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 "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;
      }
    }
  }

  /**
   * 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*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:	1668
Committed:	Fri Jan 6 19:03:05 2012 UTC (13 years, 4 months ago) by gezelter
File size:	13839 byte(s)
Log Message:	Some fixes for CMake and single precision builds
#	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			#include "utils/simError.h"
50
51			using namespace std;
52			namespace OpenMD {
53
54	gezelter	1502	Sticky::Sticky() : name_("Sticky"), initialized_(false), forceField_(NULL) {}
55	gezelter	1485
56			StickyParam Sticky::getStickyParam(AtomType* atomType) {
57
58			// Do sanity checking on the AtomType we were passed before
59			// building any data structures:
60			if (!atomType->isSticky() && !atomType->isStickyPower()) {
61			sprintf( painCave.errMsg,
62			"Sticky::getStickyParam was passed an atomType (%s) that does\n"
63			"\tnot appear to be a Sticky atom.\n",
64			atomType->getName().c_str());
65			painCave.severity = OPENMD_ERROR;
66			painCave.isFatal = 1;
67			simError();
68			}
69
70			DirectionalAtomType* daType = dynamic_cast<DirectionalAtomType*>(atomType);
71			GenericData* data = daType->getPropertyByName("Sticky");
72			if (data == NULL) {
73			sprintf( painCave.errMsg, "Sticky::getStickyParam could not find\n"
74			"\tSticky parameters for atomType %s.\n",
75			daType->getName().c_str());
76			painCave.severity = OPENMD_ERROR;
77			painCave.isFatal = 1;
78			simError();
79			}
80
81			StickyParamGenericData* stickyData = dynamic_cast<StickyParamGenericData*>(data);
82			if (stickyData == NULL) {
83			sprintf( painCave.errMsg,
84			"Sticky::getStickyParam could not convert GenericData to\n"
85			"\tStickyParamGenericData for atom type %s\n",
86			daType->getName().c_str());
87			painCave.severity = OPENMD_ERROR;
88			painCave.isFatal = 1;
89			simError();
90			}
91
92			return stickyData->getData();
93			}
94
95			void Sticky::initialize() {
96
97			ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
98			ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
99			ForceField::AtomTypeContainer::MapTypeIterator i;
100			AtomType* at;
101
102			// Sticky handles all of the Sticky-Sticky interactions
103
104			for (at = atomTypes->beginType(i); at != NULL;
105			at = atomTypes->nextType(i)) {
106
107			if (at->isSticky() \|\| at->isStickyPower())
108			addType(at);
109			}
110
111			initialized_ = true;
112			}
113
114			void Sticky::addType(AtomType* atomType){
115			// add it to the map:
116			AtomTypeProperties atp = atomType->getATP();
117
118			pair<map<int,AtomType*>::iterator,bool> ret;
119			ret = StickyMap.insert( pair<int, AtomType*>(atp.ident, atomType) );
120			if (ret.second == false) {
121			sprintf( painCave.errMsg,
122			"Sticky already had a previous entry with ident %d\n",
123			atp.ident);
124			painCave.severity = OPENMD_INFO;
125			painCave.isFatal = 0;
126			simError();
127			}
128
129			RealType w0i, v0i, v0pi, rli, rui, rlpi, rupi;
130
131			StickyParam sticky1 = getStickyParam(atomType);
132
133			// Now, iterate over all known types and add to the mixing map:
134
135			map<int, AtomType*>::iterator it;
136			for( it = StickyMap.begin(); it != StickyMap.end(); ++it) {
137
138			AtomType* atype2 = (*it).second;
139
140			StickyParam sticky2 = getStickyParam(atype2);
141
142			StickyInteractionData mixer;
143
144			// Mixing two different sticky types is silly, but if you want 2
145			// sticky types in your simulation, we'll let you do it with the
146			// Lorentz- Berthelot mixing rules (which happen to do the right thing
147			// when atomType and atype2 happen to be the same.
