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Comparing trunk/src/brains/ForceManager.cpp (file contents):
Revision 1610 by gezelter, Fri Aug 12 14:37:25 2011 UTC vs.
Revision 1915 by gezelter, Mon Jul 29 17:55:17 2013 UTC

# Line 35 | Line 35
35   *                                                                      
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).                        
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   /**
44   * @file ForceManager.cpp
45   * @author tlin
46   * @date 11/09/2004
46 – * @time 10:39am
47   * @version 1.0
48   */
49  
50 +
51   #include "brains/ForceManager.hpp"
52   #include "primitives/Molecule.hpp"
52 – #include "UseTheForce/doForces_interface.h"
53   #define __OPENMD_C
54 – #include "UseTheForce/DarkSide/fInteractionMap.h"
54   #include "utils/simError.h"
55   #include "primitives/Bond.hpp"
56   #include "primitives/Bend.hpp"
57   #include "primitives/Torsion.hpp"
58   #include "primitives/Inversion.hpp"
59 + #include "nonbonded/NonBondedInteraction.hpp"
60 + #include "perturbations/ElectricField.hpp"
61 + #include "parallel/ForceMatrixDecomposition.hpp"
62 +
63 + #include <cstdio>
64 + #include <iostream>
65 + #include <iomanip>
66 +
67 + using namespace std;
68   namespace OpenMD {
69 +  
70 +  ForceManager::ForceManager(SimInfo * info) : info_(info), switcher_(NULL),
71 +                                               initialized_(false) {
72 +    forceField_ = info_->getForceField();
73 +    interactionMan_ = new InteractionManager();
74 +    fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
75 +    thermo = new Thermo(info_);
76 +  }
77  
78 <  void ForceManager::calcForces() {
78 >  ForceManager::~ForceManager() {
79 >    perturbations_.clear();
80      
81 <    if (!info_->isFortranInitialized()) {
82 <      info_->update();
83 <    }
81 >    delete switcher_;
82 >    delete interactionMan_;
83 >    delete fDecomp_;
84 >    delete thermo;
85 >  }
86 >  
87 >  /**
88 >   * setupCutoffs
89 >   *
90 >   * Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
91 >   * and cutoffPolicy
92 >   *
93 >   * cutoffRadius : realType
94 >   *  If the cutoffRadius was explicitly set, use that value.
95 >   *  If the cutoffRadius was not explicitly set:
96 >   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
97 >   *      No electrostatic atoms?  Poll the atom types present in the
98 >   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
99 >   *      Use the maximum suggested value that was found.
100 >   *
101 >   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, TAYLOR_SHIFTED,
102 >   *                        SHIFTED_POTENTIAL, or EWALD_FULL)
103 >   *      If cutoffMethod was explicitly set, use that choice.
104 >   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
105 >   *
106 >   * cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
107 >   *      If cutoffPolicy was explicitly set, use that choice.
108 >   *      If cutoffPolicy was not explicitly set, use TRADITIONAL
109 >   *
110 >   * switchingRadius : realType
111 >   *  If the cutoffMethod was set to SWITCHED:
112 >   *      If the switchingRadius was explicitly set, use that value
113 >   *          (but do a sanity check first).
114 >   *      If the switchingRadius was not explicitly set: use 0.85 *
115 >   *      cutoffRadius_
116 >   *  If the cutoffMethod was not set to SWITCHED:
117 >   *      Set switchingRadius equal to cutoffRadius for safety.
118 >   */
119 >  void ForceManager::setupCutoffs() {
120      
121 <    preCalculation();
121 >    Globals* simParams_ = info_->getSimParams();
122 >    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
123 >    int mdFileVersion;
124 >    rCut_ = 0.0; //Needs a value for a later max() call;  
125      
126 <    calcShortRangeInteraction();
126 >    if (simParams_->haveMDfileVersion())
127 >      mdFileVersion = simParams_->getMDfileVersion();
128 >    else
129 >      mdFileVersion = 0;
130 >  
131 >    // We need the list of simulated atom types to figure out cutoffs
132 >    // as well as long range corrections.
