src/nonbonded/RepulsivePower.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/RepulsivePower.hpp"
#include "utils/simError.h"
#include "types/RepulsivePowerInteractionType.hpp"

using namespace std;

namespace OpenMD {

  RepulsivePower::RepulsivePower() : name_("RepulsivePower"), 
                                     initialized_(false), forceField_(NULL) {}
  
  void RepulsivePower::initialize() {    

    ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
    ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
    ForceField::NonBondedInteractionTypeContainer::KeyType keys;
    NonBondedInteractionType* nbt;

    for (nbt = nbiTypes->beginType(j); nbt != NULL; 
         nbt = nbiTypes->nextType(j)) {
      
      if (nbt->isRepulsivePower()) {
        keys = nbiTypes->getKeys(j);
        AtomType* at1 = forceField_->getAtomType(keys[0]);
        AtomType* at2 = forceField_->getAtomType(keys[1]);


        RepulsivePowerInteractionType* rpit = dynamic_cast<RepulsivePowerInteractionType*>(nbt);

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

        
        RealType sigma = rpit->getSigma();
        RealType epsilon = rpit->getEpsilon();
        int nRep = rpit->getNrep();

        addExplicitInteraction(at1, at2, sigma, epsilon, nRep);
      }
    }
    initialized_ = true;
  }
      
  void RepulsivePower::addExplicitInteraction(AtomType* atype1, 
                                              AtomType* atype2, 
                                              RealType sigma, 
                                              RealType epsilon, 
                                              int nRep) {

    RPInteractionData mixer;
    mixer.sigma = sigma;
    mixer.epsilon = epsilon;
    mixer.sigmai = 1.0 / mixer.sigma;
    mixer.nRep = nRep;

    pair<AtomType*, AtomType*> key1, key2;
    key1 = make_pair(atype1, atype2);
    key2 = make_pair(atype2, atype1);
    
    MixingMap[key1] = mixer;
    if (key2 != key1) {
      MixingMap[key2] = mixer;
    }    
  }
  
  void RepulsivePower::calcForce(InteractionData &idat) {

    if (!initialized_) initialize();
    
    map<pair<AtomType*, AtomType*>, RPInteractionData>::iterator it;
    it = MixingMap.find( idat.atypes );

    if (it != MixingMap.end()) {

      RPInteractionData mixer = (*it).second;
      RealType sigmai = mixer.sigmai;
      RealType epsilon = mixer.epsilon;
      int nRep = mixer.nRep;
      
      RealType ros;
      RealType rcos;
      RealType myPot = 0.0;
      RealType myPotC = 0.0;
      RealType myDeriv = 0.0;
      RealType myDerivC = 0.0;
     
      ros = *(idat.rij) * sigmai;     
      
      getNRepulsionFunc(ros, nRep, myPot, myDeriv);
      
      if (idat.shiftedPot) {
        rcos = *(idat.rcut) * sigmai;
        getNRepulsionFunc(rcos, nRep, myPotC, myDerivC);
        myDerivC = 0.0;
      } else if (idat.shiftedForce) {
        rcos = *(idat.rcut) * sigmai;
        getNRepulsionFunc(rcos, nRep, 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 RepulsivePower::getNRepulsionFunc(RealType r, int n, RealType &pot, RealType &deriv) {

    RealType ri = 1.0 / r;
    RealType rin = pow(ri, n);
    RealType rin1 = rin * ri;

    pot = rin;
    deriv = -n * rin1;
    
    return;
  }
  

  RealType RepulsivePower::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) {   
    if (!initialized_) initialize();   
    map<pair<AtomType*, AtomType*>, RPInteractionData>::iterator it;
    it = MixingMap.find(atypes);
    if (it == MixingMap.end()) 
      return 0.0;
    else  {
      RPInteractionData mixer = (*it).second;
      return 2.5 * mixer.sigma;
    }
  }

