From 4f7a62883e5e47be44856c9767c9255c1d68190d Mon Sep 17 00:00:00 2001
From: hackbard <hackbard@sage.physik.uni-augsburg.de>
Date: Mon, 5 May 2008 08:53:26 +0200
Subject: [PATCH] tool to search for bonds

---
 Makefile       |   4 +-
 search_bonds.c | 127 +++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 130 insertions(+), 1 deletion(-)
 create mode 100644 search_bonds.c

diff --git a/Makefile b/Makefile
index fbe3f59..62a137e 100644
--- a/Makefile
+++ b/Makefile
@@ -23,7 +23,7 @@ DEPS += potentials/lennard_jones.o potentials/harmonic_oscillator.o
 DEPS += potentials/tersoff.o potentials/albe.o
 
 ALL = mdrun sic fluctuation_calc postproc pair_correlation_calc diffusion_calc
-ALL += bond_analyze
+ALL += bond_analyze search_bonds
 
 all: $(ALL)
 
@@ -39,6 +39,8 @@ diffusion_calc: $(DEPS)
 
 bond_analyze: $(DEPS)
 
+search_bonds: $(DEPS)
+
 .PHONY:clean
 clean:
 	rm -vf $(ALL) *.o */*.o
diff --git a/search_bonds.c b/search_bonds.c
new file mode 100644
index 0000000..d3c1199
--- /dev/null
+++ b/search_bonds.c
@@ -0,0 +1,127 @@
+/*
+ * code searching for special types of bonds
+ *
+ * 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"
+#include "potentials/albe.h"
+
+int usage(char *prog) {
+
+	printf("\nusage:\n");
+	printf("  %s <file> <type> <bondlen> <+->\n",prog);
+	printf("    type: a - 0-0 bond\n");
+	printf("    type: b - 1-1 bond\n");
+	printf("    type: c - 0-1 / 1-0  bond\n\n");
+
+	return -1;
+}
+
+int main(int argc,char **argv) {
+
+	t_moldyn moldyn;
+	t_atom *itom,*jtom;
+	int i,j;
+	int ret;
+	t_list n[27];
+	t_list *this;
+	t_linkcell *lc;
+	t_3dvec dist;
+	double d,bondlen,bondpm;
+
+	if(argc!=5) {
+		usage(argv[0]);
+		return -1;
+	}
+
+	bondlen=atof(argv[3]);
+	bondpm=atof(argv[4]);
+
+	memset(&moldyn,0,sizeof(t_moldyn));
+
+	printf("[search bonds] reading save file ...\n");
+	ret=moldyn_read_save_file(&moldyn,argv[1]);
+	if(ret) {
+		printf("[search bonds] exit!\n");
+		return ret;
+	}
+
+	/* link cell init */
+	moldyn.cutoff=bondlen+bondpm;
+	link_cell_init(&moldyn,VERBOSE);
+	lc=&(moldyn.lc);
+
+	/* analyzing ... */
+	for(i=0;i<moldyn.count;i++) {
+		itom=&(moldyn.atom[i]);
+		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);
+		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;
+
+				switch(argv[2][0]) {
+					case 'a':
+						if(itom->brand!=0)
+							continue;
+						if(jtom->brand!=0)
+							continue;
+						break;
+					case 'b':
+						if(itom->brand!=1)
+							continue;
+						if(jtom->brand!=1)
+							continue;
+						break;
+					default:
+						if(itom->brand==jtom->brand)
+							continue;
+						break;
+				}
+
+				v3_sub(&dist,&(itom->r),&(jtom->r));
+				check_per_bound(&moldyn,&dist);
+				d=v3_norm(&dist);
+
+				if((d<=bondlen+bondpm)&(d>=bondlen-bondpm)) {
+
+					printf(" # atoms %d/%d %d/%d - %f\n",
+					       itom->tag,itom->brand,
+					       jtom->tag,jtom->brand,d);
+
+				}
+
+			} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
+		}
+	}
+
+	link_cell_shutdown(&moldyn);
+
+	moldyn_free_save_file(&moldyn);
+
+	return 0;
+}
-- 
2.39.2