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root/OpenMD/trunk/src/nonbonded/EAM.cpp
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branches/development/src/nonbonded/EAM.cpp (file contents), Revision 1478 by gezelter, Fri Jul 23 20:45:40 2010 UTC vs.
trunk/src/nonbonded/EAM.cpp (file contents), Revision 1895 by gezelter, Mon Jul 1 21:09:37 2013 UTC

# Line 35 | Line 35
35   *                                                                      
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).                        
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
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 173 | Line 90 | namespace OpenMD {
90  
91      phivals.push_back(0.0);
92  
93 <    for (int i = 1; i < rvals.size(); i++ ) {
93 >    for (unsigned 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::initialize() {
114 >  void EAM::setCutoffRadius( RealType rCut ) {
115 >    eamRcut_ = rCut;
116 >    haveCutoffRadius_ = true;
117 >  }
118  
119 +  void EAM::initialize() {
120      // set up the mixing method:
121 <    ForceFieldOptions ffo = forceField_->getForceFieldOptions();
122 <    string EAMMixMeth = toUpperCopy(ffo.getEAMMixingMethod());
123 <
121 >    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
122 >    string EAMMixMeth = fopts.getEAMMixingMethod();
123 >    toUpper(EAMMixMeth);
124 >  
125      if (EAMMixMeth == "JOHNSON")
126        mixMeth_ = eamJohnson;    
127      else if (EAMMixMeth == "DAW")
# Line 201 | Line 130 | namespace OpenMD {
130        mixMeth_ = eamUnknown;
131        
132      // find all of the EAM atom Types:
133 <    ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
134 <    ForceField::AtomTypeContainer::MapTypeIterator i;
135 <    AtomType* at;
133 >    EAMtypes.clear();
134 >    EAMtids.clear();
135 >    EAMdata.clear();
136 >    MixingMap.clear();
137 >    nEAM_ = 0;
138 >    
139 >    EAMtids.resize( forceField_->getNAtomType(), -1);
140  
141 <    for (at = atomTypes->beginType(i); at != NULL;
142 <         at = atomTypes->nextType(i)) {
143 <      
211 <      if (at->isEAM())
212 <        addType(at);
141 >    set<AtomType*>::iterator at;
142 >    for (at = simTypes_.begin(); at != simTypes_.end(); ++at) {
143 >      if ((*at)->isEAM()) nEAM_++;
144      }
145 +    EAMdata.resize(nEAM_);
146 +    MixingMap.resize(nEAM_);
147 +
148 +    for (at = simTypes_.begin(); at != simTypes_.end(); ++at) {
149 +      if ((*at)->isEAM()) addType(*at);
150 +    }
151      
152      // find all of the explicit EAM interactions (setfl):
153      ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
# Line 222 | Line 159 | namespace OpenMD {
159        
160        if (nbt->isEAM()) {
161          
162 <        std::pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes();
162 >        pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes();
163          
164          GenericData* data = nbt->getPropertyByName("EAM");
165          if (data == NULL) {
# Line 247 | Line 184 | namespace OpenMD {
184            simError();          
185          }
186          
187 <        EAMMix eamParam = eamData->getData();
187 >        EAMMixingParam eamParam = eamData->getData();
188  
189 <        vector<RealType> phiAB = eamParam.phiAB;
189 >        vector<RealType> phiAB = eamParam.phi;
190          RealType dr = eamParam.dr;
