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, 234107 (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() {    

    RPtypes.clear();
    RPtids.clear();
    MixingMap.clear();
    RPtids.resize( forceField_->getNAtomType(), -1);

    ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
    ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
    ForceField::NonBondedInteractionTypeContainer::KeyType keys;
    NonBondedInteractionType* nbt;
    int rptid1, rptid2;

    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]);

        int atid1 = at1->getIdent();
        if (RPtids[atid1] == -1) {
          rptid1 = RPtypes.size();
          RPtypes.insert(atid1);
          RPtids[atid1] = rptid1;         
        }
        int atid2 = at2->getIdent();
        if (RPtids[atid2] == -1) {
          rptid2 = RPtypes.size();
          RPtypes.insert(atid2);
          RPtids[atid2] = rptid2;         
        }
          
        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;

    int rptid1 = RPtids[atype1->getIdent()];
    int rptid2 = RPtids[atype2->getIdent()];
    int nRP = RPtypes.size();

    MixingMap.resize(nRP);
    MixingMap[rptid1].resize(nRP);
    
    MixingMap[rptid1][rptid2] = mixer;
    if (rptid2 != rptid1) {
      MixingMap[rptid2].resize(nRP);
      MixingMap[rptid2][rptid1] = mixer;
    }    
  }
  
  void RepulsivePower::calcForce(InteractionData &idat) {

    if (!initialized_) initialize();
    
    RPInteractionData &mixer = MixingMap[RPtids[idat.atid1]][RPtids[idat.atid2]];
    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(const 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();   
    
    int atid1 = atypes.first->getIdent();
    int atid2 = atypes.second->getIdent();
    int rptid1 = RPtids[atid1];
    int rptid2 = RPtids[atid2];
    
    if (rptid1 == -1 || rptid2 == -1) return 0.0;
    else {      
      RPInteractionData mixer = MixingMap[rptid1][rptid2];
      return 2.5 * mixer.sigma;
    }
  }  
}

