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/LennardJonesInteractionType.hpp"

namespace OpenMD {

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

  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(AtomType* atomType1, AtomType* atomType2) {    
    RealType sigma1 = getSigma(atomType1);
    RealType sigma2 = getSigma(atomType2);
    
    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* atomType) {    
    LJParam ljParam = getLJParam(atomType);
    return ljParam.epsilon;
  }

  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;
    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){
    RealType sigma1 = getSigma(atomType);
    RealType epsilon1 = getEpsilon(atomType);
    
    // add it to the map:
    AtomTypeProperties atp = atomType->getATP();    

    pair<map<int,AtomType*>::iterator,bool> ret;    
    ret = LJMap.insert( 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){
    
    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:	1683
Committed:	Wed Feb 29 20:33:01 2012 UTC (13 years, 2 months ago) by jmichalk
File size:	10201 byte(s)
Log Message:	LJ.cpp has been updated to more correctly deal with nonbonded interactions (i.e. explicit interactions where the species are not necessarily defined to be lennardJones type atoms)
#	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/LennardJonesInteractionType.hpp"
50
51	namespace OpenMD {
52
53	LJ::LJ() : name_("LJ"), initialized_(false), forceField_(NULL) {}
54
55	LJParam LJ::getLJParam(AtomType* atomType) {
56
57	// Do sanity checking on the AtomType we were passed before
58	// building any data structures:
59	if (!atomType->isLennardJones()) {
60	sprintf( painCave.errMsg,
61	"LJ::getLJParam was passed an atomType (%s) that does not\n"
62	"\tappear to be a Lennard-Jones atom.\n",
63	atomType->getName().c_str());
64	painCave.severity = OPENMD_ERROR;
65	painCave.isFatal = 1;
66	simError();
67	}
68
69	GenericData* data = atomType->getPropertyByName("LennardJones");
70	if (data == NULL) {
71	sprintf( painCave.errMsg, "LJ::getLJParam could not find Lennard-Jones\n"
72	"\tparameters for atomType %s.\n", atomType->getName().c_str());
73	painCave.severity = OPENMD_ERROR;
74	painCave.isFatal = 1;
75	simError();
76	}
77
78	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
79	if (ljData == NULL) {
80	sprintf( painCave.errMsg,
81	"LJ::getLJParam could not convert GenericData to LJParam for\n"
82	"\tatom type %s\n", atomType->getName().c_str());
83	painCave.severity = OPENMD_ERROR;
84	painCave.isFatal = 1;
85	simError();
86	}
87
88	return ljData->getData();
89	}
90
91	RealType LJ::getSigma(AtomType* atomType) {
92	LJParam ljParam = getLJParam(atomType);
93	return ljParam.sigma;
94	}
95
96	RealType LJ::getSigma(AtomType* atomType1, AtomType* atomType2) {
97	RealType sigma1 = getSigma(atomType1);
98	RealType sigma2 = getSigma(atomType2);
99
100	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
101	string DistanceMix = fopts.getDistanceMixingRule();
102	toUpper(DistanceMix);
103
104	if (DistanceMix == "GEOMETRIC")
105	return sqrt(sigma1 * sigma2);
106	else
107	return 0.5 * (sigma1 + sigma2);
108	}
109
110	RealType LJ::getEpsilon(AtomType* atomType) {
111	LJParam ljParam = getLJParam(atomType);
112	return ljParam.epsilon;
113	}
114
115	RealType LJ::getEpsilon(AtomType* atomType1, AtomType* atomType2) {
116	RealType epsilon1 = getEpsilon(atomType1);
117	RealType epsilon2 = getEpsilon(atomType2);
118	return sqrt(epsilon1 * epsilon2);
119	}
120
121	void LJ::initialize() {
122	ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
123	ForceField::AtomTypeContainer::MapTypeIterator i;
124	AtomType* at;
125
126	for (at = atomTypes->beginType(i); at != NULL;
127	at = atomTypes->nextType(i)) {
128	if (at->isLennardJones()){
129	addType(at);
130	}
131	}
132	ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
133	ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
134	NonBondedInteractionType* nbt;
135	ForceField::NonBondedInteractionTypeContainer::KeyType keys;
136
137
138	for (nbt = nbiTypes->beginType(j); nbt != NULL;
139	nbt = nbiTypes->nextType(j)) {
140
141	if (nbt->isLennardJones()) {
142	keys = nbiTypes->getKeys(j);
143	AtomType* at1 = forceField_->getAtomType(keys[0]);
144	AtomType* at2 = forceField_->getAtomType(keys[1]);
145
