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) { 
    if (!initialized_) initialize();
    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) {    
    if (!initialized_) initialize();
    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);
      
    f1[0] = frc.x();
    f1[1] = frc.y();
    f1[2] = frc.z();

    return;    
  }
  
  void LJ::getLJfunc(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:	1473
Committed:	Tue Jul 20 15:43:00 2010 UTC (14 years, 9 months ago) by gezelter
File size:	13197 byte(s)
Log Message:	fixing c/fortran bugs
#	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	gezelter	1473	if (!initialized_) initialize();
111	gezelter	1471	std::map<int, AtomType*> :: const_iterator it;
112			it = LJMap.find(atid);
113			if (it == LJMap.end()) {
114			sprintf( painCave.errMsg,
115			"LJ::getSigma could not find atid %d in LJMap\n",
116			(atid));
117			painCave.severity = OPENMD_ERROR;
118			painCave.isFatal = 1;
119			simError();
120			}
121			AtomType* atype = it->second;
122
123			return getSigma(atype);
124			}
125
126			RealType LJ::getSigma(AtomType* atomType1, AtomType* atomType2) {
127			RealType sigma1 = getSigma(atomType1);
128			RealType sigma2 = getSigma(atomType2);
129
130			ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
131			std::string DistanceMix = fopts.getDistanceMixingRule();
132			toUpper(DistanceMix);
133
134			if (DistanceMix == "GEOMETRIC")
135			return sqrt(sigma1 * sigma2);
136			else
137			return 0.5 * (sigma1 + sigma2);
138			}
139
140			RealType LJ::getEpsilon(AtomType* atomType) {
141			LJParam ljParam = getLJParam(atomType);
142			return ljParam.epsilon;
143			}
144
145			RealType LJ::getEpsilon(int atid) {
146	gezelter	1473	if (!initialized_) initialize();
147	gezelter	1471	std::map<int, AtomType*> :: const_iterator it;
148			it = LJMap.find(atid);
149			if (it == LJMap.end()) {
150			sprintf( painCave.errMsg,
151			"LJ::getEpsilon could not find atid %d in LJMap\n",
152			(atid));
153			painCave.severity = OPENMD_ERROR;
154			painCave.isFatal = 1;
155			simError();
156			}
157			AtomType* atype = it->second;
158
159			return getEpsilon(atype);
160			}
161
162			RealType LJ::getEpsilon(AtomType* atomType1, AtomType* atomType2) {
163			RealType epsilon1 = getEpsilon(atomType1);
164			RealType epsilon2 = getEpsilon(atomType2);
165			return sqrt(epsilon1 * epsilon2);
166			}
167
168			void LJ::initialize() {
169			ForceField::AtomTypeContainer atomTypes = forceField_->getAtomTypes();
170			ForceField::AtomTypeContainer::MapTypeIterator i;
171			AtomType* at;
172
173			for (at = atomTypes.beginType(i); at != NULL;
174			at = atomTypes.nextType(i)) {
175
176			if (at->isLennardJones())
177			addType(at);
178			}
179
180			ForceField::NonBondedInteractionTypeContainer nbiTypes = forceField_->getNonBondedInteractionTypes();
181			ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
182			NonBondedInteractionType* nbt;
183
184			for (nbt = nbiTypes.beginType(j); nbt != NULL;
185			nbt = nbiTypes.nextType(j)) {
186
187			if (nbt->isLennardJones()) {
188
189			std::pair<AtomType, AtomType> atypes = nbt->getAtomTypes();
190
191			GenericData* data = nbt->getPropertyByName("LennardJones");
192			if (data == NULL) {
193			sprintf( painCave.errMsg, "LJ::rebuildMixingMap could not find\n"
