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Revision 1505 by gezelter, Sun Oct 3 22:18:59 2010 UTC vs.
Revision 1710 by gezelter, Fri May 18 21:44:02 2012 UTC

# Line 36 | Line 36
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).                        
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>
# Line 45 | Line 46
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() : name_("Sticky"), initialized_(false), forceField_(NULL) {}
54 –  
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 –  
57    void Sticky::initialize() {    
58      
59      ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
# Line 103 | Line 66 | namespace OpenMD {
66      for (at = atomTypes->beginType(i); at != NULL;
67           at = atomTypes->nextType(i)) {
68        
69 <      if (at->isSticky() || at->isStickyPower())
70 <        addType(at);
69 >      StickyAdapter sa = StickyAdapter(at);
70 >      if (sa.isSticky()) addType(at);
71      }
72      
73      initialized_ = true;
# Line 112 | Line 75 | namespace OpenMD {
75        
76    void Sticky::addType(AtomType* atomType){
77      // add it to the map:
115 –    AtomTypeProperties atp = atomType->getATP();    
78      
79      pair<map<int,AtomType*>::iterator,bool> ret;    
80 <    ret = StickyMap.insert( pair<int, AtomType*>(atp.ident, atomType) );
80 >    ret = StickyMap.insert( pair<int, AtomType*>(atomType->getIdent(),
81 >                                                 atomType) );
82      if (ret.second == false) {
83        sprintf( painCave.errMsg,
84                 "Sticky already had a previous entry with ident %d\n",
85 <               atp.ident);
85 >               atomType->getIdent() );
86        painCave.severity = OPENMD_INFO;
87        painCave.isFatal = 0;
88        simError();        
# Line 127 | Line 90 | namespace OpenMD {
90      
91      RealType w0i, v0i, v0pi, rli, rui, rlpi, rupi;
92      
93 <    StickyParam sticky1 = getStickyParam(atomType);
93 >    StickyAdapter sticky1 = StickyAdapter(atomType);
94  
95      // Now, iterate over all known types and add to the mixing map:
96      
# Line 135 | Line 98 | namespace OpenMD {
98      for( it = StickyMap.begin(); it != StickyMap.end(); ++it) {
99        
100        AtomType* atype2 = (*it).second;
101 <    
102 <      StickyParam sticky2 = getStickyParam(atype2);
101 >      
102 >      StickyAdapter sticky2 = StickyAdapter(atype2);
103  
104        StickyInteractionData mixer;        
105            
# Line 145 | Line 108 | namespace OpenMD {
108        // Lorentz- Berthelot mixing rules (which happen to do the right thing
109        // when atomType and atype2 happen to be the same.
110        
111 <      mixer.rl   = 0.5 * ( sticky1.rl + sticky2.rl );
112 <      mixer.ru   = 0.5 * ( sticky1.ru + sticky2.ru );
113 <      mixer.rlp  = 0.5 * ( sticky1.rlp + sticky2.rlp );
114 <      mixer.rup  = 0.5 * ( sticky1.rup + sticky2.rup );
111 >      mixer.rl   = 0.5 * ( sticky1.getRl() + sticky2.getRl() );
112 >      mixer.ru   = 0.5 * ( sticky1.getRu() + sticky2.getRu() );
113 >      mixer.rlp  = 0.5 * ( sticky1.getRlp() + sticky2.getRlp() );
114 >      mixer.rup  = 0.5 * ( sticky1.getRup() + sticky2.getRup() );
115        mixer.rbig = max(mixer.ru, mixer.rup);
116 <      mixer.w0  = sqrt( sticky1.w0   * sticky2.w0  );
117 <      mixer.v0  = sqrt( sticky1.v0   * sticky2.v0  );
118 <      mixer.v0p = sqrt( sticky1.v0p  * sticky2.v0p );
119 <      mixer.isPower = atomType->isStickyPower() && atype2->isStickyPower();
116 >      mixer.w0  = sqrt( sticky1.getW0()   * sticky2.getW0()  );
117 >      mixer.v0  = sqrt( sticky1.getW0()   * sticky2.getV0()  );
118 >      mixer.v0p = sqrt( sticky1.getV0p()  * sticky2.getV0p() );
119 >      mixer.isPower = sticky1.isStickyPower() && sticky2.isStickyPower();
120  
121        CubicSpline* s = new CubicSpline();
122        s->addPoint(mixer.rl, 1.0);
# Line 186 | Line 149 | namespace OpenMD {
149     * idat structure.
