src/nonbonded/SC.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

#include <stdio.h>
#include <string.h>

#include <cmath>
#include "nonbonded/SC.hpp"
#include "utils/simError.h"
#include "types/NonBondedInteractionType.hpp"

namespace OpenMD {


  SC::SC() : name_("SC"), initialized_(false), forceField_(NULL), 
             scRcut_(0.0), np_(3000) {}
  
  SC::~SC() {
    initialized_ = false;

    MixingMap.clear();
    SCtypes.clear();
    SCdata.clear();
    SCtids.clear();
  }
        
  RealType SC::getM(AtomType* atomType1, AtomType* atomType2) {    
    SuttonChenAdapter sca1 = SuttonChenAdapter(atomType1);
    SuttonChenAdapter sca2 = SuttonChenAdapter(atomType2);
    RealType m1 = sca1.getM();
    RealType m2 = sca2.getM();
    return 0.5 * (m1 + m2);
  }

  RealType SC::getN(AtomType* atomType1, AtomType* atomType2) {    
    SuttonChenAdapter sca1 = SuttonChenAdapter(atomType1);
    SuttonChenAdapter sca2 = SuttonChenAdapter(atomType2);
    RealType n1 = sca1.getN();
    RealType n2 = sca2.getN();
    return 0.5 * (n1 + n2);
  }

  RealType SC::getAlpha(AtomType* atomType1, AtomType* atomType2) {    
    SuttonChenAdapter sca1 = SuttonChenAdapter(atomType1);
    SuttonChenAdapter sca2 = SuttonChenAdapter(atomType2);
    RealType alpha1 = sca1.getAlpha();
    RealType alpha2 = sca2.getAlpha();

    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
    std::string DistanceMix = fopts.getDistanceMixingRule();
    toUpper(DistanceMix);

    if (DistanceMix == "GEOMETRIC") 
      return sqrt(alpha1 * alpha2);
    else 
      return 0.5 * (alpha1 + alpha2);
  }

  RealType SC::getEpsilon(AtomType* atomType1, AtomType* atomType2) {   
    SuttonChenAdapter sca1 = SuttonChenAdapter(atomType1);
    SuttonChenAdapter sca2 = SuttonChenAdapter(atomType2);
    RealType epsilon1 = sca1.getEpsilon();
    RealType epsilon2 = sca2.getEpsilon();
    return sqrt(epsilon1 * epsilon2);
  }

  void SC::initialize() {      
    // find all of the SC atom Types:
    SCtypes.clear();
    SCtids.clear();
    SCdata.clear();
    MixingMap.clear();
    nSC_ = 0;

    SCtids.resize( forceField_->getNAtomType(), -1);

    set<AtomType*>::iterator at;
    for (at = simTypes_.begin(); at != simTypes_.end(); ++at) {
      if ((*at)->isSC()) nSC_++;
    }
    SCdata.resize(nSC_);
    MixingMap.resize(nSC_);
    for (at = simTypes_.begin(); at != simTypes_.end(); ++at) {
      if ((*at)->isSC()) addType((*at));
    }
    initialized_ = true;
  }
  
  
  void SC::addType(AtomType* atomType){

    SuttonChenAdapter sca = SuttonChenAdapter(atomType);
    SCAtomData scAtomData;
    
    scAtomData.c = sca.getC();
    scAtomData.m = sca.getM();
    scAtomData.n = sca.getN();
    scAtomData.alpha = sca.getAlpha();
    scAtomData.epsilon = sca.getEpsilon();
    scAtomData.rCut = 2.0 * scAtomData.alpha;
 
    // add it to the map:
    int atid = atomType->getIdent();
    int sctid = SCtypes.size();

    pair<set<int>::iterator,bool> ret;    
    ret = SCtypes.insert( atid );
    if (ret.second == false) {
      sprintf( painCave.errMsg,
               "SC already had a previous entry with ident %d\n",
               atid );
      painCave.severity = OPENMD_INFO;
      painCave.isFatal = 0;
      simError();         
    }
    
