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root/group/trunk/OOPSE/libmdtools/ForceFields.cpp
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Comparing trunk/OOPSE/libmdtools/ForceFields.cpp (file contents):
Revision 843 by mmeineke, Wed Oct 29 20:41:39 2003 UTC vs.
Revision 1180 by chrisfen, Thu May 20 20:24:07 2004 UTC

# Line 10 | Line 10 | using namespace std;
10   #endif // is_mpi
11  
12  
13 + #ifdef PROFILE
14 + #include "mdProfile.hpp"
15 + #endif
16 +
17   #include "simError.h"
18   #include "ForceFields.hpp"
19   #include "Atom.hpp"
# Line 30 | 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 50 | Line 106 | void ForceFields::doForces( int calcPot, int calcStres
106      entry_plug->atoms[i]->zeroForces();    
107    }
108  
109 + #ifdef PROFILE
110 +  startProfile(pro7);
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
120 +  endProfile( pro7 );
121 + #endif
122 +
123    config = entry_plug->getConfiguration();
124    
125    frc = config->getFrcArray();
# Line 62 | 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 70 | Line 164 | void ForceFields::doForces( int calcPot, int calcStres
164    }
165  
166  
167 + #ifdef PROFILE
168 +  startProfile(pro8);
169 + #endif
170 +
171    fortranForceLoop( pos,
172 +                    rc,
173                      A,
174                      u_l,
175                      frc,
# Line 82 | Line 181 | void ForceFields::doForces( int calcPot, int calcStres
181                      &isError );
182  
183  
184 + #ifdef PROFILE
185 +  endProfile(pro8);
186 + #endif
187  
188 +
189    if( isError ){
190      sprintf( painCave.errMsg,
191               "Error returned from the fortran force calculation.\n" );
# Line 90 | Line 193 | void ForceFields::doForces( int calcPot, int calcStres
193      simError();
194    }
195  
196 +  for(i=0; i<entry_plug->n_mol; i++ ){
197 +    entry_plug->molecules[i].atoms2rigidBodies();
198 +  }
199 +
200 +
201 +  if (entry_plug->useThermInt) {
202 +    myStunts = entry_plug->integrableObjects;
203 +
204 +    factor = pow(entry_plug->thermIntLambda, entry_plug->thermIntK);
205 +    for (i=0; i < myStunts.size(); i++) {
206 +      for (j=0; j< 3; j++)
207 +        frc[3*i + j] *= factor;
208 +      if (myStunts[i]->isDirectional()) {
209 +        for (j=0; j< 3; j++)
210 +          trq[3*i + j] *= factor;
211 +      }
212 +    }
213 +    entry_plug->vRaw = entry_plug->lrPot;
214 +    entry_plug->lrPot *= factor;
215 +    entry_plug->lrPot += entry_plug->restraint->Calc_Restraint_Forces(myStunts);
216 +    entry_plug->vHarm = entry_plug->restraint->getVharm();
217 +  }
218 +
219   #ifdef IS_MPI
220    sprintf( checkPointMsg,
221             "returned from the force calculation.\n" );
# Line 121 | Line 247 | void ForceFields::initFortran(int ljMixPolicy, int use
247   #endif // is_mpi
248    
249   }
250 +
251 +
252 + void ForceFields::initRestraints(){
253 +
254 +  // store the initial info.
255 +  entry_plug->restraint->Store_Init_Info();
256 +
257 + }
258 +
259 + void ForceFields::dumpzAngle(){
260 +
261 +  // store the initial info.
262 +  entry_plug->restraint->Write_zAngle_File();
263 +
264 + }

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