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root/OpenMD/branches/development/src/brains/ForceManager.cpp
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trunk/src/brains/ForceManager.cpp (file contents), Revision 1448 by gezelter, Thu Jun 17 14:58:49 2010 UTC vs.
branches/development/src/brains/ForceManager.cpp (file contents), Revision 1616 by gezelter, Tue Aug 30 15:45:35 2011 UTC

# Line 47 | Line 47
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 "parallel/ForceMatrixDecomposition.hpp"
61 +
62 + #include <cstdio>
63 + #include <iostream>
64 + #include <iomanip>
65 +
66 + using namespace std;
67   namespace OpenMD {
68 +  
69 +  ForceManager::ForceManager(SimInfo * info) : info_(info) {
70 +    forceField_ = info_->getForceField();
71 +    interactionMan_ = new InteractionManager();
72 +    fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
73 +  }
74  
75 <  void ForceManager::calcForces(bool needPotential, bool needStress) {
75 >  /**
76 >   * setupCutoffs
77 >   *
78 >   * Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
79 >   * and cutoffPolicy
80 >   *
81 >   * cutoffRadius : realType
82 >   *  If the cutoffRadius was explicitly set, use that value.
83 >   *  If the cutoffRadius was not explicitly set:
84 >   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
85 >   *      No electrostatic atoms?  Poll the atom types present in the
86 >   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
87 >   *      Use the maximum suggested value that was found.
88 >   *
89 >   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
90 >   *                        or SHIFTED_POTENTIAL)
91 >   *      If cutoffMethod was explicitly set, use that choice.
92 >   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
93 >   *
94 >   * cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
95 >   *      If cutoffPolicy was explicitly set, use that choice.
96 >   *      If cutoffPolicy was not explicitly set, use TRADITIONAL
97 >   *
98 >   * switchingRadius : realType
99 >   *  If the cutoffMethod was set to SWITCHED:
100 >   *      If the switchingRadius was explicitly set, use that value
101 >   *          (but do a sanity check first).
102 >   *      If the switchingRadius was not explicitly set: use 0.85 *
103 >   *      cutoffRadius_
104 >   *  If the cutoffMethod was not set to SWITCHED:
105 >   *      Set switchingRadius equal to cutoffRadius for safety.
106 >   */
107 >  void ForceManager::setupCutoffs() {
108      
109 <    if (!info_->isFortranInitialized()) {
109 >    Globals* simParams_ = info_->getSimParams();
110 >    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
111 >    int mdFileVersion;
112 >    
113 >    if (simParams_->haveMDfileVersion())
114 >      mdFileVersion = simParams_->getMDfileVersion();
115 >    else
116 >      mdFileVersion = 0;
117 >  
118 >    if (simParams_->haveCutoffRadius()) {
119 >      rCut_ = simParams_->getCutoffRadius();
120 >    } else {      
121 >      if (info_->usesElectrostaticAtoms()) {
122 >        sprintf(painCave.errMsg,
123 >                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
124 >                "\tOpenMD will use a default value of 12.0 angstroms"
125 >                "\tfor the cutoffRadius.\n");
126 >        painCave.isFatal = 0;
127 >        painCave.severity = OPENMD_INFO;
128 >        simError();
129 >        rCut_ = 12.0;
130 >      } else {
131 >        RealType thisCut;
132 >        set<AtomType*>::iterator i;
133 >        set<AtomType*> atomTypes;
134 >        atomTypes = info_->getSimulatedAtomTypes();        
135 >        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
136 >          thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
137 >          rCut_ = max(thisCut, rCut_);
138 >        }
139 >        sprintf(painCave.errMsg,
140 >                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
141 >                "\tOpenMD will use %lf angstroms.\n",
142 >                rCut_);
143 >        painCave.isFatal = 0;
144 >        painCave.severity = OPENMD_INFO;
145 >        simError();
146 >      }
147 >    }
148 >
149 >    fDecomp_->setUserCutoff(rCut_);
150 >    interactionMan_->setCutoffRadius(rCut_);
