
331 >            if (it->second == cutoffMethod_) {
332 >              theMeth = it->first;
333 >              break;
334 >            }
335 >          }
336 >          sprintf(painCave.errMsg,
337 >                  "ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
338 >                  "\tis not set to SWITCHED, so switchingRadius value\n"
339 >                  "\twill be ignored for this simulation\n", theMeth.c_str());
340 >          painCave.isFatal = 0;
341 >          painCave.severity = OPENMD_WARNING;
342 >          simError();
343 >        }
344 >      }
345 >      rSwitch_ = rCut_;
346 >    }
347      
348 +    // Default to cubic switching function.
349 +    sft_ = cubic;
350 +    if (simParams_->haveSwitchingFunctionType()) {
351 +      string funcType = simParams_->getSwitchingFunctionType();
352 +      toUpper(funcType);
353 +      if (funcType == "CUBIC") {
354 +        sft_ = cubic;
355 +      } else {
356 +        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
357 +          sft_ = fifth_order_poly;
358 +        } else {
359 +          // throw error        
360 +          sprintf( painCave.errMsg,
361 +                   "ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
362 +                   "\tswitchingFunctionType must be one of: "
363 +                   "\"cubic\" or \"fifth_order_polynomial\".",
364 +                   funcType.c_str() );
365 +          painCave.isFatal = 1;
366 +          painCave.severity = OPENMD_ERROR;
367 +          simError();
368 +        }          
369 +      }
370 +    }
371 +    switcher_->setSwitchType(sft_);
372 +    switcher_->setSwitch(rSwitch_, rCut_);
373 +    interactionMan_->setSwitchingRadius(rSwitch_);
374    }
375 +
376 +
377 +
378    
379 +  void ForceManager::initialize() {
380 +
381 +    if (!info_->isTopologyDone()) {
382 +
383 +      info_->update();
384 +      interactionMan_->setSimInfo(info_);
385 +      interactionMan_->initialize();
386 +
387 +      // We want to delay the cutoffs until after the interaction
388 +      // manager has set up the atom-atom interactions so that we can
389 +      // query them for suggested cutoff values
390 +      setupCutoffs();
391 +
392 +      info_->prepareTopology();      
393 +
394 +      doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
395 +      doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
396 +      if (doHeatFlux_) doParticlePot_ = true;
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();    
446 +  }
447 +  
448    void ForceManager::preCalculation() {
449      SimInfo::MoleculeIterator mi;
450      Molecule* mol;
# Line 82 | Line 452 | namespace OpenMD {
452      Atom* atom;
453      Molecule::RigidBodyIterator rbIter;
454      RigidBody* rb;
455 +    Molecule::CutoffGroupIterator ci;
456 +    CutoffGroup* cg;
457      
458 <    // forces are zeroed here, before any are accumulated.
459 <    // NOTE: do not rezero the forces in Fortran.
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)) {
491 >          //calculate the center of mass of cutoff group
492 >          cg->updateCOM();
493 >        }
494 >      }      
495      }
496      
497      // Zero out the stress tensor
498 <    tau *= 0.0;
499 <    
498 >    stressTensor *= 0.0;
499 >    // Zero out the heatFlux
500 >    fDecomp_->setHeatFlux( Vector3d(0.0) );    
501    }
502    
503 <  void ForceManager::calcShortRangeInteraction() {
503 >  void ForceManager::shortRangeInteractions() {
504      Molecule* mol;
505      RigidBody* rb;
506      Bond* bond;
# Line 135 | 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 143 | 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();
545 <        std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
545 >        map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
546          if (i == bendDataSets.end()) {
547            BendDataSet dataSet;
548            dataSet.prev.angle = dataSet.curr.angle = angle;
549            dataSet.prev.potential = dataSet.curr.potential = currBendPot;
550            dataSet.deltaV = 0.0;
551 <          bendDataSets.insert(std::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 167 | 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 <        std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
569 >        map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
570          if (i == torsionDataSets.end()) {
571            TorsionDataSet dataSet;
572            dataSet.prev.angle = dataSet.curr.angle = angle;
573            dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
574            dataSet.deltaV = 0.0;
575 <          torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
575 >          torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
576          }else {
577            i->second.prev.angle = i->second.curr.angle;
578            i->second.prev.potential = i->second.curr.potential;
# Line 186 | Line 582 | namespace OpenMD {
582                                     i->second.prev.potential);