191          int nr = eamParam.nr;
192  
# Line 263 | Line 200 | namespace OpenMD {
200  
201    void EAM::addType(AtomType* atomType){
202  
203 +    EAMAdapter ea = EAMAdapter(atomType);
204      EAMAtomData eamAtomData;
205  
206 <    eamAtomData.rho = getRho(atomType);
207 <    eamAtomData.F = getF(atomType);
208 <    eamAtomData.Z = getZ(atomType);
209 <    eamAtomData.rcut = getRcut(atomType);
206 >    eamAtomData.rho = ea.getRho();
207 >    eamAtomData.F = ea.getF();
208 >    eamAtomData.Z = ea.getZ();
209 >    eamAtomData.rcut = ea.getRcut();
210  
211      // add it to the map:
212 <    AtomTypeProperties atp = atomType->getATP();    
212 >    int atid = atomType->getIdent();
213 >    int eamtid = EAMtypes.size();
214  
215 <    std::pair<std::map<int,AtomType*>::iterator,bool> ret;    
216 <    ret = EAMlist.insert( std::pair<int, AtomType*>(atp.ident, atomType) );
215 >    pair<set<int>::iterator,bool> ret;    
216 >    ret = EAMtypes.insert( atid );
217      if (ret.second == false) {
218        sprintf( painCave.errMsg,
219                 "EAM already had a previous entry with ident %d\n",
220 <               atp.ident);
220 >               atid);
221        painCave.severity = OPENMD_INFO;
222        painCave.isFatal = 0;
223        simError();        
224      }
225  
226 <    EAMMap[atomType] = eamAtomData;
226 >    EAMtids[atid] = eamtid;
227 >    EAMdata[eamtid] = eamAtomData;
228 >    MixingMap[eamtid].resize(nEAM_);
229      
230      // Now, iterate over all known types and add to the mixing map:
231      
232 <    std::map<int, AtomType*>::iterator it;
233 <    for( it = EAMMap.begin(); it != EAMMap.end(); ++it) {
232 >    std::set<int>::iterator it;
233 >    for( it = EAMtypes.begin(); it != EAMtypes.end(); ++it) {
234        
235 <      AtomType* atype2 = (*it).second;
235 >      int eamtid2 = EAMtids[ (*it) ];
236 >      AtomType* atype2 = forceField_->getAtomType( (*it) );
237  
238        EAMInteractionData mixer;
239        mixer.phi = getPhi(atomType, atype2);
240        mixer.explicitlySet = false;
241  
242 <      std::pair<AtomType*, AtomType*> key1, key2;
301 <      key1 = std::make_pair(atomType, atype2);
302 <      key2 = std::make_pair(atype2, atomType);
242 >      MixingMap[eamtid2].resize( nEAM_ );
243        
244 <      MixingMap[key1] = mixer;
245 <      if (key2 != key1) {
246 <        MixingMap[key2] = mixer;
244 >      MixingMap[eamtid][eamtid2] = mixer;
245 >      if (eamtid2 != eamtid) {
246 >        MixingMap[eamtid2][eamtid] = mixer;
247        }
248      }      
249      return;
# Line 319 | Line 259 | namespace OpenMD {
259  
260      EAMInteractionData mixer;
261      CubicSpline* cs = new CubicSpline();
262 <    vector<RealType> rvals;
262 >    vector<RealType> rVals;
263  
264 <    for (int i = 0; i < nr; i++) rvals.push_back(i * dr);
264 >    for (int i = 0; i < nr; i++) rVals.push_back(i * dr);
265  
266      cs->addPoints(rVals, phiVals);
267      mixer.phi = cs;
268      mixer.explicitlySet = true;
269  
270 <    std::pair<AtomType*, AtomType*> key1, key2;
271 <    key1 = std::make_pair(atype1, atype2);
332 <    key2 = std::make_pair(atype2, atype1);
270 >    int eamtid1 = EAMtids[ atype1->getIdent() ];
271 >    int eamtid2 = EAMtids[ atype2->getIdent() ];
272      
273 <    MixingMap[key1] = mixer;
