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Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1485 by gezelter, Wed Jul 28 19:52:00 2010 UTC vs.
Revision 1712 by gezelter, Sat May 19 13:30:21 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 <                                               NBforcesInitialized_(false) {
72 <    lj_ = LJ::Instance();
73 <    lj_->setForceField(info_->getForceField());
70 >  ForceManager::ForceManager(SimInfo * info) : info_(info) {
71 >    forceField_ = info_->getForceField();
72 >    interactionMan_ = new InteractionManager();
73 >    fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
74 >  }
75  
76 <    gb_ = GB::Instance();
77 <    gb_->setForceField(info_->getForceField());
76 >  /**
77 >   * setupCutoffs
78 >   *
79 >   * Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
80 >   * and cutoffPolicy
81 >   *
82 >   * cutoffRadius : realType
83 >   *  If the cutoffRadius was explicitly set, use that value.
84 >   *  If the cutoffRadius was not explicitly set:
85 >   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
86 >   *      No electrostatic atoms?  Poll the atom types present in the
87 >   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
88 >   *      Use the maximum suggested value that was found.
89 >   *
90 >   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
91 >   *                        or SHIFTED_POTENTIAL)
92 >   *      If cutoffMethod was explicitly set, use that choice.
93 >   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
94 >   *
95 >   * cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
96 >   *      If cutoffPolicy was explicitly set, use that choice.
97 >   *      If cutoffPolicy was not explicitly set, use TRADITIONAL
98 >   *
99 >   * switchingRadius : realType
100 >   *  If the cutoffMethod was set to SWITCHED:
101 >   *      If the switchingRadius was explicitly set, use that value
102 >   *          (but do a sanity check first).
103 >   *      If the switchingRadius was not explicitly set: use 0.85 *
104 >   *      cutoffRadius_
105 >   *  If the cutoffMethod was not set to SWITCHED:
106 >   *      Set switchingRadius equal to cutoffRadius for safety.
107 >   */
108 >  void ForceManager::setupCutoffs() {
109 >    
110 >    Globals* simParams_ = info_->getSimParams();
111 >    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
112 >    int mdFileVersion;
113 >    
114 >    if (simParams_->haveMDfileVersion())
115 >      mdFileVersion = simParams_->getMDfileVersion();
116 >    else
117 >      mdFileVersion = 0;
118 >  
119 >    if (simParams_->haveCutoffRadius()) {
120 >      rCut_ = simParams_->getCutoffRadius();
121 >    } else {      
122 >      if (info_->usesElectrostaticAtoms()) {
123 >        sprintf(painCave.errMsg,
124 >                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
125 >                "\tOpenMD will use a default value of 12.0 angstroms"
126 >                "\tfor the cutoffRadius.\n");
127 >        painCave.isFatal = 0;
128 >        painCave.severity = OPENMD_INFO;
129 >        simError();
130 >        rCut_ = 12.0;
131 >      } else {
132 >        RealType thisCut;
133 >        set<AtomType*>::iterator i;
134 >        set<AtomType*> atomTypes;
135 >        atomTypes = info_->getSimulatedAtomTypes();        
136 >        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
137 >          thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
138 >          rCut_ = max(thisCut, rCut_);
139 >        }
140 >        sprintf(painCave.errMsg,
141 >                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
142 >                "\tOpenMD will use %lf angstroms.\n",
143 >                rCut_);
144 >        painCave.isFatal = 0;
145 >        painCave.severity = OPENMD_INFO;
146 >        simError();
147 >      }
148 >    }
149  
150 <    sticky_ = Sticky::Instance();
151 <    sticky_->setForceField(info_->getForceField());
150 >    fDecomp_->setUserCutoff(rCut_);
151 >    interactionMan_->setCutoffRadius(rCut_);
152  
153 <    eam_ = EAM::Instance();
154 <    eam_->setForceField(info_->getForceField());
155 <  }
156 <
157 <  void ForceManager::calcForces() {
153 >    map<string, CutoffMethod> stringToCutoffMethod;
154 >    stringToCutoffMethod["HARD"] = HARD;
