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Revision 1540 by gezelter, Mon Jan 17 21:34:36 2011 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) {
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() {
75 >
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 <    if (!info_->isFortranInitialized()) {
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 >    // 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 <      nbiMan_->setSimInfo(info_);
383 <      nbiMan_->initialize();    
384 <      info_->setupFortran();
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 95 | Line 447 | namespace OpenMD {
447      CutoffGroup* cg;
448      
449      // forces are zeroed here, before any are accumulated.
98 –    // 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()){
113 –        std::cerr << "should not see me \n";
465          for(cg = mol->beginCutoffGroup(ci); cg != NULL;
466              cg = mol->nextCutoffGroup(ci)) {
467            //calculate the center of mass of cutoff group
# Line 118 | Line 469 | namespace OpenMD {
469          }
470        }      
471      }
472 <  
472 >    
473      // Zero out the stress tensor
474      tau *= 0.0;
475      
476    }
477    
478 <  void ForceManager::calcShortRangeInteraction() {
478 >  void ForceManager::shortRangeInteractions() {
479      Molecule* mol;
480      RigidBody* rb;
481      Bond* bond;
# Line 154 | 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 162 | 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 186 | 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 205 | 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 238 | 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;
242 <    
593 >    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;    
594    }
595    
596 <  void ForceManager::calcLongRangeInteraction() {
246 <    Snapshot* curSnapshot;
247 <    DataStorage* config;
248 <    DataStorage* cgConfig;
249 <    RealType* frc;
250 <    RealType* pos;
251 <    RealType* trq;
252 <    RealType* A;
253 <    RealType* electroFrame;
254 <    RealType* rc;
255 <    RealType* particlePot;
256 <    
257 <    //get current snapshot from SimInfo
258 <    curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
259 <    
260 <    //get array pointers
261 <    config = &(curSnapshot->atomData);
262 <    cgConfig = &(curSnapshot->cgData);
263 <    frc = config->getArrayPointer(DataStorage::dslForce);
264 <    pos = config->getArrayPointer(DataStorage::dslPosition);
265 <    trq = config->getArrayPointer(DataStorage::dslTorque);
266 <    A   = config->getArrayPointer(DataStorage::dslAmat);
267 <    electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
268 <    particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
596 >  void ForceManager::longRangeInteractions() {
597  
598 <    if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
599 <      std::cerr << "should not see me \n";
600 <      rc = cgConfig->getArrayPointer(DataStorage::dslPosition);
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 >
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->updateCOM();
615 >        }
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 <    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,
293 <                trq,
294 <                tau.getArrayPointer(),
295 <                longRangePotential,
296 <                particlePot,
297 <                &isError );
298 <    
299 <    if( isError ){
300 <      sprintf( painCave.errMsg,
301 <               "Error returned from the fortran force calculation.\n" );
302 <      painCave.isFatal = 1;
303 <      simError();
304 <    }
305 <    for (int i=0; i<LR_POT_TYPES;i++){
306 <      lrPot += longRangePotential[i]; //Quick hack
659 >    loopEnd = PAIR_LOOP;
660 >    if (info_->requiresPrepair() ) {
661 >      loopStart = PREPAIR_LOOP;
662 >    } else {
663 >      loopStart = PAIR_LOOP;
664      }
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 +    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 +
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 336 | 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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