274 <    if (key2 != key1) {
275 <      MixingMap[key2] = mixer;
273 >    MixingMap[eamtid1][eamtid2] = mixer;
274 >    if (eamtid2 != eamtid1) {
275 >      MixingMap[eamtid2][eamtid1] = mixer;
276      }    
277      return;
278    }
279  
280 <  void EAM::calcDensity(AtomType* at1, AtomType* at2, Vector3d d,
281 <                        RealType rij, RealType r2, RealType rho_i_at_j,
343 <                        RealType rho_j_at_i) {
344 <
280 >  void EAM::calcDensity(InteractionData &idat) {
281 >    
282      if (!initialized_) initialize();
283 +    
284 +    EAMAtomData &data1 = EAMdata[EAMtids[idat.atid1]];
285 +    EAMAtomData &data2 = EAMdata[EAMtids[idat.atid2]];
286  
287 <    EAMAtomData data1 = EAMMap[at1];
288 <    EAMAtomData data2 = EAMMap[at2];
289 <
290 <    if (rij < data1.rcut) rho_i_at_j = data1.rho->getValueAt(rij);
291 <    if (rij < data2.rcut) rho_j_at_i = data2.rho->getValueAt(rij);
292 <    return;
287 >    if (haveCutoffRadius_)
288 >      if ( *(idat.rij) > eamRcut_) return;
289 >    
290 >    if ( *(idat.rij) < data1.rcut)
291 >      *(idat.rho1) += data1.rho->getValueAt( *(idat.rij));
292 >    
293 >      
294 >    if ( *(idat.rij) < data2.rcut)
295 >      *(idat.rho2) += data2.rho->getValueAt( *(idat.rij));
296 >    
297 >    return;  
298    }
299 <
300 <  void EAM::calcFunctional(AtomType* at1, RealType rho, RealType frho,
301 <                           RealType dfrhodrho) {
357 <
299 >  
300 >  void EAM::calcFunctional(SelfData &sdat) {
301 >    
302      if (!initialized_) initialize();
303  
304 <    EAMAtomData data1 = EAMMap[at1];
304 >    EAMAtomData &data1 = EAMdata[ EAMtids[sdat.atid] ];
305          
306 <    pair<RealType, RealType> result = data1.F->getValueAndDerivativeAt(rho);
306 >    data1.F->getValueAndDerivativeAt( *(sdat.rho), *(sdat.frho), *(sdat.dfrhodrho) );
307  
308 <    frho = result.first;
309 <    dfrhodrho = result.second;
308 >    (*(sdat.pot))[METALLIC_FAMILY] += *(sdat.frho);
309 >    if (sdat.doParticlePot) {
310 >      *(sdat.particlePot) += *(sdat.frho);
311 >    }
312 >
313      return;
314    }
315  
316  
317 <  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) {
317 >  void EAM::calcForce(InteractionData &idat) {
318  
319      if (!initialized_) initialize();
377 –    
378 –    pair<RealType, RealType> res;
379 –    
380 –    if (rij < eamRcut_) {
320  
321 <      EAMAtomData data1 = EAMMap[at1];
322 <      EAMAtomData data2 = EAMMap[at2];
323 <
385 <      // get type-specific cutoff radii
321 >    if (haveCutoffRadius_)
322 >      if ( *(idat.rij) > eamRcut_) return;
323 >  
324  
325 <      RealType rci = data1.rcut;
326 <      RealType rcj = data2.rcut;
325 >    int eamtid1 = EAMtids[idat.atid1];
326 >    int eamtid2 = EAMtids[idat.atid2];
327 >    
328 >    EAMAtomData &data1 = EAMdata[eamtid1];
329 >    EAMAtomData &data2 = EAMdata[eamtid2];
330 >    
331 >    // get type-specific cutoff radii
332 >    
333 >    RealType rci = data1.rcut;
334 >    RealType rcj = data2.rcut;
335 >    
336 >    RealType rha(0.0), drha(0.0), rhb(0.0), drhb(0.0);
337 >    RealType pha(0.0), dpha(0.0), phb(0.0), dphb(0.0);
338 >    RealType phab(0.0), dvpdr(0.0);
339 >    RealType drhoidr, drhojdr, dudr;
340 >    
341 >    if ( *(idat.rij) < rci) {
342 >      data1.rho->getValueAndDerivativeAt( *(idat.rij), rha, drha);