133  
134 <    calcLongRangeInteraction();
134 >    set<AtomType*>::iterator i;
135 >    set<AtomType*> atomTypes_;
136 >    atomTypes_ = info_->getSimulatedAtomTypes();
137  
138 <    postCalculation();
138 >    if (simParams_->haveCutoffRadius()) {
139 >      rCut_ = simParams_->getCutoffRadius();
140 >    } else {      
141 >      if (info_->usesElectrostaticAtoms()) {
142 >        sprintf(painCave.errMsg,
143 >                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
144 >                "\tOpenMD will use a default value of 12.0 angstroms"
145 >                "\tfor the cutoffRadius.\n");
146 >        painCave.isFatal = 0;
147 >        painCave.severity = OPENMD_INFO;
148 >        simError();
149 >        rCut_ = 12.0;
150 >      } else {
151 >        RealType thisCut;
152 >        for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
153 >          thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
154 >          rCut_ = max(thisCut, rCut_);
155 >        }
156 >        sprintf(painCave.errMsg,
157 >                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
158 >                "\tOpenMD will use %lf angstroms.\n",
159 >                rCut_);
160 >        painCave.isFatal = 0;
161 >        painCave.severity = OPENMD_INFO;
162 >        simError();
163 >      }
164 >    }
165 >
166 >    fDecomp_->setUserCutoff(rCut_);
167 >    interactionMan_->setCutoffRadius(rCut_);
168 >
169 >    map<string, CutoffMethod> stringToCutoffMethod;
170 >    stringToCutoffMethod["HARD"] = HARD;
171 >    stringToCutoffMethod["SWITCHED"] = SWITCHED;
172 >    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
173 >    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
174 >    stringToCutoffMethod["TAYLOR_SHIFTED"] = TAYLOR_SHIFTED;
175 >    stringToCutoffMethod["EWALD_FULL"] = EWALD_FULL;
176 >  
177 >    if (simParams_->haveCutoffMethod()) {
178 >      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
179 >      map<string, CutoffMethod>::iterator i;
180 >      i = stringToCutoffMethod.find(cutMeth);
181 >      if (i == stringToCutoffMethod.end()) {
182 >        sprintf(painCave.errMsg,
183 >                "ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
184 >                "\tShould be one of: "
185 >                "HARD, SWITCHED, SHIFTED_POTENTIAL, TAYLOR_SHIFTED,\n"
186 >                "\tSHIFTED_FORCE, or EWALD_FULL\n",
187 >                cutMeth.c_str());
188 >        painCave.isFatal = 1;
189 >        painCave.severity = OPENMD_ERROR;
190 >        simError();
191 >      } else {
192 >        cutoffMethod_ = i->second;
193 >      }
194 >    } else {
195 >      if (mdFileVersion > 1) {
196 >        sprintf(painCave.errMsg,
197 >                "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
198 >                "\tOpenMD will use SHIFTED_FORCE.\n");
199 >        painCave.isFatal = 0;
200 >        painCave.severity = OPENMD_INFO;
201 >        simError();
202 >        cutoffMethod_ = SHIFTED_FORCE;        
203 >      } else {
204 >        // handle the case where the old file version was in play
205 >        // (there should be no cutoffMethod, so we have to deduce it
206 >        // from other data).        
207 >
208 >        sprintf(painCave.errMsg,
209 >                "ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
210 >                "\tOpenMD found a file which does not set a cutoffMethod.\n"
211 >                "\tOpenMD will attempt to deduce a cutoffMethod using the\n"
212 >                "\tbehavior of the older (version 1) code.  To remove this\n"
213 >                "\twarning, add an explicit cutoffMethod and change the top\n"
214 >                "\tof the file so that it begins with <OpenMD version=2>\n");
215 >        painCave.isFatal = 0;
216 >        painCave.severity = OPENMD_WARNING;
217 >        simError();            
218 >                
219 >        // The old file version tethered the shifting behavior to the
220 >        // electrostaticSummationMethod keyword.
221 >        
222 >        if (simParams_->haveElectrostaticSummationMethod()) {
223 >          string myMethod = simParams_->getElectrostaticSummationMethod();
224 >          toUpper(myMethod);
225 >        
226 >          if (myMethod == "SHIFTED_POTENTIAL") {
227 >            cutoffMethod_ = SHIFTED_POTENTIAL;
228 >          } else if (myMethod == "SHIFTED_FORCE") {
229 >            cutoffMethod_ = SHIFTED_FORCE;
230 >          } else if (myMethod == "TAYLOR_SHIFTED") {
231 >            cutoffMethod_ = TAYLOR_SHIFTED;
232 >          } else if (myMethod == "EWALD_FULL") {
233 >            cutoffMethod_ = EWALD_FULL;
234 >          }
235 >        
236 >          if (simParams_->haveSwitchingRadius())
237 >            rSwitch_ = simParams_->getSwitchingRadius();
238 >
239 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE" ||
240 >              myMethod == "TAYLOR_SHIFTED" || myMethod == "EWALD_FULL") {
241 >            if (simParams_->haveSwitchingRadius()){
242 >              sprintf(painCave.errMsg,
243 >                      "ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
244 >                      "\tA value was set for the switchingRadius\n"
245 >                      "\teven though the electrostaticSummationMethod was\n"
