| 16 |
|
n_constraints = 0; |
| 17 |
|
n_oriented = 0; |
| 18 |
|
n_dipoles = 0; |
| 19 |
+ |
ndf = 0; |
| 20 |
+ |
ndfRaw = 0; |
| 21 |
|
the_integrator = NULL; |
| 22 |
|
setTemp = 0; |
| 23 |
|
thermalTime = 0.0; |
| 24 |
+ |
rCut = 0.0; |
| 25 |
|
|
| 26 |
|
usePBC = 0; |
| 27 |
|
useLJ = 0; |
| 31 |
|
useGB = 0; |
| 32 |
|
useEAM = 0; |
| 33 |
|
|
| 34 |
+ |
wrapMeSimInfo( this ); |
| 35 |
+ |
} |
| 36 |
|
|
| 37 |
+ |
void SimInfo::setBox(double newBox[3]) { |
| 38 |
+ |
box_x = newBox[0]; |
| 39 |
+ |
box_y = newBox[1]; |
| 40 |
+ |
box_z = newBox[2]; |
| 41 |
+ |
setFortranBoxSize(newBox); |
| 42 |
+ |
} |
| 43 |
|
|
| 44 |
< |
wrapMeSimInfo( this ); |
| 44 |
> |
void SimInfo::getBox(double theBox[3]) { |
| 45 |
> |
theBox[0] = box_x; |
| 46 |
> |
theBox[1] = box_y; |
| 47 |
> |
theBox[2] = box_z; |
| 48 |
|
} |
| 49 |
+ |
|
| 50 |
+ |
int SimInfo::getNDF(){ |
| 51 |
+ |
int ndf_local, ndf; |
| 52 |
+ |
|
| 53 |
+ |
ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints; |
| 54 |
|
|
| 55 |
+ |
#ifdef IS_MPI |
| 56 |
+ |
MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 57 |
+ |
#else |
| 58 |
+ |
ndf = ndf_local; |
| 59 |
+ |
#endif |
| 60 |
+ |
|
| 61 |
+ |
ndf = ndf - 3; |
| 62 |
+ |
|
| 63 |
+ |
return ndf; |
| 64 |
+ |
} |
| 65 |
+ |
|
| 66 |
+ |
int SimInfo::getNDFraw() { |
| 67 |
+ |
int ndfRaw_local, ndfRaw; |
| 68 |
+ |
|
| 69 |
+ |
// Raw degrees of freedom that we have to set |
| 70 |
+ |
ndfRaw_local = 3 * n_atoms + 3 * n_oriented; |
| 71 |
+ |
|
| 72 |
+ |
#ifdef IS_MPI |
| 73 |
+ |
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 74 |
+ |
#else |
| 75 |
+ |
ndfRaw = ndfRaw_local; |
| 76 |
+ |
#endif |
| 77 |
+ |
|
| 78 |
+ |
return ndfRaw; |
| 79 |
+ |
} |
| 80 |
+ |
|
| 81 |
|
void SimInfo::refreshSim(){ |
| 82 |
|
|
| 83 |
|
simtype fInfo; |
| 84 |
|
int isError; |
| 85 |
+ |
int* excl; |
| 86 |
|
|
| 87 |
|
fInfo.box[0] = box_x; |
| 88 |
|
fInfo.box[1] = box_y; |
| 90 |
|
|
| 91 |
|
fInfo.rlist = rList; |
| 92 |
|
fInfo.rcut = rCut; |
| 93 |
< |
fInfo.rrf = rRF; |
| 94 |
< |
fInfo.rt = 0.95 * rRF; |
| 93 |
> |
fInfo.rrf = ecr; |
| 94 |
> |
fInfo.rt = ecr - est; |
| 95 |
|
fInfo.dielect = dielectric; |
| 50 |
– |
|
| 96 |
|
|
| 97 |
|
fInfo.SIM_uses_PBC = usePBC; |
| 98 |
+ |
//fInfo.SIM_uses_LJ = 0; |
| 99 |
|
fInfo.SIM_uses_LJ = useLJ; |
| 100 |
|
fInfo.SIM_uses_sticky = useSticky; |
| 101 |
+ |
//fInfo.SIM_uses_sticky = 0; |
| 102 |
|
fInfo.SIM_uses_dipoles = useDipole; |
| 103 |
< |
fInfo.SIM_uses_RF = useReactionField; |
| 103 |
> |
//fInfo.SIM_uses_dipoles = 0; |
| 104 |
> |
//fInfo.SIM_uses_RF = useReactionField; |
| 105 |
> |
fInfo.SIM_uses_RF = 0; |
| 106 |
|
fInfo.SIM_uses_GB = useGB; |
| 107 |
|
fInfo.SIM_uses_EAM = useEAM; |
| 108 |
|
|
| 109 |
+ |
excl = Exclude::getArray(); |
| 110 |
|
|
| 111 |
|
isError = 0; |
| 112 |
|
|
| 113 |
< |
fInfo; |
| 114 |
< |
n_atoms; |
| 115 |
< |
identArray; |
| 116 |
< |
n_exclude; |
| 117 |
< |
excludes; |
| 118 |
< |
nGlobalExcludes; |
| 119 |
< |
globalExcludes; |
| 120 |
< |
isError; |
| 113 |
> |
// fInfo; |
| 114 |
> |
// n_atoms; |
| 115 |
> |
// identArray; |
| 116 |
> |
// n_exclude; |
| 117 |
> |
// excludes; |
| 118 |
> |
// nGlobalExcludes; |
| 119 |
> |
// globalExcludes; |
| 120 |
> |
// isError; |
| 121 |
|
|
| 122 |
< |
setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excludes, &nGlobalExcludes, globalExcludes, &isError ); |
| 122 |
> |
setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl, |
| 123 |
> |
&nGlobalExcludes, globalExcludes, &isError ); |
| 124 |
|
|
| 125 |
|
if( isError ){ |
| 126 |
|
|
| 135 |
|
"succesfully sent the simulation information to fortran.\n"); |
| 136 |
|
MPIcheckPoint(); |
| 137 |
|
#endif // is_mpi |
| 138 |
+ |
|
| 139 |
+ |
ndf = this->getNDF(); |
| 140 |
+ |
ndfRaw = this->getNDFraw(); |
| 141 |
+ |
|
| 142 |
|
} |
| 143 |
|
|
