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]  Vardeman & Gezelter, in progress (2009).                        
 */

#include <stdio.h>
#include <string.h>

#include <cmath>
#include "nonbonded/Sticky.hpp"
#include "nonbonded/LJ.hpp"
#include "utils/simError.h"

using namespace std;
namespace OpenMD {
  
  Sticky::Sticky() : name_("Sticky"), initialized_(false), forceField_(NULL) {}
  
  StickyParam Sticky::getStickyParam(AtomType* atomType) {
    
    // Do sanity checking on the AtomType we were passed before
    // building any data structures:
    if (!atomType->isSticky() && !atomType->isStickyPower()) {
      sprintf( painCave.errMsg,
               "Sticky::getStickyParam was passed an atomType (%s) that does\n"
               "\tnot appear to be a Sticky atom.\n",
               atomType->getName().c_str());
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
    
    DirectionalAtomType* daType = dynamic_cast<DirectionalAtomType*>(atomType);
    GenericData* data = daType->getPropertyByName("Sticky");
    if (data == NULL) {
      sprintf( painCave.errMsg, "Sticky::getStickyParam could not find\n"
               "\tSticky parameters for atomType %s.\n", 
               daType->getName().c_str());
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError(); 
    }
    
    StickyParamGenericData* stickyData = dynamic_cast<StickyParamGenericData*>(data);
    if (stickyData == NULL) {
      sprintf( painCave.errMsg,
               "Sticky::getStickyParam could not convert GenericData to\n"
               "\tStickyParamGenericData for atom type %s\n", 
               daType->getName().c_str());
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();          
    }
    
    return stickyData->getData();
  }
  
  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)) {
      
      if (at->isSticky() || at->isStickyPower())
        addType(at);
    }
    
    initialized_ = true;
  }
      
  void Sticky::addType(AtomType* atomType){
    // add it to the map:
    AtomTypeProperties atp = atomType->getATP();    
    
    pair<map<int,AtomType*>::iterator,bool> ret;    
    ret = StickyMap.insert( pair<int, AtomType*>(atp.ident, atomType) );
    if (ret.second == false) {
      sprintf( painCave.errMsg,
               "Sticky already had a previous entry with ident %d\n",
               atp.ident);
      painCave.severity = OPENMD_INFO;
      painCave.isFatal = 0;
      simError();         
    }
    
    RealType w0i, v0i, v0pi, rli, rui, rlpi, rupi;
    
    StickyParam sticky1 = getStickyParam(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;
    
      StickyParam sticky2 = getStickyParam(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.rl + sticky2.rl );
      mixer.ru   = 0.5 * ( sticky1.ru + sticky2.ru );
      mixer.rlp  = 0.5 * ( sticky1.rlp + sticky2.rlp );
      mixer.rup  = 0.5 * ( sticky1.rup + sticky2.rup );
      mixer.rbig = max(mixer.ru, mixer.rup);
      mixer.w0  = sqrt( sticky1.w0   * sticky2.w0  );
      mixer.v0  = sqrt( sticky1.v0   * sticky2.v0  );
      mixer.v0p = sqrt( sticky1.v0p  * sticky2.v0p );
      mixer.isPower = atomType->isStickyPower() && atype2->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;
      }
    }
  }

  void Sticky::initForce() {
        if (!initialized_) initialize();
  }

  /**
   * 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;
      
      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) {
          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*3.0*wi2*dwi + frac2*dwi;
          dwj = frac1*3.0*wj2*dwi + frac2*dwi;
          dwip = V3Zero;
          dwjp = V3Zero;
          dwidu = frac1*3.0*wi2*dwidu + frac2*dwidu;
          dwidu = frac1*3.0*wj2*dwjdu + frac2*dwjdu;
          dwipdu = V3Zero;
          dwjpdu = V3Zero;
          sp = 0.0;
          dspdr = 0.0;
        }
        
