ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/ForceFields.cpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/ForceFields.cpp (file contents):
Revision 892 by chuckv, Mon Dec 22 21:27:04 2003 UTC vs.
Revision 1258 by chrisfen, Thu Jun 10 17:09:16 2004 UTC

# Line 34 | Line 34 | void ForceFields::doForces( int calcPot, int calcStres
34      
35   }
36  
37 + void ForceFields::setRcut( double LJrcut ) {
38 +  
39 + #ifdef IS_MPI
40 +  double tempBig = bigSigma;
41 +  MPI_Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX,
42 +                 MPI_COMM_WORLD);
43 + #endif  //is_mpi
44 +  
45 +  if (LJrcut < 2.5 * bigSigma) {
46 +    sprintf( painCave.errMsg,
47 +             "Setting Lennard-Jones cutoff radius to %lf.\n"
48 +             "\tThis value is smaller than %lf, which is\n"
49 +             "\t2.5 * bigSigma, where bigSigma is the largest\n"
50 +             "\tvalue of sigma present in the simulation.\n"
51 +             "\tThis is potentially a problem since the LJ potential may\n"
52 +             "\tbe appreciable at this distance.  If you don't want the\n"
53 +             "\tsmaller cutoff, change the LJrcut variable.\n",
54 +             LJrcut, 2.5*bigSigma);
55 +    painCave.isFatal = 0;
56 +    simError();
57 +  } else {
58 +    sprintf( painCave.errMsg,
59 +             "Setting Lennard-Jones cutoff radius to %lf.\n"
60 +             "\tThis value is larger than %lf, which is\n"
61 +             "\t2.5 * bigSigma, where bigSigma is the largest\n"
62 +             "\tvalue of sigma present in the simulation. This should\n"
63 +             "\tnot be a problem, but could adversely effect performance.\n",
64 +             LJrcut, 2.5*bigSigma);
65 +    painCave.isFatal = 0;
66 +    simError();
67 +  }
68 +  
69 +  //calc rCut and rList
70 +  
71 +  entry_plug->setDefaultRcut( LJrcut );
72 + }
73 +
74   void ForceFields::doForces( int calcPot, int calcStress ){
75  
76 <  int i, isError;
76 >  int i, j, isError;
77    double* frc;
78    double* pos;
79    double* trq;
80    double* A;
81 <  double* u_l;;
81 >  double* u_l;
82 >  double* rc;
83 >  double* massRatio;
84 >  double factor;
85    SimState* config;
86  
87 +  Molecule* myMols;
88 +  Atom** myAtoms;
89 +  int numAtom;
90 +  int curIndex;
91 +  double mtot;
92 +  int numMol;
93 +  int numCutoffGroups;
94 +  CutoffGroup* myCutoffGroup;
95 +  vector<CutoffGroup*>::iterator iterCutoff;
96 +  double com[3];
97 +  vector<double> rcGroup;
98 +  
99    short int passedCalcPot = (short int)calcPot;
100    short int passedCalcStress = (short int)calcStress;
101  
# Line 59 | Line 111 | void ForceFields::doForces( int calcPot, int calcStres
111   #endif
112    
113    for(i=0; i<entry_plug->n_mol; i++ ){
114 <    entry_plug->molecules[i].calcForces();
114 >    // CalcForces in molecules takes care of mapping rigid body coordinates
115 >    // into atomic coordinates
116 >    entry_plug->molecules[i].calcForces();    
117    }
118  
119   #ifdef PROFILE
# Line 74 | Line 128 | void ForceFields::doForces( int calcPot, int calcStres
128    A   = config->getAmatArray();
129    u_l = config->getUlArray();
130  
131 +  if(entry_plug->haveCutoffGroups){
132 +    myMols = entry_plug->molecules;
133 +    numMol = entry_plug->n_mol;
134 +    for(int i  = 0; i < numMol; i++){
135 +        
136 +      numCutoffGroups = myMols[i].getNCutoffGroups();
137 +      for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL;
