src/nonbonded/LJ.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, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */

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

#include <cmath>
#include "nonbonded/LJ.hpp"
#include "utils/simError.h"


namespace OpenMD {

  bool LJ::initialized_ = false;
  bool LJ::shiftedPot_ = false;
  bool LJ::shiftedFrc_ = false;
  ForceField* LJ::forceField_ = NULL;
  std::map<int, AtomType*> LJ::LJMap;
  std::map<std::pair<AtomType*, AtomType*>, LJInteractionData> LJ::MixingMap;
  
  LJ* LJ::_instance = NULL;

  LJ* LJ::Instance() {
    if (!_instance) {
      _instance = new LJ();
    }
    return _instance;
  }

  LJParam LJ::getLJParam(AtomType* atomType) {
    
    // Do sanity checking on the AtomType we were passed before
    // building any data structures:
    if (!atomType->isLennardJones()) {
      sprintf( painCave.errMsg,
               "LJ::getLJParam was passed an atomType (%s) that does not\n"
               "\tappear to be a Lennard-Jones atom.\n",
               atomType->getName().c_str());
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
    
    GenericData* data = atomType->getPropertyByName("LennardJones");
    if (data == NULL) {
      sprintf( painCave.errMsg, "LJ::getLJParam could not find Lennard-Jones\n"
               "\tparameters for atomType %s.\n", atomType->getName().c_str());
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError(); 
    }
    
    LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
    if (ljData == NULL) {
      sprintf( painCave.errMsg,
               "LJ::getLJParam could not convert GenericData to LJParam for\n"
               "\tatom type %s\n", atomType->getName().c_str());
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();          
    }
    
    return ljData->getData();
  }

  RealType LJ::getSigma(AtomType* atomType) {    
    LJParam ljParam = getLJParam(atomType);
    return ljParam.sigma;
  }

  RealType LJ::getSigma(int atid) { 
    std::map<int, AtomType*> :: const_iterator it;
    it = LJMap.find(atid);
    if (it == LJMap.end()) {
      sprintf( painCave.errMsg,
               "LJ::getSigma could not find atid %d in LJMap\n",
               (atid));
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();          
    }
    AtomType* atype = it->second;

    return getSigma(atype);    
  }

  RealType LJ::getSigma(AtomType* atomType1, AtomType* atomType2) {    
    RealType sigma1 = getSigma(atomType1);
    RealType sigma2 = getSigma(atomType2);
    
    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
    std::string DistanceMix = fopts.getDistanceMixingRule();
    toUpper(DistanceMix);

    if (DistanceMix == "GEOMETRIC") 
      return sqrt(sigma1 * sigma2);
    else 
      return 0.5 * (sigma1 + sigma2);
  }

  RealType LJ::getEpsilon(AtomType* atomType) {    
    LJParam ljParam = getLJParam(atomType);
    return ljParam.epsilon;
  }

  RealType LJ::getEpsilon(int atid) {    
    std::map<int, AtomType*> :: const_iterator it;
    it = LJMap.find(atid);
    if (it == LJMap.end()) {
      sprintf( painCave.errMsg,
               "LJ::getEpsilon could not find atid %d in LJMap\n",
               (atid));
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();          
    }
    AtomType* atype = it->second;

    return getEpsilon(atype);    
  }

  RealType LJ::getEpsilon(AtomType* atomType1, AtomType* atomType2) {    
    RealType epsilon1 = getEpsilon(atomType1);
    RealType epsilon2 = getEpsilon(atomType2);
    return sqrt(epsilon1 * epsilon2);
  }

  void LJ::initialize() {    
    ForceField::AtomTypeContainer atomTypes = forceField_->getAtomTypes();
    ForceField::AtomTypeContainer::MapTypeIterator i;
    AtomType* at;

    for (at = atomTypes.beginType(i); at != NULL; 
         at = atomTypes.nextType(i)) {
      
      if (at->isLennardJones())
        addType(at);
    }

    ForceField::NonBondedInteractionTypeContainer nbiTypes = forceField_->getNonBondedInteractionTypes();
    ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
    NonBondedInteractionType* nbt;

    for (nbt = nbiTypes.beginType(j); nbt != NULL; 
         nbt = nbiTypes.nextType(j)) {
      
      if (nbt->isLennardJones()) {
        
        std::pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes();
        
