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]  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/LJ.hpp"
#include "utils/simError.h"
#include "types/LennardJonesAdapter.hpp"
#include "types/LennardJonesInteractionType.hpp"

namespace OpenMD {

  LJ::LJ() : name_("LJ"), initialized_(false), forceField_(NULL) {}

  RealType LJ::getSigma(AtomType* atomType1, AtomType* atomType2) {

    LennardJonesAdapter lja1 = LennardJonesAdapter(atomType1);
    LennardJonesAdapter lja2 = LennardJonesAdapter(atomType2);
    RealType sigma1 = lja1.getSigma();
    RealType sigma2 = lja2.getSigma();
    
    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
    string DistanceMix = fopts.getDistanceMixingRule();
    toUpper(DistanceMix);

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

  RealType LJ::getEpsilon(AtomType* atomType1, AtomType* atomType2) {  
    LennardJonesAdapter lja1 = LennardJonesAdapter(atomType1);
    LennardJonesAdapter lja2 = LennardJonesAdapter(atomType2);
  
    RealType epsilon1 = lja1.getEpsilon();
    RealType epsilon2 = lja2.getEpsilon();
    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)) {
      LennardJonesAdapter lja = LennardJonesAdapter(at);
      if (lja.isLennardJones()){
         addType(at);
      }
    }
    ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
    ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
    NonBondedInteractionType* nbt;
    ForceField::NonBondedInteractionTypeContainer::KeyType keys;


    for (nbt = nbiTypes->beginType(j); nbt != NULL; 
         nbt = nbiTypes->nextType(j)) {

      if (nbt->isLennardJones()) {
        keys = nbiTypes->getKeys(j);
        AtomType* at1 = forceField_->getAtomType(keys[0]);
        AtomType* at2 = forceField_->getAtomType(keys[1]);

        LennardJonesInteractionType* ljit = dynamic_cast<LennardJonesInteractionType*>(nbt);

        if (ljit == NULL) {
          sprintf( painCave.errMsg,
                   "LJ::initialize could not convert NonBondedInteractionType\n"
                   "\tto LennardJonesInteractionType for %s - %s interaction.\n", 
                   at1->getName().c_str(),
                   at2->getName().c_str());
          painCave.severity = OPENMD_ERROR;
          painCave.isFatal = 1;
          simError();          
        }

        RealType sigma = ljit->getSigma();
        RealType epsilon = ljit->getEpsilon();
        addExplicitInteraction(at1, at2, sigma, epsilon);
      }
    }  
    initialized_ = true;
  }
      

  void LJ::addType(AtomType* atomType){
    LennardJonesAdapter lja1 = LennardJonesAdapter(atomType);

    RealType sigma1 = lja1.getSigma();
    RealType epsilon1 = lja1.getEpsilon();
    
    // add it to the map:

    pair<map<int,AtomType*>::iterator,bool> ret;    
    ret = LJMap.insert( pair<int, AtomType*>(atomType->getIdent(), atomType) );
    if (ret.second == false) {
      sprintf( painCave.errMsg,
               "LJ already had a previous entry with ident %d\n",
               atomType->getIdent());
      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){
    
    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(InteractionData &idat) {
    if (!initialized_) initialize();
    map<pair<AtomType*, AtomType*>, LJInteractionData>::iterator it;
    it = MixingMap.find( idat.atypes );
    
    if (it != MixingMap.end())  {
      
      LJInteractionData mixer = (*it).second;
      
      RealType sigmai = mixer.sigmai;
      RealType epsilon = mixer.epsilon;
      
      RealType ros;
      RealType rcos;
      RealType myPot = 0.0;
      RealType myPotC = 0.0;
      RealType myDeriv = 0.0;
      RealType myDerivC = 0.0;
     
      ros = *(idat.rij) * sigmai;     
      
      getLJfunc(ros, myPot, myDeriv);
      
      if (idat.shiftedPot) {
        rcos = *(idat.rcut) * sigmai;
        getLJfunc(rcos, myPotC, myDerivC);
        myDerivC = 0.0;
      } else if (idat.shiftedForce) {
        rcos = *(idat.rcut) * sigmai;
        getLJfunc(rcos, myPotC, myDerivC);
        myPotC = myPotC + myDerivC * (*(idat.rij) - *(idat.rcut)) * sigmai;
      } else {
        myPotC = 0.0;
        myDerivC = 0.0;        
      }

      RealType pot_temp = *(idat.vdwMult) * epsilon * (myPot - myPotC);
      *(idat.vpair) += pot_temp;
      
      RealType dudr = *(idat.sw) * *(idat.vdwMult) * epsilon * (myDeriv - 
                                                                myDerivC)*sigmai;      