    SCtids[atid] = sctid;
    SCdata[sctid] = scAtomData;
    MixingMap[sctid].resize(nSC_);
    
    // Now, iterate over all known types and add to the mixing map:
    
    std::set<int>::iterator it;
    for( it = SCtypes.begin(); it != SCtypes.end(); ++it) {
      
      int sctid2 = SCtids[ (*it) ];
      AtomType* atype2 = forceField_->getAtomType( (*it) );
      
      SCInteractionData mixer;

      mixer.alpha = getAlpha(atomType, atype2);
      mixer.rCut = 2.0 * mixer.alpha;
      mixer.epsilon = getEpsilon(atomType, atype2);
      mixer.m = getM(atomType, atype2);
      mixer.n = getN(atomType, atype2);

      RealType dr = mixer.rCut / (np_ - 1);
      vector<RealType> rvals;
      vector<RealType> vvals;
      vector<RealType> phivals;
    
      rvals.push_back(0.0);
      vvals.push_back(0.0);
      phivals.push_back(0.0);

      for (int k = 1; k < np_; k++) {
        RealType r = dr * k;
        rvals.push_back(r);
        vvals.push_back( mixer.epsilon * pow(mixer.alpha/r, mixer.n) );
        phivals.push_back( pow(mixer.alpha/r, mixer.m) );
      }

      mixer.vCut = mixer.epsilon * pow(mixer.alpha/mixer.rCut, mixer.n);
    
      CubicSpline* V = new CubicSpline();
      V->addPoints(rvals, vvals);
      
      CubicSpline* phi = new CubicSpline();
      phi->addPoints(rvals, phivals);
      
      mixer.V = V;
      mixer.phi = phi;

      mixer.explicitlySet = false;

      MixingMap[sctid2].resize( nSC_ );
      
      MixingMap[sctid][sctid2] = mixer;
      if (sctid2 != sctid) {
        MixingMap[sctid2][sctid] = mixer;
      }
    }      
    return;
  }
  
  void SC::addExplicitInteraction(AtomType* atype1, AtomType* atype2, 
                                  RealType epsilon, RealType m, RealType n,
                                  RealType alpha) {
    
    // in case these weren't already in the map
    addType(atype1);
    addType(atype2);

    SCInteractionData mixer;

    mixer.epsilon = epsilon;
    mixer.m = m;
    mixer.n = n;
    mixer.alpha = alpha;
    mixer.rCut = 2.0 * mixer.alpha;
    
    RealType dr = mixer.rCut / (np_ - 1);
    vector<RealType> rvals;
    vector<RealType> vvals;
    vector<RealType> phivals;
    
    rvals.push_back(0.0);
    vvals.push_back(0.0);
    phivals.push_back(0.0);
    
    for (int k = 1; k < np_; k++) {
      RealType r = dr * k;
      rvals.push_back(r);
      vvals.push_back( mixer.epsilon * pow(mixer.alpha/r, mixer.n) );
      phivals.push_back( pow(mixer.alpha/r, mixer.m) );
    }
    
    mixer.vCut = mixer.epsilon * pow(mixer.alpha/mixer.rCut, mixer.n);
    
    CubicSpline* V = new CubicSpline();
    V->addPoints(rvals, vvals);
    
    CubicSpline* phi = new CubicSpline();
    phi->addPoints(rvals, phivals);
    
    mixer.V = V;
    mixer.phi = phi;
    
    mixer.explicitlySet = true;

    int sctid1 = SCtids[ atype1->getIdent() ];
    int sctid2 = SCtids[ atype2->getIdent() ];

    MixingMap[sctid1][sctid2] = mixer;
    if (sctid2 != sctid1) {
      MixingMap[sctid2][sctid1] = mixer;
    }    
    return;
  }

  void SC::calcDensity(InteractionData &idat) {
    
    if (!initialized_) initialize();
    int sctid1 = SCtids[idat.atid1];
    int sctid2 = SCtids[idat.atid2];
    
    SCInteractionData &mixer = MixingMap[sctid1][sctid2];

