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

using namespace std;
namespace OpenMD {
  
  Sticky::Sticky() : initialized_(false), forceField_(NULL), name_("Sticky") {}
    
  void Sticky::initialize() {    
    Stypes.clear();
    Stids.clear();
    MixingMap.clear();
    nSticky_=0;

    Stids.resize( forceField_->getNAtomType(), -1);

    // Sticky handles all of the Sticky-Sticky interactions

    set<AtomType*>::iterator at;
    for (at = simTypes_.begin(); at != simTypes_.end(); ++at) {
      if ((*at)->isSticky()) nSticky_++;
    }

    MixingMap.resize(nSticky_);

    for (at = simTypes_.begin(); at != simTypes_.end(); ++at) {
      if ((*at)->isSticky()) addType( *at );
    }
    
    initialized_ = true;
  }
      
  void Sticky::addType(AtomType* atomType){
    StickyAdapter sticky1 = StickyAdapter(atomType);

    // add it to the map:
    
    int atid = atomType->getIdent();
    int stid = Stypes.size();
  
    pair<set<int>::iterator,bool> ret;    
    ret = Stypes.insert( atid );
    if (ret.second == false) {
      sprintf( painCave.errMsg,
               "Sticky already had a previous entry with ident %d\n",
               atid) ;
      painCave.severity = OPENMD_INFO;
      painCave.isFatal = 0;
      simError();         
    }

    Stids[atid] = stid;
    MixingMap[stid].resize( nSticky_ );    


    // Now, iterate over all known types and add to the mixing map:
    
    std::set<int>::iterator it; 
    for( it = Stypes.begin(); it != Stypes.end(); ++it) {
      

      int stid2 = Stids[ (*it) ];
      AtomType* atype2 = forceField_->getAtomType( (*it) );
      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;

      MixingMap[stid2].resize( nSticky_ );

      MixingMap[stid][stid2] = mixer;
      if (stid2 != stid) {
        MixingMap[stid2][stid] = 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();
    
    StickyInteractionData &mixer = MixingMap[Stids[idat.atid1]][Stids[idat.atid2]];
    
    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;
    
    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           
          mixer.s->getValueAndDerivativeAt(*(idat.rij), s, dsdr);
        }
      }
      
      if (*(idat.rij) < rup) {
        if ( *(idat.rij) < rlp) {
          sp = 1.0;
          dspdr = 0.0;
        } else {
          // we are in the switching region           
          mixer.sp->getValueAndDerivativeAt( *(idat.rij), sp, dspdr);
        }
      }
      
      
      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();   
    int atid1 = atypes.first->getIdent();
    int atid2 = atypes.second->getIdent();
    int stid1 = Stids[atid1];
    int stid2 = Stids[atid2];
    