155 >    stringToCutoffMethod["SWITCHED"] = SWITCHED;
156 >    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
157 >    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
158 >  
159 >    if (simParams_->haveCutoffMethod()) {
160 >      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
161 >      map<string, CutoffMethod>::iterator i;
162 >      i = stringToCutoffMethod.find(cutMeth);
163 >      if (i == stringToCutoffMethod.end()) {
164 >        sprintf(painCave.errMsg,
165 >                "ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
166 >                "\tShould be one of: "
167 >                "HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
168 >                cutMeth.c_str());
169 >        painCave.isFatal = 1;
170 >        painCave.severity = OPENMD_ERROR;
171 >        simError();
172 >      } else {
173 >        cutoffMethod_ = i->second;
174 >      }
175 >    } else {
176 >      if (mdFileVersion > 1) {
177 >        sprintf(painCave.errMsg,
178 >                "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
179 >                "\tOpenMD will use SHIFTED_FORCE.\n");
180 >        painCave.isFatal = 0;
181 >        painCave.severity = OPENMD_INFO;
182 >        simError();
183 >        cutoffMethod_ = SHIFTED_FORCE;        
184 >      } else {
185 >        // handle the case where the old file version was in play
186 >        // (there should be no cutoffMethod, so we have to deduce it
187 >        // from other data).        
188 >
189 >        sprintf(painCave.errMsg,
190 >                "ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
191 >                "\tOpenMD found a file which does not set a cutoffMethod.\n"
192 >                "\tOpenMD will attempt to deduce a cutoffMethod using the\n"
193 >                "\tbehavior of the older (version 1) code.  To remove this\n"
194 >                "\twarning, add an explicit cutoffMethod and change the top\n"
195 >                "\tof the file so that it begins with <OpenMD version=2>\n");
196 >        painCave.isFatal = 0;
197 >        painCave.severity = OPENMD_WARNING;
198 >        simError();            
199 >                
200 >        // The old file version tethered the shifting behavior to the
201 >        // electrostaticSummationMethod keyword.
202 >        
203 >        if (simParams_->haveElectrostaticSummationMethod()) {
204 >          string myMethod = simParams_->getElectrostaticSummationMethod();
205 >          toUpper(myMethod);
206 >        
207 >          if (myMethod == "SHIFTED_POTENTIAL") {
208 >            cutoffMethod_ = SHIFTED_POTENTIAL;
209 >          } else if (myMethod == "SHIFTED_FORCE") {
210 >            cutoffMethod_ = SHIFTED_FORCE;
211 >          }
212 >        
213 >          if (simParams_->haveSwitchingRadius())
214 >            rSwitch_ = simParams_->getSwitchingRadius();
215 >
216 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
217 >            if (simParams_->haveSwitchingRadius()){
218 >              sprintf(painCave.errMsg,
219 >                      "ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
220 >                      "\tA value was set for the switchingRadius\n"
221 >                      "\teven though the electrostaticSummationMethod was\n"
222 >                      "\tset to %s\n", myMethod.c_str());
223 >              painCave.severity = OPENMD_WARNING;
224 >              painCave.isFatal = 1;
225 >              simError();            
226 >            }
227 >          }
228 >          if (abs(rCut_ - rSwitch_) < 0.0001) {
229 >            if (cutoffMethod_ == SHIFTED_FORCE) {              
230 >              sprintf(painCave.errMsg,
231 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
232 >                      "\tcutoffRadius and switchingRadius are set to the\n"
233 >                      "\tsame value.  OpenMD will use shifted force\n"
234 >                      "\tpotentials instead of switching functions.\n");
235 >              painCave.isFatal = 0;
236 >              painCave.severity = OPENMD_WARNING;
237 >              simError();            
238 >            } else {
239 >              cutoffMethod_ = SHIFTED_POTENTIAL;
240 >              sprintf(painCave.errMsg,
241 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
