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root/group/trunk/OOPSE/libmdtools/ForceFields.cpp
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Comparing trunk/OOPSE/libmdtools/ForceFields.cpp (file contents):
Revision 841 by mmeineke, Wed Oct 29 17:55:28 2003 UTC vs.
Revision 1097 by gezelter, Mon Apr 12 20:32:20 2004 UTC

# Line 10 | Line 10 | using namespace std;
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 30 | Line 34 | void ForceFields::calcRcut( void ){
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;
# Line 50 | Line 91 | void ForceFields::doForces( int calcPot, int calcStres
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 + #ifdef PROFILE
105 +  endProfile( pro7 );
106 + #endif
107 +
108    config = entry_plug->getConfiguration();
109    
110    frc = config->getFrcArray();
# Line 69 | Line 120 | void ForceFields::doForces( int calcPot, int calcStres
120      entry_plug->tau[i] = 0.0;
121    }
122  
72 –  std::cerr << "before\n"
73 –            << "  force[0] = " << frc[0] << "\n"
74 –            << "  pos[0]   = " << pos[0] << "\n"
75 –            << "  trq[0]   = " << trq[0] << "\n"
76 –            << "  A[0]     = " << A[0] << "\n"
77 –            << "  tau      = " << entry_plug->tau[0] << ", " << entry_plug->tau[1] << ", " << entry_plug->tau[2] << "\n"
78 –            << "             " << entry_plug->tau[3] << ", " << entry_plug->tau[4] << ", " << entry_plug->tau[5] << "\n"
79 –            << "             " << entry_plug->tau[6] << ", " << entry_plug->tau[7] << ", " << entry_plug->tau[8] << "\n\n";
123  
124 + #ifdef PROFILE
125 +  startProfile(pro8);
126 + #endif
127 +
128    fortranForceLoop( pos,
129                      A,
130                      u_l,
# Line 89 | Line 136 | void ForceFields::doForces( int calcPot, int calcStres
136                      &passedCalcStress,
137                      &isError );
138  
139 + #ifdef PROFILE
140 +  endProfile(pro8);
141 + #endif
142  
93 –  std::cerr << "after\n"
94 –            << "  force[0] = " << frc[0] << "\n"
95 –            << "  pos[0]   = " << pos[0] << "\n"
96 –            << "  trq[0]   = " << trq[0] << "\n"
97 –            << "  A[0]     = " << A[0] << "\n"
98 –            << "  tau      = " << entry_plug->tau[0] << ", " << entry_plug->tau[1] << ", " << entry_plug->tau[2] << "\n"
99 –            << "             " << entry_plug->tau[3] << ", " << entry_plug->tau[4] << ", " << entry_plug->tau[5] << "\n"
100 –            << "             " << entry_plug->tau[6] << ", " << entry_plug->tau[7] << ", " << entry_plug->tau[8] << "\n\n";
143  
144    if( isError ){
145      sprintf( painCave.errMsg,
# Line 106 | 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" );

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