194			"\tLennard-Jones parameters for %s - %s interaction.\n",
195			atypes.first->getName().c_str(),
196			atypes.second->getName().c_str());
197			painCave.severity = OPENMD_ERROR;
198			painCave.isFatal = 1;
199			simError();
200			}
201
202			LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
203			if (ljData == NULL) {
204			sprintf( painCave.errMsg,
205			"LJ::rebuildMixingMap could not convert GenericData to\n"
206			"\tLJParam for %s - %s interaction.\n",
207			atypes.first->getName().c_str(),
208			atypes.second->getName().c_str());
209			painCave.severity = OPENMD_ERROR;
210			painCave.isFatal = 1;
211			simError();
212			}
213
214			LJParam ljParam = ljData->getData();
215
216			RealType sigma = ljParam.sigma;
217			RealType epsilon = ljParam.epsilon;
218
219			addExplicitInteraction(atypes.first, atypes.second, sigma, epsilon);
220			}
221			}
222			initialized_ = true;
223			}
224
225
226
227			void LJ::addType(AtomType* atomType){
228			RealType sigma1 = getSigma(atomType);
229			RealType epsilon1 = getEpsilon(atomType);
230
231			// add it to the map:
232			AtomTypeProperties atp = atomType->getATP();
233	gezelter	1473
234			std::pair<std::map<int,AtomType*>::iterator,bool> ret;
235	gezelter	1471	ret = LJMap.insert( std::pair<int, AtomType*>(atp.ident, atomType) );
236			if (ret.second == false) {
237			sprintf( painCave.errMsg,
238			"LJ already had a previous entry with ident %d\n",
239			atp.ident);
240			painCave.severity = OPENMD_INFO;
241			painCave.isFatal = 0;
242			simError();
243			}
244
245			// Now, iterate over all known types and add to the mixing map:
246
247			std::map<int, AtomType*>::iterator it;
248			for( it = LJMap.begin(); it != LJMap.end(); ++it) {
249
250			AtomType* atype2 = (*it).second;
251
252			LJInteractionData mixer;
253			mixer.sigma = getSigma(atomType, atype2);
254			mixer.epsilon = getEpsilon(atomType, atype2);
255			mixer.sigmai = 1.0 / mixer.sigma;
256			mixer.explicitlySet = false;
257
258			std::pair<AtomType, AtomType> key1, key2;
259			key1 = std::make_pair(atomType, atype2);
260			key2 = std::make_pair(atype2, atomType);
261
262			MixingMap[key1] = mixer;
263			if (key2 != key1) {
264			MixingMap[key2] = mixer;
265			}
266			}
267			}
268
269			void LJ::addExplicitInteraction(AtomType* atype1, AtomType* atype2, RealType sigma, RealType epsilon){
270
271			// in case these weren't already in the map
272			addType(atype1);
273			addType(atype2);
274
275			LJInteractionData mixer;
276			mixer.sigma = sigma;
277			mixer.epsilon = epsilon;
278			mixer.sigmai = 1.0 / mixer.sigma;
279			mixer.explicitlySet = true;
280
281			std::pair<AtomType, AtomType> key1, key2;
282			key1 = std::make_pair(atype1, atype2);
283			key2 = std::make_pair(atype2, atype1);
284
285			MixingMap[key1] = mixer;
286			if (key2 != key1) {
287			MixingMap[key2] = mixer;
288			}
289			}
290
291	gezelter	1472	void LJ::calcForce(AtomType* at1, AtomType* at2, Vector3d d,
292			RealType rij, RealType r2, RealType rcut, RealType sw,
293			RealType vdwMult, RealType &vpair, RealType &pot,
294			Vector3d &f1) {
295	gezelter	1471
296			if (!initialized_) initialize();
297
298			RealType ros;
299			RealType rcos;
300			RealType myPot = 0.0;
301			RealType myPotC = 0.0;
302			RealType myDeriv = 0.0;