242 >                      "\tcutoffRadius and switchingRadius are set to the\n"
243 >                      "\tsame value.  OpenMD will use shifted potentials\n"
244 >                      "\tinstead of switching functions.\n");
245 >              painCave.isFatal = 0;
246 >              painCave.severity = OPENMD_WARNING;
247 >              simError();            
248 >            }
249 >          }
250 >        }
251 >      }
252 >    }
253 >
254 >    map<string, CutoffPolicy> stringToCutoffPolicy;
255 >    stringToCutoffPolicy["MIX"] = MIX;
256 >    stringToCutoffPolicy["MAX"] = MAX;
257 >    stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;    
258 >
259 >    string cutPolicy;
260 >    if (forceFieldOptions_.haveCutoffPolicy()){
261 >      cutPolicy = forceFieldOptions_.getCutoffPolicy();
262 >    }else if (simParams_->haveCutoffPolicy()) {
263 >      cutPolicy = simParams_->getCutoffPolicy();
264 >    }
265 >
266 >    if (!cutPolicy.empty()){
267 >      toUpper(cutPolicy);
268 >      map<string, CutoffPolicy>::iterator i;
269 >      i = stringToCutoffPolicy.find(cutPolicy);
270 >
271 >      if (i == stringToCutoffPolicy.end()) {
272 >        sprintf(painCave.errMsg,
273 >                "ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
274 >                "\tShould be one of: "
275 >                "MIX, MAX, or TRADITIONAL\n",
276 >                cutPolicy.c_str());
277 >        painCave.isFatal = 1;
278 >        painCave.severity = OPENMD_ERROR;
279 >        simError();
280 >      } else {
281 >        cutoffPolicy_ = i->second;
282 >      }
283 >    } else {
284 >      sprintf(painCave.errMsg,
285 >              "ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
286 >              "\tOpenMD will use TRADITIONAL.\n");
287 >      painCave.isFatal = 0;
288 >      painCave.severity = OPENMD_INFO;
289 >      simError();
290 >      cutoffPolicy_ = TRADITIONAL;        
291 >    }
292 >
293 >    fDecomp_->setCutoffPolicy(cutoffPolicy_);
294 >        
295 >    // create the switching function object:
296 >
297 >    switcher_ = new SwitchingFunction();
298 >  
299 >    if (cutoffMethod_ == SWITCHED) {
300 >      if (simParams_->haveSwitchingRadius()) {
301 >        rSwitch_ = simParams_->getSwitchingRadius();
302 >        if (rSwitch_ > rCut_) {        
303 >          sprintf(painCave.errMsg,
304 >                  "ForceManager::setupCutoffs: switchingRadius (%f) is larger "
305 >                  "than the cutoffRadius(%f)\n", rSwitch_, rCut_);
306 >          painCave.isFatal = 1;
307 >          painCave.severity = OPENMD_ERROR;
308 >          simError();
309 >        }
310 >      } else {      
311 >        rSwitch_ = 0.85 * rCut_;
312 >        sprintf(painCave.errMsg,
313 >                "ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
314 >                "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
315 >                "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
316 >        painCave.isFatal = 0;
317 >        painCave.severity = OPENMD_WARNING;
318 >        simError();
319 >      }
320 >    } else {
321 >      if (mdFileVersion > 1) {
322 >        // throw an error if we define a switching radius and don't need one.
323 >        // older file versions should not do this.
324 >        if (simParams_->haveSwitchingRadius()) {
325 >          map<string, CutoffMethod>::const_iterator it;
326 >          string theMeth;
327 >          for (it = stringToCutoffMethod.begin();
328 >               it != stringToCutoffMethod.end(); ++it) {
329 >            if (it->second == cutoffMethod_) {
330 >              theMeth = it->first;
331 >              break;
332 >            }
333 >          }
334 >          sprintf(painCave.errMsg,
335 >                  "ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
336 >                  "\tis not set to SWITCHED, so switchingRadius value\n"
337 >                  "\twill be ignored for this simulation\n", theMeth.c_str());
338 >          painCave.isFatal = 0;
339 >          painCave.severity = OPENMD_WARNING;
340 >          simError();
341 >        }
342 >      }
343 >      rSwitch_ = rCut_;
344 >    }
345      
346 <    if (!info_->isFortranInitialized()) {
346 >    // Default to cubic switching function.
