src/nonbonded/MAW.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/MAW.hpp"
#include "utils/simError.h"

using namespace std;

namespace OpenMD {

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

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

    for (nbt = nbiTypes->beginType(j); nbt != NULL; 
         nbt = nbiTypes->nextType(j)) {
      
      if (nbt->isMAW()) {
        pair<AtomType*, AtomType*> atypes = nbt->getAtomTypes();
        
        GenericData* data = nbt->getPropertyByName("MAW");
        if (data == NULL) {
          sprintf( painCave.errMsg, "MAW::initialize could not find\n"
                   "\tMAW parameters for %s - %s interaction.\n", 
                   atypes.first->getName().c_str(),
                   atypes.second->getName().c_str());
          painCave.severity = OPENMD_ERROR;
          painCave.isFatal = 1;
          simError(); 
        }
        
        MAWData* mawData = dynamic_cast<MAWData*>(data);
        if (mawData == NULL) {
          sprintf( painCave.errMsg,
                   "MAW::initialize could not convert GenericData to\n"
                   "\tMAWData for %s - %s interaction.\n", 
                   atypes.first->getName().c_str(),
                   atypes.second->getName().c_str());
          painCave.severity = OPENMD_ERROR;
          painCave.isFatal = 1;
          simError();          
        }
        
        MAWParam mawParam = mawData->getData();

        RealType De = mawParam.De;
        RealType beta = mawParam.beta;
        RealType Re = mawParam.Re;
        RealType ca1 = mawParam.ca1;
        RealType cb1 = mawParam.cb1;
        
        addExplicitInteraction(atypes.first, atypes.second, 
                               De, beta, Re, ca1, cb1);
      }
    }  
    initialized_ = true;
  }
  
  void MAW::addExplicitInteraction(AtomType* atype1, AtomType* atype2, 
                                   RealType De, RealType beta, RealType Re, 
                                   RealType ca1, RealType cb1) {

    MAWInteractionData mixer;
    mixer.De = De;
    mixer.beta = beta;
    mixer.Re = Re;
    mixer.ca1 = ca1;
    mixer.cb1 = cb1;

    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 MAW::calcForce(InteractionData &idat) {

    if (!initialized_) initialize();
    
    map<pair<AtomType*, AtomType*>, MAWInteractionData>::iterator it;
    it = MixingMap.find( idat.atypes );
    if (it != MixingMap.end()) {
      MAWInteractionData mixer = (*it).second;
      
      RealType myPot = 0.0;
      RealType myPotC = 0.0;
      RealType myDeriv = 0.0;
      RealType myDerivC = 0.0;
      
      RealType D_e = mixer.De;
      RealType R_e = mixer.Re;
      RealType beta = mixer.beta;
      RealType ca1 = mixer.ca1;
      RealType cb1 = mixer.cb1;

      bool j_is_Metal = idat.atypes.second->isMetal();

      Vector3d r;
      RotMat3x3d Atrans;
      if (j_is_Metal) {
        // rotate the inter-particle separation into the two different 
        // body-fixed coordinate systems:
        r = *(idat.A1) * *(idat.d);
        Atrans = idat.A1->transpose();
      } else {
        // negative sign because this is the vector from j to i:       
        r = -*(idat.A2) * *(idat.d);
        Atrans = idat.A2->transpose();
      }
      
      // V(r) = D_e exp(-a(r-re)(exp(-a(r-re))-2)
      
      RealType expt     = -beta*( *(idat.rij) - R_e);
      RealType expfnc   = exp(expt);
      RealType expfnc2  = expfnc*expfnc;
      
