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root/group/trunk/OOPSE/libmdtools/ForceFields.cpp
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Comparing trunk/OOPSE/libmdtools/ForceFields.cpp (file contents):
Revision 428 by mmeineke, Thu Mar 27 21:07:14 2003 UTC vs.
Revision 1167 by tim, Wed May 12 16:38:45 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 +  double* rc;
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 +  double com[3];
96 +  vector<double> rcGroup;
97 +  
98    short int passedCalcPot = (short int)calcPot;
99    short int passedCalcStress = (short int)calcStress;
100  
101 <  // forces are zeroed here, before any are acumulated.
101 >  // forces are zeroed here, before any are accumulated.
102    // NOTE: do not rezero the forces in Fortran.
103  
104    for(i=0; i<entry_plug->n_atoms; i++){
105 <    entry_plug->atoms[i]->zeroForces();
105 >    entry_plug->atoms[i]->zeroForces();    
106    }
107  
108 + #ifdef PROFILE
109 +  startProfile(pro7);
110 + #endif
111 +  
112    for(i=0; i<entry_plug->n_mol; i++ ){
113 <    entry_plug->molecules[i].calcForces();
113 >    // CalcForces in molecules takes care of mapping rigid body coordinates
114 >    // into atomic coordinates
115 >    entry_plug->molecules[i].calcForces();    
116    }
117  
118 <  frc = Atom::getFrcArray();
119 <  pos = Atom::getPosArray();
120 <  trq = Atom::getTrqArray();
63 <  A   = Atom::getAmatArray();
64 <  u_l = Atom::getUlArray();
65 <  tau = entry_plug->tau;
118 > #ifdef PROFILE
119 >  endProfile( pro7 );
120 > #endif
121  
122 +  config = entry_plug->getConfiguration();
123    
124 +  frc = config->getFrcArray();
125 +  pos = config->getPosArray();
126 +  trq = config->getTrqArray();
127 +  A   = config->getAmatArray();
128 +  u_l = config->getUlArray();
129 +
130 +  if(entry_plug->haveCutoffGroups){
131 +    myMols = entry_plug->molecules;
132 +    numMol = entry_plug->n_mol;
133 +    for(int i  = 0; i < numMol; i++){
134 +        
135 +      numCutoffGroups = myMols[i].getNCutoffGroups();
136 +      for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL;
137 +                                                    myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
138 +        //get center of mass of the cutoff group
139 +        myCutoffGroup->getCOM(com);
140 +
141 +        rcGroup.push_back(com[0]);
142 +        rcGroup.push_back(com[1]);
143 +        rcGroup.push_back(com[2]);
144 +        
145 +      }// end for(myCutoffGroup)
146 +      
147 +    }//end for(int i = 0)
148 +
149 +    rc = &rcGroup[0];
150 +  }
151 +  else{
152 +    // center of mass of the group is the same as position of the atom  if cutoff group does not exist
153 +    rc = pos;
154 +  }
155 +  
156 +
157 +
158    isError = 0;
159    entry_plug->lrPot = 0.0;
160  
161 <  
161 >  for (i=0; i<9; i++) {
162 >    entry_plug->tau[i] = 0.0;
163 >  }
164 >
165 >
166 > #ifdef PROFILE
167 >  startProfile(pro8);
168 > #endif
169 >
170    fortranForceLoop( pos,
171 +                    rc,
172                      A,
173                      u_l,
174                      frc,
175                      trq,
176 <                    tau,
176 >                    entry_plug->tau,
177                      &(entry_plug->lrPot),
178                      &passedCalcPot,
179                      &passedCalcStress,
180                      &isError );
181  
182  
183 + #ifdef PROFILE
184 +  endProfile(pro8);
185 + #endif
186 +
187 +
188    if( isError ){
189      sprintf( painCave.errMsg,
190               "Error returned from the fortran force calculation.\n" );
# Line 88 | Line 192 | void ForceFields::doForces( int calcPot, int calcStres
192      simError();
193    }
194  
195 +  for(i=0; i<entry_plug->n_mol; i++ ){
196 +    entry_plug->molecules[i].atoms2rigidBodies();
197 +  }
198 +
199 +
200   #ifdef IS_MPI
201    sprintf( checkPointMsg,
202             "returned from the force calculation.\n" );
203    MPIcheckPoint();
204   #endif // is_mpi
205 +  
206  
207   }
208  

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