first simple atom match code

diff --git a/atom_match.c b/atom_match.c
new file mode 100644 (file)
index 0000000..7eb5556
--- /dev/null
+++ b/atom_match.c
@@ -0,0 +1,228 @@
+/*
+ * atom_match.c - match atoms and process
+ *
+ * author: frank.zirkelbach@physik.uni-augsburg.de
+ *
+ */
+
+#define _GNU_SOURCE
+#include <stdio.h>
+
+#include "moldyn.h"
+
+#define PSE_NAME
+#define PSE_COL
+#include "pse.h"
+#undef PSE_NAME
+#undef PSE_COL
+
+#define ME     "[atom match]"
+
+#define LAND   0
+#define LOR    1
+
+#define SELECT         1
+#define UNSELECT       0
+
+#define S_COL_NO_OVERRIDE      0
+#define S_COL_NONE             1
+#define S_COL_BLUE             2
+#define S_COL_RED              3
+#define S_COL_BLACK            4
+
+/* rule types */
+#define RT_ELEMENT             0
+
+typedef int t_element;
+
+typedef struct s_rule {
+       u8 type;
+       u8 logic_op;
+       void *params;
+} t_rule;
+
+typedef struct s_am {
+       int count;
+       t_rule rule[32];
+       char infile[128];
+} t_am;
+
+int parse_rule(t_am *am,char *line) {
+
+       int wcnt;
+       char *wptr;
+       char word[16][64];
+
+       t_element *element;
+
+       wcnt=0;
+       while(1) {
+               if(wcnt)
+                       wptr=strtok(NULL," ");
+               else
+                       wptr=strtok(line," ");
+               if(wptr==NULL)
+                       break;
+               strncpy(word[wcnt],wptr,64);
+               wcnt+=1;
+       }
+
+       switch(word[0][0]) {
+               case 'e':
+                       am->rule[am->count].params=malloc(sizeof(t_element));
+                       element=am->rule[am->count].params;
+                       if(element==NULL) {
+                               printf("%s malloc (element).\n",ME);
+                               return -1;
+                       }
+                       *element=atoi(word[1]);
+                       break;
+               /*
+               case '':
+                       break;
+               case '':
+                       break;
+               */
+               default:
+                       return -1;
+       }
+
+       return 0;
+}
+
+int parse_argv(int argc,char **argv,t_am *am) {
+
+       int i;
+       int ret;
+
+       memset(am,0,sizeof(t_am));
+       ret=0;
+
+       for(i=1;i<argc;i++) {
+               if(argv[i][0]=='-') {
+                       switch(argv[i][1]) {
+                               case 'i':
+                                       // infile
+                                       strncpy(am->infile,argv[++i],128);
+                                       break;
+                               case 'a':
+                                       // and rule
+                                       am->rule[am->count].logic_op=LAND;
+                                       ret=parse_rule(am,argv[++i]);
+                                       am->count+=1;
+                                       break;
+                               case 'o':
+                                       // or rule
+                                       am->rule[am->count].logic_op=LOR;
+                                       ret=parse_rule(am,argv[++i]);
+                                       am->count+=1;
+                                       break;
+                               case 'p':
+                                       // how to process data
+                                       break;
+                               default:
+                                       printf("%s unknown switch: %s\n",
+                                               ME,argv[i]);
+                                       return -1;
+                       
+                       }
+               }
+               else {
+                       printf("%s unknown argument: %s\n",ME,argv[i]);
+                       return -1;
+               }
+       }
+
+       return ret;
+}
+
+int main(int argc,char **argv) {
+
+       t_am am;
+       t_moldyn moldyn;
+       u8 *sel_atom;
+       u8 *sel_color;
+       int i,j,acnt;
+       t_atom *atom;
+
+       t_element *e;
+
+       memset(&moldyn,0,sizeof(t_moldyn));
+
+       if(parse_argv(argc,argv,&am)<0) {
+               printf("%s aborted (bad args).\n",ME);
+               return -1;
+       }
+
+       if(moldyn_read_save_file(&moldyn,am.infile)<0) {
+               printf("%s aborted (bad infile).\n",ME);
+               return -1;
+       }
+
+       acnt=moldyn.count;
+       atom=moldyn.atom;
+
+       link_cell_init(&moldyn,VERBOSE);
+
+       /* alloc select status and color memory */
+       sel_atom=malloc(acnt*sizeof(u8));
+       if(sel_atom==NULL) {
+               printf("%s aborted (malloc failed).\n",ME);
+               return -1;
+       }
+       sel_color=malloc(acnt*sizeof(u8));
+       if(sel_color==NULL) {
+               printf("%s aborted (malloc failed).\n",ME);
+               return -1;
+       }
+
+       /* apply rules */
+       for(i=0;i<am.count;i++) {
+
+               /* initialize status and color in first run */
+               if(i==0) {
+                       if(am.rule[0].logic_op==LAND)
+                               memset(sel_atom,SELECT,acnt*sizeof(u8));
+                       else
+                               memset(sel_atom,UNSELECT,acnt*sizeof(u8));
+               }
+
+               /* rules */
+               switch(am.rule[i].type) {
+                       case RT_ELEMENT:
+                               e=am.rule[0].params;
+                               if(am.rule[i].type==LAND)
+                                       for(j=0;j<acnt;j++)
+                                               if(atom[j].element==*e)
+                                                       sel_atom[j]&=SELECT;
+                                               else
+                                                       sel_atom[j]&=UNSELECT;
+                               else
+                                       for(j=0;j<acnt;j++)
+                                               if(atom[j].element==*e)
+                                                       sel_atom[j]|=SELECT;
+                               break;
+                       default:
+                               printf("%s unknown rule %c -> skipped.\n",
+                                       ME,am.rule[i].type);
+                               break;
+               }
+       }
+
+       /* process data */
+       for(i=0;i<acnt;i++)
+               if(sel_atom[i]==SELECT)
+                       printf("%s %f %f %f %s %f\n",
+                              pse_name[atom[i].element],
+                              atom[i].r.x,atom[i].r.y,atom[i].r.z,
+                              pse_col[atom[i].element],
+                              atom[i].ekin);
+
+       /* exit and cleanup */
+       free(sel_atom);
+       free(sel_color);
+       link_cell_shutdown(&moldyn);
+       moldyn_free_save_file(&moldyn);
+       
+       return 0;
+}