138 +                                                    myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
139 +        //get center of mass of the cutoff group
140 +        myCutoffGroup->getCOM(com);
141 +
142 +        rcGroup.push_back(com[0]);
143 +        rcGroup.push_back(com[1]);
144 +        rcGroup.push_back(com[2]);
145 +        
146 +      }// end for(myCutoffGroup)
147 +      
148 +    }//end for(int i = 0)
149 +
150 +    rc = &rcGroup[0];
151 +  }
152 +  else{
153 +    // center of mass of the group is the same as position of the atom  if cutoff group does not exist
154 +    rc = pos;
155 +  }
156 +  
157 +
158 +
159    isError = 0;
160    entry_plug->lrPot = 0.0;
161  
# Line 87 | Line 169 | void ForceFields::doForces( int calcPot, int calcStres
169   #endif
170  
171    fortranForceLoop( pos,
172 +                    rc,
173                      A,
174                      u_l,
175                      frc,
# Line 97 | Line 180 | void ForceFields::doForces( int calcPot, int calcStres
180                      &passedCalcStress,
181                      &isError );
182  
183 +
184   #ifdef PROFILE
185    endProfile(pro8);
186   #endif
# Line 109 | Line 193 | void ForceFields::doForces( int calcPot, int calcStres
193      simError();
194    }
195  
196 +  if (entry_plug->useSolidThermInt && !entry_plug->useLiquidThermInt) {
197 +    
198 +    factor = pow(entry_plug->thermIntLambda, entry_plug->thermIntK);
199 +    for (i=0; i < entry_plug->n_atoms; i++) {
200 +      for (j=0; j< 3; j++)
201 +        frc[3*i + j] *= factor;
202 +      if (entry_plug->atoms[i]->isDirectional()) {
203 +        for (j=0; j< 3; j++)
204 +          trq[3*i + j] *= factor;
205 +      }
206 +    }
207 +    entry_plug->vRaw = entry_plug->lrPot;
208 +    entry_plug->lrPot *= factor;
209 +    entry_plug->lrPot += entry_plug->restraint->Calc_Restraint_Forces(entry_plug->integrableObjects);
210 +    entry_plug->vHarm = entry_plug->restraint->getVharm();
211 +  }
212 +  
213 +  if (entry_plug->useLiquidThermInt) {
214 +    
215 +    factor = pow(entry_plug->thermIntLambda, entry_plug->thermIntK);
216 +    for (i=0; i < entry_plug->n_atoms; i++) {
217 +      for (j=0; j< 3; j++)
218 +        frc[3*i + j] *= factor;
219 +      if (entry_plug->atoms[i]->isDirectional()) {
220 +        for (j=0; j< 3; j++)
221 +          trq[3*i + j] *= factor;
222 +      }
223 +    }
224 +    entry_plug->vRaw = entry_plug->lrPot;
225 +    entry_plug->lrPot *= factor;
226 +  }
227 +
228 +  for(i=0; i<entry_plug->n_mol; i++ ){
229 +    entry_plug->molecules[i].atoms2rigidBodies();
230 +  }
231 +
232 +
233   #ifdef IS_MPI
234    sprintf( checkPointMsg,
235             "returned from the force calculation.\n" );
# Line 140 | Line 261 | void ForceFields::initFortran(int ljMixPolicy, int use
261   #endif // is_mpi
262    
263   }
264 +
265 +
266 + void ForceFields::initRestraints(){
267 +  int i;
268 +  // store the initial info.
269 +  // set the omega values to zero
270 +  for (i=0; i<entry_plug->integrableObjects.size(); i++)
271 +    entry_plug->integrableObjects[i]->setZangle( 0.0 );
272 +
273 +  entry_plug->restraint->Store_Init_Info(entry_plug->integrableObjects);
274 +
275 + }
276 +
277 + void ForceFields::dumpzAngle(){
278 +
279 +  // store the initial info.
280 +  entry_plug->restraint->Write_zAngle_File(entry_plug->integrableObjects);
281 +
282 + }

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines