visual_atoms.c

   1 /*
   2  * code visualize atoms
   3  *
   4  * author: frank.zirkelbach@physik.uni-augsburg.de
   5  *
   6  */
   7
   8 #define _GNU_SOURCE
   9 #include <stdio.h>
  10 //#include <stdlib.h>
  11 //#include <unistd.h>
  12 //#include <string.h>
  13 //#include <sys/types.h>
  14 //#include <sys/stat.h>
  15 //#include <fcntl.h>
  16
  17 #include "moldyn.h"
  18
  19 int usage(char *prog) {
  20
  21         printf("\nusage:\n");
  22         printf("  %s <file> <centre atom> <radius> [marked atom]\n\n",prog);
  23
  24         return -1;
  25 }
  26
  27 int main(int argc,char **argv) {
  28
  29         t_moldyn moldyn;
  30         t_atom *itom,*jtom;
  31         int j;
  32         int ret;
  33         t_list n[27];
  34         t_list *this;
  35         t_linkcell *lc;
  36         t_3dvec dist;
  37         double d,radius;
  38         int ma,ca;
  39
  40         if(argc<4) {
  41                 usage(argv[0]);
  42                 return -1;
  43         }
  44
  45         ca=atoi(argv[2]);
  46         radius=atof(argv[3]);
  47
  48         ma=-1;
  49         if(argc==5)
  50                 ma=atoi(argv[4]);
  51
  52         memset(&moldyn,0,sizeof(t_moldyn));
  53
  54         printf("[visual atoms] reading save file ...\n");
  55         ret=moldyn_read_save_file(&moldyn,argv[1]);
  56         if(ret) {
  57                 printf("[visual atoms] exit!\n");
  58                 return ret;
  59         }
  60
  61         /* link cell init */
  62         moldyn.cutoff=radius;
  63         link_cell_init(&moldyn,VERBOSE);
  64         lc=&(moldyn.lc);
  65
  66         /* serach atoms */
  67         itom=&(moldyn.atom[ca]);
  68         link_cell_neighbour_index(&moldyn,
  69                                   (itom->r.x+moldyn.dim.x/2)/lc->x,
  70                                   (itom->r.y+moldyn.dim.y/2)/lc->y,
  71                                   (itom->r.z+moldyn.dim.z/2)/lc->z,
  72                                   n);
  73
  74
  75         printf("%s %f %f %f %s %f\n",
  76                pse_name[itom->element],itom->r.x,itom->r.y,itom->r.z,
  77                "Green",itom->ekin);
  78
  79         for(j=0;j<27;j++) {
  80                 this=&(n[j]);
  81                 list_reset_f(this);
  82
  83                 if(this->start==NULL)
  84                         continue;
  85
  86                 do {
  87
  88                         jtom=this->current->data;
  89
  90                         if(jtom==itom)
  91                                 continue;
  92
  93                         v3_sub(&dist,&(itom->r),&(jtom->r));
  94                         check_per_bound(&moldyn,&dist);
  95                         d=v3_norm(&dist);
  96
  97                         if(d<=radius) {
  98                                 printf("%s %f %f %f %s %f\n",
  99                                        pse_name[jtom->element],
 100                                        jtom->r.x,jtom->r.y,jtom->r.z,
 101                                        (jtom->tag==ma)?"Red":pse_col[jtom->element],
 102                                        jtom->ekin);
 103                         }
 104
 105                 } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
 106         }
 107
 108         link_cell_shutdown(&moldyn);
 109
 110         moldyn_free_save_file(&moldyn);
 111
 112         return 0;
 113 }