246 >                      "\tset to %s\n", myMethod.c_str());
247 >              painCave.severity = OPENMD_WARNING;
248 >              painCave.isFatal = 1;
249 >              simError();            
250 >            }
251 >          }
252 >          if (abs(rCut_ - rSwitch_) < 0.0001) {
253 >            if (cutoffMethod_ == SHIFTED_FORCE) {              
254 >              sprintf(painCave.errMsg,
255 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
256 >                      "\tcutoffRadius and switchingRadius are set to the\n"
257 >                      "\tsame value.  OpenMD will use shifted force\n"
258 >                      "\tpotentials instead of switching functions.\n");
259 >              painCave.isFatal = 0;
260 >              painCave.severity = OPENMD_WARNING;
261 >              simError();            
262 >            } else {
263 >              cutoffMethod_ = SHIFTED_POTENTIAL;
264 >              sprintf(painCave.errMsg,
265 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
266 >                      "\tcutoffRadius and switchingRadius are set to the\n"
267 >                      "\tsame value.  OpenMD will use shifted potentials\n"
268 >                      "\tinstead of switching functions.\n");
269 >              painCave.isFatal = 0;
270 >              painCave.severity = OPENMD_WARNING;
271 >              simError();            
272 >            }
273 >          }
274 >        }
275 >      }
276 >    }
277 >
278 >    map<string, CutoffPolicy> stringToCutoffPolicy;
279 >    stringToCutoffPolicy["MIX"] = MIX;
280 >    stringToCutoffPolicy["MAX"] = MAX;
281 >    stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;    
282 >
283 >    string cutPolicy;
284 >    if (forceFieldOptions_.haveCutoffPolicy()){
285 >      cutPolicy = forceFieldOptions_.getCutoffPolicy();
286 >    }else if (simParams_->haveCutoffPolicy()) {
287 >      cutPolicy = simParams_->getCutoffPolicy();
288 >    }
289 >
290 >    if (!cutPolicy.empty()){
291 >      toUpper(cutPolicy);
292 >      map<string, CutoffPolicy>::iterator i;
293 >      i = stringToCutoffPolicy.find(cutPolicy);
294 >
295 >      if (i == stringToCutoffPolicy.end()) {
296 >        sprintf(painCave.errMsg,
297 >                "ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
298 >                "\tShould be one of: "
299 >                "MIX, MAX, or TRADITIONAL\n",
300 >                cutPolicy.c_str());
301 >        painCave.isFatal = 1;
302 >        painCave.severity = OPENMD_ERROR;
303 >        simError();
304 >      } else {
305 >        cutoffPolicy_ = i->second;
306 >      }
307 >    } else {
308 >      sprintf(painCave.errMsg,
309 >              "ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
310 >              "\tOpenMD will use TRADITIONAL.\n");
311 >      painCave.isFatal = 0;
312 >      painCave.severity = OPENMD_INFO;
313 >      simError();
314 >      cutoffPolicy_ = TRADITIONAL;        
315 >    }
316 >
317 >    fDecomp_->setCutoffPolicy(cutoffPolicy_);
318 >        
319 >    // create the switching function object:
320 >
321 >    switcher_ = new SwitchingFunction();
322 >  
323 >    if (cutoffMethod_ == SWITCHED) {
324 >      if (simParams_->haveSwitchingRadius()) {
325 >        rSwitch_ = simParams_->getSwitchingRadius();
326 >        if (rSwitch_ > rCut_) {        
327 >          sprintf(painCave.errMsg,
328 >                  "ForceManager::setupCutoffs: switchingRadius (%f) is larger "
329 >                  "than the cutoffRadius(%f)\n", rSwitch_, rCut_);
330 >          painCave.isFatal = 1;
331 >          painCave.severity = OPENMD_ERROR;
332 >          simError();
333 >        }
334 >      } else {      
335 >        rSwitch_ = 0.85 * rCut_;
336 >        sprintf(painCave.errMsg,
337 >                "ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
338 >                "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
339 >                "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
340 >        painCave.isFatal = 0;
341 >        painCave.severity = OPENMD_WARNING;
342 >        simError();
343 >      }
344 >    } else {
345 >      if (mdFileVersion > 1) {
346 >        // throw an error if we define a switching radius and don't need one.
347 >        // older file versions should not do this.
348 >        if (simParams_->haveSwitchingRadius()) {
349 >          map<string, CutoffMethod>::const_iterator it;
350 >          string theMeth;
351 >          for (it = stringToCutoffMethod.begin();
352 >               it != stringToCutoffMethod.end(); ++it) {
353 >            if (it->second == cutoffMethod_) {
354 >              theMeth = it->first;
355 >              break;
356 >            }
357 >          }
358 >          sprintf(painCave.errMsg,
359 >                  "ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
360 >                  "\tis not set to SWITCHED, so switchingRadius value\n"
361 >                  "\twill be ignored for this simulation\n", theMeth.c_str());
362 >          painCave.isFatal = 0;
363 >          painCave.severity = OPENMD_WARNING;
364 >          simError();
365 >        }
366 >      }
367 >      rSwitch_ = rCut_;
368 >    }
369      
370 +    // Default to cubic switching function.
