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 {

  LJ::LJ() : name_("LJ"), initialized_(false), shiftedPot_(false), 
             shiftedFrc_(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;

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

    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){
    
    // 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(InteractionData idat) {
    
    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(idat.atype1, 
                                                         idat.atype2);
    LJInteractionData mixer = MixingMap[key];

    RealType sigmai = mixer.sigmai;
    RealType epsilon = mixer.epsilon;
    

    ros = idat.rij * sigmai;

    getLJfunc(ros, myPot, myDeriv);

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

}
Revision:	1502
Committed:	Sat Oct 2 19:53:32 2010 UTC (14 years, 7 months ago) by gezelter
File size:	10059 byte(s)
Log Message:	Many changes, and we're not quite done with this phase yet.
#	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	namespace OpenMD {
50
51	LJ::LJ() : name_("LJ"), initialized_(false), shiftedPot_(false),
52	shiftedFrc_(false), forceField_(NULL) {}
53
54	LJParam LJ::getLJParam(AtomType* atomType) {
55
56	// Do sanity checking on the AtomType we were passed before
57	// building any data structures:
58	if (!atomType->isLennardJones()) {
59	sprintf( painCave.errMsg,
60	"LJ::getLJParam was passed an atomType (%s) that does not\n"
61	"\tappear to be a Lennard-Jones atom.\n",
62	atomType->getName().c_str());
63	painCave.severity = OPENMD_ERROR;
64	painCave.isFatal = 1;
65	simError();
66	}
67
68	GenericData* data = atomType->getPropertyByName("LennardJones");
69	if (data == NULL) {
70	sprintf( painCave.errMsg, "LJ::getLJParam could not find Lennard-Jones\n"
71	"\tparameters for atomType %s.\n", atomType->getName().c_str());
72	painCave.severity = OPENMD_ERROR;
73	painCave.isFatal = 1;
74	simError();
75	}
76
77	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
78	if (ljData == NULL) {
79	sprintf( painCave.errMsg,
80	"LJ::getLJParam could not convert GenericData to LJParam for\n"
81	"\tatom type %s\n", atomType->getName().c_str());
82	painCave.severity = OPENMD_ERROR;
83	painCave.isFatal = 1;
84	simError();
85	}
86
87	return ljData->getData();
88	}
89
90	RealType LJ::getSigma(AtomType* atomType) {
91	LJParam ljParam = getLJParam(atomType);
92	return ljParam.sigma;
93	}
94
95	RealType LJ::getSigma(AtomType* atomType1, AtomType* atomType2) {
96	RealType sigma1 = getSigma(atomType1);
97	RealType sigma2 = getSigma(atomType2);
98
99	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
100	string DistanceMix = fopts.getDistanceMixingRule();
101	toUpper(DistanceMix);
102
103	if (DistanceMix == "GEOMETRIC")
104	return sqrt(sigma1 * sigma2);
105	else
106	return 0.5 * (sigma1 + sigma2);
107	}
108
109	RealType LJ::getEpsilon(AtomType* atomType) {
110	LJParam ljParam = getLJParam(atomType);
111	return ljParam.epsilon;
112	}
113
114	RealType LJ::getEpsilon(AtomType* atomType1, AtomType* atomType2) {
115	RealType epsilon1 = getEpsilon(atomType1);
116	RealType epsilon2 = getEpsilon(atomType2);
117	return sqrt(epsilon1 * epsilon2);
118	}
119
120	void LJ::initialize() {
121	ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
122	ForceField::AtomTypeContainer::MapTypeIterator i;
123	AtomType* at;
124
125	for (at = atomTypes->beginType(i); at != NULL;
126	at = atomTypes->nextType(i)) {
127
128	if (at->isLennardJones())
129	addType(at);
130	}
131
132	ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
133	ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
134	NonBondedInteractionType* nbt;
135
136	for (nbt = nbiTypes->beginType(j); nbt != NULL;
137	nbt = nbiTypes->nextType(j)) {
138
139	if (nbt->isLennardJones()) {
140
141	pair<AtomType, AtomType> atypes = nbt->getAtomTypes();
142
143	GenericData* data = nbt->getPropertyByName("LennardJones");
144	if (data == NULL) {
145	sprintf( painCave.errMsg, "LJ::rebuildMixingMap could not find\n"
146	"\tLennard-Jones parameters for %s - %s interaction.\n",
147	atypes.first->getName().c_str(),