}

Revision:	1656
Committed:	Tue Oct 11 19:46:51 2011 UTC (13 years, 6 months ago) by jmichalk
File size:	6739 byte(s)
Log Message:	First few fixes for explicit interactions.
#	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/RepulsivePower.hpp"
47	#include "utils/simError.h"
48	#include "types/RepulsivePowerInteractionType.hpp"
49
50	using namespace std;
51
52	namespace OpenMD {
53
54	RepulsivePower::RepulsivePower() : name_("RepulsivePower"),
55	initialized_(false), forceField_(NULL) {}
56
57	void RepulsivePower::initialize() {
58
59	ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
60	ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
61	ForceField::NonBondedInteractionTypeContainer::KeyType keys;
62	NonBondedInteractionType* nbt;
63
64	for (nbt = nbiTypes->beginType(j); nbt != NULL;
65	nbt = nbiTypes->nextType(j)) {
66
67	if (nbt->isRepulsivePower()) {
68	keys = nbiTypes->getKeys(j);
69	AtomType* at1 = forceField_->getAtomType(keys[0]);
70	AtomType* at2 = forceField_->getAtomType(keys[1]);
71
72
73	RepulsivePowerInteractionType* rpit = dynamic_cast<RepulsivePowerInteractionType*>(nbt);
74
75	if (rpit == NULL) {
76	sprintf( painCave.errMsg,
77	"RepulsivePower::initialize could not convert NonBondedInteractionType\n"
78	"\tto RepulsivePowerInteractionType for %s - %s interaction.\n",
79	at1->getName().c_str(),
80	at2->getName().c_str());
81	painCave.severity = OPENMD_ERROR;
82	painCave.isFatal = 1;
83	simError();
84	}
85
86
87	RealType sigma = rpit->getSigma();
88	RealType epsilon = rpit->getEpsilon();
89	int nRep = rpit->getNrep();
90
91	addExplicitInteraction(at1, at2, sigma, epsilon, nRep);
92	}
93	}
94	initialized_ = true;
95	}
96
97	void RepulsivePower::addExplicitInteraction(AtomType* atype1,
98	AtomType* atype2,
99	RealType sigma,
100	RealType epsilon,
101	int nRep) {
102
103	RPInteractionData mixer;
104	mixer.sigma = sigma;
105	mixer.epsilon = epsilon;
106	mixer.sigmai = 1.0 / mixer.sigma;
107	mixer.nRep = nRep;
108
109	pair<AtomType, AtomType> key1, key2;
110	key1 = make_pair(atype1, atype2);
111	key2 = make_pair(atype2, atype1);
112
113	MixingMap[key1] = mixer;
114	if (key2 != key1) {
115	MixingMap[key2] = mixer;
116	}
117	}
118
119	void RepulsivePower::calcForce(InteractionData &idat) {
120
121	if (!initialized_) initialize();
122
123	map<pair<AtomType, AtomType>, RPInteractionData>::iterator it;
124	it = MixingMap.find( idat.atypes );
125
126	if (it != MixingMap.end()) {
127
128	RPInteractionData mixer = (*it).second;
129	RealType sigmai = mixer.sigmai;
130	RealType epsilon = mixer.epsilon;
131	int nRep = mixer.nRep;
132
133	RealType ros;
134	RealType rcos;
135	RealType myPot = 0.0;
136	RealType myPotC = 0.0;
137	RealType myDeriv = 0.0;
138	RealType myDerivC = 0.0;
139
140	ros = (idat.rij) sigmai;
141
142	getNRepulsionFunc(ros, nRep, myPot, myDeriv);
143
144	if (idat.shiftedPot) {
145	rcos = (idat.rcut) sigmai;
146	getNRepulsionFunc(rcos, nRep, myPotC, myDerivC);
147	myDerivC = 0.0;
148	} else if (idat.shiftedForce) {
149	rcos = (idat.rcut) sigmai;
150	getNRepulsionFunc(rcos, nRep, myPotC, myDerivC);
151	myPotC = myPotC + myDerivC * ((idat.rij) - (idat.rcut)) * sigmai;
152	} else {
153	myPotC = 0.0;
154	myDerivC = 0.0;
155	}
156
157	RealType pot_temp = (idat.vdwMult) epsilon * (myPot - myPotC);
158	*(idat.vpair) += pot_temp;
159
160	RealType dudr = (idat.sw) (idat.vdwMult) epsilon * (myDeriv -
161	myDerivC)*sigmai;
162
163	((idat.pot))[VANDERWAALS_FAMILY] += (idat.sw) * pot_temp;
164	(idat.f1) = (idat.d) * dudr / *(idat.rij);
165	}
166	return;
167	}
168
169	void RepulsivePower::getNRepulsionFunc(RealType r, int n, RealType &pot, RealType &deriv) {
170
171	RealType ri = 1.0 / r;
172	RealType rin = pow(ri, n);
173	RealType rin1 = rin * ri;
174
175	pot = rin;
176	deriv = -n * rin1;
177
178	return;
179	}
180
181
182	RealType RepulsivePower::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
183	if (!initialized_) initialize();
184	map<pair<AtomType, AtomType>, RPInteractionData>::iterator it;
185	it = MixingMap.find(atypes);
186	if (it == MixingMap.end())
187	return 0.0;
188	else {
189	RPInteractionData mixer = (*it).second;
190	return 2.5 * mixer.sigma;
191	}
192	}
193
194	}
195