151 >
152 >    map<string, CutoffMethod> stringToCutoffMethod;
153 >    stringToCutoffMethod["HARD"] = HARD;
154 >    stringToCutoffMethod["SWITCHED"] = SWITCHED;
155 >    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
156 >    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
157 >  
158 >    if (simParams_->haveCutoffMethod()) {
159 >      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
160 >      map<string, CutoffMethod>::iterator i;
161 >      i = stringToCutoffMethod.find(cutMeth);
162 >      if (i == stringToCutoffMethod.end()) {
163 >        sprintf(painCave.errMsg,
164 >                "ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
165 >                "\tShould be one of: "
166 >                "HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
167 >                cutMeth.c_str());
168 >        painCave.isFatal = 1;
169 >        painCave.severity = OPENMD_ERROR;
170 >        simError();
171 >      } else {
172 >        cutoffMethod_ = i->second;
173 >      }
174 >    } else {
175 >      if (mdFileVersion > 1) {
176 >        sprintf(painCave.errMsg,
177 >                "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
178 >                "\tOpenMD will use SHIFTED_FORCE.\n");
179 >        painCave.isFatal = 0;
180 >        painCave.severity = OPENMD_INFO;
181 >        simError();
182 >        cutoffMethod_ = SHIFTED_FORCE;        
183 >      } else {
184 >        // handle the case where the old file version was in play
185 >        // (there should be no cutoffMethod, so we have to deduce it
186 >        // from other data).        
187 >
188 >        sprintf(painCave.errMsg,
189 >                "ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
190 >                "\tOpenMD found a file which does not set a cutoffMethod.\n"
191 >                "\tOpenMD will attempt to deduce a cutoffMethod using the\n"
192 >                "\tbehavior of the older (version 1) code.  To remove this\n"
193 >                "\twarning, add an explicit cutoffMethod and change the top\n"
194 >                "\tof the file so that it begins with <OpenMD version=2>\n");
195 >        painCave.isFatal = 0;
196 >        painCave.severity = OPENMD_WARNING;
197 >        simError();            
198 >                
199 >        // The old file version tethered the shifting behavior to the
200 >        // electrostaticSummationMethod keyword.
201 >        
202 >        if (simParams_->haveElectrostaticSummationMethod()) {
203 >          std::string myMethod = simParams_->getElectrostaticSummationMethod();
204 >          toUpper(myMethod);
205 >        
206 >          if (myMethod == "SHIFTED_POTENTIAL") {
207 >            cutoffMethod_ = SHIFTED_POTENTIAL;
208 >          } else if (myMethod == "SHIFTED_FORCE") {
209 >            cutoffMethod_ = SHIFTED_FORCE;
210 >          }
211 >        
212 >          if (simParams_->haveSwitchingRadius())
213 >            rSwitch_ = simParams_->getSwitchingRadius();
214 >
215 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
216 >            if (simParams_->haveSwitchingRadius()){
217 >              sprintf(painCave.errMsg,
218 >                      "ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
219 >                      "\tA value was set for the switchingRadius\n"
220 >                      "\teven though the electrostaticSummationMethod was\n"
221 >                      "\tset to %s\n", myMethod.c_str());
222 >              painCave.severity = OPENMD_WARNING;
223 >              painCave.isFatal = 1;
224 >              simError();            
225 >            }
226 >          }
227 >          if (abs(rCut_ - rSwitch_) < 0.0001) {
228 >            if (cutoffMethod_ == SHIFTED_FORCE) {              
229 >              sprintf(painCave.errMsg,
230 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
231 >                      "\tcutoffRadius and switchingRadius are set to the\n"
232 >                      "\tsame value.  OpenMD will use shifted force\n"
233 >                      "\tpotentials instead of switching functions.\n");
234 >              painCave.isFatal = 0;
235 >              painCave.severity = OPENMD_WARNING;
236 >              simError();            