371 +    sft_ = cubic;
372 +    if (simParams_->haveSwitchingFunctionType()) {
373 +      string funcType = simParams_->getSwitchingFunctionType();
374 +      toUpper(funcType);
375 +      if (funcType == "CUBIC") {
376 +        sft_ = cubic;
377 +      } else {
378 +        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
379 +          sft_ = fifth_order_poly;
380 +        } else {
381 +          // throw error        
382 +          sprintf( painCave.errMsg,
383 +                   "ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
384 +                   "\tswitchingFunctionType must be one of: "
385 +                   "\"cubic\" or \"fifth_order_polynomial\".",
386 +                   funcType.c_str() );
387 +          painCave.isFatal = 1;
388 +          painCave.severity = OPENMD_ERROR;
389 +          simError();
390 +        }          
391 +      }
392 +    }
393 +    switcher_->setSwitchType(sft_);
394 +    switcher_->setSwitch(rSwitch_, rCut_);
395    }
396 +
397 +
398 +
399    
400 +  void ForceManager::initialize() {
401 +
402 +    if (!info_->isTopologyDone()) {
403 +
404 +      info_->update();
405 +      interactionMan_->setSimInfo(info_);
406 +      interactionMan_->initialize();
407 +
408 +      // We want to delay the cutoffs until after the interaction
409 +      // manager has set up the atom-atom interactions so that we can
410 +      // query them for suggested cutoff values
411 +      setupCutoffs();
412 +
413 +      info_->prepareTopology();      
414 +
415 +      doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
416 +      doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
417 +      if (doHeatFlux_) doParticlePot_ = true;
418 +
419 +      doElectricField_ = info_->getSimParams()->getOutputElectricField();
420 +  
421 +    }
422 +
423 +    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
424 +    
425 +    // Force fields can set options on how to scale van der Waals and
426 +    // electrostatic interactions for atoms connected via bonds, bends
427 +    // and torsions in this case the topological distance between
428 +    // atoms is:
429 +    // 0 = topologically unconnected
430 +    // 1 = bonded together
431 +    // 2 = connected via a bend
432 +    // 3 = connected via a torsion
433 +    
434 +    vdwScale_.reserve(4);
435 +    fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
436 +
437 +    electrostaticScale_.reserve(4);
438 +    fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
439 +
440 +    vdwScale_[0] = 1.0;
441 +    vdwScale_[1] = fopts.getvdw12scale();
442 +    vdwScale_[2] = fopts.getvdw13scale();
443 +    vdwScale_[3] = fopts.getvdw14scale();
444 +    
445 +    electrostaticScale_[0] = 1.0;
446 +    electrostaticScale_[1] = fopts.getelectrostatic12scale();
447 +    electrostaticScale_[2] = fopts.getelectrostatic13scale();
448 +    electrostaticScale_[3] = fopts.getelectrostatic14scale();    
449 +    
450 +    if (info_->getSimParams()->haveElectricField()) {
451 +      ElectricField* eField = new ElectricField(info_);
452 +      perturbations_.push_back(eField);
453 +    }
454 +
455 +    usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
456 +    
457 +    fDecomp_->distributeInitialData();
458 +    
459 +    initialized_ = true;
460 +    
461 +  }
462 +  
463 +  void ForceManager::calcForces() {
464 +    
465 +    if (!initialized_) initialize();
466 +    
467 +    preCalculation();  
468 +    shortRangeInteractions();
469 +    longRangeInteractions();
470 +    postCalculation();    
471 +  }
472 +  
473    void ForceManager::preCalculation() {
474      SimInfo::MoleculeIterator mi;
475      Molecule* mol;
# Line 82 | Line 477 | namespace OpenMD {
477      Atom* atom;
478      Molecule::RigidBodyIterator rbIter;
479      RigidBody* rb;
480 +    Molecule::CutoffGroupIterator ci;
481 +    CutoffGroup* cg;
482      
483 <    // forces are zeroed here, before any are accumulated.
484 <    // NOTE: do not rezero the forces in Fortran.
483 >    // forces and potentials are zeroed here, before any are
484 >    // accumulated.