583          }      
584        }      
585 <
585 >      
586        for (inversion = mol->beginInversion(inversionIter);
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 <        std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
593 >        map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
594          if (i == inversionDataSets.end()) {
595            InversionDataSet dataSet;
596            dataSet.prev.angle = dataSet.curr.angle = angle;
597            dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
598            dataSet.deltaV = 0.0;
599 <          inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
599 >          inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
600          }else {
601            i->second.prev.angle = i->second.curr.angle;
602            i->second.prev.potential = i->second.curr.potential;
# Line 211 | 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::calcLongRangeInteraction(bool needPotential,
227 <                                              bool needStress) {
228 <    Snapshot* curSnapshot;
229 <    DataStorage* config;
230 <    RealType* frc;
231 <    RealType* pos;
232 <    RealType* trq;
233 <    RealType* A;
234 <    RealType* electroFrame;
235 <    RealType* rc;
236 <    RealType* particlePot;
237 <    
238 <    //get current snapshot from SimInfo
239 <    curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
240 <    
241 <    //get array pointers
242 <    config = &(curSnapshot->atomData);
243 <    frc = config->getArrayPointer(DataStorage::dslForce);
244 <    pos = config->getArrayPointer(DataStorage::dslPosition);
245 <    trq = config->getArrayPointer(DataStorage::dslTorque);
246 <    A   = config->getArrayPointer(DataStorage::dslAmat);
247 <    electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
248 <    particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
638 >  void ForceManager::longRangeInteractions() {
639  
640 +
641 +    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
642 +    DataStorage* config = &(curSnapshot->atomData);
643 +    DataStorage* cgConfig = &(curSnapshot->cgData);
644 +
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 <    Vector3d com;
652 <    std::vector<Vector3d> rcGroup;
257 <    
258 <    if(info_->getNCutoffGroups() > 0){
259 <      
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->getCOM(com);
265 <          rcGroup.push_back(com);
657 >          cg->updateCOM();
658          }
659 <      }// end for (mol)
268 <      
269 <      rc = rcGroup[0].getArrayPointer();
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      }
666 +
667 +    fDecomp_->zeroWorkArrays();
668 +    fDecomp_->distributeData();
669      
670 <    //initialize data before passing to fortran
671 <    RealType longRangePotential[LR_POT_TYPES];
672 <    RealType lrPot = 0.0;
673 <    Vector3d totalDipole;
674 <    short int passedCalcPot = needPotential;
675 <    short int passedCalcStress = needStress;
676 <    int isError = 0;
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, f1;
676 >    tuple3<RealType, RealType, RealType> cuts;
677 >    RealType rCutSq;
678 >    bool in_switching_region;
679 >    RealType sw, dswdr, swderiv;
680 >    vector<int> atomListColumn, atomListRow, atomListLocal;
681 >    InteractionData idat;
682 >    SelfData sdat;
683 >    RealType mf;
684 >    RealType vpair;
685 >    RealType dVdFQ1(0.0);
686 >    RealType dVdFQ2(0.0);
687 >    Vector3d eField1(0.0);
688 >    Vector3d eField2(0.0);
689 >    potVec longRangePotential(0.0);
690 >    potVec workPot(0.0);
691 >    potVec exPot(0.0);
692 >    vector<int>::iterator ia, jb;
693  
694 <    for (int i=0; i<LR_POT_TYPES;i++){
695 <      longRangePotential[i]=0.0; //Initialize array
696 <    }
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 >    sdat.doParticlePot = doParticlePot_;
713      
714 <    doForceLoop(pos,
715 <                rc,
716 <                A,
717 <                electroFrame,
718 <                frc,
293 <                trq,
294 <                tau.getArrayPointer(),
295 <                longRangePotential,
296 <                particlePot,
297 <                &passedCalcPot,
298 <                &passedCalcStress,
299 <                &isError );
300 <    
301 <    if( isError ){
302 <      sprintf( painCave.errMsg,
303 <               "Error returned from the fortran force calculation.\n" );
304 <      painCave.isFatal = 1;
305 <      simError();
714 >    loopEnd = PAIR_LOOP;
715 >    if (info_->requiresPrepair() ) {
716 >      loopStart = PREPAIR_LOOP;
717 >    } else {
718 >      loopStart = PAIR_LOOP;
719      }
720 <    for (int i=0; i<LR_POT_TYPES;i++){
308 <      lrPot += longRangePotential[i]; //Quick hack
309 <    }
720 >    for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
721      
722 <    // grab the simulation box dipole moment if specified
723 <    if (info_->getCalcBoxDipole()){