347 >    sft_ = cubic;
348 >    if (simParams_->haveSwitchingFunctionType()) {
349 >      string funcType = simParams_->getSwitchingFunctionType();
350 >      toUpper(funcType);
351 >      if (funcType == "CUBIC") {
352 >        sft_ = cubic;
353 >      } else {
354 >        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
355 >          sft_ = fifth_order_poly;
356 >        } else {
357 >          // throw error        
358 >          sprintf( painCave.errMsg,
359 >                   "ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
360 >                   "\tswitchingFunctionType must be one of: "
361 >                   "\"cubic\" or \"fifth_order_polynomial\".",
362 >                   funcType.c_str() );
363 >          painCave.isFatal = 1;
364 >          painCave.severity = OPENMD_ERROR;
365 >          simError();
366 >        }          
367 >      }
368 >    }
369 >    switcher_->setSwitchType(sft_);
370 >    switcher_->setSwitch(rSwitch_, rCut_);
371 >    interactionMan_->setSwitchingRadius(rSwitch_);
372 >  }
373 >
374 >
375 >
376 >  
377 >  void ForceManager::initialize() {
378 >
379 >    if (!info_->isTopologyDone()) {
380 >
381        info_->update();
382 +      interactionMan_->setSimInfo(info_);
383 +      interactionMan_->initialize();
384 +
385 +      // We want to delay the cutoffs until after the interaction
386 +      // manager has set up the atom-atom interactions so that we can
387 +      // query them for suggested cutoff values
388 +      setupCutoffs();
389 +
390 +      info_->prepareTopology();      
391 +
392 +      doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
393 +  
394      }
395 +
396 +    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
397      
398 <    preCalculation();
398 >    // Force fields can set options on how to scale van der Waals and
399 >    // electrostatic interactions for atoms connected via bonds, bends
400 >    // and torsions in this case the topological distance between
401 >    // atoms is:
402 >    // 0 = topologically unconnected
403 >    // 1 = bonded together
404 >    // 2 = connected via a bend
405 >    // 3 = connected via a torsion
406      
407 <    calcShortRangeInteraction();
407 >    vdwScale_.reserve(4);
408 >    fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
409  
410 <    calcLongRangeInteraction();
410 >    electrostaticScale_.reserve(4);
411 >    fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
412  
413 <    postCalculation();
413 >    vdwScale_[0] = 1.0;
414 >    vdwScale_[1] = fopts.getvdw12scale();
415 >    vdwScale_[2] = fopts.getvdw13scale();
416 >    vdwScale_[3] = fopts.getvdw14scale();
417      
418 +    electrostaticScale_[0] = 1.0;
419 +    electrostaticScale_[1] = fopts.getelectrostatic12scale();
420 +    electrostaticScale_[2] = fopts.getelectrostatic13scale();
421 +    electrostaticScale_[3] = fopts.getelectrostatic14scale();    
422 +    
423 +    fDecomp_->distributeInitialData();
424 +
425 +    initialized_ = true;
426 +
427    }
428 +
429 +  void ForceManager::calcForces() {
430 +    
431 +    if (!initialized_) initialize();
432 +
433 +    preCalculation();  
434 +    shortRangeInteractions();
435 +    longRangeInteractions();
436 +    postCalculation();    
437 +  }
438    
439    void ForceManager::preCalculation() {
440      SimInfo::MoleculeIterator mi;
# Line 98 | Line 443 | namespace OpenMD {
443      Atom* atom;
444      Molecule::RigidBodyIterator rbIter;
445      RigidBody* rb;
446 +    Molecule::CutoffGroupIterator ci;
447 +    CutoffGroup* cg;
448      
449      // forces are zeroed here, before any are accumulated.
