src/nonbonded/Sticky.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/Sticky.hpp"
#include "nonbonded/LJ.hpp"
#include "types/StickyAdapter.hpp"
#include "utils/simError.h"

using namespace std;
namespace OpenMD {
  
  Sticky::Sticky() : name_("Sticky"), initialized_(false), forceField_(NULL) {}
    
  void Sticky::initialize() {    
    
    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
    ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
    ForceField::AtomTypeContainer::MapTypeIterator i;
    AtomType* at;

    // Sticky handles all of the Sticky-Sticky interactions

    for (at = atomTypes->beginType(i); at != NULL;
         at = atomTypes->nextType(i)) {
      
      StickyAdapter sa = StickyAdapter(at);
      if (sa.isSticky()) addType(at);
    }
    
    initialized_ = true;
  }
      
  void Sticky::addType(AtomType* atomType){
    // add it to the map:
    
    pair<map<int,AtomType*>::iterator,bool> ret;    
    ret = StickyMap.insert( pair<int, AtomType*>(atomType->getIdent(), 
                                                 atomType) );
    if (ret.second == false) {
      sprintf( painCave.errMsg,
               "Sticky already had a previous entry with ident %d\n",
               atomType->getIdent() );
      painCave.severity = OPENMD_INFO;
      painCave.isFatal = 0;
      simError();         
    }   
    
    StickyAdapter sticky1 = StickyAdapter(atomType);

    // Now, iterate over all known types and add to the mixing map:
    
    map<int, AtomType*>::iterator it;
    for( it = StickyMap.begin(); it != StickyMap.end(); ++it) {
      
      AtomType* atype2 = (*it).second;
      
      StickyAdapter sticky2 = StickyAdapter(atype2);

      StickyInteractionData mixer;        
           
      // Mixing two different sticky types is silly, but if you want 2
      // sticky types in your simulation, we'll let you do it with the
      // Lorentz- Berthelot mixing rules (which happen to do the right thing 
      // when atomType and atype2 happen to be the same.
      
      mixer.rl   = 0.5 * ( sticky1.getRl() + sticky2.getRl() );
      mixer.ru   = 0.5 * ( sticky1.getRu() + sticky2.getRu() );
      mixer.rlp  = 0.5 * ( sticky1.getRlp() + sticky2.getRlp() );
      mixer.rup  = 0.5 * ( sticky1.getRup() + sticky2.getRup() );
      mixer.rbig = max(mixer.ru, mixer.rup);
      mixer.w0  = sqrt( sticky1.getW0()   * sticky2.getW0()  );
      mixer.v0  = sqrt( sticky1.getV0()   * sticky2.getV0()  );
      mixer.v0p = sqrt( sticky1.getV0p()  * sticky2.getV0p() );
      mixer.isPower = sticky1.isStickyPower() && sticky2.isStickyPower();

      CubicSpline* s = new CubicSpline();
      s->addPoint(mixer.rl, 1.0);
      s->addPoint(mixer.ru, 0.0);
      mixer.s = s;

      CubicSpline* sp = new CubicSpline();
      sp->addPoint(mixer.rlp, 1.0);
      sp->addPoint(mixer.rup, 0.0);
      mixer.sp = sp;

      
      pair<AtomType*, AtomType*> key1, key2;
      key1 = make_pair(atomType, atype2);
      key2 = make_pair(atype2, atomType);
      
      MixingMap[key1] = mixer;
      if (key2 != key1) {
        MixingMap[key2] = mixer;
      }
    }
  }

  /**
   * This function does the sticky portion of the SSD potential
   * [Chandra and Ichiye, Journal of Chemical Physics 111, 2701
   * (1999)].  The Lennard-Jones and dipolar interaction must be
   * handled separately.  We assume that the rotation matrices have
   * already been calculated and placed in the A1 & A2 entries in the
   * idat structure.
   */
  
  void Sticky::calcForce(InteractionData &idat) {
   
    if (!initialized_) initialize();
    
    map<pair<AtomType*, AtomType*>, StickyInteractionData>::iterator it;
    it = MixingMap.find(idat.atypes);
    if (it != MixingMap.end()) {