724 <      getAccumulatedBoxDipole(totalDipole.getArrayPointer());
725 <      
726 <      curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
727 <      curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
728 <      curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
722 >      if (iLoop == loopStart) {
723 >        bool update_nlist = fDecomp_->checkNeighborList();
724 >        if (update_nlist)
725 >          neighborList = fDecomp_->buildNeighborList();
726 >      }            
727 >
728 >      for (vector<pair<int, int> >::iterator it = neighborList.begin();
729 >             it != neighborList.end(); ++it) {
730 >                
731 >        cg1 = (*it).first;
732 >        cg2 = (*it).second;
733 >        
734 >        cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
735 >
736 >        d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
737 >
738 >        curSnapshot->wrapVector(d_grp);        
739 >        rgrpsq = d_grp.lengthSquare();
740 >        rCutSq = cuts.second;
741 >
742 >        if (rgrpsq < rCutSq) {
743 >          idat.rcut = &cuts.first;
744 >          if (iLoop == PAIR_LOOP) {
745 >            vij = 0.0;
746 >            fij = V3Zero;
747 >          }
748 >          
749 >          in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
750 >                                                     rgrp);
751 >
752 >          atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
753 >          atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
754 >
755 >          if (doHeatFlux_)
756 >            gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
757 >
758 >          for (ia = atomListRow.begin();
759 >               ia != atomListRow.end(); ++ia) {            
760 >            atom1 = (*ia);
761 >
762 >            for (jb = atomListColumn.begin();
763 >                 jb != atomListColumn.end(); ++jb) {              
764 >              atom2 = (*jb);
765 >
766 >              if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
767 >
768 >                vpair = 0.0;
769 >                workPot = 0.0;
770 >                exPot = 0.0;
771 >                f1 = V3Zero;
772 >                dVdFQ1 = 0.0;
773 >                dVdFQ2 = 0.0;
774 >
775 >                fDecomp_->fillInteractionData(idat, atom1, atom2);
776 >
777 >                topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
778 >                vdwMult = vdwScale_[topoDist];
779 >                electroMult = electrostaticScale_[topoDist];
780 >
781 >                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
782 >                  idat.d = &d_grp;
783 >                  idat.r2 = &rgrpsq;
784 >                  if (doHeatFlux_)
785 >                    vel2 = gvel2;
786 >                } else {
787 >                  d = fDecomp_->getInteratomicVector(atom1, atom2);
788 >                  curSnapshot->wrapVector( d );
789 >                  r2 = d.lengthSquare();
790 >                  idat.d = &d;
791 >                  idat.r2 = &r2;
792 >                  if (doHeatFlux_)
793 >                    vel2 = fDecomp_->getAtomVelocityColumn(atom2);
794 >                }
795 >              
796 >                r = sqrt( *(idat.r2) );
797 >                idat.rij = &r;
798 >              
799 >                if (iLoop == PREPAIR_LOOP) {
800 >                  interactionMan_->doPrePair(idat);
801 >                } else {
802 >                  interactionMan_->doPair(idat);
803 >                  fDecomp_->unpackInteractionData(idat, atom1, atom2);
804 >                  vij += vpair;
805 >                  fij += f1;
806 >                  stressTensor -= outProduct( *(idat.d), f1);
807 >                  if (doHeatFlux_)
808 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
809 >                }
810 >              }
811 >            }
812 >          }
813 >
814 >          if (iLoop == PAIR_LOOP) {
815 >            if (in_switching_region) {
816 >              swderiv = vij * dswdr / rgrp;
817 >              fg = swderiv * d_grp;
818 >              fij += fg;
819 >
820 >              if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
821 >                stressTensor -= outProduct( *(idat.d), fg);
822 >                if (doHeatFlux_)
823 >                  fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
824 >                
825 >              }
826 >          
827 >              for (ia = atomListRow.begin();
828 >                   ia != atomListRow.end(); ++ia) {            
829 >                atom1 = (*ia);                
830 >                mf = fDecomp_->getMassFactorRow(atom1);
831 >                // fg is the force on atom ia due to cutoff group's
832 >                // presence in switching region
833 >                fg = swderiv * d_grp * mf;
834 >                fDecomp_->addForceToAtomRow(atom1, fg);
835 >                if (atomListRow.size() > 1) {
836 >                  if (info_->usesAtomicVirial()) {
