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.
#	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, 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	}