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root/group/trunk/OOPSE/libmdtools/ForceFields.cpp
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Comparing trunk/OOPSE/libmdtools/ForceFields.cpp (file contents):
Revision 424 by mmeineke, Thu Mar 27 20:36:16 2003 UTC vs.
Revision 1136 by tim, Tue Apr 27 16:26:44 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 15 | 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;
28 <  if(entry_plug->rCut > (entry_plug->box_z / 2.0))
29 <    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 38 | Line 77 | void ForceFields::doForces( int calcPot, int calcStres
77    double* frc;
78    double* pos;
79    double* trq;
41 –  double* tau;
80    double* A;
81    double* u_l;
82 +  double* rc;
83 +  double* massRatio;
84 +  SimState* config;
85  
45 –
86    short int passedCalcPot = (short int)calcPot;
87    short int passedCalcStress = (short int)calcStress;
88  
89 <  // forces are zeroed here, before any are acumulated.
89 >  // forces are zeroed here, before any are accumulated.
90    // NOTE: do not rezero the forces in Fortran.
91  
92    for(i=0; i<entry_plug->n_atoms; i++){
93 <    entry_plug->atoms[i]->zeroForces();
93 >    entry_plug->atoms[i]->zeroForces();    
94    }
95  
96 + #ifdef PROFILE
97 +  startProfile(pro7);
98 + #endif
99 +  
100    for(i=0; i<entry_plug->n_mol; i++ ){
101 <    entry_plug->molecules[i]->calc_forces();
101 >    // CalcForces in molecules takes care of mapping rigid body coordinates
102 >    // into atomic coordinates
103 >    entry_plug->molecules[i].calcForces();
104    }
105  
106 <  frc = Atom::getFrcArray();
107 <  pos = Atom::getPosArray();
108 <  trq = Atom::getTrqArray();
63 <  A   = Atom::getAmatArray();
64 <  u_l = Atom::getUlArray();
65 <  tau = entry_plug->tau;
106 > #ifdef PROFILE
107 >  endProfile( pro7 );
108 > #endif
109  
110 +  config = entry_plug->getConfiguration();
111    
112 +  frc = config->getFrcArray();
113 +  pos = config->getPosArray();
114 +  trq = config->getTrqArray();
115 +  A   = config->getAmatArray();
116 +  u_l = config->getUlArray();
117 +  rc = config->getRcArray();
118 +  massRatio = config->getMassRatioArray();
119 +
120    isError = 0;
121    entry_plug->lrPot = 0.0;
122  
123 <  
123 >  for (i=0; i<9; i++) {
124 >    entry_plug->tau[i] = 0.0;
125 >  }
126 >
127 >
128 > #ifdef PROFILE
129 >  startProfile(pro8);
130 > #endif
131 >
132    fortranForceLoop( pos,
133                      A,
134                      u_l,
135                      frc,
136                      trq,
137 <                    tau,
137 >                    rc,
138 >                    massRatio,
139 >                    entry_plug->tau,
140                      &(entry_plug->lrPot),
141                      &passedCalcPot,
142                      &passedCalcStress,
143                      &isError );
144  
145  
146 + #ifdef PROFILE
147 +  endProfile(pro8);
148 + #endif
149 +
150 +
151    if( isError ){
152      sprintf( painCave.errMsg,
153               "Error returned from the fortran force calculation.\n" );
# Line 88 | Line 155 | void ForceFields::doForces( int calcPot, int calcStres
155      simError();
156    }
157  
158 +  for(i=0; i<entry_plug->n_mol; i++ ){
159 +    entry_plug->molecules[i].atoms2rigidBodies();
160 +  }
161 +
162 +
163   #ifdef IS_MPI
164    sprintf( checkPointMsg,
165             "returned from the force calculation.\n" );
166    MPIcheckPoint();
167   #endif // is_mpi
168 +  
169  
170   }
171  

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