From: hackbard <hackbard@sage.physik.uni-augsburg.de>
Date: Mon, 5 May 2008 08:07:01 +0000 (+0200)
Subject: search bonds using infrastructure now, new visual atoms tool
X-Git-Url: https://hackdaworld.org/cgi-bin/gitweb.cgi?a=commitdiff_plain;h=a58211f24f237b51e708b9e8b9fd463a709754a6;p=physik%2Fposic.git

search bonds using infrastructure now, new visual atoms tool
---

diff --git a/Makefile b/Makefile
index 62a137e..36c411e 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 search_bonds
+ALL += bond_analyze search_bonds visual_atoms
 
 all: $(ALL)
 
@@ -41,6 +41,8 @@ bond_analyze: $(DEPS)
 
 search_bonds: $(DEPS)
 
+visual_atoms: $(DEPS)
+
 .PHONY:clean
 clean:
 	rm -vf $(ALL) *.o */*.o
diff --git a/mdrun.h b/mdrun.h
index fa16906..ad5c0c2 100644
--- a/mdrun.h
+++ b/mdrun.h
@@ -18,9 +18,6 @@
 /* main molecular dynamics api */
 #include "moldyn.h"
 
-/* elements */
-#include "pse.h"
-
 /* list api */
 #include "list/list.h"
 
diff --git a/moldyn.c b/moldyn.c
index 82ae543..4330396 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -30,101 +30,6 @@
 #include "potentials/tersoff.h"
 #endif
 
-
-/*
- * global variables, pse and atom colors (only needed here)
- */ 
-
-static char *pse_name[]={
-	"*",
-	"H",
-	"He",
-	"Li",
-	"Be",
-	"B",
-	"C",
-	"N",
-	"O",
-	"F",
-	"Ne",
-	"Na",
-	"Mg",
-	"Al",
-	"Si",
-	"P",
-	"S",
-	"Cl",
-	"Ar",
-};
-
-static char *pse_col[]={
-	"*",
-	"White",
-	"He",
-	"Li",
-	"Be",
-	"B",
-	"Gray",
-	"N",
-	"Blue",
-	"F",
-	"Ne",
-	"Na",
-	"Mg",
-	"Al",
-	"Yellow",
-	"P",
-	"S",
-	"Cl",
-	"Ar",
-};
-
-/*
-static double pse_mass[]={
-	0,
-	0,
-	0,
-	0,
-	0,
-	0,
-	M_C,
-	0,
-	0,
-	0,
-	0,
-	0,
-	0,
-	0,
-	M_SI,
-	0,
-	0,
-	0,
-	0,
-};
-
-static double pse_lc[]={
-	0,
-	0,
-	0,
-	0,
-	0,
-	0,
-	LC_C,
-	0,
-	0,
-	0,
-	0,
-	0,
-	0,
-	0,
-	LC_SI,
-	0,
-	0,
-	0,
-	0,
-};
-*/
-
 /*
  * the moldyn functions
  */
diff --git a/moldyn.h b/moldyn.h
index cd7c5d0..ca40103 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -353,6 +353,12 @@ typedef struct s_vb {
 #define DIAMOND			0x04
 #define ZINCBLENDE		0x08
 
+/*
+ * more includes
+ */
+
+#include "pse.h"
+
 /*
  *
  * function prototypes
diff --git a/pse.h b/pse.h
index d9aff12..3391d26 100644
--- a/pse.h
+++ b/pse.h
@@ -51,3 +51,47 @@ static double pse_lc[]={
 	0,
 };
 
+static char *pse_name[]={
+	"*",
+	"H",
+	"He",
+	"Li",
+	"Be",
+	"B",
+	"C",
+	"N",
+	"O",
+	"F",
+	"Ne",
+	"Na",
+	"Mg",
+	"Al",
+	"Si",
+	"P",
+	"S",
+	"Cl",
+	"Ar",
+};
+
+static char *pse_col[]={
+	"*",
+	"White",
+	"He",
+	"Li",
+	"Be",
+	"B",
+	"Gray",
+	"N",
+	"Blue",
+	"F",
+	"Ne",
+	"Na",
+	"Mg",
+	"Al",
+	"Yellow",
+	"P",
+	"S",
+	"Cl",
+	"Ar",
+};
+
diff --git a/search_bonds.c b/search_bonds.c
index d3c1199..8291109 100644
--- a/search_bonds.c
+++ b/search_bonds.c
@@ -17,6 +17,11 @@
 #include "moldyn.h"
 #include "potentials/albe.h"
 
+typedef struct s_data {
+	double pm,len;
+	u8 type;
+} t_data;
+
 int usage(char *prog) {
 
 	printf("\nusage:\n");
@@ -28,25 +33,63 @@ int usage(char *prog) {
 	return -1;
 }
 
+int process(t_moldyn *moldyn,t_atom *ai,t_atom *aj,void *ptr,u8 bc) {
+
+	t_3dvec dist;
+	double d;
+	t_data *data;
+
+	data=ptr;
+
+	if(aj<ai)
+		return 0;
+
+	switch(data->type) {
+		case 'a':
+			if(ai->brand!=0)
+				return 0;
+			if(aj->brand!=0)
+				return 0;
+				
+			break;
+		case 'b':
+			if(ai->brand!=1)
+				return 0;
+			if(aj->brand!=1)
+				return 0;
+			break;
+		default:
+			if(ai->brand==aj->brand)
+				return 0;
+			break;
+	}
+
+	v3_sub(&dist,&(ai->r),&(aj->r));
+	check_per_bound(moldyn,&dist);
+	d=v3_norm(&dist);
+
+	if((d<=data->len+data->pm)&(d>=data->len-data->pm))
+		printf(" # atoms %d/%d %d/%d - %f\n",
+		       ai->tag,ai->brand,
+		       aj->tag,aj->brand,d);
+
+	return 0;
+}
+
 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;
+	t_data data;
 
 	if(argc!=5) {
 		usage(argv[0]);
 		return -1;
 	}
 
-	bondlen=atof(argv[3]);
-	bondpm=atof(argv[4]);
+	data.type=argv[2][0];
+	data.len=atof(argv[3]);
+	data.pm=atof(argv[4]);
 
 	memset(&moldyn,0,sizeof(t_moldyn));
 
@@ -58,67 +101,12 @@ int main(int argc,char **argv) {
 	}
 
 	/* link cell init */
-	moldyn.cutoff=bondlen+bondpm;
+	moldyn.cutoff=data.len+data.pm;
 	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);
-		}
-	}
+	process_2b_bonds(&moldyn,&data,process);
 
+	/* analyzing ... */
 	link_cell_shutdown(&moldyn);
 
 	moldyn_free_save_file(&moldyn);
diff --git a/visual_atoms.c b/visual_atoms.c
new file mode 100644
index 0000000..9baa487
--- /dev/null
+++ b/visual_atoms.c
@@ -0,0 +1,113 @@
+/*
+ * 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;
+}