148
149			mixer.rl = 0.5 * ( sticky1.rl + sticky2.rl );
150			mixer.ru = 0.5 * ( sticky1.ru + sticky2.ru );
151			mixer.rlp = 0.5 * ( sticky1.rlp + sticky2.rlp );
152			mixer.rup = 0.5 * ( sticky1.rup + sticky2.rup );
153			mixer.rbig = max(mixer.ru, mixer.rup);
154			mixer.w0 = sqrt( sticky1.w0 * sticky2.w0 );
155			mixer.v0 = sqrt( sticky1.v0 * sticky2.v0 );
156			mixer.v0p = sqrt( sticky1.v0p * sticky2.v0p );
157			mixer.isPower = atomType->isStickyPower() && atype2->isStickyPower();
158
159			CubicSpline* s = new CubicSpline();
160			s->addPoint(mixer.rl, 1.0);
161			s->addPoint(mixer.ru, 0.0);
162			mixer.s = s;
163
164			CubicSpline* sp = new CubicSpline();
165			sp->addPoint(mixer.rlp, 1.0);
166			sp->addPoint(mixer.rup, 0.0);
167			mixer.sp = sp;
168
169
170			pair<AtomType, AtomType> key1, key2;
171			key1 = make_pair(atomType, atype2);
172			key2 = make_pair(atype2, atomType);
173
174			MixingMap[key1] = mixer;
175			if (key2 != key1) {
176			MixingMap[key2] = mixer;
177			}
178			}
179			}
180
181	gezelter	1502	/**
182			* This function does the sticky portion of the SSD potential
183			* [Chandra and Ichiye, Journal of Chemical Physics 111, 2701
184			* (1999)]. The Lennard-Jones and dipolar interaction must be
185			* handled separately. We assume that the rotation matrices have
186			* already been calculated and placed in the A1 & A2 entries in the
187			* idat structure.
188			*/
189
190	gezelter	1536	void Sticky::calcForce(InteractionData &idat) {
191	gezelter	1502
192	gezelter	1485	if (!initialized_) initialize();
193
194	gezelter	1505	map<pair<AtomType, AtomType>, StickyInteractionData>::iterator it;
195	gezelter	1571	it = MixingMap.find(idat.atypes);
196	gezelter	1505	if (it != MixingMap.end()) {
197	gezelter	1485
198	gezelter	1505	StickyInteractionData mixer = (*it).second;
199
200			RealType w0 = mixer.w0;
201			RealType v0 = mixer.v0;
202			RealType v0p = mixer.v0p;
203			RealType rl = mixer.rl;
204			RealType ru = mixer.ru;
205			RealType rlp = mixer.rlp;
206			RealType rup = mixer.rup;
207			RealType rbig = mixer.rbig;
208			bool isPower = mixer.isPower;
209
210	gezelter	1554	if ( *(idat.rij) <= rbig) {
211	gezelter	1505
212	gezelter	1554	RealType r3 = (idat.r2) *(idat.rij);
213			RealType r5 = r3 * *(idat.r2);
214	gezelter	1505
215	gezelter	1554	RotMat3x3d A1trans = idat.A1->transpose();
216			RotMat3x3d A2trans = idat.A2->transpose();
217	gezelter	1505
218			// rotate the inter-particle separation into the two different
219			// body-fixed coordinate systems:
220
221	gezelter	1554	Vector3d ri = (idat.A1) *(idat.d);
222	gezelter	1505
223			// negative sign because this is the vector from j to i:
224