    if (stid1 == -1 || stid2 == -1) return 0.0;
    else {      
      return MixingMap[stid1][stid2].rbig;
    }
  }
}
Revision:	2071
Committed:	Sat Mar 7 21:41:51 2015 UTC (10 years, 2 months ago) by gezelter
File size:	11924 byte(s)
Log Message:	Reducing the number of warnings when using g++ to compile.
#	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/Sticky.hpp"
48	#include "nonbonded/LJ.hpp"
49	#include "types/StickyAdapter.hpp"
50	#include "utils/simError.h"
51
52	using namespace std;
53	namespace OpenMD {
54
55	Sticky::Sticky() : initialized_(false), forceField_(NULL), name_("Sticky") {}
56
57	void Sticky::initialize() {
58	Stypes.clear();
59	Stids.clear();
60	MixingMap.clear();
61	nSticky_=0;
62
63	Stids.resize( forceField_->getNAtomType(), -1);
64
65	// Sticky handles all of the Sticky-Sticky interactions
66
67	set<AtomType*>::iterator at;
68	for (at = simTypes_.begin(); at != simTypes_.end(); ++at) {
69	if ((*at)->isSticky()) nSticky_++;
70	}
71
72	MixingMap.resize(nSticky_);
73
74	for (at = simTypes_.begin(); at != simTypes_.end(); ++at) {
75	if ((at)->isSticky()) addType( at );
76	}
77
78	initialized_ = true;
79	}
80
81	void Sticky::addType(AtomType* atomType){
82	StickyAdapter sticky1 = StickyAdapter(atomType);
83
84	// add it to the map:
85
86	int atid = atomType->getIdent();
87	int stid = Stypes.size();
88
89	pair<set<int>::iterator,bool> ret;
90	ret = Stypes.insert( atid );
91	if (ret.second == false) {
92	sprintf( painCave.errMsg,
93	"Sticky already had a previous entry with ident %d\n",
94	atid) ;
95	painCave.severity = OPENMD_INFO;
96	painCave.isFatal = 0;
97	simError();
98	}
99
100	Stids[atid] = stid;
101	MixingMap[stid].resize( nSticky_ );
102
103
104	// Now, iterate over all known types and add to the mixing map:
105
106	std::set<int>::iterator it;
107	for( it = Stypes.begin(); it != Stypes.end(); ++it) {
108
109
110	int stid2 = Stids[ (*it) ];
111	AtomType* atype2 = forceField_->getAtomType( (*it) );
112	StickyAdapter sticky2 = StickyAdapter(atype2);
113
114	StickyInteractionData mixer;
115
116	// Mixing two different sticky types is silly, but if you want 2
117	// sticky types in your simulation, we'll let you do it with the
118	// Lorentz- Berthelot mixing rules (which happen to do the right thing
119	// when atomType and atype2 happen to be the same.
120
121	mixer.rl = 0.5 * ( sticky1.getRl() + sticky2.getRl() );
122	mixer.ru = 0.5 * ( sticky1.getRu() + sticky2.getRu() );
123	mixer.rlp = 0.5 * ( sticky1.getRlp() + sticky2.getRlp() );
124	mixer.rup = 0.5 * ( sticky1.getRup() + sticky2.getRup() );
125	mixer.rbig = max(mixer.ru, mixer.rup);
126	mixer.w0 = sqrt( sticky1.getW0() * sticky2.getW0() );
127	mixer.v0 = sqrt( sticky1.getV0() * sticky2.getV0() );
128	mixer.v0p = sqrt( sticky1.getV0p() * sticky2.getV0p() );
129	mixer.isPower = sticky1.isStickyPower() && sticky2.isStickyPower();
130
131	CubicSpline* s = new CubicSpline();
132	s->addPoint(mixer.rl, 1.0);
133	s->addPoint(mixer.ru, 0.0);
134	mixer.s = s;