148	atypes.second->getName().c_str());
149	painCave.severity = OPENMD_ERROR;
150	painCave.isFatal = 1;
151	simError();
152	}
153
154	LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
155	if (ljData == NULL) {
156	sprintf( painCave.errMsg,
157	"LJ::rebuildMixingMap could not convert GenericData to\n"
158	"\tLJParam for %s - %s interaction.\n",
159	atypes.first->getName().c_str(),
160	atypes.second->getName().c_str());
161	painCave.severity = OPENMD_ERROR;
162	painCave.isFatal = 1;
163	simError();
164	}
165
166	LJParam ljParam = ljData->getData();
167
168	RealType sigma = ljParam.sigma;
169	RealType epsilon = ljParam.epsilon;
170
171	addExplicitInteraction(atypes.first, atypes.second, sigma, epsilon);
172	}
173	}
174	initialized_ = true;
175	}
176
177
178
179	void LJ::addType(AtomType* atomType){
180	RealType sigma1 = getSigma(atomType);
181	RealType epsilon1 = getEpsilon(atomType);
182
183	// add it to the map:
184	AtomTypeProperties atp = atomType->getATP();
185
186	pair<map<int,AtomType*>::iterator,bool> ret;
187	ret = LJMap.insert( pair<int, AtomType*>(atp.ident, atomType) );
188	if (ret.second == false) {
189	sprintf( painCave.errMsg,
190	"LJ already had a previous entry with ident %d\n",
191	atp.ident);
192	painCave.severity = OPENMD_INFO;
193	painCave.isFatal = 0;
194	simError();
195	}
196
197	// Now, iterate over all known types and add to the mixing map:
198
199	std::map<int, AtomType*>::iterator it;
200	for( it = LJMap.begin(); it != LJMap.end(); ++it) {
201
202	AtomType* atype2 = (*it).second;
203
204	LJInteractionData mixer;
205	mixer.sigma = getSigma(atomType, atype2);
206	mixer.epsilon = getEpsilon(atomType, atype2);
207	mixer.sigmai = 1.0 / mixer.sigma;
208	mixer.explicitlySet = false;
209
210	std::pair<AtomType, AtomType> key1, key2;
211	key1 = std::make_pair(atomType, atype2);
212	key2 = std::make_pair(atype2, atomType);
213
214	MixingMap[key1] = mixer;
215	if (key2 != key1) {
216	MixingMap[key2] = mixer;
217	}
218	}
219	}
220
221	void LJ::addExplicitInteraction(AtomType* atype1, AtomType* atype2, RealType sigma, RealType epsilon){
222
223	// in case these weren't already in the map
224	addType(atype1);
225	addType(atype2);
226
227	LJInteractionData mixer;
228	mixer.sigma = sigma;
229	mixer.epsilon = epsilon;
230	mixer.sigmai = 1.0 / mixer.sigma;
231	mixer.explicitlySet = true;
232
233	std::pair<AtomType, AtomType> key1, key2;
234	key1 = std::make_pair(atype1, atype2);
235	key2 = std::make_pair(atype2, atype1);
236
237	MixingMap[key1] = mixer;
238	if (key2 != key1) {
239	MixingMap[key2] = mixer;
240	}
241	}
242
243	void LJ::calcForce(InteractionData idat) {
244
245	if (!initialized_) initialize();
246
247	RealType ros;
248	RealType rcos;
249	RealType myPot = 0.0;
250	RealType myPotC = 0.0;
251	RealType myDeriv = 0.0;
252	RealType myDerivC = 0.0;
253
254	std::pair<AtomType, AtomType> key = std::make_pair(idat.atype1,
255	idat.atype2);
256	LJInteractionData mixer = MixingMap[key];
257
258	RealType sigmai = mixer.sigmai;
259	RealType epsilon = mixer.epsilon;
260
261
262	ros = idat.rij * sigmai;
263
264	getLJfunc(ros, myPot, myDeriv);
265
266	if (shiftedPot_) {
267	rcos = idat.rcut * sigmai;
268	getLJfunc(rcos, myPotC, myDerivC);
269	myDerivC = 0.0;
270	} else if (LJ::shiftedFrc_) {
271	rcos = idat.rcut * sigmai;
272	getLJfunc(rcos, myPotC, myDerivC);
273	myPotC = myPotC + myDerivC * (idat.rij - idat.rcut) * sigmai;
274	} else {
275	myPotC = 0.0;
276	myDerivC = 0.0;
277	}
278
279	RealType pot_temp = idat.vdwMult * epsilon * (myPot - myPotC);
280	idat.vpair += pot_temp;
281
282	RealType dudr = idat.sw * idat.vdwMult * epsilon * (myDeriv -
283	myDerivC)*sigmai;
284
285	idat.pot += idat.sw * pot_temp;
286	idat.f1 = idat.d * dudr / idat.rij;
287
288	return;
289
290	}
291
292	void LJ::getLJfunc(RealType r, RealType &pot, RealType &deriv) {
293
294	RealType ri = 1.0 / r;
295	RealType ri2 = ri * ri;
296	RealType ri6 = ri2 * ri2 * ri2;
297	RealType ri7 = ri6 * ri;
298	RealType ri12 = ri6 * ri6;
299	RealType ri13 = ri12 * ri;
300
301	pot = 4.0 * (ri12 - ri6);
302	deriv = 24.0 * (ri7 - 2.0 * ri13);
303
304	return;
305	}
306
307
308	}