Revision:	2033
Committed:	Sat Nov 1 14:12:16 2014 UTC (10 years, 6 months ago) by gezelter
File size:	7418 byte(s)
Log Message:	Fixed a selection issue in ParticleTimeCorrFunc, other whitespace stuff
#	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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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	gezelter	1895	RPtypes.clear();
61			RPtids.clear();
62			MixingMap.clear();
63			RPtids.resize( forceField_->getNAtomType(), -1);
64
65	gezelter	1624	ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
66			ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
67	jmichalk	1656	ForceField::NonBondedInteractionTypeContainer::KeyType keys;
68	gezelter	1624	NonBondedInteractionType* nbt;
69	gezelter	1895	int rptid1, rptid2;
70	gezelter	1624
71			for (nbt = nbiTypes->beginType(j); nbt != NULL;
72			nbt = nbiTypes->nextType(j)) {
73
74			if (nbt->isRepulsivePower()) {
75	jmichalk	1656	keys = nbiTypes->getKeys(j);
76			AtomType* at1 = forceField_->getAtomType(keys[0]);
77			AtomType* at2 = forceField_->getAtomType(keys[1]);
78
79	gezelter	1895	int atid1 = at1->getIdent();
80			if (RPtids[atid1] == -1) {
81			rptid1 = RPtypes.size();
82			RPtypes.insert(atid1);
83			RPtids[atid1] = rptid1;
84			}
85			int atid2 = at2->getIdent();
86			if (RPtids[atid2] == -1) {
87			rptid2 = RPtypes.size();
88			RPtypes.insert(atid2);
89			RPtids[atid2] = rptid2;
90			}
91
92	jmichalk	1656	RepulsivePowerInteractionType* rpit = dynamic_cast<RepulsivePowerInteractionType*>(nbt);
93			if (rpit == NULL) {
94	gezelter	1624	sprintf( painCave.errMsg,
95	jmichalk	1656	"RepulsivePower::initialize could not convert NonBondedInteractionType\n"
96			"\tto RepulsivePowerInteractionType for %s - %s interaction.\n",
97			at1->getName().c_str(),
98			at2->getName().c_str());
99	gezelter	1624	painCave.severity = OPENMD_ERROR;
100			painCave.isFatal = 1;
101			simError();
102			}
103
104	jmichalk	1656	RealType sigma = rpit->getSigma();
105			RealType epsilon = rpit->getEpsilon();
106			int nRep = rpit->getNrep();
107	gezelter	1624
108	jmichalk	1656	addExplicitInteraction(at1, at2, sigma, epsilon, nRep);
109	gezelter	1624	}
110			}
111			initialized_ = true;
112			}
113
114			void RepulsivePower::addExplicitInteraction(AtomType* atype1,
115			AtomType* atype2,
116			RealType sigma,
117			RealType epsilon,
118			int nRep) {
119
120			RPInteractionData mixer;
121			mixer.sigma = sigma;
122			mixer.epsilon = epsilon;
123			mixer.sigmai = 1.0 / mixer.sigma;
124			mixer.nRep = nRep;
125
126	gezelter	1895	int rptid1 = RPtids[atype1->getIdent()];
127			int rptid2 = RPtids[atype2->getIdent()];
128			int nRP = RPtypes.size();
129
130			MixingMap.resize(nRP);
131			MixingMap[rptid1].resize(nRP);
132	gezelter	1624
133	gezelter	1895	MixingMap[rptid1][rptid2] = mixer;
134			if (rptid2 != rptid1) {
135			MixingMap[rptid2].resize(nRP);
136			MixingMap[rptid2][rptid1] = mixer;
137	gezelter	1624	}
138			}
139
140			void RepulsivePower::calcForce(InteractionData &idat) {
141
142			if (!initialized_) initialize();
143	jmichalk	2031
144	gezelter	1895	RPInteractionData &mixer = MixingMap[RPtids[idat.atid1]][RPtids[idat.atid2]];
145			RealType sigmai = mixer.sigmai;
146			RealType epsilon = mixer.epsilon;
147			int nRep = mixer.nRep;
148	gezelter	1624
149	gezelter	1895	RealType ros;
150			RealType rcos;
151			RealType myPot = 0.0;
152			RealType myPotC = 0.0;
153			RealType myDeriv = 0.0;
154			RealType myDerivC = 0.0;
155
156			ros = (idat.rij) sigmai;
157
158			getNRepulsionFunc(ros, nRep, myPot, myDeriv);
159
160			if (idat.shiftedPot) {
161			rcos = (idat.rcut) sigmai;
162			getNRepulsionFunc(rcos, nRep, myPotC, myDerivC);
163			myDerivC = 0.0;
164			} else if (idat.shiftedForce) {
165			rcos = (idat.rcut) sigmai;
166			getNRepulsionFunc(rcos, nRep, myPotC, myDerivC);
167			myPotC = myPotC + myDerivC * ((idat.rij) - (idat.rcut)) * sigmai;
168			} else {
169			myPotC = 0.0;
170			myDerivC = 0.0;
171	gezelter	1624	}
172	gezelter	1895
173			RealType pot_temp = (idat.vdwMult) epsilon * (myPot - myPotC);
174			*(idat.vpair) += pot_temp;
175
176			RealType dudr = (idat.sw) (idat.vdwMult) epsilon * (myDeriv -
177	gezelter	2033	myDerivC)*sigmai;
178	gezelter	1895
179			((idat.pot))[VANDERWAALS_FAMILY] += (idat.sw) * pot_temp;
180			(idat.f1) = (idat.d) * dudr / *(idat.rij);
181
182	gezelter	1624	return;
183			}
184
185	gezelter	2033	void RepulsivePower::getNRepulsionFunc(const RealType &r, int &n,
186			RealType &pot, RealType &deriv) {
187	gezelter	1624
188			RealType ri = 1.0 / r;
189			RealType rin = pow(ri, n);
190			RealType rin1 = rin * ri;
191
192			pot = rin;
193			deriv = -n * rin1;
194
195			return;
196			}
197
198
199			RealType RepulsivePower::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
200			if (!initialized_) initialize();
201	gezelter	1895
202			int atid1 = atypes.first->getIdent();
203			int atid2 = atypes.second->getIdent();
204			int rptid1 = RPtids[atid1];
205			int rptid2 = RPtids[atid2];
206
207			if (rptid1 == -1 \|\| rptid2 == -1) return 0.0;
208			else {
209			RPInteractionData mixer = MixingMap[rptid1][rptid2];
210	gezelter	1624	return 2.5 * mixer.sigma;
211			}
212	gezelter	1895	}
213	gezelter	1624	}
214