        GenericData* data = nbt->getPropertyByName("LennardJones");
        if (data == NULL) {
          sprintf( painCave.errMsg, "LJ::rebuildMixingMap could not find\n"
               "\tLennard-Jones parameters for %s - %s interaction.\n", 
                   atypes.first->getName().c_str(),
                   atypes.second->getName().c_str());
          painCave.severity = OPENMD_ERROR;
          painCave.isFatal = 1;
          simError(); 
        }
    
        LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
        if (ljData == NULL) {
          sprintf( painCave.errMsg,
                   "LJ::rebuildMixingMap could not convert GenericData to\n"
                   "\tLJParam for %s - %s interaction.\n", 
                   atypes.first->getName().c_str(),
                   atypes.second->getName().c_str());
          painCave.severity = OPENMD_ERROR;
          painCave.isFatal = 1;
          simError();          
        }
        
        LJParam ljParam = ljData->getData();

        RealType sigma = ljParam.sigma;
        RealType epsilon = ljParam.epsilon;

        addExplicitInteraction(atypes.first, atypes.second, sigma, epsilon);
      }
    }  
    initialized_ = true;
  }
      

  void LJ::addType(AtomType* atomType){
    RealType sigma1 = getSigma(atomType);
    RealType epsilon1 = getEpsilon(atomType);

    // add it to the map:
    AtomTypeProperties atp = atomType->getATP();    
    std::pair<std::map<int,AtomType*>::iterator,bool> ret;
    ret = LJMap.insert( std::pair<int, AtomType*>(atp.ident, atomType) );
    if (ret.second == false) {
      sprintf( painCave.errMsg,
               "LJ already had a previous entry with ident %d\n",
               atp.ident);
      painCave.severity = OPENMD_INFO;
      painCave.isFatal = 0;
      simError();         
    }
    
    // Now, iterate over all known types and add to the mixing map:
    
    std::map<int, AtomType*>::iterator it;
    for( it = LJMap.begin(); it != LJMap.end(); ++it) {
      
      AtomType* atype2 = (*it).second;

      LJInteractionData mixer;
      mixer.sigma = getSigma(atomType, atype2);
      mixer.epsilon = getEpsilon(atomType, atype2);
      mixer.sigmai = 1.0 / mixer.sigma;
      mixer.explicitlySet = false;

      std::pair<AtomType*, AtomType*> key1, key2;
      key1 = std::make_pair(atomType, atype2);
      key2 = std::make_pair(atype2, atomType);
      
      MixingMap[key1] = mixer;
      if (key2 != key1) {
        MixingMap[key2] = mixer;
      }
    }      
  }
  
  void LJ::addExplicitInteraction(AtomType* atype1, AtomType* atype2, RealType sigma, RealType epsilon){
    
    // in case these weren't already in the map
    addType(atype1);
    addType(atype2);

    LJInteractionData mixer;
    mixer.sigma = sigma;
    mixer.epsilon = epsilon;
    mixer.sigmai = 1.0 / mixer.sigma;
    mixer.explicitlySet = true;

    std::pair<AtomType*, AtomType*> key1, key2;
    key1 = std::make_pair(atype1, atype2);
    key2 = std::make_pair(atype2, atype1);
    
    MixingMap[key1] = mixer;
    if (key2 != key1) {
      MixingMap[key2] = mixer;
    }    
  }
 
  void LJ::calcForce(AtomType* at1, AtomType* at2, Vector3d d, RealType rij, 
                     RealType r2, RealType rcut, RealType sw, RealType vdwMult,
                     RealType vpair, RealType pot, Vector3d f1) {

    if (!initialized_) initialize();
    
    RealType ros;
    RealType rcos;
    RealType myPot = 0.0;
    RealType myPotC = 0.0;
    RealType myDeriv = 0.0;
    RealType myDerivC = 0.0;

    std::pair<AtomType*, AtomType*> key = std::make_pair(at1, at2);
    LJInteractionData mixer = MixingMap[key];

