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Revision 1467 by gezelter, Sat Jul 17 15:33:03 2010 UTC vs.
Revision 1715 by gezelter, Tue May 22 21:55:31 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/LJ.hpp"
60 > #include "nonbonded/NonBondedInteraction.hpp"
61 > #include "parallel/ForceMatrixDecomposition.hpp"
62  
63 + #include <cstdio>
64 + #include <iostream>
65 + #include <iomanip>
66 +
67 + using namespace std;
68   namespace OpenMD {
69 +  
70 +  ForceManager::ForceManager(SimInfo * info) : info_(info) {
71 +    forceField_ = info_->getForceField();
72 +    interactionMan_ = new InteractionManager();
73 +    fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
74 +  }
75  
76 <  void ForceManager::calcForces() {
76 >  /**
77 >   * setupCutoffs
78 >   *
79 >   * Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
80 >   * and cutoffPolicy
81 >   *
82 >   * cutoffRadius : realType
83 >   *  If the cutoffRadius was explicitly set, use that value.
84 >   *  If the cutoffRadius was not explicitly set:
85 >   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
86 >   *      No electrostatic atoms?  Poll the atom types present in the
87 >   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
88 >   *      Use the maximum suggested value that was found.
89 >   *
90 >   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
91 >   *                        or SHIFTED_POTENTIAL)
92 >   *      If cutoffMethod was explicitly set, use that choice.
93 >   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
94 >   *
95 >   * cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
96 >   *      If cutoffPolicy was explicitly set, use that choice.
97 >   *      If cutoffPolicy was not explicitly set, use TRADITIONAL
98 >   *
99 >   * switchingRadius : realType
100 >   *  If the cutoffMethod was set to SWITCHED:
101 >   *      If the switchingRadius was explicitly set, use that value
102 >   *          (but do a sanity check first).
103 >   *      If the switchingRadius was not explicitly set: use 0.85 *
104 >   *      cutoffRadius_
105 >   *  If the cutoffMethod was not set to SWITCHED:
106 >   *      Set switchingRadius equal to cutoffRadius for safety.
107 >   */
108 >  void ForceManager::setupCutoffs() {
109      
110 <    if (!info_->isFortranInitialized()) {
111 <      info_->update();
110 >    Globals* simParams_ = info_->getSimParams();
111 >    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
112 >    int mdFileVersion;
113 >    
114 >    if (simParams_->haveMDfileVersion())
115 >      mdFileVersion = simParams_->getMDfileVersion();
116 >    else
117 >      mdFileVersion = 0;
118 >  
119 >    if (simParams_->haveCutoffRadius()) {
120 >      rCut_ = simParams_->getCutoffRadius();
121 >    } else {      
122 >      if (info_->usesElectrostaticAtoms()) {
123 >        sprintf(painCave.errMsg,
124 >                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
125 >                "\tOpenMD will use a default value of 12.0 angstroms"
126 >                "\tfor the cutoffRadius.\n");
127 >        painCave.isFatal = 0;
128 >        painCave.severity = OPENMD_INFO;
129 >        simError();
130 >        rCut_ = 12.0;
131 >      } else {
132 >        RealType thisCut;
133 >        set<AtomType*>::iterator i;
134 >        set<AtomType*> atomTypes;
135 >        atomTypes = info_->getSimulatedAtomTypes();        
136 >        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
137 >          thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
138 >          rCut_ = max(thisCut, rCut_);
139 >        }
140 >        sprintf(painCave.errMsg,
141 >                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
142 >                "\tOpenMD will use %lf angstroms.\n",
143 >                rCut_);
144 >        painCave.isFatal = 0;
145 >        painCave.severity = OPENMD_INFO;
146 >        simError();
147 >      }
148      }
149 +
150 +    fDecomp_->setUserCutoff(rCut_);
151 +    interactionMan_->setCutoffRadius(rCut_);
152 +
153 +    map<string, CutoffMethod> stringToCutoffMethod;
154 +    stringToCutoffMethod["HARD"] = HARD;
155 +    stringToCutoffMethod["SWITCHED"] = SWITCHED;
156 +    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
157 +    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
158 +  
159 +    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 (!NBforcesInitialized_) {
347 <      LJ* lj = new LJ(info_->getForceField());
348 <      lj->initialize();
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 <    preCalculation();
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 <    calcShortRangeInteraction();
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 >    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 89 | 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.
