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Revision 1478 by gezelter, Fri Jul 23 20:45:40 2010 UTC vs.
Revision 1710 by gezelter, Fri May 18 21:44:02 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   #include <stdio.h>
# Line 45 | Line 46
46   #include <cmath>
47   #include "nonbonded/EAM.hpp"
48   #include "utils/simError.h"
49 + #include "types/NonBondedInteractionType.hpp"
50  
51  
52   namespace OpenMD {
53  
54 <  bool EAM::initialized_ = false;
55 <  ForceField* EAM::forceField_ = NULL;
54 <  std::map<int, AtomType*> EAM::EAMlist;
55 <  std::map<AtomType*, EAMAtomData> EAM::EAMMap;
56 <  std::map<std::pair<AtomType*, AtomType*>, EAMInteractionData> EAM::MixingMap;
54 >  EAM::EAM() : name_("EAM"), initialized_(false), forceField_(NULL),
55 >               mixMeth_(eamJohnson), eamRcut_(0.0), haveCutoffRadius_(false) {}
56    
57 <  EAM* EAM::_instance = NULL;
57 >  CubicSpline* EAM::getPhi(AtomType* atomType1, AtomType* atomType2) {  
58 >    EAMAdapter ea1 = EAMAdapter(atomType1);
59 >    EAMAdapter ea2 = EAMAdapter(atomType2);
60 >    CubicSpline* z1 = ea1.getZ();
61 >    CubicSpline* z2 = ea2.getZ();
62  
63 <  EAM* EAM::Instance() {
61 <    if (!_instance) {
62 <      _instance = new EAM();
63 <    }
64 <    return _instance;
65 <  }
66 <  
67 <  EAMParam EAM::getEAMParam(AtomType* atomType) {
68 <    
69 <    // Do sanity checking on the AtomType we were passed before
70 <    // building any data structures:
71 <    if (!atomType->isEAM()) {
72 <      sprintf( painCave.errMsg,
73 <               "EAM::getEAMParam was passed an atomType (%s) that does not\n"
74 <               "\tappear to be an embedded atom method (EAM) atom.\n",
75 <               atomType->getName().c_str());
76 <      painCave.severity = OPENMD_ERROR;
77 <      painCave.isFatal = 1;
78 <      simError();
79 <    }
80 <    
81 <    GenericData* data = atomType->getPropertyByName("EAM");
82 <    if (data == NULL) {
83 <      sprintf( painCave.errMsg, "EAM::getEAMParam could not find EAM\n"
84 <               "\tparameters for atomType %s.\n",
85 <               atomType->getName().c_str());
86 <      painCave.severity = OPENMD_ERROR;
87 <      painCave.isFatal = 1;
88 <      simError();
89 <    }
90 <    
91 <    EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data);
92 <    if (eamData == NULL) {
93 <      sprintf( painCave.errMsg,
94 <               "EAM::getEAMParam could not convert GenericData to EAMParam for\n"
95 <               "\tatom type %s\n", atomType->getName().c_str());
96 <      painCave.severity = OPENMD_ERROR;
97 <      painCave.isFatal = 1;
98 <      simError();          
99 <    }
100 <    
101 <    return eamData->getData();
102 <  }
63 >    // make the r grid:
64  
104 –  CubicSpline* EAM::getZ(AtomType* atomType) {    
105 –    EAMParam eamParam = getEAMParam(atomType);
106 –    int nr = eamParam.nr;
107 –    RealType dr = eamParam.dr;
108 –    vector<RealType> rvals;
109 –    
110 –    for (int i = 0; i < nr; i++) rvals.push_back(i * dr);
111 –      
112 –    CubicSpline* cs = new CubicSpline();
113 –    cs->addPoints(rvals, eamParam.Z);
114 –    return cs;
115 –  }
65  
66 <  CubicSpline* EAM::getRho(AtomType* atomType) {    
118 <    EAMParam eamParam = getEAMParam(atomType);
119 <    int nr = eamParam.nr;
120 <    RealType dr = eamParam.dr;
121 <    vector<RealType> rvals;
66 >    // we need phi out to the largest value we'll encounter in the radial space;
67      
68 <    for (int i = 0; i < nr; i++) rvals.push_back(i * dr);