135
136	CubicSpline* sp = new CubicSpline();
137	sp->addPoint(mixer.rlp, 1.0);
138	sp->addPoint(mixer.rup, 0.0);
139	mixer.sp = sp;
140
141	MixingMap[stid2].resize( nSticky_ );
142
143	MixingMap[stid][stid2] = mixer;
144	if (stid2 != stid) {
145	MixingMap[stid2][stid] = mixer;
146	}
147	}
148	}
149
150	/**
151	* This function does the sticky portion of the SSD potential
152	* [Chandra and Ichiye, Journal of Chemical Physics 111, 2701
153	* (1999)]. The Lennard-Jones and dipolar interaction must be
154	* handled separately. We assume that the rotation matrices have
155	* already been calculated and placed in the A1 & A2 entries in the
156	* idat structure.
157	*/
158
159	void Sticky::calcForce(InteractionData &idat) {
160
161	if (!initialized_) initialize();
162
163	StickyInteractionData &mixer = MixingMap[Stids[idat.atid1]][Stids[idat.atid2]];
164
165	RealType w0 = mixer.w0;
166	RealType v0 = mixer.v0;
167	RealType v0p = mixer.v0p;
168	RealType rl = mixer.rl;
169	RealType ru = mixer.ru;
170	RealType rlp = mixer.rlp;
171	RealType rup = mixer.rup;
172	RealType rbig = mixer.rbig;
173	bool isPower = mixer.isPower;
174
175	if ( *(idat.rij) <= rbig) {
176
177	RealType r3 = (idat.r2) *(idat.rij);
178	RealType r5 = r3 * *(idat.r2);
179
180	RotMat3x3d A1trans = idat.A1->transpose();
181	RotMat3x3d A2trans = idat.A2->transpose();
182
183	// rotate the inter-particle separation into the two different
184	// body-fixed coordinate systems:
185
186	Vector3d ri = (idat.A1) *(idat.d);
187
188	// negative sign because this is the vector from j to i:
189
190	Vector3d rj = - (idat.A2) *(idat.d);
191
192	RealType xi = ri.x();
193	RealType yi = ri.y();
194	RealType zi = ri.z();
195
196	RealType xj = rj.x();
197	RealType yj = rj.y();
198	RealType zj = rj.z();
199
200	RealType xi2 = xi * xi;
201	RealType yi2 = yi * yi;
202	RealType zi2 = zi * zi;
203
204	RealType xj2 = xj * xj;
205	RealType yj2 = yj * yj;
206	RealType zj2 = zj * zj;
207
208	// calculate the switching info. from the splines
209
210	RealType s = 0.0;
211	RealType dsdr = 0.0;
212	RealType sp = 0.0;
213	RealType dspdr = 0.0;
214
215	if ( *(idat.rij) < ru) {
216	if ( *(idat.rij) < rl) {
217	s = 1.0;
218	dsdr = 0.0;
219	} else {
220	// we are in the switching region
221	mixer.s->getValueAndDerivativeAt(*(idat.rij), s, dsdr);
222	}
223	}
224
225	if (*(idat.rij) < rup) {
226	if ( *(idat.rij) < rlp) {
227	sp = 1.0;
228	dspdr = 0.0;
229	} else {
230	// we are in the switching region
231	mixer.sp->getValueAndDerivativeAt( *(idat.rij), sp, dspdr);
232	}
233	}
234
235
236	RealType wi = 2.0(xi2-yi2)zi / r3;
237	RealType wj = 2.0(xj2-yj2)zj / r3;
238	RealType w = wi+wj;
239
240
241	RealType zif = zi/ *(idat.rij) - 0.6;
242	RealType zis = zi/ *(idat.rij) + 0.8;
243
244	RealType zjf = zj/ *(idat.rij) - 0.6;
245	RealType zjs = zj/ *(idat.rij) + 0.8;
246
247	RealType wip = zifzifzis*zis - w0;
248	RealType wjp = zjfzjfzjs*zjs - w0;
249	RealType wp = wip + wjp;
250
251	Vector3d dwi(4.0xizi/r3 - 6.0xizi*(xi2-yi2)/r5,