837 >                    // find the distance between the atom
838 >                    // and the center of the cutoff group:
839 >                    dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
840 >                    stressTensor -= outProduct(dag, fg);
841 >                    if (doHeatFlux_)
842 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
843 >                  }
844 >                }
845 >              }
846 >              for (jb = atomListColumn.begin();
847 >                   jb != atomListColumn.end(); ++jb) {              
848 >                atom2 = (*jb);
849 >                mf = fDecomp_->getMassFactorColumn(atom2);
850 >                // fg is the force on atom jb due to cutoff group's
851 >                // presence in switching region
852 >                fg = -swderiv * d_grp * mf;
853 >                fDecomp_->addForceToAtomColumn(atom2, fg);
854 >
855 >                if (atomListColumn.size() > 1) {
856 >                  if (info_->usesAtomicVirial()) {
857 >                    // find the distance between the atom
858 >                    // and the center of the cutoff group:
859 >                    dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
860 >                    stressTensor -= outProduct(dag, fg);
861 >                    if (doHeatFlux_)
862 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
863 >                  }
864 >                }
865 >              }
866 >            }
867 >            //if (!info_->usesAtomicVirial()) {
868 >            //  stressTensor -= outProduct(d_grp, fij);
869 >            //  if (doHeatFlux_)
870 >            //     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
871 >            //}
872 >          }
873 >        }
874 >      }
875 >
876 >      if (iLoop == PREPAIR_LOOP) {
877 >        if (info_->requiresPrepair()) {
878 >
879 >          fDecomp_->collectIntermediateData();
880 >
881 >          for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
882 >            fDecomp_->fillSelfData(sdat, atom1);
883 >            interactionMan_->doPreForce(sdat);
884 >          }
885 >
886 >          fDecomp_->distributeIntermediateData();
887 >
888 >        }
889 >      }
890      }
891 +  
892 +    // collects pairwise information
893 +    fDecomp_->collectData();
894 +        
895 +    if (info_->requiresSelfCorrection()) {
896 +      for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
897 +        fDecomp_->fillSelfData(sdat, atom1);
898 +        interactionMan_->doSelfCorrection(sdat);
899 +      }
900 +    }
901 +
902 +    // collects single-atom information
903 +    fDecomp_->collectSelfData();
904 +
905 +    longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
906 +      *(fDecomp_->getPairwisePotential());
907 +
908 +    curSnapshot->setLongRangePotential(longRangePotential);
909      
910 <    //store the tau and long range potential    
911 <    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
912 <    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
323 <    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
910 >    curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
911 >                                         *(fDecomp_->getExcludedPotential()));
912 >
913    }
914  
915    
916 <  void ForceManager::postCalculation(bool needStress) {
916 >  void ForceManager::postCalculation() {
917 >
918 >    vector<Perturbation*>::iterator pi;
919 >    for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
920 >      (*pi)->applyPerturbation();
921 >    }
922 >
923      SimInfo::MoleculeIterator mi;
924      Molecule* mol;
925      Molecule::RigidBodyIterator rbIter;
926      RigidBody* rb;
927      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
928 <    
928 >  
929      // collect the atomic forces onto rigid bodies
930      
931      for (mol = info_->beginMolecule(mi); mol != NULL;
932           mol = info_->nextMolecule(mi)) {
933        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
934             rb = mol->nextRigidBody(rbIter)) {
935 <        if (needStress) {          
936 <          Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
342 <          tau += rbTau;
343 <        } else{
344 <          rb->calcForcesAndTorques();
345 <        }
935 >        Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
936 >        stressTensor += rbTau;
937        }
938      }
939 <
349 <    if (needStress) {
939 >    
940   #ifdef IS_MPI
941 <      Mat3x3d tmpTau(tau);
942 <      MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
353 <                    9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
941 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
942 >                              MPI::REALTYPE, MPI::SUM);
943   #endif
944 <      curSnapshot->statData.setTau(tau);
945 <    }
944 >    curSnapshot->setStressTensor(stressTensor);
945 >    
946    }
358 –
947   } //end namespace OpenMD

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