225	gezelter	1554	Vector3d rj = - (idat.A2) *(idat.d);
226	gezelter	1505
227			RealType xi = ri.x();
228			RealType yi = ri.y();
229			RealType zi = ri.z();
230
231			RealType xj = rj.x();
232			RealType yj = rj.y();
233			RealType zj = rj.z();
234
235			RealType xi2 = xi * xi;
236			RealType yi2 = yi * yi;
237			RealType zi2 = zi * zi;
238
239			RealType xj2 = xj * xj;
240			RealType yj2 = yj * yj;
241			RealType zj2 = zj * zj;
242
243			// calculate the switching info. from the splines
244
245			RealType s = 0.0;
246			RealType dsdr = 0.0;
247			RealType sp = 0.0;
248			RealType dspdr = 0.0;
249
250	gezelter	1554	if ( *(idat.rij) < ru) {
251			if ( *(idat.rij) < rl) {
252	gezelter	1505	s = 1.0;
253			dsdr = 0.0;
254			} else {
255			// we are in the switching region
256
257	gezelter	1554	pair<RealType, RealType> res = mixer.s->getValueAndDerivativeAt(*(idat.rij));
258	gezelter	1505	s = res.first;
259			dsdr = res.second;
260			}
261	gezelter	1485	}
262	gezelter	1505
263	gezelter	1554	if (*(idat.rij) < rup) {
264			if ( *(idat.rij) < rlp) {
265	gezelter	1505	sp = 1.0;
266			dspdr = 0.0;
267			} else {
268			// we are in the switching region
269
270	gezelter	1554	pair<RealType, RealType> res =mixer.sp->getValueAndDerivativeAt( *(idat.rij));
271	gezelter	1505	sp = res.first;
272			dspdr = res.second;
273			}
274			}
275
276			RealType wi = 2.0(xi2-yi2)zi / r3;
277			RealType wj = 2.0(xj2-yj2)zj / r3;
278			RealType w = wi+wj;
279
280
281	gezelter	1554	RealType zif = zi/ *(idat.rij) - 0.6;
282			RealType zis = zi/ *(idat.rij) + 0.8;
283	gezelter	1505
284	gezelter	1554	RealType zjf = zj/ *(idat.rij) - 0.6;
285			RealType zjs = zj/ *(idat.rij) + 0.8;
286	gezelter	1505
287			RealType wip = zifzifzis*zis - w0;
288			RealType wjp = zjfzjfzjs*zjs - w0;
289			RealType wp = wip + wjp;
290
291			Vector3d dwi(4.0xizi/r3 - 6.0xizi*(xi2-yi2)/r5,
292			- 4.0yizi/r3 - 6.0yizi*(xi2-yi2)/r5,
293			2.0(xi2-yi2)/r3 - 6.0zi2*(xi2-yi2)/r5);
294
295			Vector3d dwj(4.0xjzj/r3 - 6.0xjzj*(xj2-yj2)/r5,
296			- 4.0yjzj/r3 - 6.0yjzj*(xj2-yj2)/r5,
297			2.0(xj2-yj2)/r3 - 6.0zj2*(xj2-yj2)/r5);
298
299			RealType uglyi = zifzifzis + zifziszis;
300			RealType uglyj = zjfzjfzjs + zjfzjszjs;
301	gezelter	1485
302	gezelter	1505	Vector3d dwip(-2.0xizi*uglyi/r3,
303			-2.0yizi*uglyi/r3,
304	gezelter	1554	2.0(1.0/ (idat.rij) - zi2/r3)*uglyi);
305	gezelter	1505
306			Vector3d dwjp(-2.0xjzj*uglyj/r3,
307			-2.0yjzj*uglyj/r3,
308	gezelter	1554	2.0(1.0/ (idat.rij) - zj2/r3)*uglyj);
309	gezelter	1505
310			Vector3d dwidu(4.0(yizi2 + 0.5yi(xi2-yi2))/r3,
311			4.0(xizi2 - 0.5xi(xi2-yi2))/r3,
312			- 8.0xiyi*zi/r3);
313
314			Vector3d dwjdu(4.0(yjzj2 + 0.5yj(xj2-yj2))/r3,
315			4.0(xjzj2 - 0.5xj(xj2-yj2))/r3,