237 >            } else {
238 >              cutoffMethod_ = SHIFTED_POTENTIAL;
239 >              sprintf(painCave.errMsg,
240 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
241 >                      "\tcutoffRadius and switchingRadius are set to the\n"
242 >                      "\tsame value.  OpenMD will use shifted potentials\n"
243 >                      "\tinstead of switching functions.\n");
244 >              painCave.isFatal = 0;
245 >              painCave.severity = OPENMD_WARNING;
246 >              simError();            
247 >            }
248 >          }
249 >        }
250 >      }
251 >    }
252 >
253 >    map<string, CutoffPolicy> stringToCutoffPolicy;
254 >    stringToCutoffPolicy["MIX"] = MIX;
255 >    stringToCutoffPolicy["MAX"] = MAX;
256 >    stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;    
257 >
258 >    std::string cutPolicy;
259 >    if (forceFieldOptions_.haveCutoffPolicy()){
260 >      cutPolicy = forceFieldOptions_.getCutoffPolicy();
261 >    }else if (simParams_->haveCutoffPolicy()) {
262 >      cutPolicy = simParams_->getCutoffPolicy();
263 >    }
264 >
265 >    if (!cutPolicy.empty()){
266 >      toUpper(cutPolicy);
267 >      map<string, CutoffPolicy>::iterator i;
268 >      i = stringToCutoffPolicy.find(cutPolicy);
269 >
270 >      if (i == stringToCutoffPolicy.end()) {
271 >        sprintf(painCave.errMsg,
272 >                "ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
273 >                "\tShould be one of: "
274 >                "MIX, MAX, or TRADITIONAL\n",
275 >                cutPolicy.c_str());
276 >        painCave.isFatal = 1;
277 >        painCave.severity = OPENMD_ERROR;
278 >        simError();
279 >      } else {
280 >        cutoffPolicy_ = i->second;
281 >      }
282 >    } else {
283 >      sprintf(painCave.errMsg,
284 >              "ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
285 >              "\tOpenMD will use TRADITIONAL.\n");
286 >      painCave.isFatal = 0;
287 >      painCave.severity = OPENMD_INFO;
288 >      simError();
289 >      cutoffPolicy_ = TRADITIONAL;        
290 >    }
291 >
292 >    fDecomp_->setCutoffPolicy(cutoffPolicy_);
293 >        
294 >    // create the switching function object:
295 >
296 >    switcher_ = new SwitchingFunction();
297 >  
298 >    if (cutoffMethod_ == SWITCHED) {
299 >      if (simParams_->haveSwitchingRadius()) {
300 >        rSwitch_ = simParams_->getSwitchingRadius();
301 >        if (rSwitch_ > rCut_) {        
302 >          sprintf(painCave.errMsg,
303 >                  "ForceManager::setupCutoffs: switchingRadius (%f) is larger "
304 >                  "than the cutoffRadius(%f)\n", rSwitch_, rCut_);
305 >          painCave.isFatal = 1;
306 >          painCave.severity = OPENMD_ERROR;
307 >          simError();
308 >        }
309 >      } else {      
310 >        rSwitch_ = 0.85 * rCut_;
311 >        sprintf(painCave.errMsg,
312 >                "ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
313 >                "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
314 >                "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
315 >        painCave.isFatal = 0;
316 >        painCave.severity = OPENMD_WARNING;
317 >        simError();
318 >      }
319 >    } else {
320 >      if (simParams_->haveSwitchingRadius()) {
321 >        map<string, CutoffMethod>::const_iterator it;
322 >        string theMeth;
323 >        for (it = stringToCutoffMethod.begin();
324 >             it != stringToCutoffMethod.end(); ++it) {
325 >          if (it->second == cutoffMethod_) {
326 >            theMeth = it->first;
327 >            break;
328 >          }
329 >        }
330 >        sprintf(painCave.errMsg,
331 >                "ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
332 >                "\tis not set to SWITCHED, so switchingRadius value\n"
333 >                "\twill be ignored for this simulation\n", theMeth.c_str());
334 >        painCave.isFatal = 0;
335 >        painCave.severity = OPENMD_WARNING;
336 >        simError();
337 >      }
338 >
339 >      rSwitch_ = rCut_;
340 >    }
341 >    
342 >    // Default to cubic switching function.