146	LennardJonesInteractionType* ljit = dynamic_cast<LennardJonesInteractionType*>(nbt);
147
148	if (ljit == NULL) {
149	sprintf( painCave.errMsg,
150	"LJ::initialize could not convert NonBondedInteractionType\n"
151	"\tto LennardJonesInteractionType for %s - %s interaction.\n",
152	at1->getName().c_str(),
153	at2->getName().c_str());
154	painCave.severity = OPENMD_ERROR;
155	painCave.isFatal = 1;
156	simError();
157	}
158
159	RealType sigma = ljit->getSigma();
160	RealType epsilon = ljit->getEpsilon();
161	addExplicitInteraction(at1, at2, sigma, epsilon);
162	}
163	}
164	initialized_ = true;
165	}
166
167
168
169	void LJ::addType(AtomType* atomType){
170	RealType sigma1 = getSigma(atomType);
171	RealType epsilon1 = getEpsilon(atomType);
172
173	// add it to the map:
174	AtomTypeProperties atp = atomType->getATP();
175
176	pair<map<int,AtomType*>::iterator,bool> ret;
177	ret = LJMap.insert( pair<int, AtomType*>(atp.ident, atomType) );
178	if (ret.second == false) {
179	sprintf( painCave.errMsg,
180	"LJ already had a previous entry with ident %d\n",
181	atp.ident);
182	painCave.severity = OPENMD_INFO;
183	painCave.isFatal = 0;
184	simError();
185	}
186
187	// Now, iterate over all known types and add to the mixing map:
188
189	std::map<int, AtomType*>::iterator it;
190	for( it = LJMap.begin(); it != LJMap.end(); ++it) {
191
192	AtomType* atype2 = (*it).second;
193
194	LJInteractionData mixer;
195	mixer.sigma = getSigma(atomType, atype2);
196	mixer.epsilon = getEpsilon(atomType, atype2);
197	mixer.sigmai = 1.0 / mixer.sigma;
198	mixer.explicitlySet = false;
199
200	std::pair<AtomType, AtomType> key1, key2;
201	key1 = std::make_pair(atomType, atype2);
202	key2 = std::make_pair(atype2, atomType);
203
204	MixingMap[key1] = mixer;
205	if (key2 != key1) {
206	MixingMap[key2] = mixer;
207	}
208	}
209	}
210
211	void LJ::addExplicitInteraction(AtomType* atype1, AtomType* atype2, RealType sigma, RealType epsilon){
212
213	LJInteractionData mixer;
214	mixer.sigma = sigma;
215	mixer.epsilon = epsilon;
216	mixer.sigmai = 1.0 / mixer.sigma;
217	mixer.explicitlySet = true;
218
219	std::pair<AtomType, AtomType> key1, key2;
220	key1 = std::make_pair(atype1, atype2);
221	key2 = std::make_pair(atype2, atype1);
222
223	MixingMap[key1] = mixer;
224	if (key2 != key1) {
225	MixingMap[key2] = mixer;
226	}
227	}
228
229	void LJ::calcForce(InteractionData &idat) {
230	if (!initialized_) initialize();
231	map<pair<AtomType, AtomType>, LJInteractionData>::iterator it;
232	it = MixingMap.find( idat.atypes );
233
234	if (it != MixingMap.end()) {
235
236	LJInteractionData mixer = (*it).second;
237
238	RealType sigmai = mixer.sigmai;
239	RealType epsilon = mixer.epsilon;
240
241	RealType ros;
242	RealType rcos;
243	RealType myPot = 0.0;
244	RealType myPotC = 0.0;
245	RealType myDeriv = 0.0;
246	RealType myDerivC = 0.0;
247
248	ros = (idat.rij) sigmai;
249
250	getLJfunc(ros, myPot, myDeriv);
251
252	if (idat.shiftedPot) {
253	rcos = (idat.rcut) sigmai;
254	getLJfunc(rcos, myPotC, myDerivC);
255	myDerivC = 0.0;
256	} else if (idat.shiftedForce) {
257	rcos = (idat.rcut) sigmai;
258	getLJfunc(rcos, myPotC, myDerivC);
259	myPotC = myPotC + myDerivC * ((idat.rij) - (idat.rcut)) * sigmai;
260	} else {
261	myPotC = 0.0;
262	myDerivC = 0.0;
263	}
264
265	RealType pot_temp = (idat.vdwMult) epsilon * (myPot - myPotC);
266	*(idat.vpair) += pot_temp;
267
268	RealType dudr = (idat.sw) (idat.vdwMult) epsilon * (myDeriv -
269	myDerivC)*sigmai;
270
271	((idat.pot))[VANDERWAALS_FAMILY] += (idat.sw) * pot_temp;
272	(idat.f1) += (idat.d) * dudr / *(idat.rij);
273	}
274	return;
275	}
276
277	void LJ::getLJfunc(RealType r, RealType &pot, RealType &deriv) {
278
279	RealType ri = 1.0 / r;
280	RealType ri2 = ri * ri;
281	RealType ri6 = ri2 * ri2 * ri2;
282	RealType ri7 = ri6 * ri;
283	RealType ri12 = ri6 * ri6;
284	RealType ri13 = ri12 * ri;
285
286	pot = 4.0 * (ri12 - ri6);
287	deriv = 24.0 * (ri7 - 2.0 * ri13);
288
289	return;
290	}
291
292	RealType LJ::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
293	if (!initialized_) initialize();
294	map<pair<AtomType, AtomType>, LJInteractionData>::iterator it;
295	it = MixingMap.find(atypes);
296	if (it == MixingMap.end())
297	return 0.0;
298	else {
299	LJInteractionData mixer = (*it).second;
300	return 2.5 * mixer.sigma;
301	}
302	}
303
304	}