69 <      
70 <    CubicSpline* cs = new CubicSpline();
126 <    cs->addPoints(rvals, eamParam.rho);
127 <    return cs;
128 <  }
68 >    RealType rmax = 0.0;
69 >    rmax = max(rmax, ea1.getRcut());
70 >    rmax = max(rmax, ea1.getNr() * ea1.getDr());
71  
72 <  CubicSpline* EAM::getF(AtomType* atomType) {    
73 <    EAMParam eamParam = getEAMParam(atomType);
132 <    int nrho = eamParam.nrho;
133 <    RealType drho = eamParam.drho;
134 <    vector<RealType> rhovals;
135 <    vector<RealType> scaledF;
136 <    
137 <    for (int i = 0; i < nrho; i++) {
138 <      rhovals.push_back(i * drho);
139 <      scaledF.push_back( eamParam.F[i] * 23.06054 );
140 <    }
141 <      
142 <    CubicSpline* cs = new CubicSpline();
143 <    cs->addPoints(rhovals, eamParam.F);
144 <    return cs;
145 <  }
146 <  
147 <  CubicSpline* EAM::getPhi(AtomType* atomType1, AtomType* atomType2) {    
148 <    EAMParam eamParam1 = getEAMParam(atomType1);
149 <    EAMParam eamParam2 = getEAMParam(atomType2);
150 <    CubicSpline* z1 = getZ(atomType1);
151 <    CubicSpline* z2 = getZ(atomType2);
72 >    rmax = max(rmax, ea2.getRcut());
73 >    rmax = max(rmax, ea2.getNr() * ea2.getDr());
74  
75 <    // make the r grid:
75 >    // use the smallest dr (finest grid) to build our grid:
76  
77 <    // set rcut to be the smaller of the two atomic rcuts
77 >    RealType dr = min(ea1.getDr(), ea2.getDr());
78  
79 <    RealType rcut = eamParam1.rcut < eamParam2.rcut ?
158 <      eamParam1.rcut : eamParam2.rcut;
79 >    int nr = int(rmax/dr + 0.5);
80  
160 –    // use the smallest dr (finest grid) to build our grid:
161 –
162 –    RealType dr = eamParam1.dr < eamParam2.dr ? eamParam1.dr : eamParam2.dr;
163 –    int nr = int(rcut/dr);
81      vector<RealType> rvals;
82 <    for (int i = 0; i < nr; i++) rvals.push_back(i*dr);
82 >    for (int i = 0; i < nr; i++) rvals.push_back(RealType(i*dr));
83  
84      // construct the pair potential:
85  
# Line 175 | Line 92 | namespace OpenMD {
92  
93      for (int i = 1; i < rvals.size(); i++ ) {
94        r = rvals[i];
178 –      zi = z1->getValueAt(r);
179 –      zj = z2->getValueAt(r);
95  
96 +      // only use z(r) if we're inside this atom's cutoff radius,
97 +      // otherwise, we'll use zero for the charge.  This effectively
98 +      // means that our phi grid goes out beyond the cutoff of the
99 +      // pair potential
100 +
101 +      zi = r <= ea1.getRcut() ? z1->getValueAt(r) : 0.0;
102 +      zj = r <= ea2.getRcut() ? z2->getValueAt(r) : 0.0;
103 +
104        phi = 331.999296 * (zi * zj) / r;
105 +
106        phivals.push_back(phi);
107      }
108        
# Line 187 | Line 111 | namespace OpenMD {
111      return cs;
112    }
113  
114 +  void EAM::setCutoffRadius( RealType rCut ) {
115 +    eamRcut_ = rCut;
116 +    haveCutoffRadius_ = true;
117 +  }
118 +
119    void EAM::initialize() {
120  
121      // set up the mixing method:
122 <    ForceFieldOptions ffo = forceField_->getForceFieldOptions();
123 <    string EAMMixMeth = toUpperCopy(ffo.getEAMMixingMethod());
124 <
122 >    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
123 >    string EAMMixMeth = fopts.getEAMMixingMethod();
124 >    toUpper(EAMMixMeth);
125 >  
126      if (EAMMixMeth == "JOHNSON")
127        mixMeth_ = eamJohnson;    
128      else if (EAMMixMeth == "DAW")
# Line 222 | Line 152 | namespace OpenMD {
152        
153        if (nbt->isEAM()) {
154          
155 <        std::pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes();