343 >    sft_ = cubic;
344 >    if (simParams_->haveSwitchingFunctionType()) {
345 >      string funcType = simParams_->getSwitchingFunctionType();
346 >      toUpper(funcType);
347 >      if (funcType == "CUBIC") {
348 >        sft_ = cubic;
349 >      } else {
350 >        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
351 >          sft_ = fifth_order_poly;
352 >        } else {
353 >          // throw error        
354 >          sprintf( painCave.errMsg,
355 >                   "ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
356 >                   "\tswitchingFunctionType must be one of: "
357 >                   "\"cubic\" or \"fifth_order_polynomial\".",
358 >                   funcType.c_str() );
359 >          painCave.isFatal = 1;
360 >          painCave.severity = OPENMD_ERROR;
361 >          simError();
362 >        }          
363 >      }
364 >    }
365 >    switcher_->setSwitchType(sft_);
366 >    switcher_->setSwitch(rSwitch_, rCut_);
367 >    interactionMan_->setSwitchingRadius(rSwitch_);
368 >  }
369 >
370 >
371 >
372 >  
373 >  void ForceManager::initialize() {
374 >
375 >    if (!info_->isTopologyDone()) {
376 >
377        info_->update();
378 +      interactionMan_->setSimInfo(info_);
379 +      interactionMan_->initialize();
380 +
381 +      // We want to delay the cutoffs until after the interaction
382 +      // manager has set up the atom-atom interactions so that we can
383 +      // query them for suggested cutoff values
384 +      setupCutoffs();
385 +
386 +      info_->prepareTopology();      
387      }
388 +
389 +    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
390      
391 <    preCalculation();
391 >    // Force fields can set options on how to scale van der Waals and
392 >    // electrostatic interactions for atoms connected via bonds, bends
393 >    // and torsions in this case the topological distance between
394 >    // atoms is:
395 >    // 0 = topologically unconnected
396 >    // 1 = bonded together
397 >    // 2 = connected via a bend
398 >    // 3 = connected via a torsion
399      
400 <    calcShortRangeInteraction();
400 >    vdwScale_.reserve(4);
401 >    fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
402  
403 <    calcLongRangeInteraction(needPotential, needStress);
403 >    electrostaticScale_.reserve(4);
404 >    fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
405  
406 <    postCalculation(needStress);
406 >    vdwScale_[0] = 1.0;
407 >    vdwScale_[1] = fopts.getvdw12scale();
408 >    vdwScale_[2] = fopts.getvdw13scale();
409 >    vdwScale_[3] = fopts.getvdw14scale();
410      
411 +    electrostaticScale_[0] = 1.0;
412 +    electrostaticScale_[1] = fopts.getelectrostatic12scale();
413 +    electrostaticScale_[2] = fopts.getelectrostatic13scale();
414 +    electrostaticScale_[3] = fopts.getelectrostatic14scale();    
415 +    
416 +    fDecomp_->distributeInitialData();
417 +
418 +    initialized_ = true;
419 +
420    }
421 +
422 +  void ForceManager::calcForces() {
423 +    
424 +    if (!initialized_) initialize();
425 +
426 +    preCalculation();  
427 +    shortRangeInteractions();
428 +    longRangeInteractions();
429 +    postCalculation();    
430 +  }
431    
432    void ForceManager::preCalculation() {
433      SimInfo::MoleculeIterator mi;
# Line 82 | Line 436 | namespace OpenMD {
436      Atom* atom;
437      Molecule::RigidBodyIterator rbIter;
438      RigidBody* rb;
439 +    Molecule::CutoffGroupIterator ci;
440 +    CutoffGroup* cg;
441      
442      // forces are zeroed here, before any are accumulated.
87 –    // NOTE: do not rezero the forces in Fortran.