343 >      CubicSpline* phi = MixingMap[eamtid1][eamtid1].phi;
344 >      phi->getValueAndDerivativeAt( *(idat.rij), pha, dpha);
345 >    }
346 >    
347 >    if ( *(idat.rij) < rcj) {
348 >      data2.rho->getValueAndDerivativeAt( *(idat.rij), rhb, drhb );
349 >      CubicSpline* phi = MixingMap[eamtid2][eamtid2].phi;
350 >      phi->getValueAndDerivativeAt( *(idat.rij), phb, dphb);
351 >    }
352 >
353 >    switch(mixMeth_) {
354 >    case eamJohnson:
355        
356 <      RealType rha, drha, rhb, drhb;
357 <      RealType pha, dpha, phb, dphb;
358 <      RealType phab, dvpdr;
359 <      RealType drhoidr, drhojdr, dudr;
356 >      if ( *(idat.rij) < rci) {
357 >        phab = phab + 0.5 * (rhb / rha) * pha;
358 >        dvpdr = dvpdr + 0.5*((rhb/rha)*dpha +
359 >                             pha*((drhb/rha) - (rhb*drha/rha/rha)));
360 >      }
361        
362 <      if (rij < rci) {
363 <        res = data1.rho->getValueAndDerivativeAt(rij);
364 <        rha = res.first;
365 <        drha = res.second;
366 <
367 <        res = MixingMap[make_pair(at1, at1)].phi->getValueAndDerivativeAt(rij);
401 <        pha = res.first;
402 <        dpha = res.second;
362 >      
363 >      
364 >      if ( *(idat.rij) < rcj) {
365 >        phab = phab + 0.5 * (rha / rhb) * phb;
366 >        dvpdr = dvpdr + 0.5 * ((rha/rhb)*dphb +
367 >                               phb*((drha/rhb) - (rha*drhb/rhb/rhb)));
368        }
404 –
405 –      if (rij < rcj) {
406 –        res = data2.rho->getValueAndDerivativeAt(rij);
407 –        rhb = res.first;
408 –        drhb = res.second;
409 –
410 –        res = MixingMap[make_pair(at2, at2)].phi->getValueAndDerivativeAt(rij);
411 –        phb = res.first;
412 –        dphb = res.second;
413 –      }
414 –
415 –      phab = 0.0;
416 –      dvpdr = 0.0;
417 –
418 –      switch(mixMeth_) {
419 –      case eamJohnson:
420 –      
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 –          
452 –      }
369        
370 <      drhoidr = drha;
371 <      drhojdr = drhb;
372 <
373 <      dudr = drhojdr*dfrhodrho_i + drhoidr*dfrhodrho_j + dvpdr;
374 <
375 <      f1 = d * dudr / rij;
370 >      break;
371 >      
372 >    case eamDaw:
373 >      MixingMap[eamtid1][eamtid2].phi->getValueAndDerivativeAt( *(idat.rij), phab, dvpdr);
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 >    }
387 >    
388 >    drhoidr = drha;
389 >    drhojdr = drhb;
390 >    
391 >    dudr = drhojdr* *(idat.dfrho1) + drhoidr* *(idat.dfrho2) + dvpdr;
392 >    
393 >    *(idat.f1) += *(idat.d) * dudr / *(idat.rij);
394          
395 <      // particle_pot is the difference between the full potential
396 <      // and the full potential without the presence of a particular
395 >    if (idat.doParticlePot) {
396 >      // particlePot is the difference between the full potential and
397 >      // the full potential without the presence of a particular
398        // particle (atom1).
399        //
400 <      // This reduces the density at other particle locations, so
401 <      // we need to recompute the density at atom2 assuming atom1
402 <      // didn't contribute.  This then requires recomputing the
403 <      // density functional for atom2 as well.
404 <      //
405 <      // Most of the particle_pot heavy lifting comes from the
406 <      // pair interaction, and will be handled by vpair.