    RealType rcij = mixer.rCut;

    if ( *(idat.rij)  < rcij) {
      RealType rho = mixer.phi->getValueAt( *(idat.rij) );
      *(idat.rho1) += rho;
      *(idat.rho2) += rho;
    } 
    
    return;
  }

  void SC::calcFunctional(SelfData &sdat) {

    if (!initialized_) initialize();

    SCAtomData &data1 = SCdata[SCtids[sdat.atid]];
   
    RealType u = - data1.c * data1.epsilon * sqrt( *(sdat.rho) );
    *(sdat.frho) = u;
    *(sdat.dfrhodrho) = 0.5 * *(sdat.frho) / *(sdat.rho);

    (*(sdat.pot))[METALLIC_FAMILY] += u;
    if (sdat.doParticlePot) {
      *(sdat.particlePot) += u;
    }

    return;
  }
  
 
  void SC::calcForce(InteractionData &idat) {
    
    if (!initialized_) initialize();
    
    int &sctid1 = SCtids[idat.atid1];
    int &sctid2 = SCtids[idat.atid2];

    SCAtomData &data1 = SCdata[sctid1];
    SCAtomData &data2 = SCdata[sctid2];

    SCInteractionData &mixer = MixingMap[sctid1][sctid2];

    RealType rcij = mixer.rCut;

    if ( *(idat.rij)  < rcij) {
      RealType vcij = mixer.vCut; 
      RealType rhtmp, drhodr, vptmp, dvpdr;
      
      mixer.phi->getValueAndDerivativeAt( *(idat.rij), rhtmp, drhodr );      
      mixer.V->getValueAndDerivativeAt( *(idat.rij), vptmp, dvpdr);
      
      RealType pot_temp = vptmp - vcij;
      *(idat.vpair) += pot_temp;
      
      RealType dudr = drhodr * ( *(idat.dfrho1) + *(idat.dfrho2) ) + dvpdr;
      
      *(idat.f1) += *(idat.d) * dudr / *(idat.rij) ;
        
      if (idat.doParticlePot) {
        // particlePot is the difference between the full potential and
        // the full potential without the presence of a particular
        // particle (atom1).
        //
        // This reduces the density at other particle locations, so we
        // need to recompute the density at atom2 assuming atom1 didn't
        // contribute.  This then requires recomputing the density
        // functional for atom2 as well.
        
        *(idat.particlePot1) -= data2.c * data2.epsilon * 
          sqrt( *(idat.rho2) - rhtmp) + *(idat.frho2);

        *(idat.particlePot2) -= data1.c * data1.epsilon * 
          sqrt( *(idat.rho1) - rhtmp) + *(idat.frho1);
      }
      
      (*(idat.pot))[METALLIC_FAMILY] += pot_temp;
    }
      
    return;    
  }

  RealType SC::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) {
    if (!initialized_) initialize();   

    int atid1 = atypes.first->getIdent();
    int atid2 = atypes.second->getIdent();
    int &sctid1 = SCtids[atid1];
    int &sctid2 = SCtids[atid2];
    
