int main(int argc, char *argv[]) {
int i,j;
int suc;
int pid;
char *amberhome;
if (strcmp(COLORTEXT, "YES") == 0 || strcmp(COLORTEXT, "yes") == 0) {
if (argc == 2
&& (strcmp(argv[1], "-h") == 0
|| strcmp(argv[1], "-H") == 0)) {
printf("[31mUsage: poltop -i [0m topology file name\n"
"[31m -o [0m output file name\n"
"[31m -r [0m replace the existing polarizability in the topology? \n"
"[34m 1:[0m yes (the default) \n"
"[34m 0:[0m no (use with care !)\n"
"[31m -m [0m polarizability models, suppressed by argument '-p'\n"
"[34m A1:[0m Thole linear, no 1-2 and 1-3, %83 of 1-4, variable screening lengths \n"
"[34m A2:[0m Thole exponential, no 1-2 and 1-3, %83 of 1-4, variable screening lengths \n"
"[34m A3:[0m Thole tinker-like, no 1-2 and 1-3, %83 of 1-4, variable screening lengths \n"
"[34m B0:[0m Applequist, no 1-2 and 1-3, %50 of 1-4, also known as CA\n"
"[34m B1:[0m Thole linear, no 1-2 and 1-3, %50 of 1-4, also known as CL\n"
"[34m B2:[0m Thole exponential, no 1-2 and 1-3, %50 of 1-4, also known as CE\n"
"[34m B3:[0m Thole tinker-like, no 1-2 and 1-3, %50 of 1-4, also known as CT\n"
"[34m C0:[0m Thole Applequist, no 1-2 and 1-3, %83 of 1-4, also known as BA\n"
"[34m C1:[0m Thole linear, no 1-2 and 1-3, %83 of 1-4, also known as BL\n"
"[34m C2:[0m Thole exponential, no 1-2 and 1-3, %83 of 1-4, also known as BE\n"
"[34m C3:[0m Thole tinker-like, no 1-2 and 1-3, %83 of 1-4, also known as BT\n"
"[34m D0:[0m Thole Applequist, no 1-2 and 1-3, %100 of 1-4, also known as AA\n"
"[34m D1:[0m Thole linear, no 1-2 and 1-3, %100 of 1-4, also known as AL\n"
"[34m D2:[0m Thole exponential, no 1-2 and 1-3, %100 of 1-4, also known as AE\n"
"[34m D3:[0m Thole tinker-like, no 1-2 and 1-3, %100 of 1-4, also known as AT\n"
"[31m -t [0m atom type file, optional, the default is $AMBERHOME/dat/antechamber/ATCOR2.DAT\n"
"[31m -p [0m parameter file, optional\n");
exit(1);
}
if (argc != 7 && argc !=9 && argc != 11 && argc != 13 && argc != 15) {
printf("[31mUsage: poltop -i [0m topology file name\n"
"[31m -o [0m output file name\n"
"[31m -r [0m replace the existing polarizability in the topology? \n"
"[34m 1:[0m yes (the default) \n"
"[34m 0:[0m no (use with care !)\n"
"[31m -m [0m polarizability models, suppressed by argument '-p'\n"
"[34m A1:[0m Thole linear, no 1-2 and 1-3, %83 of 1-4, variable screening lengths \n"
"[34m A2:[0m Thole exponential, no 1-2 and 1-3, %83 of 1-4, variable screening lengths \n"
"[34m A3:[0m Thole tinker-like, no 1-2 and 1-3, %83 of 1-4, variable screening lengths \n"
"[34m B0:[0m Applequist, no 1-2 and 1-3, %50 of 1-4, also known as CA\n"
"[34m B1:[0m Thole linear, no 1-2 and 1-3, %50 of 1-4, also known as CL\n"
"[34m B2:[0m Thole exponential, no 1-2 and 1-3, %50 of 1-4, also known as CE\n"
"[34m B3:[0m Thole tinker-like, no 1-2 and 1-3, %50 of 1-4, also known as CT\n"
"[34m C0:[0m Thole Applequist, no 1-2 and 1-3, %83 of 1-4, also known as BA\n"
"[34m C1:[0m Thole linear, no 1-2 and 1-3, %83 of 1-4, also known as BL\n"
"[34m C2:[0m Thole exponential, no 1-2 and 1-3, %83 of 1-4, also known as BE\n"
"[34m C3:[0m Thole tinker-like, no 1-2 and 1-3, %83 of 1-4, also known as BT\n"
"[34m D0:[0m Thole Applequist, no 1-2 and 1-3, %100 of 1-4, also known as AA\n"
"[34m D1:[0m Thole linear, no 1-2 and 1-3, %100 of 1-4, also known as AL\n"
"[34m D2:[0m Thole exponential, no 1-2 and 1-3, %100 of 1-4, also known as AE\n"
"[34m D3:[0m Thole tinker-like, no 1-2 and 1-3, %100 of 1-4, also known as AT\n"