155 >        pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes();
156          
157          GenericData* data = nbt->getPropertyByName("EAM");
158          if (data == NULL) {
# Line 247 | Line 177 | namespace OpenMD {
177            simError();          
178          }
179          
180 <        EAMMix eamParam = eamData->getData();
180 >        EAMMixingParam eamParam = eamData->getData();
181  
182 <        vector<RealType> phiAB = eamParam.phiAB;
182 >        vector<RealType> phiAB = eamParam.phi;
183          RealType dr = eamParam.dr;
184          int nr = eamParam.nr;
185  
# Line 263 | Line 193 | namespace OpenMD {
193  
194    void EAM::addType(AtomType* atomType){
195  
196 +    EAMAdapter ea = EAMAdapter(atomType);
197      EAMAtomData eamAtomData;
198  
199 <    eamAtomData.rho = getRho(atomType);
200 <    eamAtomData.F = getF(atomType);
201 <    eamAtomData.Z = getZ(atomType);
202 <    eamAtomData.rcut = getRcut(atomType);
199 >    eamAtomData.rho = ea.getRho();
200 >    eamAtomData.F = ea.getF();
201 >    eamAtomData.Z = ea.getZ();
202 >    eamAtomData.rcut = ea.getRcut();
203  
204      // add it to the map:
274 –    AtomTypeProperties atp = atomType->getATP();    
205  
206 <    std::pair<std::map<int,AtomType*>::iterator,bool> ret;    
207 <    ret = EAMlist.insert( std::pair<int, AtomType*>(atp.ident, atomType) );
206 >    pair<map<int,AtomType*>::iterator,bool> ret;    
207 >    ret = EAMlist.insert( pair<int, AtomType*>(atomType->getIdent(), atomType) );
208      if (ret.second == false) {
209        sprintf( painCave.errMsg,
210                 "EAM already had a previous entry with ident %d\n",
211 <               atp.ident);
211 >               atomType->getIdent());
212        painCave.severity = OPENMD_INFO;
213        painCave.isFatal = 0;
214        simError();        
# Line 288 | Line 218 | namespace OpenMD {
218      
219      // Now, iterate over all known types and add to the mixing map:
220      
221 <    std::map<int, AtomType*>::iterator it;
221 >    map<AtomType*, EAMAtomData>::iterator it;
222      for( it = EAMMap.begin(); it != EAMMap.end(); ++it) {
223        
224 <      AtomType* atype2 = (*it).second;
224 >      AtomType* atype2 = (*it).first;
225  
226        EAMInteractionData mixer;
227        mixer.phi = getPhi(atomType, atype2);
228        mixer.explicitlySet = false;
229  
230 <      std::pair<AtomType*, AtomType*> key1, key2;
231 <      key1 = std::make_pair(atomType, atype2);
232 <      key2 = std::make_pair(atype2, atomType);
230 >      pair<AtomType*, AtomType*> key1, key2;
231 >      key1 = make_pair(atomType, atype2);
232 >      key2 = make_pair(atype2, atomType);
233        
234        MixingMap[key1] = mixer;
235        if (key2 != key1) {
# Line 319 | Line 249 | namespace OpenMD {
249  
250      EAMInteractionData mixer;
251      CubicSpline* cs = new CubicSpline();
252 <    vector<RealType> rvals;
252 >    vector<RealType> rVals;
253  
254 <    for (int i = 0; i < nr; i++) rvals.push_back(i * dr);
254 >    for (int i = 0; i < nr; i++) rVals.push_back(i * dr);
255  
256      cs->addPoints(rVals, phiVals);
257      mixer.phi = cs;
258      mixer.explicitlySet = true;
259  
260 <    std::pair<AtomType*, AtomType*> key1, key2;
261 <    key1 = std::make_pair(atype1, atype2);
262 <    key2 = std::make_pair(atype2, atype1);
260 >    pair<AtomType*, AtomType*> key1, key2;
261 >    key1 = make_pair(atype1, atype2);
262 >    key2 = make_pair(atype2, atype1);
263      
264      MixingMap[key1] = mixer;