485      
486 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
487 +
488 +    snap->setBondPotential(0.0);
489 +    snap->setBendPotential(0.0);
490 +    snap->setTorsionPotential(0.0);
491 +    snap->setInversionPotential(0.0);
492 +
493 +    potVec zeroPot(0.0);
494 +    snap->setLongRangePotential(zeroPot);
495 +    snap->setExcludedPotentials(zeroPot);
496 +
497 +    snap->setRestraintPotential(0.0);
498 +    snap->setRawPotential(0.0);
499 +
500      for (mol = info_->beginMolecule(mi); mol != NULL;
501           mol = info_->nextMolecule(mi)) {
502 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
502 >      for(atom = mol->beginAtom(ai); atom != NULL;
503 >          atom = mol->nextAtom(ai)) {
504          atom->zeroForcesAndTorques();
505        }
506 <          
506 >      
507        //change the positions of atoms which belong to the rigidbodies
508        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
509             rb = mol->nextRigidBody(rbIter)) {
510          rb->zeroForcesAndTorques();
511        }        
512 <          
512 >      
513 >      if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
514 >        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
515 >            cg = mol->nextCutoffGroup(ci)) {
516 >          //calculate the center of mass of cutoff group
517 >          cg->updateCOM();
518 >        }
519 >      }      
520      }
521      
522      // Zero out the stress tensor
523 <    tau *= 0.0;
524 <    
523 >    stressTensor *= 0.0;
524 >    // Zero out the heatFlux
525 >    fDecomp_->setHeatFlux( Vector3d(0.0) );    
526    }
527    
528 <  void ForceManager::calcShortRangeInteraction() {
528 >  void ForceManager::shortRangeInteractions() {
529      Molecule* mol;
530      RigidBody* rb;
531      Bond* bond;
# Line 135 | Line 555 | namespace OpenMD {
555  
556        for (bond = mol->beginBond(bondIter); bond != NULL;
557             bond = mol->nextBond(bondIter)) {
558 <        bond->calcForce();
558 >        bond->calcForce(doParticlePot_);
559          bondPotential += bond->getPotential();
560        }
561  
# Line 143 | Line 563 | namespace OpenMD {
563             bend = mol->nextBend(bendIter)) {
564          
565          RealType angle;
566 <        bend->calcForce(angle);
566 >        bend->calcForce(angle, doParticlePot_);
567          RealType currBendPot = bend->getPotential();          
568          
569          bendPotential += bend->getPotential();
570 <        std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
570 >        map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
571          if (i == bendDataSets.end()) {
572            BendDataSet dataSet;
573            dataSet.prev.angle = dataSet.curr.angle = angle;
574            dataSet.prev.potential = dataSet.curr.potential = currBendPot;
575            dataSet.deltaV = 0.0;
576 <          bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
576 >          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
577 >                                                                  dataSet));
578          }else {
579            i->second.prev.angle = i->second.curr.angle;
580            i->second.prev.potential = i->second.curr.potential;
# Line 167 | Line 588 | namespace OpenMD {
588        for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
589             torsion = mol->nextTorsion(torsionIter)) {
590          RealType angle;
591 <        torsion->calcForce(angle);
591 >        torsion->calcForce(angle, doParticlePot_);
592          RealType currTorsionPot = torsion->getPotential();
593          torsionPotential += torsion->getPotential();
594 <        std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
594 >        map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
595          if (i == torsionDataSets.end()) {
596            TorsionDataSet dataSet;
597            dataSet.prev.angle = dataSet.curr.angle = angle;
598            dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
599            dataSet.deltaV = 0.0;
600 <          torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
600 >          torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
601          }else {
602            i->second.prev.angle = i->second.curr.angle;
603            i->second.prev.potential = i->second.curr.potential;
# Line 186 | Line 607 | namespace OpenMD {
607                                     i->second.prev.potential);
608          }      
609        }      
610 <
610 >      
611        for (inversion = mol->beginInversion(inversionIter);
612             inversion != NULL;
613             inversion = mol->nextInversion(inversionIter)) {
614          RealType angle;
615 <        inversion->calcForce(angle);
615 >        inversion->calcForce(angle, doParticlePot_);
616          RealType currInversionPot = inversion->getPotential();
617          inversionPotential += inversion->getPotential();
618 <        std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
618 >        map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
619          if (i == inversionDataSets.end()) {
620            InversionDataSet dataSet;
621            dataSet.prev.angle = dataSet.curr.angle = angle;
622            dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
623            dataSet.deltaV = 0.0;
624 <          inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
624 >          inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
625          }else {
626            i->second.prev.angle = i->second.curr.angle;
627            i->second.prev.potential = i->second.curr.potential;
# Line 211 | Line 632 | namespace OpenMD {
632          }      
633        }      
634      }
635 <    
636 <    RealType  shortRangePotential = bondPotential + bendPotential +
637 <      torsionPotential +  inversionPotential;    
635 >
636 > #ifdef IS_MPI
637 >    // Collect from all nodes.  This should eventually be moved into a
638 >    // SystemDecomposition, but this is a better place than in
639 >    // Thermo to do the collection.