103 –    // NOTE: do not rezero the forces in Fortran.
450      
451      for (mol = info_->beginMolecule(mi); mol != NULL;
452           mol = info_->nextMolecule(mi)) {
453 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
453 >      for(atom = mol->beginAtom(ai); atom != NULL;
454 >          atom = mol->nextAtom(ai)) {
455          atom->zeroForcesAndTorques();
456        }
457 <          
457 >      
458        //change the positions of atoms which belong to the rigidbodies
459        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
460             rb = mol->nextRigidBody(rbIter)) {
461          rb->zeroForcesAndTorques();
462        }        
463 <          
463 >      
464 >      if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
465 >        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
466 >            cg = mol->nextCutoffGroup(ci)) {
467 >          //calculate the center of mass of cutoff group
468 >          cg->updateCOM();
469 >        }
470 >      }      
471      }
472      
473      // Zero out the stress tensor
# Line 121 | Line 475 | namespace OpenMD {
475      
476    }
477    
478 <  void ForceManager::calcShortRangeInteraction() {
478 >  void ForceManager::shortRangeInteractions() {
479      Molecule* mol;
480      RigidBody* rb;
481      Bond* bond;
# Line 151 | Line 505 | namespace OpenMD {
505  
506        for (bond = mol->beginBond(bondIter); bond != NULL;
507             bond = mol->nextBond(bondIter)) {
508 <        bond->calcForce();
508 >        bond->calcForce(doParticlePot_);
509          bondPotential += bond->getPotential();
510        }
511  
# Line 159 | Line 513 | namespace OpenMD {
513             bend = mol->nextBend(bendIter)) {
514          
515          RealType angle;
516 <        bend->calcForce(angle);
516 >        bend->calcForce(angle, doParticlePot_);
517          RealType currBendPot = bend->getPotential();          
518          
519          bendPotential += bend->getPotential();
520 <        std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
520 >        map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
521          if (i == bendDataSets.end()) {
522            BendDataSet dataSet;
523            dataSet.prev.angle = dataSet.curr.angle = angle;
524            dataSet.prev.potential = dataSet.curr.potential = currBendPot;
525            dataSet.deltaV = 0.0;
526 <          bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
526 >          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
527 >                                                                  dataSet));
528          }else {
529            i->second.prev.angle = i->second.curr.angle;
530            i->second.prev.potential = i->second.curr.potential;
# Line 183 | Line 538 | namespace OpenMD {
538        for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
539             torsion = mol->nextTorsion(torsionIter)) {
540          RealType angle;
541 <        torsion->calcForce(angle);
541 >        torsion->calcForce(angle, doParticlePot_);
542          RealType currTorsionPot = torsion->getPotential();
543          torsionPotential += torsion->getPotential();
544 <        std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
544 >        map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
545          if (i == torsionDataSets.end()) {
546            TorsionDataSet dataSet;
547            dataSet.prev.angle = dataSet.curr.angle = angle;
548            dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
549            dataSet.deltaV = 0.0;
550 <          torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
550 >          torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
551          }else {
552            i->second.prev.angle = i->second.curr.angle;
553            i->second.prev.potential = i->second.curr.potential;
# Line 202 | Line 557 | namespace OpenMD {
557                                     i->second.prev.potential);
558          }      
559        }      
560 <
560 >      
561        for (inversion = mol->beginInversion(inversionIter);
562             inversion != NULL;
563             inversion = mol->nextInversion(inversionIter)) {
564          RealType angle;
565 <        inversion->calcForce(angle);
565 >        inversion->calcForce(angle, doParticlePot_);
566          RealType currInversionPot = inversion->getPotential();
567          inversionPotential += inversion->getPotential();