    RealType sigmai = mixer.sigmai;
    RealType epsilon = mixer.epsilon;
    
    ros = rij * sigmai;

    getLJfunc(ros, myPot, myDeriv);

    if (shiftedPot_) {
      rcos = rcut * sigmai;
      getLJfunc(rcos, myPotC, myDerivC);
      myDerivC = 0.0;
    } else if (LJ::shiftedFrc_) {
      rcos = rcut * sigmai;
      getLJfunc(rcos, myPotC, myDerivC);
      myPotC = myPotC + myDerivC * (rij - rcut) * sigmai;
    } else {
      myPotC = 0.0;
      myDerivC = 0.0;
    }

    RealType pot_temp = vdwMult * epsilon * (myPot - myPotC);
    vpair += pot_temp;

    RealType dudr = sw * vdwMult * epsilon * (myDeriv - myDerivC)*sigmai;
    
    pot += sw * pot_temp;
    f1 = d * dudr / rij;

    return;
  }

  void LJ::do_lj_pair(int *atid1, int *atid2, RealType *d, RealType *rij, 
                      RealType *r2, RealType *rcut, RealType *sw, 
                      RealType *vdwMult,
                      RealType *vpair, RealType *pot, RealType *f1) {

    if (!initialized_) initialize();
    
    AtomType* atype1 = LJMap[*atid1];
    AtomType* atype2 = LJMap[*atid2];
    
    Vector3d disp(d[0], d[1], d[2]);
    Vector3d frc(f1[0], f1[1], f1[2]);
    
    calcForce(atype1, atype2, disp, *rij, *r2, *rcut, *sw, *vdwMult, *vpair, 
              *pot, frc);
    return;    
  }
  
  void LJ::getLJfunc(const RealType r, RealType pot, RealType deriv) {
    RealType ri = 1.0 / r;
    RealType ri2 = ri * ri;
    RealType ri6 = ri2 * ri2 * ri2;
    RealType ri7 = ri6 * ri;
    RealType ri12 = ri6 * ri6;
    RealType ri13 = ri12 * ri;

    pot = 4.0 * (ri12 - ri6);
    deriv = 24.0 * (ri7 - 2.0 * ri13);
    return;
  }


  void LJ::setLJDefaultCutoff(RealType *thisRcut, int *sP, int *sF) {
    shiftedPot_ = (bool)(*sP);
    shiftedFrc_ = (bool)(*sF);
  }
}

extern "C" {
  
#define fortranGetSigma FC_FUNC(getsigma, GETSIGMA)
#define fortranGetEpsilon FC_FUNC(getepsilon, GETEPSILON)
#define fortranSetLJCutoff FC_FUNC(setljdefaultcutoff, SETLJDEFAULTCUTOFF)
#define fortranDoLJPair FC_FUNC(do_lj_pair, DO_LJ_PAIR)
  
  RealType fortranGetSigma(int* atid) {
    return OpenMD::LJ::Instance()->getSigma(*atid);
  }
  RealType fortranGetEpsilon(int* atid) {  
    return OpenMD::LJ::Instance()->getEpsilon(*atid);
  }
  void fortranSetLJCutoff(RealType *rcut, int *shiftedPot, int *shiftedFrc) {
    return OpenMD::LJ::Instance()->setLJDefaultCutoff(rcut, shiftedPot, 
                                                      shiftedFrc);
  }
  void fortranDoLJPair(int *atid1, int *atid2, RealType *d, RealType *rij, 
                       RealType *r2, RealType *rcut, RealType *sw, 
                       RealType *vdwMult, RealType* vpair, RealType* pot, 
                       RealType *f1){
    