407 <    
408 <      fshift_i = data1.F->getValueAt( rho_i - rhb );
409 <      fshift_j = data1.F->getValueAt( rho_j - rha );
475 <
476 <      pot += phab;
477 <
478 <      vpair += phab;
400 >      // This reduces the density at other particle locations, so we
401 >      // need to recompute the density at atom2 assuming atom1 didn't
402 >      // contribute.  This then requires recomputing the density
403 >      // functional for atom2 as well.
404 >      
405 >      *(idat.particlePot1) += data2.F->getValueAt( *(idat.rho2) - rha )
406 >        - *(idat.frho2);
407 >      
408 >      *(idat.particlePot2) += data1.F->getValueAt( *(idat.rho1) - rhb)
409 >        - *(idat.frho1);
410      }
411 <
411 >    
412 >    (*(idat.pot))[METALLIC_FAMILY] += phab;
413 >    
414 >    *(idat.vpair) += phab;
415 >  
416      return;
417      
418    }
419  
420 +  RealType EAM::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) {
421 +    if (!initialized_) initialize();  
422  
423 <  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();
423 >    RealType cut = 0.0;
424  
425 <    AtomType* atype1 = EAMlist[*atid1];
426 <    AtomType* atype2 = EAMlist[*atid2];
425 >    int atid1 = atypes.first->getIdent();
426 >    int atid2 = atypes.second->getIdent();
427 >    int eamtid1 = EAMtids[atid1];
428 >    int eamtid2 = EAMtids[atid2];
429      
430 <    Vector3d disp(d[0], d[1], d[2]);
430 >    if (eamtid1 != -1) {
431 >      EAMAtomData data1 = EAMdata[eamtid1];
432 >      cut = data1.rcut;
433 >    }
434  
435 <    calcDensity(atype1, atype2, disp, *rij, *r2, *rho_i_at_j, *rho_j_at_i);
436 <
437 <    return;    
438 <  }
439 <
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);
435 >    if (eamtid2 != -1) {
436 >      EAMAtomData data2 = EAMdata[eamtid2];
437 >      if (data2.rcut > cut)
438 >        cut = data2.rcut;
439 >    }
440      
441 <    return;    
441 >    return cut;
442    }
512 –
513 –  void EAM::do_eam_pair(int *atid1, int *atid2, RealType *d, RealType *rij,
514 –                        RealType *r2, RealType *sw, RealType *vpair,
515 –                        RealType *pot, RealType *f1, RealType *rho1,
516 –                        RealType *rho2, RealType *dfrho1, RealType *dfrho2,
517 –                        RealType *fshift1, RealType *fshift2) {
518 –
519 –    if (!initialized_) initialize();
520 –    
521 –    AtomType* atype1 = EAMMap[*atid1];
522 –    AtomType* atype2 = EAMMap[*atid2];
523 –    
524 –    Vector3d disp(d[0], d[1], d[2]);
525 –    Vector3d frc(f1[0], f1[1], f1[2]);
526 –    
527 –    calcForce(atype1, atype2, disp, *rij, *r2, *sw, *vpair,  *pot, frc,
528 –              *rho1, *rho2, *dfrho1, *dfrho2, *fshift1, *fshift2);
529 –      
530 –    f1[0] = frc.x();
531 –    f1[1] = frc.y();
532 –    f1[2] = frc.z();
533 –
534 –    return;    
535 –  }
536 –  
537 –  void EAM::setCutoffEAM(RealType *thisRcut) {
538 –    eamRcut_ = thisRcut;
539 –  }
443   }
444  
542 – extern "C" {
543 –  
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) {
552 –
553 –    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) {  
560 –
561 –    return OpenMD::EAM::Instance()->calc_eam_preforce_Frho(*atid1,
562 –                                                           *rho,
563 –                                                           *frho,
564 –                                                           *dfrhodrho);
565 –
566 –  }
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 –  }
582 – }

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