MC1p(const Par &par) : TSP(par) {
LOG << "# Read parameters" << std::endl;
read_par();
LOG << "# Set parameters" << std::endl;
#define JN_MCPSB_PAR_SET(a) par.set(PP_CAT(_mc_, a), PP_STRING3(PP_CAT(mc_, a)));
JN_MAP(JN_MCPSB_PAR_SET, JN_MC_PARS1, JN_MC_PARS2)
LOG << "# Print parameters" << std::endl;
print_parameters();
LOG << "# Read initial structure" << std::endl;
chain_read_model(_pred_chain, par.get("pdb"));
LOG << "# Set indices" << std::endl;
thread_local static std::map<char, int> m {{'A', 0}, {'U', 1}, {'G', 2}, {'C', 3}};
m_indices.resize(_seq.size());
for (int i = 0; i < _seq.size(); i++) {
m_indices[i] = m[_seq[i]];
}
LOG << "# Set 2D trees" << std::endl;
set_trees();
LOG << "# Set ranges" << std::endl;
set_ranges();
LOG << "# Print ranges" << std::endl;
print_ranges();
}
int main(int argc, char **argv){
int nsnap;
char *fileinp;
/* read parameters from parameter-file (stdin) */
/*read_par(stdin);*/
/* read parameters from parameter-file (stdin) */
fileinp=argv[1];
FP=fopen(fileinp,"r");
if(FP==NULL) {
if (MYID == 0){
printf("\n==================================================================\n");
printf(" Cannot open Denise input file %s \n",fileinp);
printf("\n==================================================================\n\n");
err(" --- ");
}
}
/* read input file */
read_par(FP);
NXG=NX;
NYG=NY;
NX = NXG/NPROCX;
NY = NYG/NPROCY;
nsnap=1+iround((TSNAP2-TSNAP1)/TSNAPINC);
FP=stdout;
switch(SNAP){
case 1 : /*particle velocity*/
merge(nsnap,1);
merge(nsnap,2);
break;
case 2 : /*pressure */
merge(nsnap,6);
break;
case 4 : /*particle velocity*/
merge(nsnap,1);
merge(nsnap,2);
case 3 :
merge(nsnap,4);
merge(nsnap,5);
break;
default :
warning(" snapmerge: cannot identify content of snapshot !");
break;
}
return 0;
}
int main(int argc, char **argv){
int nsnap;
char *fileinp;
/* read parameters from parameter-file (stdin) */
/*read_par(stdin);*/
/* read parameters from parameter-file (stdin) */
fileinp=argv[1];
FP=fopen(fileinp,"r");
if(FP==NULL) {
if (MYID == 0){
printf("\n==================================================================\n");
printf(" Cannot open Denise input file %s \n",fileinp);
printf("\n==================================================================\n\n");
err(" --- ");
}
}
if (strstr(fileinp,".json")){
/* read json formatted input file */
read_par_json(stdout,fileinp);}
else{
/* read "old" input file *.inp */
read_par(FP);}
NXG=NX;
NYG=NY;
NX = NXG/NPROCX;
NY = NYG/NPROCY;
nsnap=1+iround((TSNAP2-TSNAP1)/TSNAPINC);
FP=stdout;
switch(SNAP){
case 1 : /*particle velocity*/
merge(nsnap,1);
/*merge(nsnap,2);*/
break;
default :
warning(" snapmerge: cannot identify content of snapshot !");
break;
}
return 0;
}
// Read each item in turn.
void corrobj::read(char *parfile)
{
read_par(parfile);
kcorr = new kcorr_table(par.kcorr_file);
read_primary();
if (par.corrtype == 1 || par.corrtype == 3)
read_secondary();
else
read_random_secondary();
read_rev();
}