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root/group/trunk/OOPSE/libmdtools/ForceFields.cpp
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Comparing trunk/OOPSE/libmdtools/ForceFields.cpp (file contents):
Revision 1144 by tim, Sat May 1 18:52:38 2004 UTC vs.
Revision 1157 by tim, Tue May 11 20:33:41 2004 UTC

# Line 73 | Line 73 | void ForceFields::doForces( int calcPot, int calcStres
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;
# Line 83 | Line 83 | void ForceFields::doForces( int calcPot, int calcStres
83    double* massRatio;
84    SimState* config;
85  
86 +  Molecule* myMols;
87 +  Atom** myAtoms;
88 +  int numAtom;
89 +  int curIndex;
90 +  double mtot;
91 +  int numMol;
92 +  int numCutoffGroups;
93 +  CutoffGroup* myCutoffGroup;
94 +  vector<CutoffGroup*>::iterator iterCutoff;
95 +  Atom* cutoffAtom;
96 +  vector<Atom*>::iterator iterAtom;  
97 +  double com[3];
98 +  double tempPos[3];
99 +  int atomIndex;
100 +  
101    short int passedCalcPot = (short int)calcPot;
102    short int passedCalcStress = (short int)calcStress;
103  
# Line 100 | Line 115 | void ForceFields::doForces( int calcPot, int calcStres
115    for(i=0; i<entry_plug->n_mol; i++ ){
116      // CalcForces in molecules takes care of mapping rigid body coordinates
117      // into atomic coordinates
118 <    entry_plug->molecules[i].calcForces();
118 >    entry_plug->molecules[i].calcForces();    
119    }
120  
121   #ifdef PROFILE
# Line 114 | Line 129 | void ForceFields::doForces( int calcPot, int calcStres
129    trq = config->getTrqArray();
130    A   = config->getAmatArray();
131    u_l = config->getUlArray();
117 –  rc = config->getRcArray();
118 –  massRatio = config->getMassRatioArray();
132  
133 +  if(entry_plug->haveCutoffGroups){
134 +    //if
135 +    myMols = entry_plug->molecules;
136 +    numMol = entry_plug->n_mol;
137 +    for(int i  = 0; i < numMol; i++){
138 +      numAtom = myMols[i].getNAtoms();
139 +      myAtoms = myMols[i].getMyAtoms();
140 +
141 +      
142 +      for(int j = 0; j < numAtom; j++){
143 + #ifdef IS_MPI
144 +        atomIndex = myAtoms[j]->getGlobalIndex();
145 + #else
146 +        atomIndex = myAtoms[j]->getIndex();
147 + #endif
148 +
149 +        if(myMols[i].belongToCutoffGroup(atomIndex))
150 +          continue;
151 +        else{
152 +          myAtoms[j]->getPos(tempPos);
153 +          myAtoms[j]->setRc(tempPos);
154 +        }
155 +          
156 +      }
157 +        
158 +      numCutoffGroups = myMols[i].getNCutoffGroups();
159 +      for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL;
160 +                                                    myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
161 +        //get center of mass of the cutoff group
162 +        myCutoffGroup->getCOM(com);
163 +
164 +        for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL;
165 +                                             cutoffAtom = myCutoffGroup->beginAtom(iterAtom)){
166 +          cutoffAtom->setRc(com);
167 +        }  
168 +                                
169 +      }// end for(myCutoffGroup)
170 +      
171 +    }//end for(int i = 0)
172 +
173 +    rc = config->getRcArray();
174 +  }
175 +  else{
176 +    // center of mass of the group is the same as position of the atom  if cutoff group does not exist
177 +    rc = pos;
178 +  }
179 +  
180 +
181 +
182    isError = 0;
183    entry_plug->lrPot = 0.0;
184  

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