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 (12 years ago) by gezelter
File size:	11330 byte(s)
Log Message:	Speed!
#	User	Rev	Content
1	gezelter	1489	/*
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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	1489	*/
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	gezelter	1502	SC::SC() : name_("SC"), initialized_(false), forceField_(NULL),
55			scRcut_(0.0), np_(3000) {}
56	gezelter	1489
57	gezelter	1879	SC::~SC() {
58			initialized_ = false;
59
60			MixingMap.clear();
61	gezelter	1895	SCtypes.clear();
62			SCdata.clear();
63			SCtids.clear();
64	gezelter	1879	}
65
66	gezelter	1489	RealType SC::getM(AtomType* atomType1, AtomType* atomType2) {
67	gezelter	1710	SuttonChenAdapter sca1 = SuttonChenAdapter(atomType1);
68			SuttonChenAdapter sca2 = SuttonChenAdapter(atomType2);
69			RealType m1 = sca1.getM();
70			RealType m2 = sca2.getM();
71	gezelter	1489	return 0.5 * (m1 + m2);
72			}
73
74			RealType SC::getN(AtomType* atomType1, AtomType* atomType2) {
75	gezelter	1710	SuttonChenAdapter sca1 = SuttonChenAdapter(atomType1);
76			SuttonChenAdapter sca2 = SuttonChenAdapter(atomType2);
77			RealType n1 = sca1.getN();
78			RealType n2 = sca2.getN();
79	gezelter	1489	return 0.5 * (n1 + n2);
80			}
81
82			RealType SC::getAlpha(AtomType* atomType1, AtomType* atomType2) {
83	gezelter	1710	SuttonChenAdapter sca1 = SuttonChenAdapter(atomType1);
84			SuttonChenAdapter sca2 = SuttonChenAdapter(atomType2);
85			RealType alpha1 = sca1.getAlpha();
86			RealType alpha2 = sca2.getAlpha();
87	gezelter	1489
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	gezelter	1710	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	gezelter	1489	return sqrt(epsilon1 * epsilon2);
104			}
105
106	gezelter	1895	void SC::initialize() {
107	gezelter	1489	// find all of the SC atom Types:
108	gezelter	1895	SCtypes.clear();
109			SCtids.clear();
110			SCdata.clear();
111			MixingMap.clear();
112			nSC_ = 0;
113	gezelter	1489
114	gezelter	1895	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	gezelter	1489	initialized_ = true;
126			}
127
128
129
130			void SC::addType(AtomType* atomType){
131
132	gezelter	1710	SuttonChenAdapter sca = SuttonChenAdapter(atomType);
133	gezelter	1489	SCAtomData scAtomData;
134
135	gezelter	1710	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	gezelter	1489	scAtomData.rCut = 2.0 * scAtomData.alpha;
141	gezelter	1895
142	gezelter	1489	// add it to the map:
143	gezelter	1895	int atid = atomType->getIdent();
144			int sctid = SCtypes.size();
145	gezelter	1489
146	gezelter	1895	pair<set<int>::iterator,bool> ret;
147			ret = SCtypes.insert( atid );
148	gezelter	1489	if (ret.second == false) {
149			sprintf( painCave.errMsg,
150			"SC already had a previous entry with ident %d\n",
151	gezelter	1895	atid );
152	gezelter	1489	painCave.severity = OPENMD_INFO;
153			painCave.isFatal = 0;
154			simError();
155			}
156
157	gezelter	1895	SCtids[atid] = sctid;
158			SCdata[sctid] = scAtomData;
159			MixingMap[sctid].resize(nSC_);
160
161	gezelter	1489	// Now, iterate over all known types and add to the mixing map:
162
163	gezelter	1895	std::set<int>::iterator it;
164			for( it = SCtypes.begin(); it != SCtypes.end(); ++it) {
165	gezelter	1489
166	gezelter	1895	int sctid2 = SCtids[ (*it) ];
167			AtomType* atype2 = forceField_->getAtomType( (*it) );
168	gezelter	1489