        *(idat.vpair) += 0.5*(v0*s*w + v0p*sp*wp);
        (*(idat.pot))[HYDROGENBONDING_FAMILY] += 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 = 0.5* *(idat.sw) *(v0*s*dwidu + v0p*sp*dwipdu);
        Vector3d tj = 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) += 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:	1614
Committed:	Tue Aug 23 20:55:51 2011 UTC (13 years, 11 months ago) by mciznick
File size:	13743 byte(s)
Log Message:	Updated scalability of OpenMP threads.
#	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			* [4] Vardeman & Gezelter, in progress (2009).
40			*/
41
42			#include <stdio.h>
43			#include <string.h>
44
45			#include <cmath>
46			#include "nonbonded/Sticky.hpp"
47			#include "nonbonded/LJ.hpp"
48			#include "utils/simError.h"
49
50			using namespace std;
51			namespace OpenMD {
52
53	gezelter	1502	Sticky::Sticky() : name_("Sticky"), initialized_(false), forceField_(NULL) {}
54	gezelter	1485
55			StickyParam Sticky::getStickyParam(AtomType* atomType) {
56
57			// Do sanity checking on the AtomType we were passed before
58			// building any data structures:
59			if (!atomType->isSticky() && !atomType->isStickyPower()) {
60			sprintf( painCave.errMsg,
61			"Sticky::getStickyParam was passed an atomType (%s) that does\n"
62			"\tnot appear to be a Sticky atom.\n",
63			atomType->getName().c_str());
64			painCave.severity = OPENMD_ERROR;
65			painCave.isFatal = 1;
66			simError();
67			}
68
69			DirectionalAtomType* daType = dynamic_cast<DirectionalAtomType*>(atomType);
70			GenericData* data = daType->getPropertyByName("Sticky");
71			if (data == NULL) {
72			sprintf( painCave.errMsg, "Sticky::getStickyParam could not find\n"
73			"\tSticky parameters for atomType %s.\n",
74			daType->getName().c_str());
75			painCave.severity = OPENMD_ERROR;
76			painCave.isFatal = 1;
77			simError();
78			}
79
80			StickyParamGenericData* stickyData = dynamic_cast<StickyParamGenericData*>(data);
81			if (stickyData == NULL) {
82			sprintf( painCave.errMsg,
83			"Sticky::getStickyParam could not convert GenericData to\n"
84			"\tStickyParamGenericData for atom type %s\n",
85			daType->getName().c_str());
86			painCave.severity = OPENMD_ERROR;
87			painCave.isFatal = 1;
88			simError();
89			}
90
91			return stickyData->getData();
92			}
93
94			void Sticky::initialize() {
95
96			ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
97			ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
98			ForceField::AtomTypeContainer::MapTypeIterator i;
99			AtomType* at;
100
101			// Sticky handles all of the Sticky-Sticky interactions
102
103			for (at = atomTypes->beginType(i); at != NULL;
104			at = atomTypes->nextType(i)) {
105
106			if (at->isSticky() \|\| at->isStickyPower())
107			addType(at);
108			}
109
110			initialized_ = true;
111			}
112
113			void Sticky::addType(AtomType* atomType){
114			// add it to the map:
115			AtomTypeProperties atp = atomType->getATP();
116
117			pair<map<int,AtomType*>::iterator,bool> ret;