      StickyInteractionData mixer = (*it).second;
      
      RealType w0  = mixer.w0;
      RealType v0  = mixer.v0; 
      RealType v0p = mixer.v0p;
      RealType rl  = mixer.rl; 
      RealType ru  = mixer.ru; 
      RealType rlp = mixer.rlp;
      RealType rup = mixer.rup;
      RealType rbig = mixer.rbig;
      bool isPower = mixer.isPower;
      
      cerr << rl << " " << ru << " " << rlp << " " << rup << " " << rbig << " " << w0 << " " << v0 << " " << v0p << "\n";
      if ( *(idat.rij) <= rbig) {
        
        RealType r3 = *(idat.r2) * *(idat.rij);
        RealType r5 = r3 * *(idat.r2);
        
        RotMat3x3d A1trans = idat.A1->transpose();
        RotMat3x3d A2trans = idat.A2->transpose();
        
        // rotate the inter-particle separation into the two different
        // body-fixed coordinate systems:
        
        Vector3d ri = *(idat.A1) * *(idat.d);
        
        // negative sign because this is the vector from j to i:
        
        Vector3d rj = - *(idat.A2) * *(idat.d);
        
        RealType xi = ri.x();
        RealType yi = ri.y();
        RealType zi = ri.z();
        
        RealType xj = rj.x();
        RealType yj = rj.y();
        RealType zj = rj.z();
        
        RealType xi2 = xi * xi;
        RealType yi2 = yi * yi;
        RealType zi2 = zi * zi;
        
        RealType xj2 = xj * xj;
        RealType yj2 = yj * yj;
        RealType zj2 = zj * zj;     
        
        // calculate the switching info. from the splines
        
        RealType s = 0.0;
        RealType dsdr = 0.0;
        RealType sp = 0.0;
        RealType dspdr = 0.0;
        
        if ( *(idat.rij) < ru) {
          if ( *(idat.rij) < rl) {
            s = 1.0;
            dsdr = 0.0;
          } else {          
            // we are in the switching region 
            
            pair<RealType, RealType> res = mixer.s->getValueAndDerivativeAt(*(idat.rij));
            s = res.first;
            dsdr = res.second;
          }
        }
        
        if (*(idat.rij) < rup) {
          if ( *(idat.rij) < rlp) {
            sp = 1.0;
            dspdr = 0.0;
          } else {
            // we are in the switching region 
            
            pair<RealType, RealType> res =mixer.sp->getValueAndDerivativeAt( *(idat.rij));
            sp = res.first;
            dspdr = res.second;
          }
        }
        

        RealType wi = 2.0*(xi2-yi2)*zi / r3;
        RealType wj = 2.0*(xj2-yj2)*zj / r3;
        RealType w = wi+wj;
        
        
        RealType zif = zi/ *(idat.rij)  - 0.6;
        RealType zis = zi/ *(idat.rij)  + 0.8;
        
        RealType zjf = zj/ *(idat.rij)  - 0.6;
        RealType zjs = zj/ *(idat.rij)  + 0.8;
        
        RealType wip = zif*zif*zis*zis - w0;
        RealType wjp = zjf*zjf*zjs*zjs - w0;
        RealType wp = wip + wjp;
        
        Vector3d dwi(4.0*xi*zi/r3  - 6.0*xi*zi*(xi2-yi2)/r5, 
                     - 4.0*yi*zi/r3  - 6.0*yi*zi*(xi2-yi2)/r5,
                     2.0*(xi2-yi2)/r3  - 6.0*zi2*(xi2-yi2)/r5);
        