568 <        std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
568 >        map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
569          if (i == inversionDataSets.end()) {
570            InversionDataSet dataSet;
571            dataSet.prev.angle = dataSet.curr.angle = angle;
572            dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
573            dataSet.deltaV = 0.0;
574 <          inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
574 >          inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
575          }else {
576            i->second.prev.angle = i->second.curr.angle;
577            i->second.prev.potential = i->second.curr.potential;
# Line 235 | Line 590 | namespace OpenMD {
590      curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
591      curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
592      curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
593 <    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
239 <    
593 >    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;    
594    }
595    
596 <  void ForceManager::calcLongRangeInteraction() {
243 <    Snapshot* curSnapshot;
244 <    DataStorage* config;
245 <    RealType* frc;
246 <    RealType* pos;
247 <    RealType* trq;
248 <    RealType* A;
249 <    RealType* electroFrame;
250 <    RealType* rc;
251 <    RealType* particlePot;
252 <    
253 <    //get current snapshot from SimInfo
254 <    curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
255 <    
256 <    //get array pointers
257 <    config = &(curSnapshot->atomData);
258 <    frc = config->getArrayPointer(DataStorage::dslForce);
259 <    pos = config->getArrayPointer(DataStorage::dslPosition);
260 <    trq = config->getArrayPointer(DataStorage::dslTorque);
261 <    A   = config->getArrayPointer(DataStorage::dslAmat);
262 <    electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
263 <    particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
596 >  void ForceManager::longRangeInteractions() {
597  
598 +    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
599 +    DataStorage* config = &(curSnapshot->atomData);
600 +    DataStorage* cgConfig = &(curSnapshot->cgData);
601 +
602      //calculate the center of mass of cutoff group
603 +
604      SimInfo::MoleculeIterator mi;
605      Molecule* mol;
606      Molecule::CutoffGroupIterator ci;
607      CutoffGroup* cg;
608 <    Vector3d com;
609 <    std::vector<Vector3d> rcGroup;
272 <    
273 <    if(info_->getNCutoffGroups() > 0){
274 <      
608 >
609 >    if(info_->getNCutoffGroups() > 0){      
610        for (mol = info_->beginMolecule(mi); mol != NULL;
611             mol = info_->nextMolecule(mi)) {
612          for(cg = mol->beginCutoffGroup(ci); cg != NULL;
613              cg = mol->nextCutoffGroup(ci)) {
614 <          cg->getCOM(com);
280 <          rcGroup.push_back(com);
614 >          cg->updateCOM();
615          }
616 <      }// end for (mol)
283 <      
284 <      rc = rcGroup[0].getArrayPointer();
616 >      }      
617      } else {
618        // center of mass of the group is the same as position of the atom  
619        // if cutoff group does not exist
620 <      rc = pos;
620 >      cgConfig->position = config->position;
621      }
622 +
623 +    fDecomp_->zeroWorkArrays();
624 +    fDecomp_->distributeData();
625      
626 <    //initialize data before passing to fortran
627 <    RealType longRangePotential[LR_POT_TYPES];
628 <    RealType lrPot = 0.0;
629 <    Vector3d totalDipole;
630 <    int isError = 0;
626 >    int cg1, cg2, atom1, atom2, topoDist;
627 >    Vector3d d_grp, dag, d;
628 >    RealType rgrpsq, rgrp, r2, r;
629 >    RealType electroMult, vdwMult;
630 >    RealType vij;
631 >    Vector3d fij, fg, f1;
632 >    tuple3<RealType, RealType, RealType> cuts;
633 >    RealType rCutSq;
634 >    bool in_switching_region;
635 >    RealType sw, dswdr, swderiv;
636 >    vector<int> atomListColumn, atomListRow, atomListLocal;
637 >    InteractionData idat;
638 >    SelfData sdat;
639 >    RealType mf;
640 >    RealType lrPot;
641 >    RealType vpair;
642 >    potVec longRangePotential(0.0);
643 >    potVec workPot(0.0);
644  
645 <    for (int i=0; i<LR_POT_TYPES;i++){
646 <      longRangePotential[i]=0.0; //Initialize array
647 <    }
645 >    int loopStart, loopEnd;
646 >
647 >    idat.vdwMult = &vdwMult;
648 >    idat.electroMult = &electroMult;
649 >    idat.pot = &workPot;