118			ret = StickyMap.insert( pair<int, AtomType*>(atp.ident, atomType) );
119			if (ret.second == false) {
120			sprintf( painCave.errMsg,
121			"Sticky already had a previous entry with ident %d\n",
122			atp.ident);
123			painCave.severity = OPENMD_INFO;
124			painCave.isFatal = 0;
125			simError();
126			}
127
128			RealType w0i, v0i, v0pi, rli, rui, rlpi, rupi;
129
130			StickyParam sticky1 = getStickyParam(atomType);
131
132			// Now, iterate over all known types and add to the mixing map:
133
134			map<int, AtomType*>::iterator it;
135			for( it = StickyMap.begin(); it != StickyMap.end(); ++it) {
136
137			AtomType* atype2 = (*it).second;
138
139			StickyParam sticky2 = getStickyParam(atype2);
140
141			StickyInteractionData mixer;
142
143			// Mixing two different sticky types is silly, but if you want 2
144			// sticky types in your simulation, we'll let you do it with the
145			// Lorentz- Berthelot mixing rules (which happen to do the right thing
146			// when atomType and atype2 happen to be the same.
147
148			mixer.rl = 0.5 * ( sticky1.rl + sticky2.rl );
149			mixer.ru = 0.5 * ( sticky1.ru + sticky2.ru );
150			mixer.rlp = 0.5 * ( sticky1.rlp + sticky2.rlp );
151			mixer.rup = 0.5 * ( sticky1.rup + sticky2.rup );
152			mixer.rbig = max(mixer.ru, mixer.rup);
153			mixer.w0 = sqrt( sticky1.w0 * sticky2.w0 );
154			mixer.v0 = sqrt( sticky1.v0 * sticky2.v0 );
155			mixer.v0p = sqrt( sticky1.v0p * sticky2.v0p );
156			mixer.isPower = atomType->isStickyPower() && atype2->isStickyPower();
157
158			CubicSpline* s = new CubicSpline();
159			s->addPoint(mixer.rl, 1.0);
160			s->addPoint(mixer.ru, 0.0);
161			mixer.s = s;
162
163			CubicSpline* sp = new CubicSpline();
164			sp->addPoint(mixer.rlp, 1.0);
165			sp->addPoint(mixer.rup, 0.0);
166			mixer.sp = sp;
167
168
169			pair<AtomType, AtomType> key1, key2;
170			key1 = make_pair(atomType, atype2);
171			key2 = make_pair(atype2, atomType);
172
173			MixingMap[key1] = mixer;
174			if (key2 != key1) {
175			MixingMap[key2] = mixer;
176			}
177			}
178			}
179
180	mciznick	1614	void Sticky::initForce() {
181			if (!initialized_) initialize();
182			}
183
184	gezelter	1502	/**
185			* This function does the sticky portion of the SSD potential
186			* [Chandra and Ichiye, Journal of Chemical Physics 111, 2701
187			* (1999)]. The Lennard-Jones and dipolar interaction must be
188			* handled separately. We assume that the rotation matrices have
189			* already been calculated and placed in the A1 & A2 entries in the
190			* idat structure.
191			*/
192
193	gezelter	1536	void Sticky::calcForce(InteractionData &idat) {
194	gezelter	1502
195	gezelter	1485	if (!initialized_) initialize();
196
197	gezelter	1505	map<pair<AtomType, AtomType>, StickyInteractionData>::iterator it;
198	gezelter	1571	it = MixingMap.find(idat.atypes);
199	gezelter	1505	if (it != MixingMap.end()) {
200	gezelter	1485
201	gezelter	1505	StickyInteractionData mixer = (*it).second;
202
203			RealType w0 = mixer.w0;
204			RealType v0 = mixer.v0;
