From 4bf9958c9ed62371b6d620c7ca167bd9993d2148 Mon Sep 17 00:00:00 2001
From: hackbard <hackbard>
Date: Thu, 30 Nov 2006 23:54:37 +0000
Subject: [PATCH] vel scaling issues, tersoff still segfaulting!

---
 moldyn.c | 27 ++++++++++++++++++++++-----
 sic.c    | 14 ++++++--------
 2 files changed, 28 insertions(+), 13 deletions(-)

diff --git a/moldyn.c b/moldyn.c
index 26f298f..80f4fa1 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -72,7 +72,7 @@ int set_cutoff(t_moldyn *moldyn,double cutoff) {
 }
 
 int set_temperature(t_moldyn *moldyn,double t) {
-	
+
 	moldyn->t=t;
 
 	return 0;
@@ -331,6 +331,7 @@ int scale_velocity(t_moldyn *moldyn,u8 type) {
 	int i;
 	double e,scale;
 	t_atom *atom;
+	int count;
 
 	atom=moldyn->atom;
 
@@ -339,13 +340,29 @@ int scale_velocity(t_moldyn *moldyn,u8 type) {
 	 */
 
 	e=0.0;
-	for(i=0;i<moldyn->count;i++)
-		e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
-	scale=(1.5*moldyn->count*K_BOLTZMANN*moldyn->t)/e;
+	count=0;
+	for(i=0;i<moldyn->count;i++) {
+		if(atom[i].attr&ATOM_ATTR_HB) {
+			e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+			count+=1;
+		}
+	}
+
+	/* temporary hack for e,t = 0 */
+	if(e==0.0) {
+		if(moldyn->t!=0.0)
+			thermal_init(moldyn);
+		else
+			return 0;
+	}
+
+	/* direct scaling */
+	scale=(1.5*count*K_BOLTZMANN*moldyn->t)/e;
 	if(type&VSCALE_INIT_EQUI) scale*=2.0; /* equipartition theorem */
 	scale=sqrt(scale);
 	for(i=0;i<moldyn->count;i++)
-		v3_scale(&(atom[i].v),&(atom[i].v),scale);
+		if(atom[i].attr&ATOM_ATTR_HB)
+			v3_scale(&(atom[i].v),&(atom[i].v),scale);
 
 	return 0;
 }
diff --git a/sic.c b/sic.c
index 82b3710..fa1cb66 100644
--- a/sic.c
+++ b/sic.c
@@ -15,7 +15,6 @@
 #include "posic.h"
 
 int main(int argc,char **argv) {
-printf("%d\n",sizeof(t_atom));
 	/* main moldyn structure */
 	t_moldyn md;
 
@@ -86,7 +85,6 @@ printf("%d\n",sizeof(t_atom));
 	/* cutoff radius */
 	printf("[sic] setting cutoff radius\n");
 	set_cutoff(&md,TM_S_SI);
-	//set_cutoff(&md,1.0*LC_SI);
 
 	/* set (initial) dimensions of simulation volume */
 	printf("[sic] setting dimensions\n");
@@ -99,8 +97,8 @@ printf("%d\n",sizeof(t_atom));
 	/* create the lattice / place atoms */
 	printf("[sic] creating atoms\n");
 	create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
-	               ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP,
-	               //ATOM_ATTR_2BP,
+	               ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+	               //ATOM_ATTR_2BP|ATOM_ATTR_HB,
 	               0,4,4,4);
 
 	/* setting a nearest neighbour distance for the moldyn checks */
@@ -108,7 +106,7 @@ printf("%d\n",sizeof(t_atom));
 
 	/* set temperature */
 	printf("[sic] setting temperature\n");
-	set_temperature(&md,10.0);
+	set_temperature(&md,273.0);
 	
 	/* initial thermal fluctuations of particles */
 	printf("[sic] thermal init\n");
@@ -116,12 +114,12 @@ printf("%d\n",sizeof(t_atom));
 
 	/* create the simulation schedule */
 	printf("[sic] adding schedule\n");
-	moldyn_add_schedule(&md,1000,1.0e-15);
+	moldyn_add_schedule(&md,100,1.0e-15);
 
 	/* activate logging */
 	printf("[sic] activate logging\n");
-	moldyn_set_log(&md,LOG_TOTAL_ENERGY,"saves/test-energy",10);
-	moldyn_set_log(&md,VISUAL_STEP,"saves/test-visual",10);
+	moldyn_set_log(&md,LOG_TOTAL_ENERGY,"saves/test-energy",1);
+	moldyn_set_log(&md,VISUAL_STEP,"saves/test-visual",1);
 
 	/*
 	 * let's do the actual md algorithm now
-- 
2.20.1