316			- 8.0xjyj*zj/r3);
317
318	gezelter	1554	Vector3d dwipdu(2.0yiuglyi/ *(idat.rij) ,
319			-2.0xiuglyi/ *(idat.rij) ,
320	gezelter	1505	0.0);
321
322	gezelter	1554	Vector3d dwjpdu(2.0yjuglyj/ *(idat.rij) ,
323			-2.0xjuglyj/ *(idat.rij) ,
324	gezelter	1505	0.0);
325
326			if (isPower) {
327			RealType frac1 = 0.25;
328			RealType frac2 = 0.75;
329			RealType wi2 = wi*wi;
330			RealType wj2 = wj*wj;
331			// sticky power has no w' function:
332			w = frac1 * wi * wi2 + frac2wi + frac1wjwj2 + frac2wj + v0p;
333			wp = 0.0;
334	gezelter	1668	dwi = frac1RealType(3.0)wi2dwi + frac2dwi;
335			dwj = frac1RealType(3.0)wj2dwi + frac2dwi;
336	gezelter	1505	dwip = V3Zero;
337			dwjp = V3Zero;
338	gezelter	1668	dwidu = frac1RealType(3.0)wi2dwidu + frac2dwidu;
339			dwidu = frac1RealType(3.0)wj2dwjdu + frac2dwjdu;
340	gezelter	1505	dwipdu = V3Zero;
341			dwjpdu = V3Zero;
342			sp = 0.0;
343	gezelter	1485	dspdr = 0.0;
344			}
345	gezelter	1505
346	gezelter	1668	(idat.vpair) += RealType(0.5)(v0sw + v0pspwp);
347			((idat.pot))[HYDROGENBONDING_FAMILY] += RealType(0.5)(v0sw + v0pspwp)* *(idat.sw) ;
348	gezelter	1505
349			// do the torques first since they are easy:
350			// remember that these are still in the body-fixed axes
351
352	gezelter	1668	Vector3d ti = RealType(0.5)* (idat.sw) (v0sdwidu + v0pspdwipdu);
353			Vector3d tj = RealType(0.5)* (idat.sw) (v0sdwjdu + v0pspdwjpdu);
354	gezelter	1505
355			// go back to lab frame using transpose of rotation matrix:
356
357	gezelter	1554	(idat.t1) += A1trans ti;
358			(idat.t2) += A2trans tj;
359	gezelter	1505
360			// Now, on to the forces:
361
362			// first rotate the i terms back into the lab frame:
363
364	gezelter	1554	Vector3d radcomi = (v0 * s * dwi + v0p * sp * dwip) * *(idat.sw);
365			Vector3d radcomj = (v0 * s * dwj + v0p * sp * dwjp) * *(idat.sw);
366	gezelter	1505
367			Vector3d fii = A1trans * radcomi;
368			Vector3d fjj = A2trans * radcomj;
369
370			// now assemble these with the radial-only terms:
371
372	gezelter	1668	(idat.f1) += RealType(0.5) ((v0dsdrw + v0pdspdrwp) * *(idat.d) /
373			*(idat.rij) + fii - fjj);
374	gezelter	1505
375	gezelter	1485	}
376			}
377
378	gezelter	1505	return;
379	gezelter	1485	}
380	gezelter	1505
381	gezelter	1545	RealType Sticky::getSuggestedCutoffRadius(pair<AtomType, AtomType> atypes) {
382	gezelter	1505	if (!initialized_) initialize();
383			map<pair<AtomType, AtomType>, StickyInteractionData>::iterator it;
384	gezelter	1545	it = MixingMap.find(atypes);
385	gezelter	1505	if (it == MixingMap.end())
386			return 0.0;
387			else {
388			StickyInteractionData mixer = (*it).second;
389			return mixer.rbig;
390			}
391			}
392	gezelter	1485	}