From 60f40345bc4fcd8448d724dc67bbb512ec081bd4 Mon Sep 17 00:00:00 2001
From: hackbard <hackbard>
Date: Thu, 14 Dec 2006 00:06:18 +0000
Subject: [PATCH] new linked list system, still a pain inthe ...

---
 Makefile    |   6 +--
 init/init.c |  91 ----------------------------------------
 init/init.h |  20 ---------
 moldyn.c    | 118 +++++++++++++++++++++++++++++++++++++++++++---------
 moldyn.h    |   3 ++
 sic.c       |   5 +--
 6 files changed, 105 insertions(+), 138 deletions(-)
 delete mode 100644 init/init.c
 delete mode 100644 init/init.h

diff --git a/Makefile b/Makefile
index 6f3e39e..0250883 100644
--- a/Makefile
+++ b/Makefile
@@ -1,12 +1,12 @@
 CC=gcc-3.4
 #CC=gcc
-CFLAGS=-Wall -O3 #-DSIMPLE_TESTING
+CFLAGS=-Wall# -O3 #-DSIMPLE_TESTING
 LDFLAGS=-lm
 
-OBJS=init/init.o visual/visual.o random/random.o list/list.o
+OBJS=visual/visual.o random/random.o
 OBJS+=moldyn.o
 
-all: sic
+all: clean sic
 
 sic: $(OBJS)
 
diff --git a/init/init.c b/init/init.c
deleted file mode 100644
index daeb3b1..0000000
--- a/init/init.c
+++ /dev/null
@@ -1,91 +0,0 @@
-/*
- * init.c - create initial conditions
- *
- * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
- *
- */
-
-#include "../math/math.h"
-#include "../moldyn.h"
-
-/* fcc lattice init */
-int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
-
-	int count;
-	int i,j;
-	t_3dvec o,r,n;
-	t_3dvec basis[3];
-	double help[3];
-	double x,y,z;
-
-	x=a*lc;
-	y=b*lc;
-	z=c*lc;
-
-	if(origin) v3_copy(&o,origin);
-	else v3_zero(&o);
-
-	/* construct the basis */
-	for(i=0;i<3;i++) {
-		for(j=0;j<3;j++) {
-			if(i!=j) help[j]=0.5*lc;
-			else help[j]=.0;
-		}
-		v3_set(&basis[i],help);
-	}
-
-	v3_zero(&r);
-	count=0;
-	
-	/* fill up the room */
-	r.x=o.x;
-	while(r.x<x) {
-		r.y=o.y;
-		while(r.y<y) {
-			r.z=o.z;
-			while(r.z<z) {
-				v3_copy(&(atom[count].r),&r);
-				atom[count].element=1;
-				count+=1;
-				for(i=0;i<3;i++) {
-					v3_add(&n,&r,&basis[i]);
-					if((n.x<x+o.x)&&(n.y<y+o.y)&&(n.z<z+o.z)) {
-						v3_copy(&(atom[count].r),&n);
-						count+=1;
-					}
-				}
-				r.z+=lc;	
-			}
-			r.y+=lc;
-		}
-		r.x+=lc;
-	}
-
-	/* coordinate transformation */
-	help[0]=x/2.0;
-	help[1]=y/2.0;
-	help[2]=z/2.0;
-	v3_set(&n,help);
-	for(i=0;i<count;i++)
-		v3_sub(&(atom[i].r),&(atom[i].r),&n);
-		
-	return count;
-}
-
-int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
-
-	int count;
-	t_3dvec o;
-
-	count=fcc_init(a,b,c,lc,atom,origin);
-
-	o.x=0.25*lc;
-	o.y=0.25*lc;
-	o.z=0.25*lc;
-
-	if(origin) v3_add(&o,&o,origin);
-
-	count+=fcc_init(a,b,c,lc,&atom[count],&o);
-
-	return count;
-}
diff --git a/init/init.h b/init/init.h
deleted file mode 100644
index 8f4e93c..0000000
--- a/init/init.h
+++ /dev/null
@@ -1,20 +0,0 @@
-/*
- * init.h - create initial conditions
- *
- * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
- *
- */
-
-#ifndef INIT_H
-#define INIT_H
-
-#include "../moldyn.h"
-
-/* datattypes */
-
-/* function prototypes */
-
-int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
-int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
-
-#endif
diff --git a/moldyn.c b/moldyn.c
index b6fa8d3..7a77898 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -17,13 +17,6 @@
 
 #include "moldyn.h"
 
-#include "math/math.h"
-#include "init/init.h"
-#include "random/random.h"
-#include "visual/visual.h"
-#include "list/list.h"
-
-
 int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 
 	//int ret;
@@ -551,9 +544,6 @@ int link_cell_init(t_moldyn *moldyn) {
 
 	t_linkcell *lc;
 	int i;
-	int fd;
-
-	fd=open("/dev/null",O_WRONLY);
 
 	lc=&(moldyn->lc);
 
@@ -571,8 +561,7 @@ int link_cell_init(t_moldyn *moldyn) {
 	printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
 
 	for(i=0;i<lc->cells;i++)
-		//list_init(&(lc->subcell[i]),1);
-		list_init(&(lc->subcell[i]),fd);
+		list_init_f(&(lc->subcell[i]));
 
  	link_cell_update(moldyn);
 	