94 –    // 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 112 | 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 142 | 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 150 | 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 174 | 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 193 | 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 226 | 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;
230 <    
593 >    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;    
594    }
595    
596 <  void ForceManager::calcLongRangeInteraction() {
234 <    Snapshot* curSnapshot;
235 <    DataStorage* config;
236 <    RealType* frc;
237 <    RealType* pos;
238 <    RealType* trq;
239 <    RealType* A;
240 <    RealType* electroFrame;
241 <    RealType* rc;
242 <    RealType* particlePot;
243 <    
244 <    //get current snapshot from SimInfo
245 <    curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
246 <    
247 <    //get array pointers
248 <    config = &(curSnapshot->atomData);
249 <    frc = config->getArrayPointer(DataStorage::dslForce);
250 <    pos = config->getArrayPointer(DataStorage::dslPosition);
251 <    trq = config->getArrayPointer(DataStorage::dslTorque);
252 <    A   = config->getArrayPointer(DataStorage::dslAmat);
253 <    electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
254 <    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;
263 <    
264 <    if(info_->getNCutoffGroups() > 0){
265 <      
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);
271 <          rcGroup.push_back(com);
614 >          cg->updateCOM();
615          }
616 <      }// end for (mol)
274 <      
275 <      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 >    vector<int>::iterator ia, jb;
645  
646 <    for (int i=0; i<LR_POT_TYPES;i++){
647 <      longRangePotential[i]=0.0; //Initialize array
648 <    }
646 >    int loopStart, loopEnd;
647 >
648 >    idat.vdwMult = &vdwMult;
649 >    idat.electroMult = &electroMult;
650 >    idat.pot = &workPot;
651 >    sdat.pot = fDecomp_->getEmbeddingPotential();
652 >    idat.vpair = &vpair;
653 >    idat.f1 = &f1;
654 >    idat.sw = &sw;
655 >    idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
656 >    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
657 >    idat.doParticlePot = doParticlePot_;
658 >    sdat.doParticlePot = doParticlePot_;
659      
660 <    doForceLoop(pos,
661 <                rc,
662 <                A,
663 <                electroFrame,
664 <                frc,
297 <                trq,
298 <                tau.getArrayPointer(),
299 <                longRangePotential,
300 <                particlePot,
301 <                &isError );
302 <    
303 <    if( isError ){
304 <      sprintf( painCave.errMsg,
305 <               "Error returned from the fortran force calculation.\n" );
306 <      painCave.isFatal = 1;
307 <      simError();
660 >    loopEnd = PAIR_LOOP;
661 >    if (info_->requiresPrepair() ) {
662 >      loopStart = PREPAIR_LOOP;
663 >    } else {
664 >      loopStart = PAIR_LOOP;
665      }
666 <    for (int i=0; i<LR_POT_TYPES;i++){
667 <      lrPot += longRangePotential[i]; //Quick hack
666 >  
667 >    for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
668 >    
669 >      if (iLoop == loopStart) {
670 >        bool update_nlist = fDecomp_->checkNeighborList();
671 >        if (update_nlist)
672 >          neighborList = fDecomp_->buildNeighborList();
673 >      }            
674 >
675 >      for (vector<pair<int, int> >::iterator it = neighborList.begin();
676 >             it != neighborList.end(); ++it) {
677 >                
678 >        cg1 = (*it).first;
679 >        cg2 = (*it).second;
680 >        
681 >        cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
682 >
683 >        d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
684 >
685 >        curSnapshot->wrapVector(d_grp);        
686 >        rgrpsq = d_grp.lengthSquare();
687 >        rCutSq = cuts.second;
688 >
689 >        if (rgrpsq < rCutSq) {
690 >          idat.rcut = &cuts.first;
691 >          if (iLoop == PAIR_LOOP) {
692 >            vij = 0.0;
693 >            fij = V3Zero;
694 >          }
695 >          
696 >          in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
697 >                                                     rgrp);
698 >          
699 >          atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
700 >          atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
701 >
702 >          for (ia = atomListRow.begin();
703 >               ia != atomListRow.end(); ++ia) {            
704 >            atom1 = (*ia);
705 >            
706 >            for (jb = atomListColumn.begin();
707 >                 jb != atomListColumn.end(); ++jb) {              
708 >              atom2 = (*jb);
709 >
710 >              if (!fDecomp_->skipAtomPair(atom1, atom2)) {
711 >                vpair = 0.0;
712 >                workPot = 0.0;
713 >                f1 = V3Zero;
714 >
715 >                fDecomp_->fillInteractionData(idat, atom1, atom2);
716 >                
717 >                topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
718 >                vdwMult = vdwScale_[topoDist];
719 >                electroMult = electrostaticScale_[topoDist];
720 >
721 >                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
722 >                  idat.d = &d_grp;