        Vector3d dwj(4.0*xj*zj/r3  - 6.0*xj*zj*(xj2-yj2)/r5,
                     - 4.0*yj*zj/r3  - 6.0*yj*zj*(xj2-yj2)/r5,
                     2.0*(xj2-yj2)/r3  - 6.0*zj2*(xj2-yj2)/r5);
        
        RealType uglyi = zif*zif*zis + zif*zis*zis;
        RealType uglyj = zjf*zjf*zjs + zjf*zjs*zjs;

        Vector3d dwip(-2.0*xi*zi*uglyi/r3, 
                      -2.0*yi*zi*uglyi/r3,
                      2.0*(1.0/ *(idat.rij)  - zi2/r3)*uglyi);
        
        Vector3d dwjp(-2.0*xj*zj*uglyj/r3,
                      -2.0*yj*zj*uglyj/r3,
                      2.0*(1.0/ *(idat.rij)  - zj2/r3)*uglyj);
        
        Vector3d dwidu(4.0*(yi*zi2 + 0.5*yi*(xi2-yi2))/r3,
                       4.0*(xi*zi2 - 0.5*xi*(xi2-yi2))/r3,
                       - 8.0*xi*yi*zi/r3);
        
        Vector3d dwjdu(4.0*(yj*zj2 + 0.5*yj*(xj2-yj2))/r3,
                       4.0*(xj*zj2 - 0.5*xj*(xj2-yj2))/r3,
                       - 8.0*xj*yj*zj/r3);
        
        Vector3d dwipdu(2.0*yi*uglyi/ *(idat.rij) ,
                        -2.0*xi*uglyi/ *(idat.rij) ,
                        0.0);
        
        Vector3d dwjpdu(2.0*yj*uglyj/ *(idat.rij) ,
                        -2.0*xj*uglyj/ *(idat.rij) ,
                        0.0);
        
        if (isPower) {
          cerr << "This is probably an error!\n";
          RealType frac1 = 0.25;
          RealType frac2 = 0.75;      
          RealType wi2 = wi*wi;
          RealType wj2 = wj*wj;
          // sticky power has no w' function:
          w = frac1 * wi * wi2 + frac2*wi + frac1*wj*wj2 + frac2*wj + v0p; 
          wp = 0.0;
          dwi = frac1*RealType(3.0)*wi2*dwi + frac2*dwi;
          dwj = frac1*RealType(3.0)*wj2*dwi + frac2*dwi;
          dwip = V3Zero;
          dwjp = V3Zero;
          dwidu = frac1*RealType(3.0)*wi2*dwidu + frac2*dwidu;
          dwidu = frac1*RealType(3.0)*wj2*dwjdu + frac2*dwjdu;
          dwipdu = V3Zero;
          dwjpdu = V3Zero;
          sp = 0.0;
          dspdr = 0.0;
        }
        
        *(idat.vpair) += RealType(0.5)*(v0*s*w + v0p*sp*wp);
        (*(idat.pot))[HYDROGENBONDING_FAMILY] += RealType(0.5)*(v0*s*w + v0p*sp*wp)* *(idat.sw) ;
        
        // do the torques first since they are easy:
        // remember that these are still in the body-fixed axes
        
        Vector3d ti = RealType(0.5)* *(idat.sw) *(v0*s*dwidu + v0p*sp*dwipdu);
        Vector3d tj = RealType(0.5)* *(idat.sw) *(v0*s*dwjdu + v0p*sp*dwjpdu);
        
        // go back to lab frame using transpose of rotation matrix:
        
        *(idat.t1) += A1trans * ti;
        *(idat.t2) += A2trans * tj;
        
        // Now, on to the forces:
        
        // first rotate the i terms back into the lab frame:
        
        Vector3d radcomi = (v0 * s * dwi + v0p * sp * dwip) *  *(idat.sw);
        Vector3d radcomj = (v0 * s * dwj + v0p * sp * dwjp) *  *(idat.sw);
        