"[31m -t [0m atom type file, optional, the default is $AMBERHOME/dat/antechamber/ATCOR2.DAT\n"
"[31m -p [0m parameter file, optional\n");
exit(1);
}
} else {
if (argc == 2)
if (strcmp(argv[1], "-h") == 0 || strcmp(argv[1], "-H") == 0) {
printf("Usage: poltop -i topology file name\n"
" -o output file name\n"
" -r replace the existing polarizability in the topology? \n"
" 1: yes (the default) \n"
" 0: no (use with care !)\n"
" -m polarizability models, suppressed by argument '-p'\n"
" A1: Thole linear, no 1-2 and 1-3, %83 of 1-4, variable screening lengths \n"
" A2: Thole exponential, no 1-2 and 1-3, %83 of 1-4, variable screening lengths \n"
" A3: Thole tinker-like, no 1-2 and 1-3, %83 of 1-4, variable screening lengths \n"
" B0: Applequist, no 1-2 and 1-3, %50 of 1-4, also known as CA\n"
" B1: Thole linear, no 1-2 and 1-3, %50 of 1-4, also known as CL\n"
" B2: Thole exponential, no 1-2 and 1-3, %50 of 1-4, also known as CE\n"
" B3: Thole tinker-like, no 1-2 and 1-3, %50 of 1-4, also known as CT\n"
" C0: Thole Applequist, no 1-2 and 1-3, %83 of 1-4, also known as BA\n"
" C1: Thole linear, no 1-2 and 1-3, %83 of 1-4, also known as BL\n"
" C2: Thole exponential, no 1-2 and 1-3, %83 of 1-4, also known as BE\n"
" C3: Thole tinker-like, no 1-2 and 1-3, %83 of 1-4, also known as BT\n"
" D0: Thole Applequist, no 1-2 and 1-3, %100 of 1-4, also known as AA\n"
" D1: Thole linear, no 1-2 and 1-3, %100 of 1-4, also known as AL\n"
" D2: Thole exponential, no 1-2 and 1-3, %100 of 1-4, also known as AE\n"
" D3: Thole tinker-like, no 1-2 and 1-3, %100 of 1-4, also known as AT\n"
" -t atom type file, optional, the default is $AMBERHOME/dat/antechamber/ATCOR2.DAT\n"
" -p parameter file, optional\n");
exit(1);
}
if (argc != 7 && argc !=9 && argc != 11 && argc != 13) {
printf("Usage: poltop -i topology file name\n"
" -o output file name\n"
" -r replace the existing polarizability in the topology? \n"
" 1: yes (the default) \n"
" 0: no (use with care !)\n"
" -m polarizability models, suppressed by argument '-p'\n"
" A1: Thole linear, no 1-2 and 1-3, %83 of 1-4, variable screening lengths \n"
" A2: Thole exponential, no 1-2 and 1-3, %83 of 1-4, variable screening lengths \n"
" A3: Thole tinker-like, no 1-2 and 1-3, %83 of 1-4, variable screening lengths \n"
" B0: Applequist, no 1-2 and 1-3, %50 of 1-4, also known as CA\n"
" B1: Thole linear, no 1-2 and 1-3, %50 of 1-4, also known as CL\n"
" B2: Thole exponential, no 1-2 and 1-3, %50 of 1-4, also known as CE\n"
" B3: Thole tinker-like, no 1-2 and 1-3, %50 of 1-4, also known as CT\n"
" C0: Thole Applequist, no 1-2 and 1-3, %83 of 1-4, also known as BA\n"
" C1: Thole linear, no 1-2 and 1-3, %83 of 1-4, also known as BL\n"
" C2: Thole exponential, no 1-2 and 1-3, %83 of 1-4, also known as BE\n"
" C3: Thole tinker-like, no 1-2 and 1-3, %83 of 1-4, also known as BT\n"
" D0: Thole Applequist, no 1-2 and 1-3, %100 of 1-4, also known as AA\n"
" D1: Thole linear, no 1-2 and 1-3, %100 of 1-4, also known as AL\n"
" D2: Thole exponential, no 1-2 and 1-3, %100 of 1-4, also known as AE\n"
" D3: Thole tinker-like, no 1-2 and 1-3, %100 of 1-4, also known as AT\n"
" -t atom type file, optional, the default is $AMBERHOME/dat/antechamber/ATCOR2.DAT\n"
" -p parameter file, optional\n");
exit(1);
}
}
ireplace = 1;
ireadat = 0;
ireadparm = 0;
strcpy(model, "A0");
for (i = 1; i < argc; i += 2) {
if (strcmp(argv[i], "-i") == 0)
strcpy(ifilename, argv[i + 1]);
if (strcmp(argv[i], "-o") == 0)
strcpy(ofilename, argv[i + 1]);
