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]  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/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:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	6805 byte(s)
Log Message:	updated copyright notices
#	User	Rev	Content
1	gezelter	1624	/*
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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	1624	*/
42
43			#include <stdio.h>
44			#include <string.h>
45
46			#include <cmath>
47			#include "nonbonded/RepulsivePower.hpp"
48			#include "utils/simError.h"
49	jmichalk	1656	#include "types/RepulsivePowerInteractionType.hpp"
50	gezelter	1624
51			using namespace std;
52
53			namespace OpenMD {
54
55			RepulsivePower::RepulsivePower() : name_("RepulsivePower"),
56			initialized_(false), forceField_(NULL) {}
57
58			void RepulsivePower::initialize() {
59
60			ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
61			ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
62	jmichalk	1656	ForceField::NonBondedInteractionTypeContainer::KeyType keys;
63	gezelter	1624	NonBondedInteractionType* nbt;
64
65			for (nbt = nbiTypes->beginType(j); nbt != NULL;
66			nbt = nbiTypes->nextType(j)) {
67
68			if (nbt->isRepulsivePower()) {
69	jmichalk	1656	keys = nbiTypes->getKeys(j);
70			AtomType* at1 = forceField_->getAtomType(keys[0]);
71			AtomType* at2 = forceField_->getAtomType(keys[1]);
72
73
74			RepulsivePowerInteractionType* rpit = dynamic_cast<RepulsivePowerInteractionType*>(nbt);
75
76			if (rpit == NULL) {
77	gezelter	1624	sprintf( painCave.errMsg,
78	jmichalk	1656	"RepulsivePower::initialize could not convert NonBondedInteractionType\n"
79			"\tto RepulsivePowerInteractionType for %s - %s interaction.\n",
80			at1->getName().c_str(),
81			at2->getName().c_str());
82	gezelter	1624	painCave.severity = OPENMD_ERROR;
83			painCave.isFatal = 1;
84			simError();
85			}
86	jmichalk	1656
87	gezelter	1624
88	jmichalk	1656	RealType sigma = rpit->getSigma();
89			RealType epsilon = rpit->getEpsilon();
90			int nRep = rpit->getNrep();
91	gezelter	1624
92	jmichalk	1656	addExplicitInteraction(at1, at2, sigma, epsilon, nRep);
93	gezelter	1624	}
94			}
95			initialized_ = true;
96			}
97
98			void RepulsivePower::addExplicitInteraction(AtomType* atype1,
99			AtomType* atype2,
100			RealType sigma,
101			RealType epsilon,
102			int nRep) {
103
104			RPInteractionData mixer;
105			mixer.sigma = sigma;
106			mixer.epsilon = epsilon;
107			mixer.sigmai = 1.0 / mixer.sigma;
108			mixer.nRep = nRep;
109
110			pair<AtomType, AtomType> key1, key2;
111			key1 = make_pair(atype1, atype2);
112			key2 = make_pair(atype2, atype1);
113
114			MixingMap[key1] = mixer;
115			if (key2 != key1) {
116			MixingMap[key2] = mixer;
117			}
118			}
119
120			void RepulsivePower::calcForce(InteractionData &idat) {
121
122			if (!initialized_) initialize();
123
124			map<pair<AtomType, AtomType>, RPInteractionData>::iterator it;
125			it = MixingMap.find( idat.atypes );
126
127			if (it != MixingMap.end()) {
128
129			RPInteractionData mixer = (*it).second;
130			RealType sigmai = mixer.sigmai;
131			RealType epsilon = mixer.epsilon;
132			int nRep = mixer.nRep;
133
134			RealType ros;
135			RealType rcos;
136			RealType myPot = 0.0;
137			RealType myPotC = 0.0;
138			RealType myDeriv = 0.0;
139			RealType myDerivC = 0.0;
140
141			ros = (idat.rij) sigmai;
142
143			getNRepulsionFunc(ros, nRep, myPot, myDeriv);
144
145			if (idat.shiftedPot) {
146			rcos = (idat.rcut) sigmai;
147			getNRepulsionFunc(rcos, nRep, myPotC, myDerivC);
148			myDerivC = 0.0;
149			} else if (idat.shiftedForce) {
150			rcos = (idat.rcut) sigmai;
151			getNRepulsionFunc(rcos, nRep, myPotC, myDerivC);
152			myPotC = myPotC + myDerivC * ((idat.rij) - (idat.rcut)) * sigmai;
153			} else {
154			myPotC = 0.0;
155			myDerivC = 0.0;
156			}
157
158			RealType pot_temp = (idat.vdwMult) epsilon * (myPot - myPotC);
159			*(idat.vpair) += pot_temp;
160
161			RealType dudr = (idat.sw) (idat.vdwMult) epsilon * (myDeriv -
162			myDerivC)*sigmai;
163
164			((idat.pot))[VANDERWAALS_FAMILY] += (idat.sw) * pot_temp;
165			(idat.f1) = (idat.d) * dudr / *(idat.rij);
166			}
167			return;
168			}
169
170			void RepulsivePower::getNRepulsionFunc(RealType r, int n, RealType &pot, RealType &deriv) {
171
172			RealType ri = 1.0 / r;
173			RealType rin = pow(ri, n);
174			RealType rin1 = rin * ri;
175
176			pot = rin;
177			deriv = -n * rin1;
178
179			return;
180			}
181
182
183			RealType RepulsivePower::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
184			if (!initialized_) initialize();
185			map<pair<AtomType, AtomType>, RPInteractionData>::iterator it;
186			it = MixingMap.find(atypes);
187			if (it == MixingMap.end())
188			return 0.0;
189			else {
190			RPInteractionData mixer = (*it).second;
191			return 2.5 * mixer.sigma;
192			}
193			}
194
195			}
196