    if (sctid1 == -1 || sctid2 == -1) {
      return 0.0;
    } else {
      return MixingMap[sctid1][sctid2].rCut;
    }
  }
}
Revision:	1895
Committed:	Mon Jul 1 21:09:37 2013 UTC (11 years, 10 months ago) by gezelter
File size:	11330 byte(s)
Log Message:	Speed!
#	Content
1	/*
2	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	*
4	* The University of Notre Dame grants you ("Licensee") a
5	* non-exclusive, royalty free, license to use, modify and
6	* redistribute this software in source and binary code form, provided
7	* that the following conditions are met:
8	*
9	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* notice, this list of conditions and the following disclaimer in the
14	* documentation and/or other materials provided with the
15	* distribution.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
28	* arising out of the use of or inability to use software, even if the
29	* University of Notre Dame has been advised of the possibility of
30	* such damages.
31	*
32	* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33	* research, please cite the appropriate papers when you publish your
34	* work. Good starting points are:
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, 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>
44	#include <string.h>
45
46	#include <cmath>
47	#include "nonbonded/SC.hpp"
48	#include "utils/simError.h"
49	#include "types/NonBondedInteractionType.hpp"
50
51	namespace OpenMD {
52
53
54	SC::SC() : name_("SC"), initialized_(false), forceField_(NULL),
55	scRcut_(0.0), np_(3000) {}
56
57	SC::~SC() {
58	initialized_ = false;
59
60	MixingMap.clear();
61	SCtypes.clear();
62	SCdata.clear();
63	SCtids.clear();
64	}
65
66	RealType SC::getM(AtomType* atomType1, AtomType* atomType2) {
67	SuttonChenAdapter sca1 = SuttonChenAdapter(atomType1);
68	SuttonChenAdapter sca2 = SuttonChenAdapter(atomType2);
69	RealType m1 = sca1.getM();
70	RealType m2 = sca2.getM();
71	return 0.5 * (m1 + m2);
72	}
73
74	RealType SC::getN(AtomType* atomType1, AtomType* atomType2) {
75	SuttonChenAdapter sca1 = SuttonChenAdapter(atomType1);
76	SuttonChenAdapter sca2 = SuttonChenAdapter(atomType2);
77	RealType n1 = sca1.getN();
78	RealType n2 = sca2.getN();
79	return 0.5 * (n1 + n2);
80	}
81
82	RealType SC::getAlpha(AtomType* atomType1, AtomType* atomType2) {
83	SuttonChenAdapter sca1 = SuttonChenAdapter(atomType1);
84	SuttonChenAdapter sca2 = SuttonChenAdapter(atomType2);
85	RealType alpha1 = sca1.getAlpha();
86	RealType alpha2 = sca2.getAlpha();
87
88	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
89	std::string DistanceMix = fopts.getDistanceMixingRule();
90	toUpper(DistanceMix);
91
92	if (DistanceMix == "GEOMETRIC")
93	return sqrt(alpha1 * alpha2);
94	else
95	return 0.5 * (alpha1 + alpha2);
96	}
97
98	RealType SC::getEpsilon(AtomType* atomType1, AtomType* atomType2) {
99	SuttonChenAdapter sca1 = SuttonChenAdapter(atomType1);
100	SuttonChenAdapter sca2 = SuttonChenAdapter(atomType2);
101	RealType epsilon1 = sca1.getEpsilon();
102	RealType epsilon2 = sca2.getEpsilon();
103	return sqrt(epsilon1 * epsilon2);
104	}
105
106	void SC::initialize() {
107	// find all of the SC atom Types:
108	SCtypes.clear();
109	SCtids.clear();
110	SCdata.clear();
111	MixingMap.clear();
112	nSC_ = 0;
113
114	SCtids.resize( forceField_->getNAtomType(), -1);
115
116	set<AtomType*>::iterator at;