443      
444      for (mol = info_->beginMolecule(mi); mol != NULL;
445           mol = info_->nextMolecule(mi)) {
446 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
446 >      for(atom = mol->beginAtom(ai); atom != NULL;
447 >          atom = mol->nextAtom(ai)) {
448          atom->zeroForcesAndTorques();
449        }
450 <          
450 >      
451        //change the positions of atoms which belong to the rigidbodies
452        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
453             rb = mol->nextRigidBody(rbIter)) {
454          rb->zeroForcesAndTorques();
455        }        
456 <          
456 >      
457 >      if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
458 >        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
459 >            cg = mol->nextCutoffGroup(ci)) {
460 >          //calculate the center of mass of cutoff group
461 >          cg->updateCOM();
462 >        }
463 >      }      
464      }
465      
466      // Zero out the stress tensor
# Line 105 | Line 468 | namespace OpenMD {
468      
469    }
470    
471 <  void ForceManager::calcShortRangeInteraction() {
471 >  void ForceManager::shortRangeInteractions() {
472      Molecule* mol;
473      RigidBody* rb;
474      Bond* bond;
# Line 147 | Line 510 | namespace OpenMD {
510          RealType currBendPot = bend->getPotential();          
511          
512          bendPotential += bend->getPotential();
513 <        std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
513 >        map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
514          if (i == bendDataSets.end()) {
515            BendDataSet dataSet;
516            dataSet.prev.angle = dataSet.curr.angle = angle;
517            dataSet.prev.potential = dataSet.curr.potential = currBendPot;
518            dataSet.deltaV = 0.0;
519 <          bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
519 >          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
520 >                                                                  dataSet));
521          }else {
522            i->second.prev.angle = i->second.curr.angle;
523            i->second.prev.potential = i->second.curr.potential;
# Line 170 | Line 534 | namespace OpenMD {
534          torsion->calcForce(angle);
535          RealType currTorsionPot = torsion->getPotential();
536          torsionPotential += torsion->getPotential();
537 <        std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
537 >        map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
538          if (i == torsionDataSets.end()) {
539            TorsionDataSet dataSet;
540            dataSet.prev.angle = dataSet.curr.angle = angle;
541            dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
542            dataSet.deltaV = 0.0;
543 <          torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
543 >          torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
544          }else {
545            i->second.prev.angle = i->second.curr.angle;
546            i->second.prev.potential = i->second.curr.potential;
# Line 186 | Line 550 | namespace OpenMD {
550                                     i->second.prev.potential);
551          }      
552        }      
553 <
553 >      
554        for (inversion = mol->beginInversion(inversionIter);
555             inversion != NULL;
556             inversion = mol->nextInversion(inversionIter)) {
# Line 194 | Line 558 | namespace OpenMD {
558          inversion->calcForce(angle);
559          RealType currInversionPot = inversion->getPotential();
560          inversionPotential += inversion->getPotential();
561 <        std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
561 >        map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
562          if (i == inversionDataSets.end()) {
563            InversionDataSet dataSet;
564            dataSet.prev.angle = dataSet.curr.angle = angle;
565            dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
566            dataSet.deltaV = 0.0;
567 <          inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
567 >          inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
568          }else {
569            i->second.prev.angle = i->second.curr.angle;
570            i->second.prev.potential = i->second.curr.potential;
# Line 219 | Line 583 | namespace OpenMD {
583      curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
584      curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
585      curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