        Vector3d fii = A1trans * radcomi;
        Vector3d fjj = A2trans * radcomj;
        
        // now assemble these with the radial-only terms:
       
        *(idat.f1) += RealType(0.5) * ((v0*dsdr*w + v0p*dspdr*wp) * *(idat.d) / 
                                       *(idat.rij)  + fii - fjj);
        
      }
    }
    
    return;      
  }

  RealType Sticky::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) {
    if (!initialized_) initialize();   
    map<pair<AtomType*, AtomType*>, StickyInteractionData>::iterator it;
    it = MixingMap.find(atypes);
    if (it == MixingMap.end()) 
      return 0.0;
    else  {
      StickyInteractionData mixer = (*it).second;
      return mixer.rbig;
    }
  }
}
Revision:	1834
Committed:	Tue Jan 15 16:28:42 2013 UTC (12 years, 6 months ago) by gezelter
File size:	12648 byte(s)
Log Message:	Bug fix in Sticky potential, label in stats
#	User	Rev	Content
1	gezelter	1485	/*
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	1485	*/
42
43			#include <stdio.h>
44			#include <string.h>
45
46			#include <cmath>
47			#include "nonbonded/Sticky.hpp"
48			#include "nonbonded/LJ.hpp"
49	gezelter	1710	#include "types/StickyAdapter.hpp"
50	gezelter	1485	#include "utils/simError.h"
51
52			using namespace std;
53			namespace OpenMD {
54
55	gezelter	1502	Sticky::Sticky() : name_("Sticky"), initialized_(false), forceField_(NULL) {}
56	gezelter	1485
57			void Sticky::initialize() {
58
59			ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
60			ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
61			ForceField::AtomTypeContainer::MapTypeIterator i;
62			AtomType* at;
63
64			// Sticky handles all of the Sticky-Sticky interactions
65
66			for (at = atomTypes->beginType(i); at != NULL;
67			at = atomTypes->nextType(i)) {
68
69	gezelter	1710	StickyAdapter sa = StickyAdapter(at);
70			if (sa.isSticky()) addType(at);
71	gezelter	1485	}
72
73			initialized_ = true;
74			}
75
76			void Sticky::addType(AtomType* atomType){
77			// add it to the map:
78
79			pair<map<int,AtomType*>::iterator,bool> ret;
80	gezelter	1710	ret = StickyMap.insert( pair<int, AtomType*>(atomType->getIdent(),
81			atomType) );
82	gezelter	1485	if (ret.second == false) {
83			sprintf( painCave.errMsg,
84			"Sticky already had a previous entry with ident %d\n",
85	gezelter	1710	atomType->getIdent() );
86	gezelter	1485	painCave.severity = OPENMD_INFO;
87			painCave.isFatal = 0;
88			simError();
89	gezelter	1767	}
90	gezelter	1485
91	gezelter	1710	StickyAdapter sticky1 = StickyAdapter(atomType);
92	gezelter	1485
93			// Now, iterate over all known types and add to the mixing map:
94
95			map<int, AtomType*>::iterator it;
96			for( it = StickyMap.begin(); it != StickyMap.end(); ++it) {
97
98			AtomType* atype2 = (*it).second;
99	gezelter	1710
100			StickyAdapter sticky2 = StickyAdapter(atype2);
101	gezelter	1485
102			StickyInteractionData mixer;