723 >                  idat.r2 = &rgrpsq;
724 >                } else {
725 >                  d = fDecomp_->getInteratomicVector(atom1, atom2);
726 >                  curSnapshot->wrapVector( d );
727 >                  r2 = d.lengthSquare();
728 >                  idat.d = &d;
729 >                  idat.r2 = &r2;
730 >                }
731 >              
732 >                r = sqrt( *(idat.r2) );
733 >                idat.rij = &r;
734 >              
735 >                if (iLoop == PREPAIR_LOOP) {
736 >                  interactionMan_->doPrePair(idat);
737 >                } else {
738 >                  interactionMan_->doPair(idat);
739 >                  fDecomp_->unpackInteractionData(idat, atom1, atom2);
740 >                  vij += vpair;
741 >                  fij += f1;
742 >                  tau -= outProduct( *(idat.d), f1);
743 >                }
744 >              }
745 >            }
746 >          }
747 >
748 >          if (iLoop == PAIR_LOOP) {
749 >            if (in_switching_region) {
750 >              swderiv = vij * dswdr / rgrp;
751 >              fg = swderiv * d_grp;
752 >              fij += fg;
753 >
754 >              if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
755 >                tau -= outProduct( *(idat.d), fg);
756 >              }
757 >          
758 >              for (ia = atomListRow.begin();
759 >                   ia != atomListRow.end(); ++ia) {            
760 >                atom1 = (*ia);                
761 >                mf = fDecomp_->getMassFactorRow(atom1);
762 >                // fg is the force on atom ia due to cutoff group's
763 >                // presence in switching region
764 >                fg = swderiv * d_grp * mf;
765 >                fDecomp_->addForceToAtomRow(atom1, fg);
766 >                if (atomListRow.size() > 1) {
767 >                  if (info_->usesAtomicVirial()) {
768 >                    // find the distance between the atom
769 >                    // and the center of the cutoff group:
770 >                    dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
771 >                    tau -= outProduct(dag, fg);
772 >                  }
773 >                }
774 >              }
775 >              for (jb = atomListColumn.begin();
776 >                   jb != atomListColumn.end(); ++jb) {              
777 >                atom2 = (*jb);
778 >                mf = fDecomp_->getMassFactorColumn(atom2);
779 >                // fg is the force on atom jb due to cutoff group's
780 >                // presence in switching region
781 >                fg = -swderiv * d_grp * mf;
782 >                fDecomp_->addForceToAtomColumn(atom2, fg);
783 >
784 >                if (atomListColumn.size() > 1) {
785 >                  if (info_->usesAtomicVirial()) {
786 >                    // find the distance between the atom
787 >                    // and the center of the cutoff group:
788 >                    dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
789 >                    tau -= outProduct(dag, fg);
790 >                  }
791 >                }
792 >              }
793 >            }
794 >            //if (!info_->usesAtomicVirial()) {
795 >            //  tau -= outProduct(d_grp, fij);
796 >            //}
797 >          }
798 >        }
799 >      }
800 >
801 >      if (iLoop == PREPAIR_LOOP) {
802 >        if (info_->requiresPrepair()) {
803 >
804 >          fDecomp_->collectIntermediateData();
805 >
806 >          for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
807 >            fDecomp_->fillSelfData(sdat, atom1);
808 >            interactionMan_->doPreForce(sdat);
809 >          }
810 >
811 >          fDecomp_->distributeIntermediateData();
812 >
813 >        }
814 >      }
815      }
816      
817 <    // grab the simulation box dipole moment if specified
818 <    if (info_->getCalcBoxDipole()){
819 <      getAccumulatedBoxDipole(totalDipole.getArrayPointer());
820 <      
821 <      curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
822 <      curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
823 <      curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
817 >    fDecomp_->collectData();
818 >        
819 >    if (info_->requiresSelfCorrection()) {
820 >
821 >      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {          
822 >        fDecomp_->fillSelfData(sdat, atom1);
823 >        interactionMan_->doSelfCorrection(sdat);
824 >      }
825 >
826      }
827 <    
827 >
828 >    longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
829 >      *(fDecomp_->getPairwisePotential());
830 >
831 >    lrPot = longRangePotential.sum();
832 >
833      //store the tau and long range potential    
834      curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
835 <    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
836 <    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
835 >    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
836 >    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
837    }
838  
839    
# Line 349 | Line 860 | namespace OpenMD {
860      MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
861                    9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
862   #endif
863 <    curSnapshot->statData.setTau(tau);
863 >    curSnapshot->setTau(tau);
864    }
865  
866   } //end namespace OpenMD

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