      RealType exptC = 0.0;
      RealType expfncC = 0.0;
      RealType expfnc2C = 0.0;

      myPot  = D_e * (expfnc2  - 2.0 * expfnc);
      myDeriv   = 2.0 * D_e * beta * (expfnc - expfnc2);
      
      if (idat.shiftedPot || idat.shiftedForce) {
        exptC     = -beta*( *(idat.rcut)  - R_e);
        expfncC   = exp(exptC);
        expfnc2C  = expfncC*expfncC;
      }
      
      if (idat.shiftedPot) {
        myPotC = D_e * (expfnc2C - 2.0 * expfncC);
        myDerivC = 0.0;
      } else if (idat.shiftedForce) {
        myPotC = D_e * (expfnc2C - 2.0 * expfncC);
        myDerivC  = 2.0 * D_e * beta * (expfnc2C - expfnc2C);
        myPotC += myDerivC * ( *(idat.rij)  -  *(idat.rcut) );
      } else {
        myPotC = 0.0;
        myDerivC = 0.0;
      }

      RealType x = r.x();
      RealType y = r.y();
      RealType z = r.z();
      RealType x2 = x * x;
      RealType y2 = y * y;
      RealType z2 = z * z;

      RealType r3 = *(idat.r2) *  *(idat.rij) ;
      RealType r4 = *(idat.r2) *  *(idat.r2);

      // angular modulation of morse part of potential to approximate 
      // the squares of the two HOMO lone pair orbitals in water:
      //********************** old form*************************
      // s = 1 / (4 pi)
      // ta1 = (s - pz)^2 = (1 - sqrt(3)*cos(theta))^2 / (4 pi)
      // b1 = px^2 = 3 * (sin(theta)*cos(phi))^2 / (4 pi)   
      //********************** old form*************************
      // we'll leave out the 4 pi for now
      
      // new functional form just using the p orbitals.
      // Vmorse(r)*[a*p_x + b p_z + (1-a-b)]
      // which is 
      // Vmorse(r)*[a sin^2(theta) cos^2(phi) + b cos(theta) + (1-a-b)]
      // Vmorse(r)*[a*x2/r2 + b*z/r + (1-a-b)]
       
      RealType Vmorse = (myPot - myPotC);
      RealType Vang = ca1 * x2 / *(idat.r2) + 
        cb1 * z /  *(idat.rij)  + (0.8 - ca1 / 3.0);
      
      RealType pot_temp = *(idat.vdwMult) * Vmorse * Vang;
      *(idat.vpair) += pot_temp;
      (*(idat.pot))[VANDERWAALS_FAMILY] += *(idat.sw) * pot_temp;
           
      Vector3d dVmorsedr = (myDeriv - myDerivC) * Vector3d(x, y, z) /  *(idat.rij) ;
      
      Vector3d dVangdr = Vector3d(-2.0 * ca1 * x2 * x / r4 + 2.0 * ca1 * x / *(idat.r2) - cb1 * x * z / r3,
                                  -2.0 * ca1 * x2 * y / r4 - cb1 * z * y / r3,
                                  -2.0 * ca1 * x2 * z / r4 + cb1 /  *(idat.rij)           - cb1 * z2  / r3);
      
      // chain rule to put these back on x, y, z

      Vector3d dvdr = Vang * dVmorsedr + Vmorse * dVangdr;

      // Torques for Vang using method of Price:
      // S. L. Price, A. J. Stone, and M. Alderton, Mol. Phys. 52, 987 (1984).
      
      Vector3d dVangdu = Vector3d(cb1 * y /  *(idat.rij) ,
                                  2.0 * ca1 * x * z / *(idat.r2) - cb1 * x /  *(idat.rij),
                                  -2.0 * ca1 * y * x / *(idat.r2));

      // do the torques first since they are easy:
      // remember that these are still in the body fixed axes    

      Vector3d trq = *(idat.vdwMult) * Vmorse * dVangdu * *(idat.sw);

      // go back to lab frame using transpose of rotation matrix:
      
      if (j_is_Metal) {
        *(idat.t1) += Atrans * trq;
      } else {
        *(idat.t2) += Atrans * trq;
      }

      // Now, on to the forces (still in body frame of water)

      Vector3d ftmp = *(idat.vdwMult) * *(idat.sw) * dvdr;