150     */
151    
152 <  void Sticky::calcForce(InteractionData idat) {
152 >  void Sticky::calcForce(InteractionData &idat) {
153    
154      if (!initialized_) initialize();
155      
193 –    pair<AtomType*, AtomType*> key = make_pair(idat.atype1, idat.atype2);
156      map<pair<AtomType*, AtomType*>, StickyInteractionData>::iterator it;
157 <    it = MixingMap.find(key);
157 >    it = MixingMap.find(idat.atypes);
158      if (it != MixingMap.end()) {
159  
160        StickyInteractionData mixer = (*it).second;
# Line 207 | Line 169 | namespace OpenMD {
169        RealType rbig = mixer.rbig;
170        bool isPower = mixer.isPower;
171        
172 <      if (idat.rij <= rbig) {
211 <        
212 <        RealType r3 = idat.r2 * idat.rij;
213 <        RealType r5 = r3 * idat.r2;
172 >      if ( *(idat.rij) <= rbig) {
173          
174 <        RotMat3x3d A1trans = idat.A1.transpose();
175 <        RotMat3x3d A2trans = idat.A2.transpose();
174 >        RealType r3 = *(idat.r2) * *(idat.rij);
175 >        RealType r5 = r3 * *(idat.r2);
176          
177 +        RotMat3x3d A1trans = idat.A1->transpose();
178 +        RotMat3x3d A2trans = idat.A2->transpose();
179 +        
180          // rotate the inter-particle separation into the two different
181          // body-fixed coordinate systems:
182          
183 <        Vector3d ri = idat.A1 * idat.d;
183 >        Vector3d ri = *(idat.A1) * *(idat.d);
184          
185          // negative sign because this is the vector from j to i:
186          
187 <        Vector3d rj = - idat.A2 * idat.d;
187 >        Vector3d rj = - *(idat.A2) * *(idat.d);
188          
189          RealType xi = ri.x();
190          RealType yi = ri.y();
# Line 247 | Line 209 | namespace OpenMD {
209          RealType sp = 0.0;
210          RealType dspdr = 0.0;
211          
212 <        if (idat.rij < ru) {
213 <          if (idat.rij < rl) {
212 >        if ( *(idat.rij) < ru) {
213 >          if ( *(idat.rij) < rl) {
214              s = 1.0;
215              dsdr = 0.0;
216            } else {          
217              // we are in the switching region
218              
219 <            pair<RealType, RealType> res = mixer.s->getValueAndDerivativeAt(idat.rij);
219 >            pair<RealType, RealType> res = mixer.s->getValueAndDerivativeAt(*(idat.rij));
220              s = res.first;
221              dsdr = res.second;
222            }
223          }
224          
225 <        if (idat.rij < rup) {
226 <          if (idat.rij < rlp) {
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              
232 <            pair<RealType, RealType> res =mixer.sp->getValueAndDerivativeAt(idat.rij);
232 >            pair<RealType, RealType> res =mixer.sp->getValueAndDerivativeAt( *(idat.rij));
233              sp = res.first;
234              dspdr = res.second;
235            }
# Line 278 | Line 240 | namespace OpenMD {
240          RealType w = wi+wj;
241          
242          
243 <        RealType zif = zi/idat.rij - 0.6;
244 <        RealType zis = zi/idat.rij + 0.8;
243 >        RealType zif = zi/ *(idat.rij)  - 0.6;
244 >        RealType zis = zi/ *(idat.rij)  + 0.8;
245          
246 <        RealType zjf = zj/idat.rij - 0.6;
247 <        RealType zjs = zj/idat.rij + 0.8;
246 >        RealType zjf = zj/ *(idat.rij)  - 0.6;
247 >        RealType zjs = zj/ *(idat.rij)  + 0.8;
248          
249          RealType wip = zif*zif*zis*zis - w0;
250          RealType wjp = zjf*zjf*zjs*zjs - w0;
# Line 301 | Line 263 | namespace OpenMD {
263  
264          Vector3d dwip(-2.0*xi*zi*uglyi/r3,
265                        -2.0*yi*zi*uglyi/r3,
266 <                      2.0*(1.0/idat.rij - zi2/r3)*uglyi);
266 >                      2.0*(1.0/ *(idat.rij)  - zi2/r3)*uglyi);
267          
268          Vector3d dwjp(-2.0*xj*zj*uglyj/r3,
269                        -2.0*yj*zj*uglyj/r3,
270 <                      2.0*(1.0/idat.rij - zj2/r3)*uglyj);
270 >                      2.0*(1.0/ *(idat.rij)  - zj2/r3)*uglyj);
271          
272          Vector3d dwidu(4.0*(yi*zi2 + 0.5*yi*(xi2-yi2))/r3,
273                         4.0*(xi*zi2 - 0.5*xi*(xi2-yi2))/r3,