    return OpenMD::LJ::Instance()->do_lj_pair(atid1, atid2, d, rij, r2, rcut,
                                              sw, vdwMult, vpair, pot, f1);
  }
}
Revision:	1471
Committed:	Mon Jul 19 18:59:59 2010 UTC (14 years, 9 months ago) by gezelter
File size:	13013 byte(s)
Log Message:	Added nonbonded directory. Compiles, links, runs, but gives incorrect answer.
#	User	Rev	Content
1	gezelter	1471	/*
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, 24107 (2008).
39			* [4] Vardeman & Gezelter, in progress (2009).
40			*/
41
42			#include <stdio.h>
43			#include <string.h>
44
45			#include <cmath>
46			#include "nonbonded/LJ.hpp"
47			#include "utils/simError.h"
48
49
50			namespace OpenMD {
51
52			bool LJ::initialized_ = false;
53			bool LJ::shiftedPot_ = false;
54			bool LJ::shiftedFrc_ = false;
55			ForceField* LJ::forceField_ = NULL;
56			std::map<int, AtomType*> LJ::LJMap;
57			std::map<std::pair<AtomType, AtomType>, LJInteractionData> LJ::MixingMap;
58
59			LJ* LJ::_instance = NULL;
60
61			LJ* LJ::Instance() {
62			if (!_instance) {
63			_instance = new LJ();
64			}
65			return _instance;
66			}
67
68			LJParam LJ::getLJParam(AtomType* atomType) {
69
70			// Do sanity checking on the AtomType we were passed before
71			// building any data structures:
72			if (!atomType->isLennardJones()) {
73			sprintf( painCave.errMsg,
74			"LJ::getLJParam was passed an atomType (%s) that does not\n"
75			"\tappear to be a Lennard-Jones atom.\n",
76			atomType->getName().c_str());
77			painCave.severity = OPENMD_ERROR;
78			painCave.isFatal = 1;
79			simError();
80			}
81
82			GenericData* data = atomType->getPropertyByName("LennardJones");
83			if (data == NULL) {
84			sprintf( painCave.errMsg, "LJ::getLJParam could not find Lennard-Jones\n"
85			"\tparameters for atomType %s.\n", atomType->getName().c_str());
86			painCave.severity = OPENMD_ERROR;
87			painCave.isFatal = 1;
88			simError();
89			}
90
91			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
92			if (ljData == NULL) {
93			sprintf( painCave.errMsg,
94			"LJ::getLJParam could not convert GenericData to LJParam 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 ljData->getData();
102			}
103
104			RealType LJ::getSigma(AtomType* atomType) {
105			LJParam ljParam = getLJParam(atomType);
106			return ljParam.sigma;
107			}
108
109			RealType LJ::getSigma(int atid) {
110			std::map<int, AtomType*> :: const_iterator it;
111			it = LJMap.find(atid);
112			if (it == LJMap.end()) {
113			sprintf( painCave.errMsg,
114			"LJ::getSigma could not find atid %d in LJMap\n",
115			(atid));
116			painCave.severity = OPENMD_ERROR;
117			painCave.isFatal = 1;
118			simError();
119			}
120			AtomType* atype = it->second;
121
122			return getSigma(atype);
123			}
124
125			RealType LJ::getSigma(AtomType* atomType1, AtomType* atomType2) {
126			RealType sigma1 = getSigma(atomType1);
127			RealType sigma2 = getSigma(atomType2);
128
129			ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
130			std::string DistanceMix = fopts.getDistanceMixingRule();
131			toUpper(DistanceMix);
132
133			if (DistanceMix == "GEOMETRIC")
134			return sqrt(sigma1 * sigma2);
135			else
136			return 0.5 * (sigma1 + sigma2);
137			}
138
139			RealType LJ::getEpsilon(AtomType* atomType) {
140			LJParam ljParam = getLJParam(atomType);
141			return ljParam.epsilon;
142			}
143
144			RealType LJ::getEpsilon(int atid) {
145			std::map<int, AtomType*> :: const_iterator it;
146			it = LJMap.find(atid);
147			if (it == LJMap.end()) {
148			sprintf( painCave.errMsg,
149			"LJ::getEpsilon could not find atid %d in LJMap\n",
150			(atid));
151			painCave.severity = OPENMD_ERROR;
152			painCave.isFatal = 1;
153			simError();
154			}