      // rotate the terms back into the lab frame:
      Vector3d flab;
      if (j_is_Metal) {
        flab = Atrans * ftmp;
      } else {
        flab = - Atrans * ftmp;
      }
      
      *(idat.f1) += flab;
    }
    return;
    
  }
    
  RealType MAW::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) {
    if (!initialized_) initialize();   
    map<pair<AtomType*, AtomType*>, MAWInteractionData>::iterator it;
    it = MixingMap.find(atypes);
    if (it == MixingMap.end()) 
      return 0.0;
    else  {
      MAWInteractionData mixer = (*it).second;

      RealType R_e = mixer.Re;
      RealType beta = mixer.beta;
      // This value of the r corresponds to an energy about 1.48% of 
      // the energy at the bottom of the Morse well.  For comparison, the
      // Lennard-Jones function is about 1.63% of it's minimum value at
      // a distance of 2.5 sigma.
      return (4.9 + beta * R_e) / beta;
    }
  }
}

Revision:	1583
Committed:	Thu Jun 16 22:00:08 2011 UTC (14 years, 1 month ago) by gezelter
File size:	10338 byte(s)
Log Message:	Bug squashing
#	User	Rev	Content
1	gezelter	1532	/*
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			#include <cmath>
45
46			#include "nonbonded/MAW.hpp"
47			#include "utils/simError.h"
48
49			using namespace std;
50
51			namespace OpenMD {
52
53	gezelter	1583	MAW::MAW() : name_("MAW"), initialized_(false), forceField_(NULL) {}
54	gezelter	1532
55			void MAW::initialize() {
56
57			ForceField::NonBondedInteractionTypeContainer* nbiTypes = forceField_->getNonBondedInteractionTypes();
58			ForceField::NonBondedInteractionTypeContainer::MapTypeIterator j;
59			NonBondedInteractionType* nbt;
60
61			for (nbt = nbiTypes->beginType(j); nbt != NULL;
62			nbt = nbiTypes->nextType(j)) {
63
64			if (nbt->isMAW()) {
65			pair<AtomType, AtomType> atypes = nbt->getAtomTypes();
66
67			GenericData* data = nbt->getPropertyByName("MAW");
68			if (data == NULL) {
69			sprintf( painCave.errMsg, "MAW::initialize could not find\n"
70			"\tMAW parameters for %s - %s interaction.\n",
71			atypes.first->getName().c_str(),
72			atypes.second->getName().c_str());
73			painCave.severity = OPENMD_ERROR;
74			painCave.isFatal = 1;
75			simError();
76			}
77
78			MAWData* mawData = dynamic_cast<MAWData*>(data);
79			if (mawData == NULL) {
80			sprintf( painCave.errMsg,
81			"MAW::initialize could not convert GenericData to\n"
82			"\tMAWData for %s - %s interaction.\n",
83			atypes.first->getName().c_str(),
84			atypes.second->getName().c_str());
85			painCave.severity = OPENMD_ERROR;
86			painCave.isFatal = 1;
87			simError();
88			}
89
90			MAWParam mawParam = mawData->getData();
91
92			RealType De = mawParam.De;
93			RealType beta = mawParam.beta;
94			RealType Re = mawParam.Re;
95			RealType ca1 = mawParam.ca1;
96			RealType cb1 = mawParam.cb1;
97
98			addExplicitInteraction(atypes.first, atypes.second,
99			De, beta, Re, ca1, cb1);
100			}
101			}
102			initialized_ = true;
103			}
104
105			void MAW::addExplicitInteraction(AtomType* atype1, AtomType* atype2,
106			RealType De, RealType beta, RealType Re,
107			RealType ca1, RealType cb1) {
108
109			MAWInteractionData mixer;