586 <    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
223 <    
586 >    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;    
587    }
588    
589 <  void ForceManager::calcLongRangeInteraction(bool needPotential,
227 <                                              bool needStress) {
228 <    Snapshot* curSnapshot;
229 <    DataStorage* config;
230 <    RealType* frc;
231 <    RealType* pos;
232 <    RealType* trq;
233 <    RealType* A;
234 <    RealType* electroFrame;
235 <    RealType* rc;
236 <    RealType* particlePot;
237 <    
238 <    //get current snapshot from SimInfo
239 <    curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
240 <    
241 <    //get array pointers
242 <    config = &(curSnapshot->atomData);
243 <    frc = config->getArrayPointer(DataStorage::dslForce);
244 <    pos = config->getArrayPointer(DataStorage::dslPosition);
245 <    trq = config->getArrayPointer(DataStorage::dslTorque);
246 <    A   = config->getArrayPointer(DataStorage::dslAmat);
247 <    electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
248 <    particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
589 >  void ForceManager::longRangeInteractions() {
590  
591 +    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
592 +    DataStorage* config = &(curSnapshot->atomData);
593 +    DataStorage* cgConfig = &(curSnapshot->cgData);
594 +
595      //calculate the center of mass of cutoff group
596 +
597      SimInfo::MoleculeIterator mi;
598      Molecule* mol;
599      Molecule::CutoffGroupIterator ci;
600      CutoffGroup* cg;
601 <    Vector3d com;
602 <    std::vector<Vector3d> rcGroup;
257 <    
258 <    if(info_->getNCutoffGroups() > 0){
259 <      
601 >
602 >    if(info_->getNCutoffGroups() > 0){      
603        for (mol = info_->beginMolecule(mi); mol != NULL;
604             mol = info_->nextMolecule(mi)) {
605          for(cg = mol->beginCutoffGroup(ci); cg != NULL;
606              cg = mol->nextCutoffGroup(ci)) {
607 <          cg->getCOM(com);
265 <          rcGroup.push_back(com);
607 >          cg->updateCOM();
608          }
609 <      }// end for (mol)
268 <      
269 <      rc = rcGroup[0].getArrayPointer();
609 >      }      
610      } else {
611        // center of mass of the group is the same as position of the atom  
612        // if cutoff group does not exist
613 <      rc = pos;
613 >      cgConfig->position = config->position;
614      }
615 +
616 +    fDecomp_->zeroWorkArrays();
617 +    fDecomp_->distributeData();
618      
619 <    //initialize data before passing to fortran
620 <    RealType longRangePotential[LR_POT_TYPES];
621 <    RealType lrPot = 0.0;
622 <    Vector3d totalDipole;
623 <    short int passedCalcPot = needPotential;
624 <    short int passedCalcStress = needStress;
625 <    int isError = 0;
619 >    int cg1, cg2, atom1, atom2, topoDist;
620 >    Vector3d d_grp, dag, d;
621 >    RealType rgrpsq, rgrp, r2, r;
622 >    RealType electroMult, vdwMult;
623 >    RealType vij;
624 >    Vector3d fij, fg, f1;
625 >    tuple3<RealType, RealType, RealType> cuts;
626 >    RealType rCutSq;
627 >    bool in_switching_region;
628 >    RealType sw, dswdr, swderiv;
629 >    vector<int> atomListColumn, atomListRow, atomListLocal;
630 >    InteractionData idat;
631 >    SelfData sdat;
632 >    RealType mf;
633 >    RealType lrPot;
634 >    RealType vpair;
635 >    potVec longRangePotential(0.0);
636 >    potVec workPot(0.0);
637  
638 <    for (int i=0; i<LR_POT_TYPES;i++){
639 <      longRangePotential[i]=0.0; //Initialize array
640 <    }
638 >    int loopStart, loopEnd;
639 >
640 >    idat.vdwMult = &vdwMult;
641 >    idat.electroMult = &electroMult;
642 >    idat.pot = &workPot;
643 >    sdat.pot = fDecomp_->getEmbeddingPotential();
644 >    idat.vpair = &vpair;
645 >    idat.f1 = &f1;
646 >    idat.sw = &sw;
647 >    idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
648 >    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
649      
650 <    doForceLoop(pos,
651 <                rc,
652 <                A,
653 <                electroFrame,
654 <                frc,
293 <                trq,
294 <                tau.getArrayPointer(),
295 <                longRangePotential,
296 <                particlePot,
297 <                &passedCalcPot,
298 <                &passedCalcStress,
299 <                &isError );
300 <    
301 <    if( isError ){
302 <      sprintf( painCave.errMsg,
303 <               "Error returned from the fortran force calculation.\n" );