650 >    sdat.pot = fDecomp_->getEmbeddingPotential();
651 >    idat.vpair = &vpair;
652 >    idat.f1 = &f1;
653 >    idat.sw = &sw;
654 >    idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
655 >    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
656 >    idat.doParticlePot = doParticlePot_;
657 >    sdat.doParticlePot = doParticlePot_;
658      
659 <    doForceLoop(pos,
660 <                rc,
661 <                A,
662 <                electroFrame,
663 <                frc,
306 <                trq,
307 <                tau.getArrayPointer(),
308 <                longRangePotential,
309 <                particlePot,
310 <                &isError );
311 <    
312 <    if( isError ){
313 <      sprintf( painCave.errMsg,
314 <               "Error returned from the fortran force calculation.\n" );
315 <      painCave.isFatal = 1;
316 <      simError();
659 >    loopEnd = PAIR_LOOP;
660 >    if (info_->requiresPrepair() ) {
661 >      loopStart = PREPAIR_LOOP;
662 >    } else {
663 >      loopStart = PAIR_LOOP;
664      }
665 <    for (int i=0; i<LR_POT_TYPES;i++){
666 <      lrPot += longRangePotential[i]; //Quick hack
665 >  
666 >    for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
667 >    
668 >      if (iLoop == loopStart) {
669 >        bool update_nlist = fDecomp_->checkNeighborList();
670 >        if (update_nlist)
671 >          neighborList = fDecomp_->buildNeighborList();
672 >      }            
673 >
674 >      for (vector<pair<int, int> >::iterator it = neighborList.begin();
675 >             it != neighborList.end(); ++it) {
676 >                
677 >        cg1 = (*it).first;
678 >        cg2 = (*it).second;
679 >        
680 >        cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
681 >
682 >        d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
683 >
684 >        curSnapshot->wrapVector(d_grp);        
685 >        rgrpsq = d_grp.lengthSquare();
686 >        rCutSq = cuts.second;
687 >
688 >        if (rgrpsq < rCutSq) {
689 >          idat.rcut = &cuts.first;
690 >          if (iLoop == PAIR_LOOP) {
691 >            vij = 0.0;
692 >            fij = V3Zero;
693 >          }
694 >          
695 >          in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
696 >                                                     rgrp);
697 >          
698 >          atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
699 >          atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
700 >
701 >          for (vector<int>::iterator ia = atomListRow.begin();
702 >               ia != atomListRow.end(); ++ia) {            
703 >            atom1 = (*ia);
704 >            
705 >            for (vector<int>::iterator jb = atomListColumn.begin();
706 >                 jb != atomListColumn.end(); ++jb) {              
707 >              atom2 = (*jb);
708 >
709 >              if (!fDecomp_->skipAtomPair(atom1, atom2)) {
710 >                vpair = 0.0;
711 >                workPot = 0.0;
712 >                f1 = V3Zero;
713 >
714 >                fDecomp_->fillInteractionData(idat, atom1, atom2);
715 >                
716 >                topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
717 >                vdwMult = vdwScale_[topoDist];
718 >                electroMult = electrostaticScale_[topoDist];
719 >
720 >                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
721 >                  idat.d = &d_grp;
722 >                  idat.r2 = &rgrpsq;
723 >                } else {
724 >                  d = fDecomp_->getInteratomicVector(atom1, atom2);
725 >                  curSnapshot->wrapVector( d );
726 >                  r2 = d.lengthSquare();
727 >                  idat.d = &d;
728 >                  idat.r2 = &r2;
729 >                }
730 >              
731 >                r = sqrt( *(idat.r2) );
732 >                idat.rij = &r;
733 >              
734 >                if (iLoop == PREPAIR_LOOP) {
735 >                  interactionMan_->doPrePair(idat);
736 >                } else {
737 >                  interactionMan_->doPair(idat);
738 >                  fDecomp_->unpackInteractionData(idat, atom1, atom2);
739 >                  vij += vpair;
740 >                  fij += f1;
741 >                  tau -= outProduct( *(idat.d), f1);
742 >                }
743 >              }
744 >            }
745 >          }
746 >
747 >          if (iLoop == PAIR_LOOP) {
748 >            if (in_switching_region) {
