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root/group/trunk/OOPSE/libmdtools/ForceFields.cpp
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Comparing trunk/OOPSE/libmdtools/ForceFields.cpp (file contents):
Revision 626 by mmeineke, Wed Jul 16 21:30:56 2003 UTC vs.
Revision 1142 by tim, Thu Apr 29 02:11:49 2004 UTC

# Line 3 | Line 3 | using namespace std;
3   using namespace std;
4  
5  
6 < #include <cstdlib>
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 26 | Line 30 | void ForceFields::calcRcut( void ){
30  
31    //calc rCut and rList
32  
33 <  entry_plug->setRcut( 2.5 * bigSigma );  
33 >  entry_plug->setDefaultRcut( 2.5 * bigSigma );  
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 36 | Line 78 | void ForceFields::doForces( int calcPot, int calcStres
78    double* pos;
79    double* trq;
80    double* A;
81 <  double* u_l;;
82 <  DirectionalAtom* dAtom;
81 >  double* u_l;
82 >  double* rc;
83 >  double* massRatio;
84 >  SimState* config;
85  
86    short int passedCalcPot = (short int)calcPot;
87    short int passedCalcStress = (short int)calcStress;
# Line 49 | Line 93 | void ForceFields::doForces( int calcPot, int calcStres
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 +    // CalcForces in molecules takes care of mapping rigid body coordinates
102 +    // into atomic coordinates
103      entry_plug->molecules[i].calcForces();
104    }
105  
106 + #ifdef PROFILE
107 +  endProfile( pro7 );
108 + #endif
109 +
110 +  config = entry_plug->getConfiguration();
111    
112 <  
113 <  frc = Atom::getFrcArray();
114 <  pos = Atom::getPosArray();
115 <  trq = Atom::getTrqArray();
116 <  A   = Atom::getAmatArray();
117 <  u_l = Atom::getUlArray();
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;
# Line 68 | Line 124 | void ForceFields::doForces( int calcPot, int calcStres
124      entry_plug->tau[i] = 0.0;
125    }
126  
127 +
128 + #ifdef PROFILE
129 +  startProfile(pro8);
130 + #endif
131 +
132    fortranForceLoop( pos,
133 +                    rc,
134 +                    massRatio,
135                      A,
136                      u_l,
137                      frc,
# Line 79 | Line 142 | void ForceFields::doForces( int calcPot, int calcStres
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 86 | 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" );

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