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root/group/trunk/OOPSE/libmdtools/ForceFields.cpp
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Comparing trunk/OOPSE/libmdtools/ForceFields.cpp (file contents):
Revision 443 by mmeineke, Wed Apr 2 22:19:03 2003 UTC vs.
Revision 1212 by chrisfen, Tue Jun 1 17:15:43 2004 UTC

# Line 1 | Line 1
1 < #include <cstdlib>
1 > #include <iostream>
2  
3 + using namespace std;
4 +
5 +
6 + #include <stdlib.h>
7 +
8   #ifdef IS_MPI
9   #include <mpi.h>
5 – #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 16 | Line 24 | void ForceFields::calcRcut( void ){
24  
25   #ifdef IS_MPI
26    double tempBig = bigSigma;
27 <  MPI::COMM_WORLD.Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX );
27 >  MPI_Allreduce( &tempBig, &bigSigma, 1, MPI_DOUBLE, MPI_MAX,
28 >                 MPI_COMM_WORLD);
29   #endif  //is_mpi
30  
31    //calc rCut and rList
32  
33 <  entry_plug->rCut = 2.5 * bigSigma;
34 <  if(entry_plug->rCut > (entry_plug->box_x / 2.0))
35 <    entry_plug->rCut = entry_plug->box_x / 2.0;
36 <  if(entry_plug->rCut > (entry_plug->box_y / 2.0))
37 <    entry_plug->rCut = entry_plug->box_y / 2.0;
29 <  if(entry_plug->rCut > (entry_plug->box_z / 2.0))
30 <    entry_plug->rCut = entry_plug->box_z / 2.0;
33 >  entry_plug->setDefaultRcut( 2.5 * bigSigma );  
34 >    
35 > }
36 >
37 > void ForceFields::setRcut( double LJrcut ) {
38    
39 <  entry_plug->rList = entry_plug->rCut + 1.0;
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;
42 –  double* tau;
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 <  double ut[3];
88 <
89 <  //u_l = new double[entry_plug->n_atoms];
90 <
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  
102 <  // forces are zeroed here, before any are acumulated.
102 >  // forces are zeroed here, before any are accumulated.
103    // NOTE: do not rezero the forces in Fortran.
104  
57 –
105    for(i=0; i<entry_plug->n_atoms; i++){
106 <    entry_plug->atoms[i]->zeroForces();
60 <
61 <    if( entry_plug->atoms[i]->isDirectional() ){
62 <      dAtom = (DirectionalAtom *)entry_plug->atoms[i];
63 <      dAtom->getU(ut);
64 <    
65 <
66 <      if(dAtom->getIndex()== 1){
67 <        std::cerr << "atom 2's u_l = " << ut[0] << ", " << ut[1]
68 <                  << ", " << ut[2] << "\n";
69 <      }
70 <    }
71 <    
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 <  frc = Atom::getFrcArray();
120 <  pos = Atom::getPosArray();
121 <  trq = Atom::getTrqArray();
81 <  A   = Atom::getAmatArray();
82 <  u_l = Atom::getUlArray();
83 <  tau = entry_plug->tau;
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 +  
157 +
158 +
159    isError = 0;
160    entry_plug->lrPot = 0.0;
161  
162 +  for (i=0; i<9; i++) {
163 +    entry_plug->tau[i] = 0.0;
164 +  }
165  
166 <  
166 >
167 > #ifdef PROFILE
168 >  startProfile(pro8);
169 > #endif
170 >
171    fortranForceLoop( pos,
172 +                    rc,
173                      A,
174                      u_l,
175                      frc,
176                      trq,
177 <                    tau,
177 >                    entry_plug->tau,
178                      &(entry_plug->lrPot),
179                      &passedCalcPot,
180                      &passedCalcStress,
181                      &isError );
182  
183  
184 <  //  delete[] u_l;
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 109 | 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" );
238    MPIcheckPoint();
239   #endif // is_mpi
240 +  
241  
242   }
243  
# Line 139 | 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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