155			AtomType* atype = it->second;
156
157			return getEpsilon(atype);
158			}
159
160			RealType LJ::getEpsilon(AtomType* atomType1, AtomType* atomType2) {
161			RealType epsilon1 = getEpsilon(atomType1);
162			RealType epsilon2 = getEpsilon(atomType2);
163			return sqrt(epsilon1 * epsilon2);
164			}
165
166			void LJ::initialize() {
167			ForceField::AtomTypeContainer atomTypes = forceField_->getAtomTypes();
168			ForceField::AtomTypeContainer::MapTypeIterator i;
169			AtomType* at;
170
171			for (at = atomTypes.beginType(i); at != NULL;
172			at = atomTypes.nextType(i)) {
173
174			if (at->isLennardJones())
175			addType(at);
176			}
177
178			ForceField::NonBondedInteractionTypeContainer nbiTypes = forceField_->getNonBondedInteractionTypes();
179			ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
180			NonBondedInteractionType* nbt;
181
182			for (nbt = nbiTypes.beginType(j); nbt != NULL;
183			nbt = nbiTypes.nextType(j)) {
184
185			if (nbt->isLennardJones()) {
186
187			std::pair<AtomType, AtomType> atypes = nbt->getAtomTypes();
188
189			GenericData* data = nbt->getPropertyByName("LennardJones");
190			if (data == NULL) {
191			sprintf( painCave.errMsg, "LJ::rebuildMixingMap could not find\n"
192			"\tLennard-Jones parameters for %s - %s interaction.\n",
193			atypes.first->getName().c_str(),
194			atypes.second->getName().c_str());
195			painCave.severity = OPENMD_ERROR;
196			painCave.isFatal = 1;
197			simError();
198			}
199
200			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
201			if (ljData == NULL) {
202			sprintf( painCave.errMsg,
203			"LJ::rebuildMixingMap could not convert GenericData to\n"
204			"\tLJParam for %s - %s interaction.\n",
205			atypes.first->getName().c_str(),
206			atypes.second->getName().c_str());
207			painCave.severity = OPENMD_ERROR;
208			painCave.isFatal = 1;
209			simError();
210			}
211
212			LJParam ljParam = ljData->getData();
213
214			RealType sigma = ljParam.sigma;
215			RealType epsilon = ljParam.epsilon;
216
217			addExplicitInteraction(atypes.first, atypes.second, sigma, epsilon);
218			}
219			}
220			initialized_ = true;
221			}
222
223
224
225			void LJ::addType(AtomType* atomType){
226			RealType sigma1 = getSigma(atomType);
227			RealType epsilon1 = getEpsilon(atomType);
228
229			// add it to the map:
230			AtomTypeProperties atp = atomType->getATP();
231			std::pair<std::map<int,AtomType*>::iterator,bool> ret;
232			ret = LJMap.insert( std::pair<int, AtomType*>(atp.ident, atomType) );
233			if (ret.second == false) {
234			sprintf( painCave.errMsg,
235			"LJ already had a previous entry with ident %d\n",
236			atp.ident);
237			painCave.severity = OPENMD_INFO;
238			painCave.isFatal = 0;
239			simError();
240			}
241
242			// Now, iterate over all known types and add to the mixing map:
243
244			std::map<int, AtomType*>::iterator it;
245			for( it = LJMap.begin(); it != LJMap.end(); ++it) {
246
247			AtomType* atype2 = (*it).second;
248
249			LJInteractionData mixer;
250			mixer.sigma = getSigma(atomType, atype2);
251			mixer.epsilon = getEpsilon(atomType, atype2);
252			mixer.sigmai = 1.0 / mixer.sigma;
253			mixer.explicitlySet = false;
254
255			std::pair<AtomType, AtomType> key1, key2;
256			key1 = std::make_pair(atomType, atype2);
257			key2 = std::make_pair(atype2, atomType);
258
259			MixingMap[key1] = mixer;
260			if (key2 != key1) {
261			MixingMap[key2] = mixer;
262			}
263			}
264			}
265
266			void LJ::addExplicitInteraction(AtomType* atype1, AtomType* atype2, RealType sigma, RealType epsilon){
267
268			// in case these weren't already in the map
269			addType(atype1);
270			addType(atype2);
271
272			LJInteractionData mixer;
273			mixer.sigma = sigma;
274			mixer.epsilon = epsilon;