205			RealType v0p = mixer.v0p;
206			RealType rl = mixer.rl;
207			RealType ru = mixer.ru;
208			RealType rlp = mixer.rlp;
209			RealType rup = mixer.rup;
210			RealType rbig = mixer.rbig;
211			bool isPower = mixer.isPower;
212
213	gezelter	1554	if ( *(idat.rij) <= rbig) {
214	gezelter	1505
215	gezelter	1554	RealType r3 = (idat.r2) *(idat.rij);
216			RealType r5 = r3 * *(idat.r2);
217	gezelter	1505
218	gezelter	1554	RotMat3x3d A1trans = idat.A1->transpose();
219			RotMat3x3d A2trans = idat.A2->transpose();
220	gezelter	1505
221			// rotate the inter-particle separation into the two different
222			// body-fixed coordinate systems:
223
224	gezelter	1554	Vector3d ri = (idat.A1) *(idat.d);
225	gezelter	1505
226			// negative sign because this is the vector from j to i:
227
228	gezelter	1554	Vector3d rj = - (idat.A2) *(idat.d);
229	gezelter	1505
230			RealType xi = ri.x();
231			RealType yi = ri.y();
232			RealType zi = ri.z();
233
234			RealType xj = rj.x();
235			RealType yj = rj.y();
236			RealType zj = rj.z();
237
238			RealType xi2 = xi * xi;
239			RealType yi2 = yi * yi;
240			RealType zi2 = zi * zi;
241
242			RealType xj2 = xj * xj;
243			RealType yj2 = yj * yj;
244			RealType zj2 = zj * zj;
245
246			// calculate the switching info. from the splines
247
248			RealType s = 0.0;
249			RealType dsdr = 0.0;
250			RealType sp = 0.0;
251			RealType dspdr = 0.0;
252
253	gezelter	1554	if ( *(idat.rij) < ru) {
254			if ( *(idat.rij) < rl) {
255	gezelter	1505	s = 1.0;
256			dsdr = 0.0;
257			} else {
258			// we are in the switching region
259
260	gezelter	1554	pair<RealType, RealType> res = mixer.s->getValueAndDerivativeAt(*(idat.rij));
261	gezelter	1505	s = res.first;
262			dsdr = res.second;
263			}
264	gezelter	1485	}
265	gezelter	1505
266	gezelter	1554	if (*(idat.rij) < rup) {
267			if ( *(idat.rij) < rlp) {
268	gezelter	1505	sp = 1.0;
269			dspdr = 0.0;
270			} else {
271			// we are in the switching region
272
273	gezelter	1554	pair<RealType, RealType> res =mixer.sp->getValueAndDerivativeAt( *(idat.rij));
274	gezelter	1505	sp = res.first;
275			dspdr = res.second;
276			}
277			}
278
279			RealType wi = 2.0(xi2-yi2)zi / r3;
280			RealType wj = 2.0(xj2-yj2)zj / r3;
281			RealType w = wi+wj;
282
283
284	gezelter	1554	RealType zif = zi/ *(idat.rij) - 0.6;
285			RealType zis = zi/ *(idat.rij) + 0.8;
286	gezelter	1505
287	gezelter	1554	RealType zjf = zj/ *(idat.rij) - 0.6;
288			RealType zjs = zj/ *(idat.rij) + 0.8;
289	gezelter	1505
290			RealType wip = zifzifzis*zis - w0;
291			RealType wjp = zjfzjfzjs*zjs - w0;
292			RealType wp = wip + wjp;
293
294			Vector3d dwi(4.0xizi/r3 - 6.0xizi*(xi2-yi2)/r5,
295			- 4.0yizi/r3 - 6.0yizi*(xi2-yi2)/r5,
296			2.0(xi2-yi2)/r3 - 6.0zi2*(xi2-yi2)/r5);
297
298			Vector3d dwj(4.0xjzj/r3 - 6.0xjzj*(xj2-yj2)/r5,
299			- 4.0yjzj/r3 - 6.0yjzj*(xj2-yj2)/r5,
300			2.0(xj2-yj2)/r3 - 6.0zj2*(xj2-yj2)/r5);
301
302			RealType uglyi = zifzifzis + zifziszis;
303			RealType uglyj = zjfzjfzjs + zjfzjszjs;
304	gezelter	1485