103
104			// Mixing two different sticky types is silly, but if you want 2
105			// sticky types in your simulation, we'll let you do it with the
106			// Lorentz- Berthelot mixing rules (which happen to do the right thing
107			// when atomType and atype2 happen to be the same.
108
109	gezelter	1710	mixer.rl = 0.5 * ( sticky1.getRl() + sticky2.getRl() );
110			mixer.ru = 0.5 * ( sticky1.getRu() + sticky2.getRu() );
111			mixer.rlp = 0.5 * ( sticky1.getRlp() + sticky2.getRlp() );
112			mixer.rup = 0.5 * ( sticky1.getRup() + sticky2.getRup() );
113	gezelter	1485	mixer.rbig = max(mixer.ru, mixer.rup);
114	gezelter	1710	mixer.w0 = sqrt( sticky1.getW0() * sticky2.getW0() );
115	gezelter	1834	mixer.v0 = sqrt( sticky1.getV0() * sticky2.getV0() );
116	gezelter	1710	mixer.v0p = sqrt( sticky1.getV0p() * sticky2.getV0p() );
117			mixer.isPower = sticky1.isStickyPower() && sticky2.isStickyPower();
118	gezelter	1485
119			CubicSpline* s = new CubicSpline();
120			s->addPoint(mixer.rl, 1.0);
121			s->addPoint(mixer.ru, 0.0);
122			mixer.s = s;
123
124			CubicSpline* sp = new CubicSpline();
125			sp->addPoint(mixer.rlp, 1.0);
126			sp->addPoint(mixer.rup, 0.0);
127			mixer.sp = sp;
128
129
130			pair<AtomType, AtomType> key1, key2;
131			key1 = make_pair(atomType, atype2);
132			key2 = make_pair(atype2, atomType);
133
134			MixingMap[key1] = mixer;
135			if (key2 != key1) {
136			MixingMap[key2] = mixer;
137			}
138			}
139			}
140
141	gezelter	1502	/**
142			* This function does the sticky portion of the SSD potential
143			* [Chandra and Ichiye, Journal of Chemical Physics 111, 2701
144			* (1999)]. The Lennard-Jones and dipolar interaction must be
145			* handled separately. We assume that the rotation matrices have
146			* already been calculated and placed in the A1 & A2 entries in the
147			* idat structure.
148			*/
149
150	gezelter	1536	void Sticky::calcForce(InteractionData &idat) {
151	gezelter	1502
152	gezelter	1485	if (!initialized_) initialize();
153
154	gezelter	1505	map<pair<AtomType, AtomType>, StickyInteractionData>::iterator it;
155	gezelter	1571	it = MixingMap.find(idat.atypes);
156	gezelter	1505	if (it != MixingMap.end()) {
157	gezelter	1485
158	gezelter	1505	StickyInteractionData mixer = (*it).second;
159
160			RealType w0 = mixer.w0;
161			RealType v0 = mixer.v0;
162			RealType v0p = mixer.v0p;
163			RealType rl = mixer.rl;
164			RealType ru = mixer.ru;
165			RealType rlp = mixer.rlp;
166			RealType rup = mixer.rup;
167			RealType rbig = mixer.rbig;
168			bool isPower = mixer.isPower;
169
170	gezelter	1834	cerr << rl << " " << ru << " " << rlp << " " << rup << " " << rbig << " " << w0 << " " << v0 << " " << v0p << "\n";
171	gezelter	1554	if ( *(idat.rij) <= rbig) {
172	gezelter	1505
173	gezelter	1554	RealType r3 = (idat.r2) *(idat.rij);
174			RealType r5 = r3 * *(idat.r2);
175	gezelter	1505
176	gezelter	1554	RotMat3x3d A1trans = idat.A1->transpose();