117	for (at = simTypes_.begin(); at != simTypes_.end(); ++at) {
118	if ((*at)->isSC()) nSC_++;
119	}
120	SCdata.resize(nSC_);
121	MixingMap.resize(nSC_);
122	for (at = simTypes_.begin(); at != simTypes_.end(); ++at) {
123	if ((at)->isSC()) addType((at));
124	}
125	initialized_ = true;
126	}
127
128
129
130	void SC::addType(AtomType* atomType){
131
132	SuttonChenAdapter sca = SuttonChenAdapter(atomType);
133	SCAtomData scAtomData;
134
135	scAtomData.c = sca.getC();
136	scAtomData.m = sca.getM();
137	scAtomData.n = sca.getN();
138	scAtomData.alpha = sca.getAlpha();
139	scAtomData.epsilon = sca.getEpsilon();
140	scAtomData.rCut = 2.0 * scAtomData.alpha;
141
142	// add it to the map:
143	int atid = atomType->getIdent();
144	int sctid = SCtypes.size();
145
146	pair<set<int>::iterator,bool> ret;
147	ret = SCtypes.insert( atid );
148	if (ret.second == false) {
149	sprintf( painCave.errMsg,
150	"SC already had a previous entry with ident %d\n",
151	atid );
152	painCave.severity = OPENMD_INFO;
153	painCave.isFatal = 0;
154	simError();
155	}
156
157	SCtids[atid] = sctid;
158	SCdata[sctid] = scAtomData;
159	MixingMap[sctid].resize(nSC_);
160
161	// Now, iterate over all known types and add to the mixing map:
162
163	std::set<int>::iterator it;
164	for( it = SCtypes.begin(); it != SCtypes.end(); ++it) {
165
166	int sctid2 = SCtids[ (*it) ];
167	AtomType* atype2 = forceField_->getAtomType( (*it) );
168
169	SCInteractionData mixer;
170
171	mixer.alpha = getAlpha(atomType, atype2);
172	mixer.rCut = 2.0 * mixer.alpha;
173	mixer.epsilon = getEpsilon(atomType, atype2);
174	mixer.m = getM(atomType, atype2);
175	mixer.n = getN(atomType, atype2);
176
177	RealType dr = mixer.rCut / (np_ - 1);
178	vector<RealType> rvals;
179	vector<RealType> vvals;
180	vector<RealType> phivals;
181
182	rvals.push_back(0.0);
183	vvals.push_back(0.0);
184	phivals.push_back(0.0);
185
186	for (int k = 1; k < np_; k++) {
187	RealType r = dr * k;
188	rvals.push_back(r);
189	vvals.push_back( mixer.epsilon * pow(mixer.alpha/r, mixer.n) );
190	phivals.push_back( pow(mixer.alpha/r, mixer.m) );
191	}
192
193	mixer.vCut = mixer.epsilon * pow(mixer.alpha/mixer.rCut, mixer.n);
194
195	CubicSpline* V = new CubicSpline();
196	V->addPoints(rvals, vvals);
197
198	CubicSpline* phi = new CubicSpline();
199	phi->addPoints(rvals, phivals);
200
201	mixer.V = V;
202	mixer.phi = phi;
203
204	mixer.explicitlySet = false;
205
206	MixingMap[sctid2].resize( nSC_ );
207
208	MixingMap[sctid][sctid2] = mixer;
209	if (sctid2 != sctid) {
210	MixingMap[sctid2][sctid] = mixer;
211	}
212	}
213	return;
214	}
215
216	void SC::addExplicitInteraction(AtomType* atype1, AtomType* atype2,
217	RealType epsilon, RealType m, RealType n,
218	RealType alpha) {
219
220	// in case these weren't already in the map
221	addType(atype1);
222	addType(atype2);
223
224	SCInteractionData mixer;
225
226	mixer.epsilon = epsilon;
227	mixer.m = m;
228	mixer.n = n;
229	mixer.alpha = alpha;
230	mixer.rCut = 2.0 * mixer.alpha;
231
232	RealType dr = mixer.rCut / (np_ - 1);
233	vector<RealType> rvals;
234	vector<RealType> vvals;
235	vector<RealType> phivals;
236
237	rvals.push_back(0.0);
238	vvals.push_back(0.0);
239	phivals.push_back(0.0);
240
241	for (int k = 1; k < np_; k++) {
242	RealType r = dr * k;
243	rvals.push_back(r);
244	vvals.push_back( mixer.epsilon * pow(mixer.alpha/r, mixer.n) );
245	phivals.push_back( pow(mixer.alpha/r, mixer.m) );