      (*(idat.pot))[VANDERWAALS_FAMILY] += *(idat.sw) * pot_temp;
      *(idat.f1) += *(idat.d) * dudr / *(idat.rij);
    }
    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;
  }
  
  RealType LJ::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) {
    if (!initialized_) initialize();   
    map<pair<AtomType*, AtomType*>, LJInteractionData>::iterator it;
    it = MixingMap.find(atypes);
    if (it == MixingMap.end()) 
      return 0.0;
    else  {
      LJInteractionData mixer = (*it).second;
      return 2.5 * mixer.sigma;
    }
  }

}
Revision:	1710
Committed:	Fri May 18 21:44:02 2012 UTC (12 years, 11 months ago) by gezelter
File size:	9037 byte(s)
Log Message:	Added an adapter layer between the AtomType and the rest of the code to handle the bolt-on capabilities of new types. Fixed a long-standing bug in how storageLayout was being set to the maximum possible value. Started to add infrastructure for Polarizable and fluc-Q calculations.
#	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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	#include <stdio.h>
44	#include <string.h>
45
46	#include <cmath>
47	#include "nonbonded/LJ.hpp"
48	#include "utils/simError.h"
49	#include "types/LennardJonesAdapter.hpp"
50	#include "types/LennardJonesInteractionType.hpp"
51
52	namespace OpenMD {
53
54	LJ::LJ() : name_("LJ"), initialized_(false), forceField_(NULL) {}
55
56	RealType LJ::getSigma(AtomType* atomType1, AtomType* atomType2) {
57
58	LennardJonesAdapter lja1 = LennardJonesAdapter(atomType1);
59	LennardJonesAdapter lja2 = LennardJonesAdapter(atomType2);
60	RealType sigma1 = lja1.getSigma();
61	RealType sigma2 = lja2.getSigma();
62
63	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
64	string DistanceMix = fopts.getDistanceMixingRule();
65	toUpper(DistanceMix);
66
67	if (DistanceMix == "GEOMETRIC")
68	return sqrt(sigma1 * sigma2);
69	else
70	return 0.5 * (sigma1 + sigma2);
71	}
72
73	RealType LJ::getEpsilon(AtomType* atomType1, AtomType* atomType2) {
74	LennardJonesAdapter lja1 = LennardJonesAdapter(atomType1);
75	LennardJonesAdapter lja2 = LennardJonesAdapter(atomType2);
76
77	RealType epsilon1 = lja1.getEpsilon();
78	RealType epsilon2 = lja2.getEpsilon();
79	return sqrt(epsilon1 * epsilon2);
80	}
81
82	void LJ::initialize() {
83	ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
84	ForceField::AtomTypeContainer::MapTypeIterator i;
85	AtomType* at;
86
87	for (at = atomTypes->beginType(i); at != NULL;
88	at = atomTypes->nextType(i)) {
89	LennardJonesAdapter lja = LennardJonesAdapter(at);
90	if (lja.isLennardJones()){
91	addType(at);
92	}
93	}
94	ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
95	ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
96	NonBondedInteractionType* nbt;
97	ForceField::NonBondedInteractionTypeContainer::KeyType keys;
98
99
100	for (nbt = nbiTypes->beginType(j); nbt != NULL;
101	nbt = nbiTypes->nextType(j)) {
102
103	if (nbt->isLennardJones()) {
104	keys = nbiTypes->getKeys(j);
105	AtomType* at1 = forceField_->getAtomType(keys[0]);
106	AtomType* at2 = forceField_->getAtomType(keys[1]);
107
108	LennardJonesInteractionType* ljit = dynamic_cast<LennardJonesInteractionType*>(nbt);
109
110	if (ljit == NULL) {
111	sprintf( painCave.errMsg,
112	"LJ::initialize could not convert NonBondedInteractionType\n"
113	"\tto LennardJonesInteractionType for %s - %s interaction.\n",
114	at1->getName().c_str(),
115	at2->getName().c_str());
116	painCave.severity = OPENMD_ERROR;
117	painCave.isFatal = 1;
118	simError();
119	}
120
121	RealType sigma = ljit->getSigma();
122	RealType epsilon = ljit->getEpsilon();
123	addExplicitInteraction(at1, at2, sigma, epsilon);
124	}
125	}
126	initialized_ = true;
127	}
128
129
130
