X-Git-Url: https://hackdaworld.org/cgi-bin/gitweb.cgi?a=blobdiff_plain;f=moldyn.c;h=e961ca23b45316fbf15b664b889e70dd1f9976bc;hb=9f9a3d935831d0eefa1b67f94510c2956a78aed4;hp=2fdf4c2e0b8a7bf47a3f3fb7dc76d235465c48e6;hpb=5b64e8a2762ea3248792a3c8cb57add0ecb5442c;p=physik%2Fposic.git

diff --git a/moldyn.c b/moldyn.c
index 2fdf4c2..e961ca2 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -24,6 +24,9 @@ int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 
 	memset(moldyn,0,sizeof(t_moldyn));
 
+	moldyn->argc=argc;
+	moldyn->args=argv;
+
 	rand_init(&(moldyn->random),NULL,1);
 	moldyn->random.status|=RAND_STAT_VERBOSE;
 
@@ -510,6 +513,7 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 		atom[ret].brand=brand;
 		atom[ret].tag=count+ret;
 		check_per_bound(moldyn,&(atom[ret].r));
+		atom[ret].r_0=atom[ret].r;
 	}
 
 	/* update total system mass */
@@ -518,6 +522,40 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 	return ret;
 }
 
+int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
+             t_3dvec *r,t_3dvec *v) {
+
+	t_atom *atom;
+	void *ptr;
+	int count;
+	
+	atom=moldyn->atom;
+	count=(moldyn->count)++;
+
+	ptr=realloc(atom,(count+1)*sizeof(t_atom));
+	if(!ptr) {
+		perror("[moldyn] realloc (add atom)");
+		return -1;
+	}
+	moldyn->atom=ptr;
+
+	atom=moldyn->atom;
+	atom[count].r=*r;
+	atom[count].v=*v;
+	atom[count].element=element;
+	atom[count].mass=mass;
+	atom[count].brand=brand;
+	atom[count].tag=count;
+	atom[count].attr=attr;
+	check_per_bound(moldyn,&(atom[count].r));
+	atom[count].r_0=atom[count].r;
+
+	/* update total system mass */
+	total_mass_calc(moldyn);
+
+	return 0;
+}
+
 /* cubic init */
 int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 
@@ -630,38 +668,6 @@ int diamond_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 	return count;
 }
 
-int add_atom(t_moldyn *moldyn,int element,double mass,u8 brand,u8 attr,
-             t_3dvec *r,t_3dvec *v) {
-
-	t_atom *atom;
-	void *ptr;
-	int count;
-	
-	atom=moldyn->atom;
-	count=(moldyn->count)++;
-
-	ptr=realloc(atom,(count+1)*sizeof(t_atom));
-	if(!ptr) {
-		perror("[moldyn] realloc (add atom)");
-		return -1;
-	}
-	moldyn->atom=ptr;
-
-	atom=moldyn->atom;
-	atom[count].r=*r;
-	atom[count].v=*v;
-	atom[count].element=element;
-	atom[count].mass=mass;
-	atom[count].brand=brand;
-	atom[count].tag=count;
-	atom[count].attr=attr;
-
-	/* update total system mass */
-	total_mass_calc(moldyn);
-
-	return 0;
-}
-
 int destroy_atoms(t_moldyn *moldyn) {
 
 	if(moldyn->atom) free(moldyn->atom);
@@ -1097,8 +1103,10 @@ double e_kin_calc(t_moldyn *moldyn) {
 	atom=moldyn->atom;
 	moldyn->ekin=0.0;
 
-	for(i=0;i<moldyn->count;i++)
-		moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+	for(i=0;i<moldyn->count;i++) {
+		atom[i].ekin=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+		moldyn->ekin+=atom[i].ekin;
+	}
 
 	return moldyn->ekin;
 }
@@ -1456,7 +1464,8 @@ return 0;
 			if(!(i%s)) {
 				snprintf(dir,128,"%s/s-%07.f.save",
 				         moldyn->vlsdir,moldyn->time);
-				fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT);
+				fd=open(dir,O_WRONLY|O_TRUNC|O_CREAT,
+				        S_IRUSR|S_IWUSR);
 				if(fd<0) perror("[moldyn] save fd open");
 				else {
 					write(fd,moldyn,sizeof(t_moldyn));
@@ -1478,7 +1487,7 @@ return 0;
 	printf("\rsched:%d, steps:%d, T:%3.1f/%3.1f P:%4.1f/%4.1f V:%6.1f",
 	       sched->count,i,
 	       moldyn->t,moldyn->t_avg,
-	       moldyn->p_avg/BAR,moldyn->p/BAR,
+	       moldyn->p_avg/BAR,moldyn->gp_avg/BAR,
 	       moldyn->volume);
 	fflush(stdout);
 		}
@@ -1490,13 +1499,11 @@ return 0;
 	}
 
 		/* check for hooks */
-		if(sched->count+1<sched->total_sched) {
-			if(sched->hook) {
-				printf("\n ## schedule hook %d/%d start ##\n",
-				       sched->count+1,sched->total_sched-1);
-				sched->hook(moldyn,sched->hook_params);
-				printf(" ## schedule hook end ##\n");
-			}
+		if(sched->hook) {
+			printf("\n ## schedule hook %d/%d start ##\n",
+			       sched->count+1,sched->total_sched-1);
+			sched->hook(moldyn,sched->hook_params);
+			printf(" ## schedule hook end ##\n");
 		}
 
 		/* increase the schedule counter */
@@ -1917,6 +1924,17 @@ int moldyn_bc_check(t_moldyn *moldyn) {
 	return 0;
 }
 
+/*
+ * restore function
+ */
+
+int moldyn_load(t_moldyn *moldyn) {
+
+	// later ...
+
+	return 0;
+}
+
 /*
  * post processing functions
  */
@@ -1939,3 +1957,11 @@ int get_line(int fd,char *line,int max) {
 	}
 }
 
+int analyze_bonds(t_moldyn *moldyn) {
+
+	
+	
+
+	return 0;
+}
+