304 <      painCave.isFatal = 1;
305 <      simError();
650 >    loopEnd = PAIR_LOOP;
651 >    if (info_->requiresPrepair() ) {
652 >      loopStart = PREPAIR_LOOP;
653 >    } else {
654 >      loopStart = PAIR_LOOP;
655      }
656 <    for (int i=0; i<LR_POT_TYPES;i++){
657 <      lrPot += longRangePotential[i]; //Quick hack
309 <    }
656 >  
657 >    for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
658      
659 <    // grab the simulation box dipole moment if specified
660 <    if (info_->getCalcBoxDipole()){
661 <      getAccumulatedBoxDipole(totalDipole.getArrayPointer());
662 <      
663 <      curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
664 <      curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
665 <      curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
659 >      if (iLoop == loopStart) {
660 >        bool update_nlist = fDecomp_->checkNeighborList();
661 >        if (update_nlist)
662 >          neighborList = fDecomp_->buildNeighborList();
663 >      }            
664 >
665 >      for (vector<pair<int, int> >::iterator it = neighborList.begin();
666 >             it != neighborList.end(); ++it) {
667 >                
668 >        cg1 = (*it).first;
669 >        cg2 = (*it).second;
670 >        
671 >        cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
672 >
673 >        d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
674 >
675 >        curSnapshot->wrapVector(d_grp);        
676 >        rgrpsq = d_grp.lengthSquare();
677 >        rCutSq = cuts.second;
678 >
679 >        if (rgrpsq < rCutSq) {
680 >          idat.rcut = &cuts.first;
681 >          if (iLoop == PAIR_LOOP) {
682 >            vij = 0.0;
683 >            fij = V3Zero;
684 >          }
685 >          
686 >          in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
687 >                                                     rgrp);
688 >          
689 >          atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
690 >          atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
691 >
692 >          for (vector<int>::iterator ia = atomListRow.begin();
693 >               ia != atomListRow.end(); ++ia) {            
694 >            atom1 = (*ia);
695 >            
696 >            for (vector<int>::iterator jb = atomListColumn.begin();
697 >                 jb != atomListColumn.end(); ++jb) {              
698 >              atom2 = (*jb);
699 >
700 >              if (!fDecomp_->skipAtomPair(atom1, atom2)) {
701 >                vpair = 0.0;
702 >                workPot = 0.0;
703 >                f1 = V3Zero;
704 >
705 >                fDecomp_->fillInteractionData(idat, atom1, atom2);
706 >                
707 >                topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
708 >                vdwMult = vdwScale_[topoDist];
709 >                electroMult = electrostaticScale_[topoDist];
710 >
711 >                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
712 >                  idat.d = &d_grp;
713 >                  idat.r2 = &rgrpsq;
714 >                } else {
715 >                  d = fDecomp_->getInteratomicVector(atom1, atom2);
716 >                  curSnapshot->wrapVector( d );
717 >                  r2 = d.lengthSquare();
718 >                  idat.d = &d;
719 >                  idat.r2 = &r2;
720 >                }
721 >              
722 >                r = sqrt( *(idat.r2) );
723 >                idat.rij = &r;
724 >              
725 >                if (iLoop == PREPAIR_LOOP) {
726 >                  interactionMan_->doPrePair(idat);
727 >                } else {
728 >                  interactionMan_->doPair(idat);
729 >                  fDecomp_->unpackInteractionData(idat, atom1, atom2);
730 >                  vij += vpair;
731 >                  fij += f1;
732 >                  tau -= outProduct( *(idat.d), f1);
733 >                }
734 >              }
735 >            }
736 >          }
737 >
738 >          if (iLoop == PAIR_LOOP) {
739 >            if (in_switching_region) {
740 >              swderiv = vij * dswdr / rgrp;
741 >              fg = swderiv * d_grp;
742 >              fij += fg;
743 >
744 >              if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
745 >                tau -= outProduct( *(idat.d), fg);
746 >              }
747 >          
748 >              for (vector<int>::iterator ia = atomListRow.begin();
749 >                   ia != atomListRow.end(); ++ia) {            
750 >                atom1 = (*ia);                
751 >                mf = fDecomp_->getMassFactorRow(atom1);