# Line 315 | Line 277 | namespace OpenMD {
277                         4.0*(xj*zj2 - 0.5*xj*(xj2-yj2))/r3,
278                         - 8.0*xj*yj*zj/r3);
279          
280 <        Vector3d dwipdu(2.0*yi*uglyi/idat.rij,
281 <                        -2.0*xi*uglyi/idat.rij,
280 >        Vector3d dwipdu(2.0*yi*uglyi/ *(idat.rij) ,
281 >                        -2.0*xi*uglyi/ *(idat.rij) ,
282                          0.0);
283          
284 <        Vector3d dwjpdu(2.0*yj*uglyj/idat.rij,
285 <                        -2.0*xj*uglyj/idat.rij,
284 >        Vector3d dwjpdu(2.0*yj*uglyj/ *(idat.rij) ,
285 >                        -2.0*xj*uglyj/ *(idat.rij) ,
286                          0.0);
287          
288          if (isPower) {
# Line 331 | Line 293 | namespace OpenMD {
293            // sticky power has no w' function:
294            w = frac1 * wi * wi2 + frac2*wi + frac1*wj*wj2 + frac2*wj + v0p;
295            wp = 0.0;
296 <          dwi = frac1*3.0*wi2*dwi + frac2*dwi;
297 <          dwj = frac1*3.0*wj2*dwi + frac2*dwi;
296 >          dwi = frac1*RealType(3.0)*wi2*dwi + frac2*dwi;
297 >          dwj = frac1*RealType(3.0)*wj2*dwi + frac2*dwi;
298            dwip = V3Zero;
299            dwjp = V3Zero;
300 <          dwidu = frac1*3.0*wi2*dwidu + frac2*dwidu;
301 <          dwidu = frac1*3.0*wj2*dwjdu + frac2*dwjdu;
300 >          dwidu = frac1*RealType(3.0)*wi2*dwidu + frac2*dwidu;
301 >          dwidu = frac1*RealType(3.0)*wj2*dwjdu + frac2*dwjdu;
302            dwipdu = V3Zero;
303            dwjpdu = V3Zero;
304            sp = 0.0;
305            dspdr = 0.0;
306          }
307          
308 <        idat.vpair += 0.5*(v0*s*w + v0p*sp*wp);
309 <        idat.pot += 0.5*(v0*s*w + v0p*sp*wp)*idat.sw;
308 >        *(idat.vpair) += RealType(0.5)*(v0*s*w + v0p*sp*wp);
309 >        (*(idat.pot))[HYDROGENBONDING_FAMILY] += RealType(0.5)*(v0*s*w + v0p*sp*wp)* *(idat.sw) ;
310          
311          // do the torques first since they are easy:
312          // remember that these are still in the body-fixed axes
313          
314 <        Vector3d ti = 0.5*idat.sw*(v0*s*dwidu + v0p*sp*dwipdu);
315 <        Vector3d tj = 0.5*idat.sw*(v0*s*dwjdu + v0p*sp*dwjpdu);
314 >        Vector3d ti = RealType(0.5)* *(idat.sw) *(v0*s*dwidu + v0p*sp*dwipdu);
315 >        Vector3d tj = RealType(0.5)* *(idat.sw) *(v0*s*dwjdu + v0p*sp*dwjpdu);
316          
317          // go back to lab frame using transpose of rotation matrix:
318          
319 <        idat.t1 += A1trans * ti;
320 <        idat.t2 += A2trans * tj;
319 >        *(idat.t1) += A1trans * ti;
320 >        *(idat.t2) += A2trans * tj;
321          
322          // Now, on to the forces:
323          
324          // first rotate the i terms back into the lab frame:
325          
326 <        Vector3d radcomi = (v0 * s * dwi + v0p * sp * dwip) * idat.sw;
327 <        Vector3d radcomj = (v0 * s * dwj + v0p * sp * dwjp) * idat.sw;
326 >        Vector3d radcomi = (v0 * s * dwi + v0p * sp * dwip) *  *(idat.sw);
327 >        Vector3d radcomj = (v0 * s * dwj + v0p * sp * dwjp) *  *(idat.sw);
328          
329          Vector3d fii = A1trans * radcomi;
330          Vector3d fjj = A2trans * radcomj;
331          
332          // now assemble these with the radial-only terms:
333          
334 <        idat.f1 += 0.5 * ((v0*dsdr*w + v0p*dspdr*wp) * idat.d /
335 <                          idat.rij + fii - fjj);
334 >        *(idat.f1) += RealType(0.5) * ((v0*dsdr*w + v0p*dspdr*wp) * *(idat.d) /
335 >                                       *(idat.rij)  + fii - fjj);
336          
337        }
338      }
# Line 378 | Line 340 | namespace OpenMD {
340      return;      
341    }
342  
343 <  RealType Sticky::getSuggestedCutoffRadius(AtomType* at1, AtomType* at2) {
343 >  RealType Sticky::getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) {
344      if (!initialized_) initialize();  
383 –    pair<AtomType*, AtomType*> key = make_pair(at1, at2);
345      map<pair<AtomType*, AtomType*>, StickyInteractionData>::iterator it;
346 <    it = MixingMap.find(key);
346 >    it = MixingMap.find(atypes);
347      if (it == MixingMap.end())
348        return 0.0;
349      else  {

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