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:	1895
Committed:	Mon Jul 1 21:09:37 2013 UTC (12 years, 5 months ago) by gezelter
File size:	7379 byte(s)
Log Message:	Speed!
#	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, 234107 (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/RepulsivePower.hpp"
48	#include "utils/simError.h"
49	#include "types/RepulsivePowerInteractionType.hpp"
50
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	RPtypes.clear();
61	RPtids.clear();
62	MixingMap.clear();
63	RPtids.resize( forceField_->getNAtomType(), -1);
64
65	ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
66	ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
67	ForceField::NonBondedInteractionTypeContainer::KeyType keys;
68	NonBondedInteractionType* nbt;
69	int rptid1, rptid2;
70
71	for (nbt = nbiTypes->beginType(j); nbt != NULL;
72	nbt = nbiTypes->nextType(j)) {
73
74	if (nbt->isRepulsivePower()) {
75	keys = nbiTypes->getKeys(j);
76	AtomType* at1 = forceField_->getAtomType(keys[0]);
77	AtomType* at2 = forceField_->getAtomType(keys[1]);
78
79	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	RepulsivePowerInteractionType* rpit = dynamic_cast<RepulsivePowerInteractionType*>(nbt);
93	if (rpit == NULL) {
94	sprintf( painCave.errMsg,
95	"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	painCave.severity = OPENMD_ERROR;
100	painCave.isFatal = 1;
101	simError();
102	}
103
104	RealType sigma = rpit->getSigma();
105	RealType epsilon = rpit->getEpsilon();
106	int nRep = rpit->getNrep();
107
108	addExplicitInteraction(at1, at2, sigma, epsilon, nRep);
109	}
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	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
133	MixingMap[rptid1][rptid2] = mixer;
134	if (rptid2 != rptid1) {
135	MixingMap[rptid2].resize(nRP);
136	MixingMap[rptid2][rptid1] = mixer;
137	}
138	}
139
140	void RepulsivePower::calcForce(InteractionData &idat) {
141
142	if (!initialized_) initialize();
143
144	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
149	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	}
172
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	myDerivC)*sigmai;
178
179	((idat.pot))[VANDERWAALS_FAMILY] += (idat.sw) * pot_temp;
180	(idat.f1) = (idat.d) * dudr / *(idat.rij);
181
182	return;
183	}
184
185	void RepulsivePower::getNRepulsionFunc(const RealType &r, int &n, RealType &pot, RealType &deriv) {
186
187	RealType ri = 1.0 / r;
188	RealType rin = pow(ri, n);
189	RealType rin1 = rin * ri;
190
191	pot = rin;
192	deriv = -n * rin1;
193
194	return;
195	}
196
197
198	RealType RepulsivePower::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
199	if (!initialized_) initialize();
200
201	int atid1 = atypes.first->getIdent();
202	int atid2 = atypes.second->getIdent();
203	int rptid1 = RPtids[atid1];
204	int rptid2 = RPtids[atid2];
205
206	if (rptid1 == -1 \|\| rptid2 == -1) return 0.0;
207	else {
208	RPInteractionData mixer = MixingMap[rptid1][rptid2];
209	return 2.5 * mixer.sigma;
210	}
211	}
212	}
213