752 >                // fg is the force on atom ia due to cutoff group's
753 >                // presence in switching region
754 >                fg = swderiv * d_grp * mf;
755 >                fDecomp_->addForceToAtomRow(atom1, fg);
756 >                if (atomListRow.size() > 1) {
757 >                  if (info_->usesAtomicVirial()) {
758 >                    // find the distance between the atom
759 >                    // and the center of the cutoff group:
760 >                    dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
761 >                    tau -= outProduct(dag, fg);
762 >                  }
763 >                }
764 >              }
765 >              for (vector<int>::iterator jb = atomListColumn.begin();
766 >                   jb != atomListColumn.end(); ++jb) {              
767 >                atom2 = (*jb);
768 >                mf = fDecomp_->getMassFactorColumn(atom2);
769 >                // fg is the force on atom jb due to cutoff group's
770 >                // presence in switching region
771 >                fg = -swderiv * d_grp * mf;
772 >                fDecomp_->addForceToAtomColumn(atom2, fg);
773 >
774 >                if (atomListColumn.size() > 1) {
775 >                  if (info_->usesAtomicVirial()) {
776 >                    // find the distance between the atom
777 >                    // and the center of the cutoff group:
778 >                    dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
779 >                    tau -= outProduct(dag, fg);
780 >                  }
781 >                }
782 >              }
783 >            }
784 >            //if (!info_->usesAtomicVirial()) {
785 >            //  tau -= outProduct(d_grp, fij);
786 >            //}
787 >          }
788 >        }
789 >      }
790 >
791 >      if (iLoop == PREPAIR_LOOP) {
792 >        if (info_->requiresPrepair()) {
793 >
794 >          fDecomp_->collectIntermediateData();
795 >
796 >          for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
797 >            fDecomp_->fillSelfData(sdat, atom1);
798 >            interactionMan_->doPreForce(sdat);
799 >          }
800 >
801 >          fDecomp_->distributeIntermediateData();
802 >
803 >        }
804 >      }
805      }
806      
807 +    fDecomp_->collectData();
808 +        
809 +    if (info_->requiresSelfCorrection()) {
810 +
811 +      for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {          
812 +        fDecomp_->fillSelfData(sdat, atom1);
813 +        interactionMan_->doSelfCorrection(sdat);
814 +      }
815 +
816 +    }
817 +
818 +    longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
819 +      *(fDecomp_->getPairwisePotential());
820 +
821 +    lrPot = longRangePotential.sum();
822 +
823      //store the tau and long range potential    
824      curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
825 <    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
826 <    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
825 >    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
826 >    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
827    }
828  
829    
830 <  void ForceManager::postCalculation(bool needStress) {
830 >  void ForceManager::postCalculation() {
831      SimInfo::MoleculeIterator mi;
832      Molecule* mol;
833      Molecule::RigidBodyIterator rbIter;
# Line 337 | Line 840 | namespace OpenMD {
840           mol = info_->nextMolecule(mi)) {
841        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
842             rb = mol->nextRigidBody(rbIter)) {
843 <        if (needStress) {          
844 <          Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
342 <          tau += rbTau;
343 <        } else{
344 <          rb->calcForcesAndTorques();
345 <        }
843 >        Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
844 >        tau += rbTau;
845        }
846      }
847 <
349 <    if (needStress) {
847 >    
848   #ifdef IS_MPI
849 <      Mat3x3d tmpTau(tau);
850 <      MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
851 <                    9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
849 >    Mat3x3d tmpTau(tau);
850 >    MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
851 >                  9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
852   #endif
853 <      curSnapshot->statData.setTau(tau);
356 <    }
853 >    curSnapshot->statData.setTau(tau);
854    }
855  
856   } //end namespace OpenMD

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