265      if (key2 != key1) {
# Line 338 | Line 268 | namespace OpenMD {
268      return;
269    }
270  
271 <  void EAM::calcDensity(AtomType* at1, AtomType* at2, Vector3d d,
272 <                        RealType rij, RealType r2, RealType rho_i_at_j,
343 <                        RealType rho_j_at_i) {
344 <
271 >  void EAM::calcDensity(InteractionData &idat) {
272 >    
273      if (!initialized_) initialize();
274 <
275 <    EAMAtomData data1 = EAMMap[at1];
276 <    EAMAtomData data2 = EAMMap[at2];
277 <
278 <    if (rij < data1.rcut) rho_i_at_j = data1.rho->getValueAt(rij);
279 <    if (rij < data2.rcut) rho_j_at_i = data2.rho->getValueAt(rij);
280 <    return;
274 >    
275 >    EAMAtomData data1 = EAMMap[idat.atypes.first];
276 >    EAMAtomData data2 = EAMMap[idat.atypes.second];
277 >    
278 >    if (haveCutoffRadius_)
279 >      if ( *(idat.rij) > eamRcut_) return;
280 >    
281 >    if ( *(idat.rij) < data1.rcut)
282 >      *(idat.rho1) += data1.rho->getValueAt( *(idat.rij));
283 >    
284 >      
285 >    if ( *(idat.rij) < data2.rcut)
286 >      *(idat.rho2) += data2.rho->getValueAt( *(idat.rij));
287 >    
288 >    return;  
289    }
290 <
291 <  void EAM::calcFunctional(AtomType* at1, RealType rho, RealType frho,
292 <                           RealType dfrhodrho) {
357 <
290 >  
291 >  void EAM::calcFunctional(SelfData &sdat) {
292 >    
293      if (!initialized_) initialize();
294  
295 <    EAMAtomData data1 = EAMMap[at1];
295 >    EAMAtomData data1 = EAMMap[ sdat.atype ];
296          
297 <    pair<RealType, RealType> result = data1.F->getValueAndDerivativeAt(rho);
297 >    pair<RealType, RealType> result = data1.F->getValueAndDerivativeAt( *(sdat.rho) );
298  
299 <    frho = result.first;
300 <    dfrhodrho = result.second;
299 >    *(sdat.frho) = result.first;
300 >    *(sdat.dfrhodrho) = result.second;
301 >
302 >    (*(sdat.pot))[METALLIC_FAMILY] += result.first;
303 >    *(sdat.particlePot) += result.first;
304 >
305      return;
306    }
307  
308  
309 <  void EAM::calcForce(AtomType* at1, AtomType* at2, Vector3d d,
371 <                      RealType rij, RealType r2, RealType sw,
372 <                      RealType &vpair, RealType &pot, Vector3d &f1,
373 <                      RealType rho1, RealType rho2, RealType dfrho1,
374 <                      RealType dfrho2, RealType fshift1, RealType fshift2) {
309 >  void EAM::calcForce(InteractionData &idat) {
310  
311      if (!initialized_) initialize();
312 <    
312 >
313 >    if (haveCutoffRadius_)
314 >      if ( *(idat.rij) > eamRcut_) return;
315 >  
316      pair<RealType, RealType> res;
317      
318 <    if (rij < eamRcut_) {
319 <
320 <      EAMAtomData data1 = EAMMap[at1];
321 <      EAMAtomData data2 = EAMMap[at2];
322 <
323 <      // get type-specific cutoff radii
324 <
325 <      RealType rci = data1.rcut;
326 <      RealType rcj = data2.rcut;
327 <      
328 <      RealType rha, drha, rhb, drhb;
329 <      RealType pha, dpha, phb, dphb;
330 <      RealType phab, dvpdr;
331 <      RealType drhoidr, drhojdr, dudr;
332 <      
333 <      if (rij < rci) {
334 <        res = data1.rho->getValueAndDerivativeAt(rij);
335 <        rha = res.first;
336 <        drha = res.second;
337 <
338 <        res = MixingMap[make_pair(at1, at1)].phi->getValueAndDerivativeAt(rij);
339 <        pha = res.first;
340 <        dpha = res.second;
341 <      }
342 <
343 <      if (rij < rcj) {
344 <        res = data2.rho->getValueAndDerivativeAt(rij);
345 <        rhb = res.first;