640 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
641 >                              MPI::SUM);
642 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
643 >                              MPI::SUM);
644 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
645 >                              MPI::REALTYPE, MPI::SUM);
646 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
647 >                              MPI::REALTYPE, MPI::SUM);
648 > #endif
649 >
650      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
651 <    curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
652 <    curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
653 <    curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
654 <    curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
655 <    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
651 >
652 >    curSnapshot->setBondPotential(bondPotential);
653 >    curSnapshot->setBendPotential(bendPotential);
654 >    curSnapshot->setTorsionPotential(torsionPotential);
655 >    curSnapshot->setInversionPotential(inversionPotential);
656      
657 +    // RealType shortRangePotential = bondPotential + bendPotential +
658 +    //   torsionPotential +  inversionPotential;    
659 +
660 +    // curSnapshot->setShortRangePotential(shortRangePotential);
661    }
662    
663 <  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);
663 >  void ForceManager::longRangeInteractions() {
664  
665 +    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
666 +    DataStorage* config = &(curSnapshot->atomData);
667 +    DataStorage* cgConfig = &(curSnapshot->cgData);
668 +
669      //calculate the center of mass of cutoff group
670 +
671      SimInfo::MoleculeIterator mi;
672      Molecule* mol;
673      Molecule::CutoffGroupIterator ci;
674      CutoffGroup* cg;
675 <    Vector3d com;
676 <    std::vector<Vector3d> rcGroup;
256 <    
257 <    if(info_->getNCutoffGroups() > 0){
258 <      
675 >
676 >    if(info_->getNCutoffGroups() > 0){      
677        for (mol = info_->beginMolecule(mi); mol != NULL;
678             mol = info_->nextMolecule(mi)) {
679          for(cg = mol->beginCutoffGroup(ci); cg != NULL;
680              cg = mol->nextCutoffGroup(ci)) {
681 <          cg->getCOM(com);
264 <          rcGroup.push_back(com);
681 >          cg->updateCOM();
682          }
683 <      }// end for (mol)
267 <      
268 <      rc = rcGroup[0].getArrayPointer();
683 >      }      
684      } else {
685        // center of mass of the group is the same as position of the atom  
686        // if cutoff group does not exist
687 <      rc = pos;
687 >      cgConfig->position = config->position;
688 >      cgConfig->velocity = config->velocity;
689      }
690 +
691 +    fDecomp_->zeroWorkArrays();
692 +    fDecomp_->distributeData();
693      
694 <    //initialize data before passing to fortran
695 <    RealType longRangePotential[LR_POT_TYPES];
696 <    RealType lrPot = 0.0;
697 <    Vector3d totalDipole;
698 <    int isError = 0;
694 >    int cg1, cg2, atom1, atom2, topoDist;
695 >    Vector3d d_grp, dag, d, gvel2, vel2;
696 >    RealType rgrpsq, rgrp, r2, r;
697 >    RealType electroMult, vdwMult;
698 >    RealType vij;
699 >    Vector3d fij, fg, f1;
700 >    tuple3<RealType, RealType, RealType> cuts;
701 >    RealType rCut, rCutSq, rListSq;
702 >    bool in_switching_region;
703 >    RealType sw, dswdr, swderiv;
704 >    vector<int> atomListColumn, atomListRow;
705 >    InteractionData idat;
706 >    SelfData sdat;
707 >    RealType mf;
708 >    RealType vpair;
709 >    RealType dVdFQ1(0.0);
710 >    RealType dVdFQ2(0.0);
711 >    potVec longRangePotential(0.0);
712 >    potVec workPot(0.0);
713 >    potVec exPot(0.0);
714 >    Vector3d eField1(0.0);
715 >    Vector3d eField2(0.0);
716 >    vector<int>::iterator ia, jb;
717  
718 <    for (int i=0; i<LR_POT_TYPES;i++){
282 <      longRangePotential[i]=0.0; //Initialize array
283 <    }
718 >    int loopStart, loopEnd;
719      
720 <    doForceLoop(pos,
721 <                rc,
722 <                A,
723 <                electroFrame,
724 <                frc,
725 <                trq,
726 <                tau.getArrayPointer(),
727 <                longRangePotential,
728 <                particlePot,
729 <                &isError );
720 >    idat.rcut = &rCut;
721 >    idat.vdwMult = &vdwMult;
722 >    idat.electroMult = &electroMult;
723 >    idat.pot = &workPot;
724 >    idat.excludedPot = &exPot;
725 >    sdat.pot = fDecomp_->getEmbeddingPotential();
726 >    sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
727 >    idat.vpair = &vpair;
728 >    idat.dVdFQ1 = &dVdFQ1;
729 >    idat.dVdFQ2 = &dVdFQ2;
730 >    idat.eField1 = &eField1;
731 >    idat.eField2 = &eField2;  
732 >    idat.f1 = &f1;
733 >    idat.sw = &sw;
734 >    idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
735 >    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE || cutoffMethod_ == TAYLOR_SHIFTED) ? true : false;
736 >    idat.doParticlePot = doParticlePot_;
737 >    idat.doElectricField = doElectricField_;
738 >    sdat.doParticlePot = doParticlePot_;
739      
740 <    if( isError ){
741 <      sprintf( painCave.errMsg,
742 <               "Error returned from the fortran force calculation.\n" );
743 <      painCave.isFatal = 1;
744 <      simError();
740 >    loopEnd = PAIR_LOOP;
741 >    if (info_->requiresPrepair() ) {
742 >      loopStart = PREPAIR_LOOP;
743 >    } else {
744 >      loopStart = PAIR_LOOP;
745      }
746 <    for (int i=0; i<LR_POT_TYPES;i++){
747 <      lrPot += longRangePotential[i]; //Quick hack
746 >    for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
747 >    
748 >      if (iLoop == loopStart) {
749 >        bool update_nlist = fDecomp_->checkNeighborList();