303			RealType myDerivC = 0.0;
304
305			std::pair<AtomType, AtomType> key = std::make_pair(at1, at2);
306			LJInteractionData mixer = MixingMap[key];
307
308			RealType sigmai = mixer.sigmai;
309			RealType epsilon = mixer.epsilon;
310
311	gezelter	1473
312	gezelter	1471	ros = rij * sigmai;
313
314			getLJfunc(ros, myPot, myDeriv);
315
316			if (shiftedPot_) {
317			rcos = rcut * sigmai;
318			getLJfunc(rcos, myPotC, myDerivC);
319			myDerivC = 0.0;
320			} else if (LJ::shiftedFrc_) {
321			rcos = rcut * sigmai;
322			getLJfunc(rcos, myPotC, myDerivC);
323			myPotC = myPotC + myDerivC * (rij - rcut) * sigmai;
324			} else {
325			myPotC = 0.0;
326			myDerivC = 0.0;
327			}
328
329			RealType pot_temp = vdwMult * epsilon * (myPot - myPotC);
330			vpair += pot_temp;
331
332			RealType dudr = sw * vdwMult * epsilon * (myDeriv - myDerivC)*sigmai;
333
334			pot += sw * pot_temp;
335			f1 = d * dudr / rij;
336
337			return;
338	gezelter	1473
339
340
341	gezelter	1471	}
342
343			void LJ::do_lj_pair(int atid1, int atid2, RealType d, RealType rij,
344			RealType r2, RealType rcut, RealType *sw,
345			RealType *vdwMult,
346			RealType vpair, RealType pot, RealType *f1) {
347
348			if (!initialized_) initialize();
349
350			AtomType* atype1 = LJMap[*atid1];
351			AtomType* atype2 = LJMap[*atid2];
352
353			Vector3d disp(d[0], d[1], d[2]);
354			Vector3d frc(f1[0], f1[1], f1[2]);
355
356			calcForce(atype1, atype2, disp, rij, r2, rcut, sw, vdwMult, vpair,
357			*pot, frc);
358	gezelter	1472
359			f1[0] = frc.x();
360			f1[1] = frc.y();
361			f1[2] = frc.z();
362	gezelter	1473
363	gezelter	1471	return;
364			}
365
366	gezelter	1472	void LJ::getLJfunc(RealType r, RealType &pot, RealType &deriv) {
367
368	gezelter	1471	RealType ri = 1.0 / r;
369			RealType ri2 = ri * ri;
370			RealType ri6 = ri2 * ri2 * ri2;
371			RealType ri7 = ri6 * ri;
372			RealType ri12 = ri6 * ri6;
373			RealType ri13 = ri12 * ri;
374	gezelter	1472
375	gezelter	1471	pot = 4.0 * (ri12 - ri6);
376			deriv = 24.0 * (ri7 - 2.0 * ri13);
377	gezelter	1472
378	gezelter	1471	return;
379			}
380	gezelter	1472
381	gezelter	1471
382			void LJ::setLJDefaultCutoff(RealType thisRcut, int sP, int *sF) {
383			shiftedPot_ = (bool)(*sP);
384			shiftedFrc_ = (bool)(*sF);
385			}
386			}
387
388			extern "C" {
389
390			#define fortranGetSigma FC_FUNC(getsigma, GETSIGMA)
391			#define fortranGetEpsilon FC_FUNC(getepsilon, GETEPSILON)
392			#define fortranSetLJCutoff FC_FUNC(setljdefaultcutoff, SETLJDEFAULTCUTOFF)
393			#define fortranDoLJPair FC_FUNC(do_lj_pair, DO_LJ_PAIR)
394
395			RealType fortranGetSigma(int* atid) {
396			return OpenMD::LJ::Instance()->getSigma(*atid);
397			}
398			RealType fortranGetEpsilon(int* atid) {
399			return OpenMD::LJ::Instance()->getEpsilon(*atid);
400			}
401			void fortranSetLJCutoff(RealType rcut, int shiftedPot, int *shiftedFrc) {
402			return OpenMD::LJ::Instance()->setLJDefaultCutoff(rcut, shiftedPot,
403			shiftedFrc);
404			}
405			void fortranDoLJPair(int atid1, int atid2, RealType d, RealType rij,
406			RealType r2, RealType rcut, RealType *sw,
407			RealType vdwMult, RealType vpair, RealType* pot,
408			RealType *f1){
409
410			return OpenMD::LJ::Instance()->do_lj_pair(atid1, atid2, d, rij, r2, rcut,
411			sw, vdwMult, vpair, pot, f1);
412			}
413			}