110			mixer.De = De;
111			mixer.beta = beta;
112			mixer.Re = Re;
113			mixer.ca1 = ca1;
114			mixer.cb1 = cb1;
115
116			pair<AtomType, AtomType> key1, key2;
117			key1 = make_pair(atype1, atype2);
118			key2 = make_pair(atype2, atype1);
119
120			MixingMap[key1] = mixer;
121			if (key2 != key1) {
122			MixingMap[key2] = mixer;
123			}
124			}
125
126	gezelter	1536	void MAW::calcForce(InteractionData &idat) {
127	gezelter	1532
128			if (!initialized_) initialize();
129
130			map<pair<AtomType, AtomType>, MAWInteractionData>::iterator it;
131	gezelter	1571	it = MixingMap.find( idat.atypes );
132	gezelter	1532	if (it != MixingMap.end()) {
133			MAWInteractionData mixer = (*it).second;
134
135			RealType myPot = 0.0;
136			RealType myPotC = 0.0;
137			RealType myDeriv = 0.0;
138			RealType myDerivC = 0.0;
139
140			RealType D_e = mixer.De;
141			RealType R_e = mixer.Re;
142			RealType beta = mixer.beta;
143			RealType ca1 = mixer.ca1;
144			RealType cb1 = mixer.cb1;
145
146	gezelter	1571	bool j_is_Metal = idat.atypes.second->isMetal();
147	gezelter	1532
148			Vector3d r;
149			RotMat3x3d Atrans;
150			if (j_is_Metal) {
151			// rotate the inter-particle separation into the two different
152			// body-fixed coordinate systems:
153	gezelter	1554	r = (idat.A1) *(idat.d);
154			Atrans = idat.A1->transpose();
155	gezelter	1532	} else {
156			// negative sign because this is the vector from j to i:
157	gezelter	1554	r = -(idat.A2) *(idat.d);
158			Atrans = idat.A2->transpose();
159	gezelter	1532	}
160
161			// V(r) = D_e exp(-a(r-re)(exp(-a(r-re))-2)
162
163	gezelter	1554	RealType expt = -beta( (idat.rij) - R_e);
164	gezelter	1532	RealType expfnc = exp(expt);
165			RealType expfnc2 = expfnc*expfnc;
166
167			RealType exptC = 0.0;
168			RealType expfncC = 0.0;
169			RealType expfnc2C = 0.0;
170
171			myPot = D_e * (expfnc2 - 2.0 * expfnc);
172			myDeriv = 2.0 * D_e * beta * (expfnc - expfnc2);
173
174	gezelter	1583	if (idat.shiftedPot \|\| idat.shiftedForce) {
175	gezelter	1554	exptC = -beta( (idat.rcut) - R_e);
176	gezelter	1532	expfncC = exp(exptC);
177			expfnc2C = expfncC*expfncC;
178			}
179
180	gezelter	1583	if (idat.shiftedPot) {
181	gezelter	1532	myPotC = D_e * (expfnc2C - 2.0 * expfncC);
182			myDerivC = 0.0;
183	gezelter	1583	} else if (idat.shiftedForce) {
184	gezelter	1532	myPotC = D_e * (expfnc2C - 2.0 * expfncC);
185			myDerivC = 2.0 * D_e * beta * (expfnc2C - expfnc2C);
186	gezelter	1554	myPotC += myDerivC * ( (idat.rij) - (idat.rcut) );
187	gezelter	1532	} else {
188			myPotC = 0.0;
189			myDerivC = 0.0;
190			}
191
192			RealType x = r.x();
193			RealType y = r.y();
194			RealType z = r.z();
195			RealType x2 = x * x;
196			RealType y2 = y * y;
197			RealType z2 = z * z;
198
199	gezelter	1554	RealType r3 = (idat.r2) *(idat.rij) ;
200			RealType r4 = (idat.r2) *(idat.r2);
201	gezelter	1532
202			// angular modulation of morse part of potential to approximate
203			// the squares of the two HOMO lone pair orbitals in water:
204			//******************** old form***********************
205			// s = 1 / (4 pi)
206			// ta1 = (s - pz)^2 = (1 - sqrt(3)*cos(theta))^2 / (4 pi)