@@ -594,14 +583,14 @@ int link_cell_update(t_moldyn *moldyn) {
 	nz=lc->nz;
 
 	for(i=0;i<lc->cells;i++)
-		list_destroy(&(moldyn->lc.subcell[i]));
+		list_destroy_f(&(moldyn->lc.subcell[i]));
 	
 	for(count=0;count<moldyn->count;count++) {
 		i=(atom[count].r.x+(moldyn->dim.x/2))/lc->x;
 		j=(atom[count].r.y+(moldyn->dim.y/2))/lc->y;
 		k=(atom[count].r.z+(moldyn->dim.z/2))/lc->z;
-		list_add_immediate_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
-		                       &(atom[count]));
+		list_add_immediate_f(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
+		                     &(atom[count]));
 	}
 
 	return 0;
@@ -671,7 +660,9 @@ int link_cell_shutdown(t_moldyn *moldyn) {
 	lc=&(moldyn->lc);
 
 	for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
-		list_shutdown(&(moldyn->lc.subcell[i]));
+		list_destroy_f(&(moldyn->lc.subcell[i]));
+
+	free(lc->subcell);
 
 	return 0;
 }
@@ -950,7 +941,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 		for(j=0;j<27;j++) {
 
 			this=&(neighbour_i[j]);
-			list_reset(this);
+			list_reset_f(this);
 
 			if(this->start==NULL)
 				continue;
@@ -985,7 +976,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 				for(k=0;k<27;k++) {
 
 					that=&(neighbour_i2[k]);
-					list_reset(that);
+					list_reset_f(that);
 					
 					if(that->start==NULL)
 						continue;
@@ -1011,7 +1002,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 						               ktom,
 						               bc_ik|bc_ij);
 
-					} while(list_next(that)!=\
+					} while(list_next_f(that)!=\
 					        L_NO_NEXT_ELEMENT);
 
 				}
@@ -1023,7 +1014,7 @@ int potential_force_calc(t_moldyn *moldyn) {
 					                    jtom,bc_ij);
 				}
 					
-			} while(list_next(this)!=L_NO_NEXT_ELEMENT);
+			} while(list_next_f(this)!=L_NO_NEXT_ELEMENT);
 		
 		}
 
@@ -1756,3 +1747,90 @@ x=dim->x/2;
 	return 0;
 }
 
+/*
+ * lattice creation functions
+ */
+
+/* fcc lattice init */
+int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+
+	int count;
+	int i,j;
+	t_3dvec o,r,n;
+	t_3dvec basis[3];
+	double help[3];
+	double x,y,z;
+
+	x=a*lc;
+	y=b*lc;
+	z=c*lc;
+
+	if(origin) v3_copy(&o,origin);
+	else v3_zero(&o);
+
+	/* construct the basis */
+	for(i=0;i<3;i++) {
+		for(j=0;j<3;j++) {
+			if(i!=j) help[j]=0.5*lc;
+			else help[j]=.0;
+		}
+		v3_set(&basis[i],help);
+	}
+
+	v3_zero(&r);
+	count=0;
+	
+	/* fill up the room */
+	r.x=o.x;
+	while(r.x<x) {
+		r.y=o.y;
+		while(r.y<y) {
+			r.z=o.z;
+			while(r.z<z) {
+				v3_copy(&(atom[count].r),&r);
+				atom[count].element=1;
+				count+=1;
+				for(i=0;i<3;i++) {
+					v3_add(&n,&r,&basis[i]);
+					if((n.x<x+o.x)&&
+					   (n.y<y+o.y)&&
+					   (n.z<z+o.z)) {
+						v3_copy(&(atom[count].r),&n);
+						count+=1;
+					}
+				}
+				r.z+=lc;	
+			}
+			r.y+=lc;
+		}
+		r.x+=lc;
+	}
+
+	/* coordinate transformation */
+	help[0]=x/2.0;
+	help[1]=y/2.0;
+	help[2]=z/2.0;
+	v3_set(&n,help);
+	for(i=0;i<count;i++)
+		v3_sub(&(atom[i].r),&(atom[i].r),&n);
+		
+	return count;
+}
+
+int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
+
+	int count;
+	t_3dvec o;
+
+	count=fcc_init(a,b,c,lc,atom,origin);
+
+	o.x=0.25*lc;
+	o.y=0.25*lc;
+	o.z=0.25*lc;
+
+	if(origin) v3_add(&o,&o,origin);
+
+	count+=fcc_init(a,b,c,lc,&atom[count],&o);
+
+	return count;
+}
diff --git a/moldyn.h b/moldyn.h
index 4203c79..af54cef 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -415,4 +415,7 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc);
 
 int moldyn_bc_check(t_moldyn *moldyn);
 
+int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
+int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin);
+
 #endif
diff --git a/sic.c b/sic.c
index 516ee01..45e671f 100644
--- a/sic.c
+++ b/sic.c
@@ -8,9 +8,6 @@
 #include <math.h>
  
 #include "moldyn.h"
-#include "math/math.h"
-#include "init/init.h"
-#include "visual/visual.h"
 
 #include "posic.h"
 
@@ -157,7 +154,7 @@ int main(int argc,char **argv) {
 
 	/* activate logging */
 	printf("[sic] activate logging\n");
-	moldyn_set_log_dir(&md,"saves/test");
+	moldyn_set_log_dir(&md,"saves/si_melting_point");
 	moldyn_set_log(&md,LOG_TOTAL_ENERGY,200);
 	moldyn_set_log(&md,VISUAL_STEP,200);
 
-- 
2.20.1