346 <        drhb = res.second;
318 >    EAMAtomData data1 = EAMMap[idat.atypes.first];
319 >    EAMAtomData data2 = EAMMap[idat.atypes.second];
320 >    
321 >    // get type-specific cutoff radii
322 >    
323 >    RealType rci = data1.rcut;
324 >    RealType rcj = data2.rcut;
325 >    
326 >    RealType rha(0.0), drha(0.0), rhb(0.0), drhb(0.0);
327 >    RealType pha(0.0), dpha(0.0), phb(0.0), dphb(0.0);
328 >    RealType phab(0.0), dvpdr(0.0);
329 >    RealType drhoidr, drhojdr, dudr;
330 >    
331 >    if ( *(idat.rij) < rci) {
332 >      res = data1.rho->getValueAndDerivativeAt( *(idat.rij));
333 >      rha = res.first;
334 >      drha = res.second;
335 >      
336 >      res = MixingMap[make_pair(idat.atypes.first, idat.atypes.first)].phi->getValueAndDerivativeAt( *(idat.rij) );
337 >      pha = res.first;
338 >      dpha = res.second;
339 >    }
340 >    
341 >    if ( *(idat.rij) < rcj) {
342 >      res = data2.rho->getValueAndDerivativeAt( *(idat.rij) );
343 >      rhb = res.first;
344 >      drhb = res.second;
345 >      
346 >      res = MixingMap[make_pair(idat.atypes.second, idat.atypes.second)].phi->getValueAndDerivativeAt( *(idat.rij) );
347 >      phb = res.first;
348 >      dphb = res.second;
349 >    }
350  
351 <        res = MixingMap[make_pair(at2, at2)].phi->getValueAndDerivativeAt(rij);
352 <        phb = res.first;
353 <        dphb = res.second;
351 >    switch(mixMeth_) {
352 >    case eamJohnson:
353 >      
354 >      if ( *(idat.rij) < rci) {
355 >        phab = phab + 0.5 * (rhb / rha) * pha;
356 >        dvpdr = dvpdr + 0.5*((rhb/rha)*dpha +
357 >                             pha*((drhb/rha) - (rhb*drha/rha/rha)));
358        }
359 <
360 <      phab = 0.0;
361 <      dvpdr = 0.0;
362 <
363 <      switch(mixMeth_) {
364 <      case eamJohnson:
365 <      
421 <        if (rij < rci) {
422 <          phab = phab + 0.5 * (rhb / rha) * pha;
423 <          dvpdr = dvpdr + 0.5*((rhb/rha)*dpha +
424 <                               pha*((drhb/rha) - (rhb*drha/rha/rha)));
425 <        }
426 <
427 <        if (rij < rcj) {
428 <          phab = phab + 0.5 * (rha / rhb) * phb;
429 <          dvpdr = dvpdr + 0.5 * ((rha/rhb)*dphb +
430 <                                 phb*((drha/rhb) - (rha*drhb/rhb/rhb)));
431 <        }
432 <
433 <        break;
434 <
435 <      case eamDaw:
436 <                
437 <        res = MixingMap[make_pair(at1,at2)].phi->getValueAndDerivativeAt(rij);
438 <        phab = res.first;
439 <        dvpdr = res.second;
440 <
441 <        break;
442 <      case eamUnknown:
443 <      default:
444 <
445 <        sprintf(painCave.errMsg,
446 <                "EAM::calcForce hit a mixing method it doesn't know about!\n"
447 <                );
448 <        painCave.severity = OPENMD_ERROR;
449 <        painCave.isFatal = 1;
450 <        simError();        
451 <          
359 >      
360 >      
361 >      
362 >      if ( *(idat.rij) < rcj) {
363 >        phab = phab + 0.5 * (rha / rhb) * phb;
364 >        dvpdr = dvpdr + 0.5 * ((rha/rhb)*dphb +
365 >                               phb*((drha/rhb) - (rha*drhb/rhb/rhb)));
366        }
367        
368 <      drhoidr = drha;
369 <      drhojdr = drhb;
370 <
371 <      dudr = drhojdr*dfrhodrho_i + drhoidr*dfrhodrho_j + dvpdr;
372 <
373 <      f1 = d * dudr / rij;
374 <        
375 <      // particle_pot is the difference between the full potential
376 <      // and the full potential without the presence of a particular
377 <      // particle (atom1).