177			RotMat3x3d A2trans = idat.A2->transpose();
178	gezelter	1505
179			// rotate the inter-particle separation into the two different
180			// body-fixed coordinate systems:
181
182	gezelter	1554	Vector3d ri = (idat.A1) *(idat.d);
183	gezelter	1505
184			// negative sign because this is the vector from j to i:
185
186	gezelter	1554	Vector3d rj = - (idat.A2) *(idat.d);
187	gezelter	1505
188			RealType xi = ri.x();
189			RealType yi = ri.y();
190			RealType zi = ri.z();
191
192			RealType xj = rj.x();
193			RealType yj = rj.y();
194			RealType zj = rj.z();
195
196			RealType xi2 = xi * xi;
197			RealType yi2 = yi * yi;
198			RealType zi2 = zi * zi;
199
200			RealType xj2 = xj * xj;
201			RealType yj2 = yj * yj;
202			RealType zj2 = zj * zj;
203
204			// calculate the switching info. from the splines
205
206			RealType s = 0.0;
207			RealType dsdr = 0.0;
208			RealType sp = 0.0;
209			RealType dspdr = 0.0;
210
211	gezelter	1554	if ( *(idat.rij) < ru) {
212			if ( *(idat.rij) < rl) {
213	gezelter	1505	s = 1.0;
214			dsdr = 0.0;
215			} else {
216			// we are in the switching region
217
218	gezelter	1554	pair<RealType, RealType> res = mixer.s->getValueAndDerivativeAt(*(idat.rij));
219	gezelter	1505	s = res.first;
220			dsdr = res.second;
221			}
222	gezelter	1485	}
223	gezelter	1505
224	gezelter	1554	if (*(idat.rij) < rup) {
225			if ( *(idat.rij) < rlp) {
226	gezelter	1505	sp = 1.0;
227			dspdr = 0.0;
228			} else {
229			// we are in the switching region
230
231	gezelter	1554	pair<RealType, RealType> res =mixer.sp->getValueAndDerivativeAt( *(idat.rij));
232	gezelter	1505	sp = res.first;
233			dspdr = res.second;
234			}
235			}
236
237	gezelter	1834
238	gezelter	1505	RealType wi = 2.0(xi2-yi2)zi / r3;
239			RealType wj = 2.0(xj2-yj2)zj / r3;
240			RealType w = wi+wj;
241
242
243	gezelter	1554	RealType zif = zi/ *(idat.rij) - 0.6;
244			RealType zis = zi/ *(idat.rij) + 0.8;
245	gezelter	1505
246	gezelter	1554	RealType zjf = zj/ *(idat.rij) - 0.6;
247			RealType zjs = zj/ *(idat.rij) + 0.8;
248	gezelter	1505
249			RealType wip = zifzifzis*zis - w0;
250			RealType wjp = zjfzjfzjs*zjs - w0;
251			RealType wp = wip + wjp;
252
253			Vector3d dwi(4.0xizi/r3 - 6.0xizi*(xi2-yi2)/r5,
254			- 4.0yizi/r3 - 6.0yizi*(xi2-yi2)/r5,
255			2.0(xi2-yi2)/r3 - 6.0zi2*(xi2-yi2)/r5);
256
257			Vector3d dwj(4.0xjzj/r3 - 6.0xjzj*(xj2-yj2)/r5,
258			- 4.0yjzj/r3 - 6.0yjzj*(xj2-yj2)/r5,
259			2.0(xj2-yj2)/r3 - 6.0zj2*(xj2-yj2)/r5);
260
261			RealType uglyi = zifzifzis + zifziszis;
262			RealType uglyj = zjfzjfzjs + zjfzjszjs;
263	gezelter	1485
264	gezelter	1505	Vector3d dwip(-2.0xizi*uglyi/r3,
265			-2.0yizi*uglyi/r3,
266	gezelter	1554	2.0(1.0/ (idat.rij) - zi2/r3)*uglyi);
267	gezelter	1505
268			Vector3d dwjp(-2.0xjzj*uglyj/r3,
269			-2.0yjzj*uglyj/r3,
270	gezelter	1554	2.0(1.0/ (idat.rij) - zj2/r3)*uglyj);
271	gezelter	1505
272			Vector3d dwidu(4.0(yizi2 + 0.5yi(xi2-yi2))/r3,