750 >        if (update_nlist) {
751 >          if (!usePeriodicBoundaryConditions_)
752 >            Mat3x3d bbox = thermo->getBoundingBox();
753 >          fDecomp_->buildNeighborList(neighborList_);
754 >        }
755 >      }
756 >
757 >      for (vector<pair<int, int> >::iterator it = neighborList_.begin();
758 >             it != neighborList_.end(); ++it) {
759 >                
760 >        cg1 = (*it).first;
761 >        cg2 = (*it).second;
762 >        
763 >        fDecomp_->getGroupCutoffs(cg1, cg2, rCut, rCutSq, rListSq);
764 >
765 >        d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
766 >
767 >        // already wrapped in the getIntergroupVector call:
768 >        // curSnapshot->wrapVector(d_grp);        
769 >        rgrpsq = d_grp.lengthSquare();
770 >
771 >        if (rgrpsq < rCutSq) {
772 >
773 >          if (iLoop == PAIR_LOOP) {
774 >            vij = 0.0;
775 >            fij.zero();
776 >            eField1.zero();
777 >            eField2.zero();
778 >          }
779 >          
780 >          in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
781 >                                                     rgrp);
782 >
783 >          atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
784 >          atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
785 >
786 >          if (doHeatFlux_)
787 >            gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
788 >
789 >          for (ia = atomListRow.begin();
790 >               ia != atomListRow.end(); ++ia) {            
791 >            atom1 = (*ia);
792 >
793 >            for (jb = atomListColumn.begin();
794 >                 jb != atomListColumn.end(); ++jb) {              
795 >              atom2 = (*jb);
796 >
797 >              if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
798 >
799 >                vpair = 0.0;
800 >                workPot = 0.0;
801 >                exPot = 0.0;
802 >                f1.zero();
803 >                dVdFQ1 = 0.0;
804 >                dVdFQ2 = 0.0;
805 >
806 >                fDecomp_->fillInteractionData(idat, atom1, atom2);
807 >
808 >                topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
809 >                vdwMult = vdwScale_[topoDist];
810 >                electroMult = electrostaticScale_[topoDist];
811 >
812 >                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
813 >                  idat.d = &d_grp;
814 >                  idat.r2 = &rgrpsq;
815 >                  if (doHeatFlux_)
816 >                    vel2 = gvel2;
817 >                } else {
818 >                  d = fDecomp_->getInteratomicVector(atom1, atom2);
819 >                  curSnapshot->wrapVector( d );
820 >                  r2 = d.lengthSquare();
821 >                  idat.d = &d;
822 >                  idat.r2 = &r2;
823 >                  if (doHeatFlux_)
824 >                    vel2 = fDecomp_->getAtomVelocityColumn(atom2);
825 >                }
826 >              
827 >                r = sqrt( *(idat.r2) );
828 >                idat.rij = &r;
829 >              
830 >                if (iLoop == PREPAIR_LOOP) {
831 >                  interactionMan_->doPrePair(idat);
832 >                } else {
833 >                  interactionMan_->doPair(idat);
834 >                  fDecomp_->unpackInteractionData(idat, atom1, atom2);
835 >                  vij += vpair;
836 >                  fij += f1;
837 >                  stressTensor -= outProduct( *(idat.d), f1);
838 >                  if (doHeatFlux_)
839 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
840 >                }
841 >              }
842 >            }
843 >          }
844 >
845 >          if (iLoop == PAIR_LOOP) {
846 >            if (in_switching_region) {
847 >              swderiv = vij * dswdr / rgrp;
848 >              fg = swderiv * d_grp;
849 >              fij += fg;
850 >
851 >              if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
852 >                if (!fDecomp_->skipAtomPair(atomListRow[0],
853 >                                            atomListColumn[0],
854 >                                            cg1, cg2)) {
855 >                  stressTensor -= outProduct( *(idat.d), fg);
856 >                  if (doHeatFlux_)
857 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
858 >                }                
859 >              }
860 >          
861 >              for (ia = atomListRow.begin();
862 >                   ia != atomListRow.end(); ++ia) {            
863 >                atom1 = (*ia);                
864 >                mf = fDecomp_->getMassFactorRow(atom1);
865 >                // fg is the force on atom ia due to cutoff group's
866 >                // presence in switching region
867 >                fg = swderiv * d_grp * mf;
868 >                fDecomp_->addForceToAtomRow(atom1, fg);
869 >                if (atomListRow.size() > 1) {
870 >                  if (info_->usesAtomicVirial()) {
871 >                    // find the distance between the atom
872 >                    // and the center of the cutoff group:
873 >                    dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
874 >                    stressTensor -= outProduct(dag, fg);
875 >                    if (doHeatFlux_)
876 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
877 >                  }
878 >                }
879 >              }
880 >              for (jb = atomListColumn.begin();
881 >                   jb != atomListColumn.end(); ++jb) {              
882 >                atom2 = (*jb);
883 >                mf = fDecomp_->getMassFactorColumn(atom2);
884 >                // fg is the force on atom jb due to cutoff group's
885 >                // presence in switching region