378 <      //
379 <      // This reduces the density at other particle locations, so
380 <      // we need to recompute the density at atom2 assuming atom1
381 <      // didn't contribute.  This then requires recomputing the
382 <      // density functional for atom2 as well.
383 <      //
384 <      // Most of the particle_pot heavy lifting comes from the
385 <      // pair interaction, and will be handled by vpair.
472 <    
473 <      fshift_i = data1.F->getValueAt( rho_i - rhb );
474 <      fshift_j = data1.F->getValueAt( rho_j - rha );
475 <
476 <      pot += phab;
477 <
478 <      vpair += phab;
368 >      break;
369 >      
370 >    case eamDaw:
371 >      res = MixingMap[idat.atypes].phi->getValueAndDerivativeAt( *(idat.rij));
372 >      phab = res.first;
373 >      dvpdr = res.second;
374 >      
375 >      break;
376 >    case eamUnknown:
377 >    default:
378 >      
379 >      sprintf(painCave.errMsg,
380 >              "EAM::calcForce hit a mixing method it doesn't know about!\n"
381 >              );
382 >      painCave.severity = OPENMD_ERROR;
383 >      painCave.isFatal = 1;
384 >      simError();        
385 >      
386      }
480 –
481 –    return;
387      
388 <  }
389 <
485 <
486 <  void EAM::calc_eam_prepair_rho(int *atid1, int *atid2, RealType *d,
487 <                                 RealType *rij, RealType *r2,
488 <                                 RealType* rho_i_at_j, RealType* rho_j_at_i){
489 <    if (!initialized_) initialize();
490 <
491 <    AtomType* atype1 = EAMlist[*atid1];
492 <    AtomType* atype2 = EAMlist[*atid2];
388 >    drhoidr = drha;
389 >    drhojdr = drhb;
390      
391 <    Vector3d disp(d[0], d[1], d[2]);
495 <
496 <    calcDensity(atype1, atype2, disp, *rij, *r2, *rho_i_at_j, *rho_j_at_i);
497 <
498 <    return;    
499 <  }
500 <
501 <  void EAM::calc_eam_preforce_Frho(int *atid1, RealType *rho, RealType *frho,
502 <                                   RealType *dfrhodrho) {
503 <
504 <    if (!initialized_) initialize();
505 <
506 <    AtomType* atype1 = EAMlist[*atid1];  
507 <
508 <    calcFunctional(atype1, *rho, *frho, *dfrhodrho);
391 >    dudr = drhojdr* *(idat.dfrho1) + drhoidr* *(idat.dfrho2) + dvpdr;
392      
393 <    return;    
394 <  }
395 <
396 <  void EAM::do_eam_pair(int *atid1, int *atid2, RealType *d, RealType *rij,
397 <                        RealType *r2, RealType *sw, RealType *vpair,
398 <                        RealType *pot, RealType *f1, RealType *rho1,
399 <                        RealType *rho2, RealType *dfrho1, RealType *dfrho2,
400 <                        RealType *fshift1, RealType *fshift2) {
401 <
402 <    if (!initialized_) initialize();
393 >    *(idat.f1) += *(idat.d) * dudr / *(idat.rij);
394 >        
395 >    // particlePot is the difference between the full potential and
396 >    // the full potential without the presence of a particular
397 >    // particle (atom1).
398 >    //
399 >    // This reduces the density at other particle locations, so we
400 >    // need to recompute the density at atom2 assuming atom1 didn't
401 >    // contribute.  This then requires recomputing the density
402 >    // functional for atom2 as well.