275			mixer.sigmai = 1.0 / mixer.sigma;
276			mixer.explicitlySet = true;
277
278			std::pair<AtomType, AtomType> key1, key2;
279			key1 = std::make_pair(atype1, atype2);
280			key2 = std::make_pair(atype2, atype1);
281
282			MixingMap[key1] = mixer;
283			if (key2 != key1) {
284			MixingMap[key2] = mixer;
285			}
286			}
287
288			void LJ::calcForce(AtomType* at1, AtomType* at2, Vector3d d, RealType rij,
289			RealType r2, RealType rcut, RealType sw, RealType vdwMult,
290			RealType vpair, RealType pot, Vector3d f1) {
291
292			if (!initialized_) initialize();
293
294			RealType ros;
295			RealType rcos;
296			RealType myPot = 0.0;
297			RealType myPotC = 0.0;
298			RealType myDeriv = 0.0;
299			RealType myDerivC = 0.0;
300
301			std::pair<AtomType, AtomType> key = std::make_pair(at1, at2);
302			LJInteractionData mixer = MixingMap[key];
303
304			RealType sigmai = mixer.sigmai;
305			RealType epsilon = mixer.epsilon;
306
307			ros = rij * sigmai;
308
309			getLJfunc(ros, myPot, myDeriv);
310
311			if (shiftedPot_) {
312			rcos = rcut * sigmai;
313			getLJfunc(rcos, myPotC, myDerivC);
314			myDerivC = 0.0;
315			} else if (LJ::shiftedFrc_) {
316			rcos = rcut * sigmai;
317			getLJfunc(rcos, myPotC, myDerivC);
318			myPotC = myPotC + myDerivC * (rij - rcut) * sigmai;
319			} else {
320			myPotC = 0.0;
321			myDerivC = 0.0;
322			}
323
324			RealType pot_temp = vdwMult * epsilon * (myPot - myPotC);
325			vpair += pot_temp;
326
327			RealType dudr = sw * vdwMult * epsilon * (myDeriv - myDerivC)*sigmai;
328
329			pot += sw * pot_temp;
330			f1 = d * dudr / rij;
331
332			return;
333			}
334
335			void LJ::do_lj_pair(int atid1, int atid2, RealType d, RealType rij,
336			RealType r2, RealType rcut, RealType *sw,
337			RealType *vdwMult,
338			RealType vpair, RealType pot, RealType *f1) {
339
340			if (!initialized_) initialize();
341
342			AtomType* atype1 = LJMap[*atid1];
343			AtomType* atype2 = LJMap[*atid2];
344
345			Vector3d disp(d[0], d[1], d[2]);
346			Vector3d frc(f1[0], f1[1], f1[2]);
347
348			calcForce(atype1, atype2, disp, rij, r2, rcut, sw, vdwMult, vpair,
349			*pot, frc);
350			return;
351			}
352
353			void LJ::getLJfunc(const RealType r, RealType pot, RealType deriv) {
354			RealType ri = 1.0 / r;
355			RealType ri2 = ri * ri;
356			RealType ri6 = ri2 * ri2 * ri2;
357			RealType ri7 = ri6 * ri;
358			RealType ri12 = ri6 * ri6;
359			RealType ri13 = ri12 * ri;
360
361			pot = 4.0 * (ri12 - ri6);
362			deriv = 24.0 * (ri7 - 2.0 * ri13);
363			return;
364			}
365
366
367			void LJ::setLJDefaultCutoff(RealType thisRcut, int sP, int *sF) {
368			shiftedPot_ = (bool)(*sP);
369			shiftedFrc_ = (bool)(*sF);
370			}
371			}
372
373			extern "C" {
374
375			#define fortranGetSigma FC_FUNC(getsigma, GETSIGMA)
376			#define fortranGetEpsilon FC_FUNC(getepsilon, GETEPSILON)
377			#define fortranSetLJCutoff FC_FUNC(setljdefaultcutoff, SETLJDEFAULTCUTOFF)
378			#define fortranDoLJPair FC_FUNC(do_lj_pair, DO_LJ_PAIR)
379
380			RealType fortranGetSigma(int* atid) {
381			return OpenMD::LJ::Instance()->getSigma(*atid);
382			}
383			RealType fortranGetEpsilon(int* atid) {
384			return OpenMD::LJ::Instance()->getEpsilon(*atid);
385			}
386			void fortranSetLJCutoff(RealType rcut, int shiftedPot, int *shiftedFrc) {
387			return OpenMD::LJ::Instance()->setLJDefaultCutoff(rcut, shiftedPot,
388			shiftedFrc);
389			}
390			void fortranDoLJPair(int atid1, int atid2, RealType d, RealType rij,
391			RealType r2, RealType rcut, RealType *sw,
392			RealType vdwMult, RealType vpair, RealType* pot,
393			RealType *f1){
394
395			return OpenMD::LJ::Instance()->do_lj_pair(atid1, atid2, d, rij, r2, rcut,
396			sw, vdwMult, vpair, pot, f1);
397			}
398			}