886 >                fg = -swderiv * d_grp * mf;
887 >                fDecomp_->addForceToAtomColumn(atom2, fg);
888 >
889 >                if (atomListColumn.size() > 1) {
890 >                  if (info_->usesAtomicVirial()) {
891 >                    // find the distance between the atom
892 >                    // and the center of the cutoff group:
893 >                    dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
894 >                    stressTensor -= outProduct(dag, fg);
895 >                    if (doHeatFlux_)
896 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
897 >                  }
898 >                }
899 >              }
900 >            }
901 >            //if (!info_->usesAtomicVirial()) {
902 >            //  stressTensor -= outProduct(d_grp, fij);
903 >            //  if (doHeatFlux_)
904 >            //     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
905 >            //}
906 >          }
907 >        }
908 >      }
909 >
910 >      if (iLoop == PREPAIR_LOOP) {
911 >        if (info_->requiresPrepair()) {
912 >
913 >          fDecomp_->collectIntermediateData();
914 >
915 >          for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
916 >            fDecomp_->fillSelfData(sdat, atom1);
917 >            interactionMan_->doPreForce(sdat);
918 >          }
919 >
920 >          fDecomp_->distributeIntermediateData();
921 >
922 >        }
923 >      }
924      }
925 <  
926 <    // grab the simulation box dipole moment if specified
927 <    if (info_->getCalcBoxDipole()){
928 <      getAccumulatedBoxDipole(totalDipole.getArrayPointer());
929 <      
310 <      curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
311 <      curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
312 <      curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
925 >    
926 >    // collects pairwise information
927 >    fDecomp_->collectData();
928 >    if (cutoffMethod_ == EWALD_FULL) {
929 >      interactionMan_->doReciprocalSpaceSum();
930      }
931 +        
932 +    if (info_->requiresSelfCorrection()) {
933 +      for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
934 +        fDecomp_->fillSelfData(sdat, atom1);
935 +        interactionMan_->doSelfCorrection(sdat);
936 +      }
937 +    }
938 +
939 +    // collects single-atom information
940 +    fDecomp_->collectSelfData();
941 +
942 +    longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
943 +      *(fDecomp_->getPairwisePotential());
944 +
945 +    curSnapshot->setLongRangePotential(longRangePotential);
946      
947 <    //store the tau and long range potential    
948 <    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
949 <    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
318 <    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
947 >    curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
948 >                                         *(fDecomp_->getExcludedPotential()));
949 >
950    }
951  
952    
953    void ForceManager::postCalculation() {
954 +
955 +    vector<Perturbation*>::iterator pi;
956 +    for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
957 +      (*pi)->applyPerturbation();
958 +    }
959 +
960      SimInfo::MoleculeIterator mi;
961      Molecule* mol;
962      Molecule::RigidBodyIterator rbIter;
963      RigidBody* rb;
964      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
965 <    
965 >  
966      // collect the atomic forces onto rigid bodies
967      
968      for (mol = info_->beginMolecule(mi); mol != NULL;
# Line 333 | Line 970 | namespace OpenMD {
970        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
971             rb = mol->nextRigidBody(rbIter)) {
972          Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
973 <        tau += rbTau;
973 >        stressTensor += rbTau;
974        }
975      }
976      
977   #ifdef IS_MPI
978 <    Mat3x3d tmpTau(tau);
979 <    MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
343 <                  9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
978 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
979 >                              MPI::REALTYPE, MPI::SUM);
980   #endif
981 <    curSnapshot->statData.setTau(tau);
982 <  }
981 >    curSnapshot->setStressTensor(stressTensor);
982 >    
983 >    if (info_->getSimParams()->getUseLongRangeCorrections()) {
984 >      /*
985 >      RealType vol = curSnapshot->getVolume();
986 >      RealType Elrc(0.0);
987 >      RealType Wlrc(0.0);
988  
989 < } //end namespace OpenMD
989 >      set<AtomType*>::iterator i;
990 >      set<AtomType*>::iterator j;
991 >    
992 >      RealType n_i, n_j;
993 >      RealType rho_i, rho_j;
994 >      pair<RealType, RealType> LRI;
995 >      
996 >      for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
997 >        n_i = RealType(info_->getGlobalCountOfType(*i));
998 >        rho_i = n_i /  vol;
999 >        for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) {
1000 >          n_j = RealType(info_->getGlobalCountOfType(*j));
1001 >          rho_j = n_j / vol;
1002 >          
1003 >          LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) );
1004 >
1005 >          Elrc += n_i   * rho_j * LRI.first;
1006 >          Wlrc -= rho_i * rho_j * LRI.second;
1007 >        }
1008 >      }
1009 >      Elrc *= 2.0 * NumericConstant::PI;
1010 >      Wlrc *= 2.0 * NumericConstant::PI;
1011 >
1012 >      RealType lrp = curSnapshot->getLongRangePotential();
1013 >      curSnapshot->setLongRangePotential(lrp + Elrc);
1014 >      stressTensor += Wlrc * SquareMatrix3<RealType>::identity();
1015 >      curSnapshot->setStressTensor(stressTensor);
1016 >      */
1017 >    
1018 >    }
1019 >  }
1020 > }

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