403      
404 <    AtomType* atype1 = EAMMap[*atid1];
405 <    AtomType* atype2 = EAMMap[*atid2];
404 >    *(idat.particlePot1) += data2.F->getValueAt( *(idat.rho2) - rha )
405 >      - *(idat.frho2);
406      
407 <    Vector3d disp(d[0], d[1], d[2]);
408 <    Vector3d frc(f1[0], f1[1], f1[2]);
407 >    *(idat.particlePot2) += data1.F->getValueAt( *(idat.rho1) - rhb)
408 >      - *(idat.frho1);
409      
410 <    calcForce(atype1, atype2, disp, *rij, *r2, *sw, *vpair,  *pot, frc,
411 <              *rho1, *rho2, *dfrho1, *dfrho2, *fshift1, *fshift2);
412 <      
530 <    f1[0] = frc.x();
531 <    f1[1] = frc.y();
532 <    f1[2] = frc.z();
533 <
534 <    return;    
535 <  }
410 >    (*(idat.pot))[METALLIC_FAMILY] += phab;
411 >    
412 >    *(idat.vpair) += phab;
413    
414 <  void EAM::setCutoffEAM(RealType *thisRcut) {
415 <    eamRcut_ = thisRcut;
414 >    return;
415 >    
416    }
540 – }
417  
418 < extern "C" {
419 <  
544 < #define fortranCalcDensity FC_FUNC(calc_eam_prepair_rho, CALC_EAM_PREPAIR_RHO)
545 < #define fortranCalcFunctional FC_FUNC(calc_eam_preforce_frho, CALC_EAM_PREFORCE_FRHO)
546 < #define fortranCalcForce FC_FUNC(do_eam_pair, DO_EAM_PAIR)
547 < #define fortranSetCutoffEAM FC_FUNC(setcutoffeam, SETCUTOFFEAM)
548 <  
549 <  RealType fortranCalcDensity(int *atid1, int *atid2, RealType *d,
550 <                              RealType *rij, RealType *r2,
551 <                              RealType *rho_i_at_j, RealType *rho_j_at_i) {
418 >  RealType EAM::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) {
419 >    if (!initialized_) initialize();  
420  
421 <    return OpenMD::EAM::Instance()->calc_eam_prepair_rho(*atid1, *atid2, *d,
554 <                                                         *rij, *r2,
555 <                                                         *rho_i_at_j,  
556 <                                                         *rho_j_at_i);
557 <  }
558 <  RealType fortranCalcFunctional(int *atid1, RealType *rho, RealType *frho,
559 <                                 RealType *dfrhodrho) {  
421 >    RealType cut = 0.0;
422  
423 <    return OpenMD::EAM::Instance()->calc_eam_preforce_Frho(*atid1,
562 <                                                           *rho,
563 <                                                           *frho,
564 <                                                           *dfrhodrho);
423 >    map<AtomType*, EAMAtomData>::iterator it;
424  
425 +    it = EAMMap.find(atypes.first);
426 +    if (it != EAMMap.end()) {
427 +      EAMAtomData data1 = (*it).second;
428 +      cut = data1.rcut;
429 +    }
430 +
431 +    it = EAMMap.find(atypes.second);
432 +    if (it != EAMMap.end()) {
433 +      EAMAtomData data2 = (*it).second;
434 +      if (data2.rcut > cut)
435 +        cut = data2.rcut;
436 +    }
437 +
438 +    return cut;
439    }
567 –  void fortranSetEAMCutoff(RealType *rcut) {
568 –    return OpenMD::EAM::Instance()->setCutoffEAM(rcut);
569 –  }
570 –  void fortranDoEAMPair(int *atid1, int *atid2, RealType *d, RealType *rij,
571 –                        RealType *r2, RealType *sw, RealType *vpair,
572 –                        RealType *pot, RealType *f1, RealType *rho1,
573 –                        RealType *rho2, RealType *dfrho1, RealType *dfrho2,
574 –                        RealType *fshift1, RealType *fshift2){
575 –    
576 –    return OpenMD::EAM::Instance()->do_eam_pair(*atid1, *atid2, *d, *rij,
577 –                                                *r2, *sw,  *vpair,
578 –                                                *pot, *f1,  *rho1,
579 –                                                *rho2,  *dfrho1,  *dfrho2,
580 –                                                *fshift1,  *fshift2);
581 –  }
440   }
441 +

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