273			4.0(xizi2 - 0.5xi(xi2-yi2))/r3,
274			- 8.0xiyi*zi/r3);
275
276			Vector3d dwjdu(4.0(yjzj2 + 0.5yj(xj2-yj2))/r3,
277			4.0(xjzj2 - 0.5xj(xj2-yj2))/r3,
278			- 8.0xjyj*zj/r3);
279
280	gezelter	1554	Vector3d dwipdu(2.0yiuglyi/ *(idat.rij) ,
281			-2.0xiuglyi/ *(idat.rij) ,
282	gezelter	1505	0.0);
283
284	gezelter	1554	Vector3d dwjpdu(2.0yjuglyj/ *(idat.rij) ,
285			-2.0xjuglyj/ *(idat.rij) ,
286	gezelter	1505	0.0);
287
288			if (isPower) {
289	gezelter	1834	cerr << "This is probably an error!\n";
290	gezelter	1505	RealType frac1 = 0.25;
291			RealType frac2 = 0.75;
292			RealType wi2 = wi*wi;
293			RealType wj2 = wj*wj;
294			// sticky power has no w' function:
295			w = frac1 * wi * wi2 + frac2wi + frac1wjwj2 + frac2wj + v0p;
296			wp = 0.0;
297	gezelter	1668	dwi = frac1RealType(3.0)wi2dwi + frac2dwi;
298			dwj = frac1RealType(3.0)wj2dwi + frac2dwi;
299	gezelter	1505	dwip = V3Zero;
300			dwjp = V3Zero;
301	gezelter	1668	dwidu = frac1RealType(3.0)wi2dwidu + frac2dwidu;
302			dwidu = frac1RealType(3.0)wj2dwjdu + frac2dwjdu;
303	gezelter	1505	dwipdu = V3Zero;
304			dwjpdu = V3Zero;
305			sp = 0.0;
306	gezelter	1485	dspdr = 0.0;
307			}
308	gezelter	1505
309	gezelter	1668	(idat.vpair) += RealType(0.5)(v0sw + v0pspwp);
310			((idat.pot))[HYDROGENBONDING_FAMILY] += RealType(0.5)(v0sw + v0pspwp)* *(idat.sw) ;
311	gezelter	1505
312			// do the torques first since they are easy:
313			// remember that these are still in the body-fixed axes
314
315	gezelter	1668	Vector3d ti = RealType(0.5)* (idat.sw) (v0sdwidu + v0pspdwipdu);
316			Vector3d tj = RealType(0.5)* (idat.sw) (v0sdwjdu + v0pspdwjpdu);
317	gezelter	1505
318			// go back to lab frame using transpose of rotation matrix:
319
320	gezelter	1554	(idat.t1) += A1trans ti;
321			(idat.t2) += A2trans tj;
322	gezelter	1505
323			// Now, on to the forces:
324
325			// first rotate the i terms back into the lab frame:
326
327	gezelter	1554	Vector3d radcomi = (v0 * s * dwi + v0p * sp * dwip) * *(idat.sw);
328			Vector3d radcomj = (v0 * s * dwj + v0p * sp * dwjp) * *(idat.sw);
329	gezelter	1505
330			Vector3d fii = A1trans * radcomi;
331			Vector3d fjj = A2trans * radcomj;
332
333			// now assemble these with the radial-only terms:
334	gezelter	1834
335	gezelter	1668	(idat.f1) += RealType(0.5) ((v0dsdrw + v0pdspdrwp) * *(idat.d) /
336			*(idat.rij) + fii - fjj);
337	gezelter	1505
338	gezelter	1485	}
339			}
340
341	gezelter	1505	return;
342	gezelter	1485	}
343	gezelter	1505
344	gezelter	1545	RealType Sticky::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
345	gezelter	1505	if (!initialized_) initialize();
346			map<pair<AtomType, AtomType>, StickyInteractionData>::iterator it;
347	gezelter	1545	it = MixingMap.find(atypes);
348	gezelter	1505	if (it == MixingMap.end())
349			return 0.0;
350			else {
351			StickyInteractionData mixer = (*it).second;
352			return mixer.rbig;
353			}
354			}
355	gezelter	1485	}