207			// b1 = px^2 = 3 * (sin(theta)*cos(phi))^2 / (4 pi)
208			//******************** old form***********************
209			// we'll leave out the 4 pi for now
210
211			// new functional form just using the p orbitals.
212			// Vmorse(r)[ap_x + b p_z + (1-a-b)]
213			// which is
214			// Vmorse(r)*[a sin^2(theta) cos^2(phi) + b cos(theta) + (1-a-b)]
215			// Vmorse(r)[ax2/r2 + b*z/r + (1-a-b)]
216
217			RealType Vmorse = (myPot - myPotC);
218	gezelter	1554	RealType Vang = ca1 * x2 / *(idat.r2) +
219			cb1 * z / *(idat.rij) + (0.8 - ca1 / 3.0);
220
221			RealType pot_temp = (idat.vdwMult) Vmorse * Vang;
222			*(idat.vpair) += pot_temp;
223	gezelter	1582	((idat.pot))[VANDERWAALS_FAMILY] += (idat.sw) * pot_temp;
224	gezelter	1532
225	gezelter	1554	Vector3d dVmorsedr = (myDeriv - myDerivC) * Vector3d(x, y, z) / *(idat.rij) ;
226	gezelter	1532
227	gezelter	1554	Vector3d dVangdr = Vector3d(-2.0 * ca1 * x2 * x / r4 + 2.0 * ca1 * x / (idat.r2) - cb1 x * z / r3,
228			-2.0 * ca1 * x2 * y / r4 - cb1 * z * y / r3,
229			-2.0 * ca1 * x2 * z / r4 + cb1 / (idat.rij) - cb1 z2 / r3);
230
231	gezelter	1532	// chain rule to put these back on x, y, z
232
233			Vector3d dvdr = Vang * dVmorsedr + Vmorse * dVangdr;
234
235			// Torques for Vang using method of Price:
236			// S. L. Price, A. J. Stone, and M. Alderton, Mol. Phys. 52, 987 (1984).
237
238	gezelter	1554	Vector3d dVangdu = Vector3d(cb1 * y / *(idat.rij) ,
239			2.0 * ca1 * x * z / (idat.r2) - cb1 x / *(idat.rij),
240			-2.0 * ca1 * y * x / *(idat.r2));
241	gezelter	1532
242			// do the torques first since they are easy:
243			// remember that these are still in the body fixed axes
244
245	gezelter	1554	Vector3d trq = (idat.vdwMult) Vmorse * dVangdu * *(idat.sw);
246	gezelter	1532
247			// go back to lab frame using transpose of rotation matrix:
248
249			if (j_is_Metal) {
250	gezelter	1554	(idat.t1) += Atrans trq;
251	gezelter	1532	} else {
252	gezelter	1554	(idat.t2) += Atrans trq;
253	gezelter	1532	}
254
255			// Now, on to the forces (still in body frame of water)
256
257	gezelter	1554	Vector3d ftmp = (idat.vdwMult) (idat.sw) dvdr;
258	gezelter	1532
259			// rotate the terms back into the lab frame:
260			Vector3d flab;
261			if (j_is_Metal) {
262			flab = Atrans * ftmp;
263			} else {
264			flab = - Atrans * ftmp;
265			}
266
267	gezelter	1554	*(idat.f1) += flab;
268	gezelter	1532	}
269			return;
270
271			}
272
273	gezelter	1545	RealType MAW::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
274	gezelter	1532	if (!initialized_) initialize();
275			map<pair<AtomType, AtomType>, MAWInteractionData>::iterator it;
276	gezelter	1545	it = MixingMap.find(atypes);
277	gezelter	1532	if (it == MixingMap.end())
278			return 0.0;
279			else {
280			MAWInteractionData mixer = (*it).second;
281
282			RealType R_e = mixer.Re;
283			RealType beta = mixer.beta;
284			// This value of the r corresponds to an energy about 1.48% of
285			// the energy at the bottom of the Morse well. For comparison, the
286			// Lennard-Jones function is about 1.63% of it's minimum value at
287			// a distance of 2.5 sigma.
288			return (4.9 + beta * R_e) / beta;
289			}
290			}
291			}
292