252	- 4.0yizi/r3 - 6.0yizi*(xi2-yi2)/r5,
253	2.0(xi2-yi2)/r3 - 6.0zi2*(xi2-yi2)/r5);
254
255	Vector3d dwj(4.0xjzj/r3 - 6.0xjzj*(xj2-yj2)/r5,
256	- 4.0yjzj/r3 - 6.0yjzj*(xj2-yj2)/r5,
257	2.0(xj2-yj2)/r3 - 6.0zj2*(xj2-yj2)/r5);
258
259	RealType uglyi = zifzifzis + zifziszis;
260	RealType uglyj = zjfzjfzjs + zjfzjszjs;
261
262	Vector3d dwip(-2.0xizi*uglyi/r3,
263	-2.0yizi*uglyi/r3,
264	2.0(1.0/ (idat.rij) - zi2/r3)*uglyi);
265
266	Vector3d dwjp(-2.0xjzj*uglyj/r3,
267	-2.0yjzj*uglyj/r3,
268	2.0(1.0/ (idat.rij) - zj2/r3)*uglyj);
269
270	Vector3d dwidu(4.0(yizi2 + 0.5yi(xi2-yi2))/r3,
271	4.0(xizi2 - 0.5xi(xi2-yi2))/r3,
272	- 8.0xiyi*zi/r3);
273
274	Vector3d dwjdu(4.0(yjzj2 + 0.5yj(xj2-yj2))/r3,
275	4.0(xjzj2 - 0.5xj(xj2-yj2))/r3,
276	- 8.0xjyj*zj/r3);
277
278	Vector3d dwipdu(2.0yiuglyi/ *(idat.rij) ,
279	-2.0xiuglyi/ *(idat.rij) ,
280	0.0);
281
282	Vector3d dwjpdu(2.0yjuglyj/ *(idat.rij) ,
283	-2.0xjuglyj/ *(idat.rij) ,
284	0.0);
285
286	if (isPower) {
287	cerr << "This is probably an error!\n";
288	RealType frac1 = 0.25;
289	RealType frac2 = 0.75;
290	RealType wi2 = wi*wi;
291	RealType wj2 = wj*wj;
292	// sticky power has no w' function:
293	w = frac1 * wi * wi2 + frac2wi + frac1wjwj2 + frac2wj + v0p;
294	wp = 0.0;
295	dwi = frac1RealType(3.0)wi2dwi + frac2dwi;
296	dwj = frac1RealType(3.0)wj2dwi + frac2dwi;
297	dwip = V3Zero;
298	dwjp = V3Zero;
299	dwidu = frac1RealType(3.0)wi2dwidu + frac2dwidu;
300	dwidu = frac1RealType(3.0)wj2dwjdu + frac2dwjdu;
301	dwipdu = V3Zero;
302	dwjpdu = V3Zero;
303	sp = 0.0;
304	dspdr = 0.0;
305	}
306
307
308
309	(idat.vpair) += RealType(0.5)(v0sw + v0pspwp);
310	((idat.pot))[HYDROGENBONDING_FAMILY] += RealType(0.5)(v0sw + v0pspwp)* *(idat.sw) ;
311
312	// do the torques first since they are easy:
313	// remember that these are still in the body-fixed axes
314
315	Vector3d ti = RealType(0.5)* (idat.sw) (v0sdwidu + v0pspdwipdu);
316	Vector3d tj = RealType(0.5)* (idat.sw) (v0sdwjdu + v0pspdwjpdu);
317
318	// go back to lab frame using transpose of rotation matrix:
319
320	(idat.t1) += A1trans ti;
321	(idat.t2) += A2trans tj;
322
323	// Now, on to the forces:
324
325	// first rotate the i terms back into the lab frame:
326
327	Vector3d radcomi = (v0 * s * dwi + v0p * sp * dwip) * *(idat.sw);
328	Vector3d radcomj = (v0 * s * dwj + v0p * sp * dwjp) * *(idat.sw);
329
330	Vector3d fii = A1trans * radcomi;
331	Vector3d fjj = A2trans * radcomj;
332
333	// now assemble these with the radial-only terms:
334
335	(idat.f1) += RealType(0.5) ((v0dsdrw + v0pdspdrwp) * *(idat.d) /
336	*(idat.rij) + fii - fjj);
337
338	}
339
340	return;
341	}
342
343	RealType Sticky::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
344	if (!initialized_) initialize();
345	int atid1 = atypes.first->getIdent();
346	int atid2 = atypes.second->getIdent();
347	int stid1 = Stids[atid1];
348	int stid2 = Stids[atid2];
349
350	if (stid1 == -1 \|\| stid2 == -1) return 0.0;
351	else {
352	return MixingMap[stid1][stid2].rbig;
353	}
354	}
355	}