246	}
247
248	mixer.vCut = mixer.epsilon * pow(mixer.alpha/mixer.rCut, mixer.n);
249
250	CubicSpline* V = new CubicSpline();
251	V->addPoints(rvals, vvals);
252
253	CubicSpline* phi = new CubicSpline();
254	phi->addPoints(rvals, phivals);
255
256	mixer.V = V;
257	mixer.phi = phi;
258
259	mixer.explicitlySet = true;
260
261	int sctid1 = SCtids[ atype1->getIdent() ];
262	int sctid2 = SCtids[ atype2->getIdent() ];
263
264	MixingMap[sctid1][sctid2] = mixer;
265	if (sctid2 != sctid1) {
266	MixingMap[sctid2][sctid1] = mixer;
267	}
268	return;
269	}
270
271	void SC::calcDensity(InteractionData &idat) {
272
273	if (!initialized_) initialize();
274	int sctid1 = SCtids[idat.atid1];
275	int sctid2 = SCtids[idat.atid2];
276
277	SCInteractionData &mixer = MixingMap[sctid1][sctid2];
278
279	RealType rcij = mixer.rCut;
280
281	if ( *(idat.rij) < rcij) {
282	RealType rho = mixer.phi->getValueAt( *(idat.rij) );
283	*(idat.rho1) += rho;
284	*(idat.rho2) += rho;
285	}
286
287	return;
288	}
289
290	void SC::calcFunctional(SelfData &sdat) {
291
292	if (!initialized_) initialize();
293
294	SCAtomData &data1 = SCdata[SCtids[sdat.atid]];
295
296	RealType u = - data1.c * data1.epsilon * sqrt( *(sdat.rho) );
297	*(sdat.frho) = u;
298	(sdat.dfrhodrho) = 0.5 (sdat.frho) / (sdat.rho);
299
300	(*(sdat.pot))[METALLIC_FAMILY] += u;
301	if (sdat.doParticlePot) {
302	*(sdat.particlePot) += u;
303	}
304
305	return;
306	}
307
308
309	void SC::calcForce(InteractionData &idat) {
310
311	if (!initialized_) initialize();
312
313	int &sctid1 = SCtids[idat.atid1];
314	int &sctid2 = SCtids[idat.atid2];
315
316	SCAtomData &data1 = SCdata[sctid1];
317	SCAtomData &data2 = SCdata[sctid2];
318
319	SCInteractionData &mixer = MixingMap[sctid1][sctid2];
320
321	RealType rcij = mixer.rCut;
322
323	if ( *(idat.rij) < rcij) {
324	RealType vcij = mixer.vCut;
325	RealType rhtmp, drhodr, vptmp, dvpdr;
326
327	mixer.phi->getValueAndDerivativeAt( *(idat.rij), rhtmp, drhodr );
328	mixer.V->getValueAndDerivativeAt( *(idat.rij), vptmp, dvpdr);
329
330	RealType pot_temp = vptmp - vcij;
331	*(idat.vpair) += pot_temp;
332
333	RealType dudr = drhodr * ( (idat.dfrho1) + (idat.dfrho2) ) + dvpdr;
334
335	(idat.f1) += (idat.d) * dudr / *(idat.rij) ;
336
337	if (idat.doParticlePot) {
338	// particlePot is the difference between the full potential and
339	// the full potential without the presence of a particular
340	// particle (atom1).
341	//
342	// This reduces the density at other particle locations, so we
343	// need to recompute the density at atom2 assuming atom1 didn't
344	// contribute. This then requires recomputing the density
345	// functional for atom2 as well.
346
347	(idat.particlePot1) -= data2.c data2.epsilon *
348	sqrt( (idat.rho2) - rhtmp) + (idat.frho2);
349
350	(idat.particlePot2) -= data1.c data1.epsilon *
351	sqrt( (idat.rho1) - rhtmp) + (idat.frho1);
352	}
353
354	(*(idat.pot))[METALLIC_FAMILY] += pot_temp;
355	}
356
357	return;
358	}
359
360	RealType SC::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
361	if (!initialized_) initialize();
362
363	int atid1 = atypes.first->getIdent();
364	int atid2 = atypes.second->getIdent();
365	int &sctid1 = SCtids[atid1];
366	int &sctid2 = SCtids[atid2];
367
368	if (sctid1 == -1 \|\| sctid2 == -1) {
369	return 0.0;
370	} else {
371	return MixingMap[sctid1][sctid2].rCut;
372	}
373	}
374	}