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	gezelter	1895	MixingMap[sctid2].resize( nSC_ );
207	gezelter	1489
208	gezelter	1895	MixingMap[sctid][sctid2] = mixer;
209			if (sctid2 != sctid) {
210			MixingMap[sctid2][sctid] = mixer;
211	gezelter	1489	}
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	gezelter	1895	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	gezelter	1489	}
268			return;
269			}
270
271	gezelter	1545	void SC::calcDensity(InteractionData &idat) {
272	gezelter	1489
273			if (!initialized_) initialize();
274	gezelter	1895	int sctid1 = SCtids[idat.atid1];
275			int sctid2 = SCtids[idat.atid2];
276	gezelter	1489
277	gezelter	1895	SCInteractionData &mixer = MixingMap[sctid1][sctid2];
278	gezelter	1489
279	gezelter	1502	RealType rcij = mixer.rCut;
280	gezelter	1489
281	gezelter	1554	if ( *(idat.rij) < rcij) {
282	gezelter	1575	RealType rho = mixer.phi->getValueAt( *(idat.rij) );
283			*(idat.rho1) += rho;
284			*(idat.rho2) += rho;
285			}
286	gezelter	1554
287	gezelter	1489	return;
288			}
289
290	gezelter	1545	void SC::calcFunctional(SelfData &sdat) {
291	gezelter	1489
292			if (!initialized_) initialize();
293
294	gezelter	1895	SCAtomData &data1 = SCdata[SCtids[sdat.atid]];
295	gezelter	1575
296			RealType u = - data1.c * data1.epsilon * sqrt( *(sdat.rho) );
297			*(sdat.frho) = u;
298	gezelter	1554	(sdat.dfrhodrho) = 0.5 (sdat.frho) / (sdat.rho);
299	gezelter	1575
300	gezelter	1583	(*(sdat.pot))[METALLIC_FAMILY] += u;
301	gezelter	1711	if (sdat.doParticlePot) {
302			*(sdat.particlePot) += u;
303			}
304
305	gezelter	1489	return;
306			}
307	gezelter	1502
308	gezelter	1489
309	gezelter	1536	void SC::calcForce(InteractionData &idat) {
310	gezelter	1489
311			if (!initialized_) initialize();
312
313	gezelter	1895	int &sctid1 = SCtids[idat.atid1];
314			int &sctid2 = SCtids[idat.atid2];
315	gezelter	1489
316	gezelter	1895	SCAtomData &data1 = SCdata[sctid1];
317			SCAtomData &data2 = SCdata[sctid2];
318	gezelter	1489
319	gezelter	1895	SCInteractionData &mixer = MixingMap[sctid1][sctid2];
320
321	gezelter	1489	RealType rcij = mixer.rCut;
322
323	gezelter	1554	if ( *(idat.rij) < rcij) {
324	gezelter	1895	RealType vcij = mixer.vCut;
325			RealType rhtmp, drhodr, vptmp, dvpdr;
326	gezelter	1502
327	gezelter	1895	mixer.phi->getValueAndDerivativeAt( *(idat.rij), rhtmp, drhodr );
328			mixer.V->getValueAndDerivativeAt( *(idat.rij), vptmp, dvpdr);
329	gezelter	1502
330			RealType pot_temp = vptmp - vcij;
331	gezelter	1554	*(idat.vpair) += pot_temp;
332	gezelter	1502
333	gezelter	1554	RealType dudr = drhodr * ( (idat.dfrho1) + (idat.dfrho2) ) + dvpdr;
334	gezelter	1502
335	gezelter	1554	(idat.f1) += (idat.d) * dudr / *(idat.rij) ;
336	gezelter	1489
337	gezelter	1711	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	gezelter	1575
350	gezelter	1711	(idat.particlePot2) -= data1.c data1.epsilon *
351			sqrt( (idat.rho1) - rhtmp) + (idat.frho1);
352			}
353	gezelter	1489
354	gezelter	1582	(*(idat.pot))[METALLIC_FAMILY] += pot_temp;
355	gezelter	1502	}
356
357	gezelter	1489	return;
358			}
359	gezelter	1505
360	gezelter	1545	RealType SC::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
361	gezelter	1505	if (!initialized_) initialize();
362	gezelter	1545
363	gezelter	1895	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	gezelter	1505	return 0.0;
370	gezelter	1895	} else {
371			return MixingMap[sctid1][sctid2].rCut;
372	gezelter	1505	}
373			}
374	gezelter	1489	}