749 >              swderiv = vij * dswdr / rgrp;
750 >              fg = swderiv * d_grp;
751 >              fij += fg;
752 >
753 >              if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
754 >                tau -= outProduct( *(idat.d), fg);
755 >              }
756 >          
757 >              for (vector<int>::iterator ia = atomListRow.begin();
758 >                   ia != atomListRow.end(); ++ia) {            
759 >                atom1 = (*ia);                
760 >                mf = fDecomp_->getMassFactorRow(atom1);
761 >                // fg is the force on atom ia due to cutoff group's
762 >                // presence in switching region
763 >                fg = swderiv * d_grp * mf;
764 >                fDecomp_->addForceToAtomRow(atom1, fg);
765 >                if (atomListRow.size() > 1) {
766 >                  if (info_->usesAtomicVirial()) {
767 >                    // find the distance between the atom
768 >                    // and the center of the cutoff group:
769 >                    dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
770 >                    tau -= outProduct(dag, fg);
771 >                  }
772 >                }
773 >              }
774 >              for (vector<int>::iterator jb = atomListColumn.begin();
775 >                   jb != atomListColumn.end(); ++jb) {              
776 >                atom2 = (*jb);
777 >                mf = fDecomp_->getMassFactorColumn(atom2);
778 >                // fg is the force on atom jb due to cutoff group's
779 >                // presence in switching region
780 >                fg = -swderiv * d_grp * mf;
781 >                fDecomp_->addForceToAtomColumn(atom2, fg);
782 >
783 >                if (atomListColumn.size() > 1) {
784 >                  if (info_->usesAtomicVirial()) {
785 >                    // find the distance between the atom
786 >                    // and the center of the cutoff group:
787 >                    dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
788 >                    tau -= outProduct(dag, fg);
789 >                  }
790 >                }
791 >              }
792 >            }
793 >            //if (!info_->usesAtomicVirial()) {
794 >            //  tau -= outProduct(d_grp, fij);
795 >            //}
796 >          }
797 >        }
798 >      }
799 >
800 >      if (iLoop == PREPAIR_LOOP) {
801 >        if (info_->requiresPrepair()) {
802 >
803 >          fDecomp_->collectIntermediateData();
804 >
805 >          for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
806 >            fDecomp_->fillSelfData(sdat, atom1);
807 >            interactionMan_->doPreForce(sdat);
808 >          }
809 >
810 >          fDecomp_->distributeIntermediateData();
811 >
812 >        }
813 >      }
814      }
815      
816 <    // grab the simulation box dipole moment if specified
817 <    if (info_->getCalcBoxDipole()){
818 <      getAccumulatedBoxDipole(totalDipole.getArrayPointer());
819 <      
820 <      curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
821 <      curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
822 <      curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
816 >    fDecomp_->collectData();
817 >        
818 >    if (info_->requiresSelfCorrection()) {
819 >
820 >      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {          
821 >        fDecomp_->fillSelfData(sdat, atom1);
822 >        interactionMan_->doSelfCorrection(sdat);
823 >      }
824 >
825      }
826 <    
826 >
827 >    longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
828 >      *(fDecomp_->getPairwisePotential());
829 >
830 >    lrPot = longRangePotential.sum();
831 >
832      //store the tau and long range potential    
833      curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
834 <    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
835 <    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
834 >    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
835 >    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
836    }
837  
838    
# Line 358 | Line 859 | namespace OpenMD {
859      MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
860                    9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
861   #endif
862 <    curSnapshot->statData.setTau(tau);
862 >    curSnapshot->setTau(tau);
863    }
864  
865   } //end namespace OpenMD

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