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root/group/trunk/OOPSE/libmdtools/ForceFields.cpp
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Comparing trunk/OOPSE/libmdtools/ForceFields.cpp (file contents):
Revision 472 by mmeineke, Mon Apr 7 21:16:35 2003 UTC vs.
Revision 1097 by gezelter, Mon Apr 12 20:32:20 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>
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 21 | Line 30 | void ForceFields::calcRcut( void ){
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 ){
# Line 39 | Line 77 | void ForceFields::doForces( int calcPot, int calcStres
77    double* frc;
78    double* pos;
79    double* trq;
42 –  double* tau;
80    double* A;
81    double* u_l;;
82 <  DirectionalAtom* dAtom;
82 >  SimState* config;
83  
47 –  double ut[3];
48 –
49 –  //u_l = new double[entry_plug->n_atoms];
50 –
84    short int passedCalcPot = (short int)calcPot;
85    short int passedCalcStress = (short int)calcStress;
86  
87 <  // forces are zeroed here, before any are acumulated.
87 >  // forces are zeroed here, before any are accumulated.
88    // NOTE: do not rezero the forces in Fortran.
89  
57 –
90    for(i=0; i<entry_plug->n_atoms; i++){
91 <    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 <    
91 >    entry_plug->atoms[i]->zeroForces();    
92    }
93  
94 + #ifdef PROFILE
95 +  startProfile(pro7);
96 + #endif
97 +  
98    for(i=0; i<entry_plug->n_mol; i++ ){
99 +    // CalcForces in molecules takes care of mapping rigid body coordinates
100 +    // into atomic coordinates
101      entry_plug->molecules[i].calcForces();
102    }
103  
104 <  frc = Atom::getFrcArray();
105 <  pos = Atom::getPosArray();
106 <  trq = Atom::getTrqArray();
81 <  A   = Atom::getAmatArray();
82 <  u_l = Atom::getUlArray();
83 <  tau = entry_plug->tau;
104 > #ifdef PROFILE
105 >  endProfile( pro7 );
106 > #endif
107  
108 +  config = entry_plug->getConfiguration();
109    
110 +  frc = config->getFrcArray();
111 +  pos = config->getPosArray();
112 +  trq = config->getTrqArray();
113 +  A   = config->getAmatArray();
114 +  u_l = config->getUlArray();
115 +
116    isError = 0;
117    entry_plug->lrPot = 0.0;
88 –  tau[0] = 0.0;
89 –  tau[1] = 0.0;
90 –  tau[2] = 0.0;
91 –  
118  
119 +  for (i=0; i<9; i++) {
120 +    entry_plug->tau[i] = 0.0;
121 +  }
122  
123 <  
123 >
124 > #ifdef PROFILE
125 >  startProfile(pro8);
126 > #endif
127 >
128    fortranForceLoop( pos,
129                      A,
130                      u_l,
131                      frc,
132                      trq,
133 <                    tau,
133 >                    entry_plug->tau,
134                      &(entry_plug->lrPot),
135                      &passedCalcPot,
136                      &passedCalcStress,
137                      &isError );
138  
139 + #ifdef PROFILE
140 +  endProfile(pro8);
141 + #endif
142  
107 –  //  delete[] u_l;
143  
144    if( isError ){
145      sprintf( painCave.errMsg,
# Line 113 | Line 148 | void ForceFields::doForces( int calcPot, int calcStres
148      simError();
149    }
150  
151 +  for(i=0; i<entry_plug->n_mol; i++ ){
152 +    entry_plug->molecules[i].atoms2rigidBodies();
153 +  }
154 +
155 +
156   #ifdef IS_MPI
157    sprintf( checkPointMsg,
158             "returned from the force calculation.\n" );
159    MPIcheckPoint();
160   #endif // is_mpi
161 +  
162  
163   }
164  

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