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 /* pse */
  20 #define PSE_NAME
  21 #define PSE_COL
  22 #include "pse.h"
  23 #undef PSE_NAME
  24 #undef PSE_COL
  25
  26 typedef struct s_data {
  27         int ca;
  28         double radius;
  29         double lc;
  30         int ma;
  31         double ox,oy,oz;
  32 } t_data;
  33
  34 int usage(char *prog) {
  35
  36         printf("\nusage:\n");
  37         printf("  %s <file> <centre atom> <radius> <lc> [marked atom]\n\n",
  38                prog);
  39
  40         return -1;
  41 }
  42
  43 int process(t_moldyn *moldyn,t_atom *itom,t_atom *jtom,void *ptr,u8 bc) {
  44
  45         t_3dvec dist;
  46         double d;
  47         t_data *data;
  48
  49         data=ptr;
  50
  51         v3_sub(&dist,&(itom->r),&(jtom->r));
  52         if(bc) check_per_bound(moldyn,&dist);
  53         d=v3_norm(&dist);
  54
  55         if(d<=data->radius) {
  56                 printf("%s %f %f %f %s %f\n",
  57                        pse_name[jtom->element],
  58                        jtom->r.x+data->ox,jtom->r.y+data->oy,jtom->r.z+data->oz,
  59                        (jtom->tag==data->ma)?"Red":pse_col[jtom->element],
  60                        jtom->ekin);
  61         }
  62
  63         return 0;
  64 }
  65
  66 int main(int argc,char **argv) {
  67
  68         t_moldyn moldyn;
  69         t_data data;
  70         int ret;
  71         t_atom *atom;
  72
  73         if(argc<4) {
  74                 usage(argv[0]);
  75                 return -1;
  76         }
  77
  78         data.ca=atoi(argv[2]);
  79         data.radius=atof(argv[3]);
  80         data.lc=atof(argv[4]);
  81         data.ma=-1;
  82         if(argc==6)
  83                 data.ma=atoi(argv[5]);
  84
  85         memset(&moldyn,0,sizeof(t_moldyn));
  86
  87         printf("[visual atoms] reading save file ...\n");
  88         ret=moldyn_read_save_file(&moldyn,argv[1]);
  89         if(ret) {
  90                 printf("[visual atoms] exit!\n");
  91                 return ret;
  92         }
  93
  94         /* link cell init */
  95         moldyn.cutoff=data.radius;
  96         link_cell_init(&moldyn,VERBOSE);
  97
  98         atom=&(moldyn.atom[data.ca]);
  99
 100         /* prepare offset */
 101         data.ox=0.0;
 102         if(atom->r.x<0) {
 103                 while((atom->r.x+data.ox)<(-data.lc/2.0))
 104                         data.ox+=data.lc;
 105         }
 106         else {
 107                 while((atom->r.x+data.ox)>(data.lc/2.0))
 108                         data.ox-=data.lc;
 109         }
 110
 111         data.oy=0.0;
 112         if(atom->r.y<0) {
 113                 while((atom->r.y+data.oy)<(-data.lc/2.0))
 114                         data.oy+=data.lc;
 115         }
 116         else {
 117                 while((atom->r.y+data.oy)>(data.lc/2.0))
 118                         data.oy-=data.lc;
 119         }
 120
 121         data.oz=0.0;
 122         if(atom->r.z<0) {
 123                 while((atom->r.z+data.oz)<(-data.lc/2.0))
 124                         data.oz+=data.lc;
 125         }
 126         else {
 127                 while((atom->r.z+data.oz)>(data.lc/2.0))
 128                         data.oz-=data.lc;
 129         }
 130
 131         /* print the centered atom */
 132         printf("%s %f %f %f %s %f\n",
 133                pse_name[atom->element],atom->r.x+data.ox,atom->r.y+data.oy,
 134                atom->r.z+data.oz,"Green",atom->ekin);
 135
 136         process_neighbours(&moldyn,&data,atom,process);
 137
 138         link_cell_shutdown(&moldyn);
 139         moldyn_free_save_file(&moldyn);
 140
 141         return 0;
 142 }
 143