305	gezelter	1505	Vector3d dwip(-2.0xizi*uglyi/r3,
306			-2.0yizi*uglyi/r3,
307	gezelter	1554	2.0(1.0/ (idat.rij) - zi2/r3)*uglyi);
308	gezelter	1505
309			Vector3d dwjp(-2.0xjzj*uglyj/r3,
310			-2.0yjzj*uglyj/r3,
311	gezelter	1554	2.0(1.0/ (idat.rij) - zj2/r3)*uglyj);
312	gezelter	1505
313			Vector3d dwidu(4.0(yizi2 + 0.5yi(xi2-yi2))/r3,
314			4.0(xizi2 - 0.5xi(xi2-yi2))/r3,
315			- 8.0xiyi*zi/r3);
316
317			Vector3d dwjdu(4.0(yjzj2 + 0.5yj(xj2-yj2))/r3,
318			4.0(xjzj2 - 0.5xj(xj2-yj2))/r3,
319			- 8.0xjyj*zj/r3);
320
321	gezelter	1554	Vector3d dwipdu(2.0yiuglyi/ *(idat.rij) ,
322			-2.0xiuglyi/ *(idat.rij) ,
323	gezelter	1505	0.0);
324
325	gezelter	1554	Vector3d dwjpdu(2.0yjuglyj/ *(idat.rij) ,
326			-2.0xjuglyj/ *(idat.rij) ,
327	gezelter	1505	0.0);
328
329			if (isPower) {
330			RealType frac1 = 0.25;
331			RealType frac2 = 0.75;
332			RealType wi2 = wi*wi;
333			RealType wj2 = wj*wj;
334			// sticky power has no w' function:
335			w = frac1 * wi * wi2 + frac2wi + frac1wjwj2 + frac2wj + v0p;
336			wp = 0.0;
337			dwi = frac13.0wi2dwi + frac2dwi;
338			dwj = frac13.0wj2dwi + frac2dwi;
339			dwip = V3Zero;
340			dwjp = V3Zero;
341			dwidu = frac13.0wi2dwidu + frac2dwidu;
342			dwidu = frac13.0wj2dwjdu + frac2dwjdu;
343			dwipdu = V3Zero;
344			dwjpdu = V3Zero;
345			sp = 0.0;
346	gezelter	1485	dspdr = 0.0;
347			}
348	gezelter	1505
349	gezelter	1554	(idat.vpair) += 0.5(v0sw + v0pspwp);
350	gezelter	1582	((idat.pot))[HYDROGENBONDING_FAMILY] += 0.5(v0sw + v0pspwp)* *(idat.sw) ;
351	gezelter	1505
352			// do the torques first since they are easy:
353			// remember that these are still in the body-fixed axes
354
355	gezelter	1554	Vector3d ti = 0.5* (idat.sw) (v0sdwidu + v0pspdwipdu);
356			Vector3d tj = 0.5* (idat.sw) (v0sdwjdu + v0pspdwjpdu);
357	gezelter	1505
358			// go back to lab frame using transpose of rotation matrix:
359
360	gezelter	1554	(idat.t1) += A1trans ti;
361			(idat.t2) += A2trans tj;
362	gezelter	1505
363			// Now, on to the forces:
364
365			// first rotate the i terms back into the lab frame:
366
367	gezelter	1554	Vector3d radcomi = (v0 * s * dwi + v0p * sp * dwip) * *(idat.sw);
368			Vector3d radcomj = (v0 * s * dwj + v0p * sp * dwjp) * *(idat.sw);
369	gezelter	1505
370			Vector3d fii = A1trans * radcomi;
371			Vector3d fjj = A2trans * radcomj;
372
373			// now assemble these with the radial-only terms:
374
375	gezelter	1554	(idat.f1) += 0.5 ((v0dsdrw + v0pdspdrwp) * *(idat.d) /
376			*(idat.rij) + fii - fjj);
377	gezelter	1505
378	gezelter	1485	}
379			}
380
381	gezelter	1505	return;
382	gezelter	1485	}
383	gezelter	1505
384	gezelter	1545	RealType Sticky::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
385	gezelter	1505	if (!initialized_) initialize();
386			map<pair<AtomType, AtomType>, StickyInteractionData>::iterator it;
387	gezelter	1545	it = MixingMap.find(atypes);
388	gezelter	1505	if (it == MixingMap.end())
389			return 0.0;
390			else {
391			StickyInteractionData mixer = (*it).second;
392			return mixer.rbig;
393			}
394			}
395	gezelter	1485	}