--- /dev/null
+/*
+ * code visualize atoms
+ *
+ * author: frank.zirkelbach@physik.uni-augsburg.de
+ *
+ */
+
+#define _GNU_SOURCE
+#include <stdio.h>
+//#include <stdlib.h>
+//#include <unistd.h>
+//#include <string.h>
+//#include <sys/types.h>
+//#include <sys/stat.h>
+//#include <fcntl.h>
+
+#include "moldyn.h"
+
+int usage(char *prog) {
+
+ printf("\nusage:\n");
+ printf(" %s <file> <centre atom> <radius> [marked atom]\n\n",prog);
+
+ return -1;
+}
+
+int main(int argc,char **argv) {
+
+ t_moldyn moldyn;
+ t_atom *itom,*jtom;
+ int j;
+ int ret;
+ t_list n[27];
+ t_list *this;
+ t_linkcell *lc;
+ t_3dvec dist;
+ double d,radius;
+ int ma,ca;
+
+ if(argc<4) {
+ usage(argv[0]);
+ return -1;
+ }
+
+ ca=atoi(argv[2]);
+ radius=atof(argv[3]);
+
+ ma=-1;
+ if(argc==5)
+ ma=atoi(argv[4]);
+
+ memset(&moldyn,0,sizeof(t_moldyn));
+
+ printf("[visual atoms] reading save file ...\n");
+ ret=moldyn_read_save_file(&moldyn,argv[1]);
+ if(ret) {
+ printf("[visual atoms] exit!\n");
+ return ret;
+ }
+
+ /* link cell init */
+ moldyn.cutoff=radius;
+ link_cell_init(&moldyn,VERBOSE);
+ lc=&(moldyn.lc);
+
+ /* serach atoms */
+ itom=&(moldyn.atom[ca]);
+ link_cell_neighbour_index(&moldyn,
+ (itom->r.x+moldyn.dim.x/2)/lc->x,
+ (itom->r.y+moldyn.dim.y/2)/lc->y,
+ (itom->r.z+moldyn.dim.z/2)/lc->z,
+ n);
+
+
+ printf("%s %f %f %f %s %f\n",
+ pse_name[itom->element],itom->r.x,itom->r.y,itom->r.z,
+ "Green",itom->ekin);
+
+ for(j=0;j<27;j++) {
+ this=&(n[j]);
+ list_reset_f(this);
+
+ if(this->start==NULL)
+ continue;
+
+ do {
+
+ jtom=this->current->data;
+
+ if(jtom==itom)
+ continue;
+
+ v3_sub(&dist,&(itom->r),&(jtom->r));
+ check_per_bound(&moldyn,&dist);
+ d=v3_norm(&dist);
+
+ if(d<=radius) {
+ printf("%s %f %f %f %s %f\n",
+ pse_name[jtom->element],
+ jtom->r.x,jtom->r.y,jtom->r.z,
+ (jtom->tag==ma)?"Red":pse_col[jtom->element],
+ jtom->ekin);
+ }
+
+ } while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+ }
+
+ link_cell_shutdown(&moldyn);
+
+ moldyn_free_save_file(&moldyn);
+
+ return 0;
+}