131	void LJ::addType(AtomType* atomType){
132	LennardJonesAdapter lja1 = LennardJonesAdapter(atomType);
133
134	RealType sigma1 = lja1.getSigma();
135	RealType epsilon1 = lja1.getEpsilon();
136
137	// add it to the map:
138
139	pair<map<int,AtomType*>::iterator,bool> ret;
140	ret = LJMap.insert( pair<int, AtomType*>(atomType->getIdent(), atomType) );
141	if (ret.second == false) {
142	sprintf( painCave.errMsg,
143	"LJ already had a previous entry with ident %d\n",
144	atomType->getIdent());
145	painCave.severity = OPENMD_INFO;
146	painCave.isFatal = 0;
147	simError();
148	}
149
150	// Now, iterate over all known types and add to the mixing map:
151
152	std::map<int, AtomType*>::iterator it;
153	for( it = LJMap.begin(); it != LJMap.end(); ++it) {
154
155	AtomType* atype2 = (*it).second;
156
157	LJInteractionData mixer;
158	mixer.sigma = getSigma(atomType, atype2);
159	mixer.epsilon = getEpsilon(atomType, atype2);
160	mixer.sigmai = 1.0 / mixer.sigma;
161	mixer.explicitlySet = false;
162
163	std::pair<AtomType, AtomType> key1, key2;
164	key1 = std::make_pair(atomType, atype2);
165	key2 = std::make_pair(atype2, atomType);
166
167	MixingMap[key1] = mixer;
168	if (key2 != key1) {
169	MixingMap[key2] = mixer;
170	}
171	}
172	}
173
174	void LJ::addExplicitInteraction(AtomType* atype1, AtomType* atype2, RealType sigma, RealType epsilon){
175
176	LJInteractionData mixer;
177	mixer.sigma = sigma;
178	mixer.epsilon = epsilon;
179	mixer.sigmai = 1.0 / mixer.sigma;
180	mixer.explicitlySet = true;
181
182	std::pair<AtomType, AtomType> key1, key2;
183	key1 = std::make_pair(atype1, atype2);
184	key2 = std::make_pair(atype2, atype1);
185
186	MixingMap[key1] = mixer;
187	if (key2 != key1) {
188	MixingMap[key2] = mixer;
189	}
190	}
191
192	void LJ::calcForce(InteractionData &idat) {
193	if (!initialized_) initialize();
194	map<pair<AtomType, AtomType>, LJInteractionData>::iterator it;
195	it = MixingMap.find( idat.atypes );
196
197	if (it != MixingMap.end()) {
198
199	LJInteractionData mixer = (*it).second;
200
201	RealType sigmai = mixer.sigmai;
202	RealType epsilon = mixer.epsilon;
203
204	RealType ros;
205	RealType rcos;
206	RealType myPot = 0.0;
207	RealType myPotC = 0.0;
208	RealType myDeriv = 0.0;
209	RealType myDerivC = 0.0;
210
211	ros = (idat.rij) sigmai;
212
213	getLJfunc(ros, myPot, myDeriv);
214
215	if (idat.shiftedPot) {
216	rcos = (idat.rcut) sigmai;
217	getLJfunc(rcos, myPotC, myDerivC);
218	myDerivC = 0.0;
219	} else if (idat.shiftedForce) {
220	rcos = (idat.rcut) sigmai;
221	getLJfunc(rcos, myPotC, myDerivC);
222	myPotC = myPotC + myDerivC * ((idat.rij) - (idat.rcut)) * sigmai;
223	} else {
224	myPotC = 0.0;
225	myDerivC = 0.0;
226	}
227
228	RealType pot_temp = (idat.vdwMult) epsilon * (myPot - myPotC);
229	*(idat.vpair) += pot_temp;
230
231	RealType dudr = (idat.sw) (idat.vdwMult) epsilon * (myDeriv -
232	myDerivC)*sigmai;
233
234	((idat.pot))[VANDERWAALS_FAMILY] += (idat.sw) * pot_temp;
235	(idat.f1) += (idat.d) * dudr / *(idat.rij);
236	}
237	return;
238	}
239
240	void LJ::getLJfunc(RealType r, RealType &pot, RealType &deriv) {
241
242	RealType ri = 1.0 / r;
243	RealType ri2 = ri * ri;
244	RealType ri6 = ri2 * ri2 * ri2;
245	RealType ri7 = ri6 * ri;
246	RealType ri12 = ri6 * ri6;
247	RealType ri13 = ri12 * ri;
248
249	pot = 4.0 * (ri12 - ri6);
250	deriv = 24.0 * (ri7 - 2.0 * ri13);
251
252	return;
253	}
254
255	RealType LJ::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
256	if (!initialized_) initialize();
257	map<pair<AtomType, AtomType>, LJInteractionData>::iterator it;
258	it = MixingMap.find(atypes);
259	if (it == MixingMap.end())
260	return 0.0;
261	else {
262	LJInteractionData mixer = (*it).second;
263	return 2.5 * mixer.sigma;
264	}
265	}
266
267	}