if (strcmp(argv[i], "-p") == 0) {
strcpy(pfilename, argv[i + 1]);
ireadparm = 1;
}
if (strcmp(argv[i], "-t") == 0) {
strcpy(tfilename, argv[i + 1]);
ireadat = 1;
}
if (strcmp(argv[i], "-r") == 0)
ireplace = atoi(argv[i + 1]);
if (strcmp(argv[i], "-m") == 0)
strcpy(model, argv[i + 1]);
}
if((fpin=fopen(ifilename,"r"))==NULL) {
fprintf(stdout, "\n Cannot open topology file: %s, exit", ifilename);
exit(1);
}
if((fpout=fopen(ofilename,"w"))==NULL) {
fprintf(stdout, "\n Cannot open file to write: %s, exit", ofilename);
exit(1);
}
rtopparm();
atom = (ATOM *) malloc(sizeof(ATOM) * (atomnum + 10));
if (atom == NULL) {
fprintf(stdout, "memory allocation error for *atom\n");
exit(1);
}
if(ireadparm == 0) {
amberhome = (char *) getenv("AMBERHOME");
if( amberhome == NULL ){
fprintf( stdout, "AMBERHOME is not set!\n" );
exit(1);
}
strcpy(pfilename, amberhome);
strcat(pfilename, "/dat/antechamber/POL.PARM");
rparm();
}
else if(ireadparm == 1) rparm2();
if(ireadat == 0) {
amberhome = (char *) getenv("AMBERHOME");
if( amberhome == NULL ){
fprintf( stdout, "AMBERHOME is not set!\n" );
exit(1);
}
strcpy(tfilename, amberhome);
strcat(tfilename, "/dat/antechamber/ATCOR2.DAT");
}
rcorr();
rewind(fpin);
rtopatom();
// find the parameters
for(i=0;i<atomnum;i++) {
suc = 0;
for(j=0;j<typenum;j++) {
if(strcmp(atom[i].type, type[j].name) == 0) {
pid = type[j].pid;
if(ireplace == 1) atom[i].pol = parm[pid].pol;
atom[i].damp_factor = parm[pid].damp_factor;
suc = 1;
break;
}
}
if(suc == 0) {
fprintf(stdout, "The atom type (%s) does not show up in the atom type file %s !\n", atom[i].type, tfilename);
exit(0);
}
if(debug == 1) {
printf("ATOM %d %5s %5s %9.5lf %9.5lf\n", i+1, atom[i].name, atom[i].type, atom[i].pol, atom[i].damp_factor);
}
}
if(atom[0].damp_factor < -999990) idamp_factor = 0;
rewind(fpin);
wtop();
fclose(fpin);
fclose(fpout);
return(0);
}
int
main(int argc, char *argv[])
{
int prompt;
complex **qin;
Real *q;
double starttime, endtime;
int jflav, k;
int key[4] = {1,1,1,1}; /* 4D Fourier transform */
initialize_machine(&argc,&argv);
/* Remap standard I/O */
if(remap_stdio_from_args(argc, argv) == 1)terminate(1);
g_sync();
starttime=dclock();
/* set up */
prompt = setup();
/* Set up for Fourier transform in all directions */
if(prompt != 2)setup_restrict_fourier(key, NULL);
/* loop over input sets */
while( readin(prompt) == 0){
if(prompt == 2)continue; /* For testing */
/* Create qin array */
qin = (complex **)malloc(sizeof(complex *)*param.nrand);
if(qin == NULL){
node0_printf("main: No room for qin\n");
terminate(1);
}
for(k = 0; k < param.nrand; k++){
qin[k] = create_c_array_field(NMU);
if(qin[k] == NULL){
node0_printf("main: No room for qin[%d]\n",k);
terminate(1);
}
}
for(jflav = 0; jflav < param.nflav; jflav++){
/* Allocate space and read all the data for flavor "jflav" */
/* Accumulate the result in qin, weighted by the charge */
accumulate_current_density(param.fname[jflav], qin, param.charges[jflav],
¶m.mass[jflav], param.nrand);
}
/* Calculate the density-density correlator q */
q = rcorr(qin, param.nrand);
/* Destroy qin array */
for(k = 0; k < param.nrand; k++)
destroy_c_array_field(qin[k], NMU);
free(qin);
/* Symmetrize over hypercubic group transformations */
symmetrize(q);
/* Write the results to the specified file */
print_result(q, param.nrand);
destroy_r_field(q);
} /* readin(prompt) */
node0_printf("RUNNING COMPLETED\n");
endtime=dclock();
node0_printf("Time = %e seconds\n",(double)(endtime-starttime));
normal_exit(0);
return 0;
}
