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root/group/trunk/OOPSE/libmdtools/ForceFields.cpp
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Comparing trunk/OOPSE/libmdtools/ForceFields.cpp (file contents):
Revision 626 by mmeineke, Wed Jul 16 21:30:56 2003 UTC vs.
Revision 1212 by chrisfen, Tue Jun 1 17:15:43 2004 UTC

# Line 3 | Line 3 | using namespace std;
3   using namespace std;
4  
5  
6 < #include <cstdlib>
6 > #include <stdlib.h>
7  
8   #ifdef IS_MPI
9   #include <mpi.h>
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 26 | Line 30 | void ForceFields::calcRcut( void ){
30  
31    //calc rCut and rList
32  
33 <  entry_plug->setRcut( 2.5 * bigSigma );  
33 >  entry_plug->setDefaultRcut( 2.5 * bigSigma );  
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;;
82 <  DirectionalAtom* dAtom;
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 49 | 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();
126 +  pos = config->getPosArray();
127 +  trq = config->getTrqArray();
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    
58 –  frc = Atom::getFrcArray();
59 –  pos = Atom::getPosArray();
60 –  trq = Atom::getTrqArray();
61 –  A   = Atom::getAmatArray();
62 –  u_l = Atom::getUlArray();
157  
158 +
159    isError = 0;
160    entry_plug->lrPot = 0.0;
161  
# Line 68 | Line 163 | void ForceFields::doForces( int calcPot, int calcStres
163      entry_plug->tau[i] = 0.0;
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 79 | Line 180 | void ForceFields::doForces( int calcPot, int calcStres
180                      &passedCalcStress,
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 86 | 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->useSolidThermInt && !entry_plug->useLiquidThermInt) {
202 +
203 +    factor = pow(entry_plug->thermIntLambda, entry_plug->thermIntK);
204 +    for (i=0; i < entry_plug->integrableObjects.size(); i++) {
205 +      for (j=0; j< 3; j++)
206 +        frc[3*i + j] *= factor;
207 +      if (entry_plug->integrableObjects[i]->isDirectional()) {
208 +        for (j=0; j< 3; j++)
209 +          trq[3*i + j] *= factor;
210 +      }
211 +    }
212 +    entry_plug->vRaw = entry_plug->lrPot;
213 +    entry_plug->lrPot *= factor;
214 +    entry_plug->lrPot += entry_plug->restraint->Calc_Restraint_Forces(entry_plug->integrableObjects);
215 +    entry_plug->vHarm = entry_plug->restraint->getVharm();
216 +  }
217 +
218 +  if (entry_plug->useLiquidThermInt) {
219 +
220 +    factor = pow(entry_plug->thermIntLambda, entry_plug->thermIntK);
221 +    for (i=0; i < entry_plug->integrableObjects.size(); i++) {
222 +      for (j=0; j< 3; j++)
223 +        frc[3*i + j] *= factor;
224 +      if (entry_plug->integrableObjects[i]->isDirectional()) {
225 +        for (j=0; j< 3; j++)
226 +          trq[3*i + j] *= factor;
227 +      }
228 +    }
229 +    entry_plug->vRaw = entry_plug->lrPot;
230 +    entry_plug->lrPot *= factor;
231 +    entry_plug->lrPot += entry_plug->restraint->Calc_Restraint_Forces(entry_plug->integrableObjects);
232 +    entry_plug->vHarm = entry_plug->restraint->getVharm();
233 +  }
234 +
235   #ifdef IS_MPI
236    sprintf( checkPointMsg,
237             "returned from the force calculation.\n" );
# Line 117 | Line 263 | void ForceFields::initFortran(int ljMixPolicy, int use
263   #endif // is_mpi
264    
265   }
266 +
267 +
268 + void ForceFields::initRestraints(){
269 +  int i;
270 +  // store the initial info.
271 +  // set the omega values to zero
272 +  for (i=0; i<entry_plug->integrableObjects.size(); i++)
273 +    entry_plug->integrableObjects[i]->setZangle( 0.0 );
274 +
275 +  entry_plug->restraint->Store_Init_Info(entry_plug->integrableObjects);
276 +
277 + }
278 +
279 + void ForceFields::dumpzAngle(){
280 +
281 +  // store the initial info.
282 +  entry_plug->restraint->Write_zAngle_File(entry_plug->integrableObjects);
283 +
284 + }

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