more updates -> testing

diff --git a/moldyn.c b/moldyn.c
index a978541..eb2c606 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -618,10 +618,6 @@ int moldyn_integrate(t_moldyn *moldyn) {
        /* calculate initial forces */
        potential_force_calc(moldyn);
 
-       /* accuracy check */
-       ds=0.5*moldyn->tau_square*v3_norm(&(atom[0].f))/atom[0].mass;
-       if(ds>moldyn->lc.
-
        /* zero absolute time */
        moldyn->time=0.0;
 

diff --git a/run b/run
index 841b377..b1a2ceb 100755 (executable)
--- a/run
+++ b/run
@@ -1,6 +1,6 @@
 mkdir -p saves video
 ./clean
-./posic $@
+./sic $@
 if [ "$?" == "0" ]; then
        ./perms
        argv="`echo $@ | grep -- '-V'`"

diff --git a/sic.c b/sic.c
index 9cb2c55..5d85534 100644 (file)
--- a/sic.c
+++ b/sic.c
@@ -25,7 +25,7 @@ int main(int argc,char **argv) {
        /* potential parameters */
        t_lj_params lj;
        t_ho_params ho;
-       t_tersoff_mult_params tp;
+       //t_tersoff_mult_params tp;
 
        /* misc variables, mainly to initialize stuff */
        t_3dvec r,v;
@@ -64,11 +64,12 @@ int main(int argc,char **argv) {
 
        /* cutoff radius */
        printf("[sic] setting cutoff radius\n");
-       set_cutoff(&md,LC_SI);
+       set_cutoff(&md,5*LC_SI);
 
        /* set (initial) dimensions of simulation volume */
        printf("[sic] setting dimensions\n");
        set_dim(&md,10*LC_SI,10*LC_SI,10*LC_SI,TRUE);
+       printf("%.15f <---\n",md.vis.dim.x);
 
        /* set periodic boundary conditions in all directions */
        printf("[sic] setting periodic boundary conditions\n");
@@ -83,10 +84,6 @@ int main(int argc,char **argv) {
        add_atom(&md,SI,M_SI,0,ATOM_ATTR_2BP,&r,&v);
        r.x=-r.x;
        add_atom(&md,SI,M_SI,0,ATOM_ATTR_2BP,&r,&v);
-       printf("[sic] check: there are %d atoms\n",md.count);
-       printf("[sic] check: atoms x pos: %.15f %.15f\n",md.atom[0].r.x,md.atom[1].r.x);
-       printf("[sic] check: atoms x vel: %.15f %.15f\n",md.atom[0].v.x,md.atom[1].v.x);
-       printf("[sic] check: atoms mass: %.35f %.35f\n",md.atom[0].mass,md.atom[1].mass);
 
        /* set temperature */
        printf("[sic] setting temperature\n");
@@ -95,18 +92,15 @@ int main(int argc,char **argv) {
        /* initial thermal fluctuations of particles */
        printf("[sic] thermal init\n");
        thermal_init(&md);
-       printf("[sic] check: there are %d atoms\n",md.count);
-       printf("[sic] check: atoms x pos: %.15f %.15f\n",md.atom[0].r.x,md.atom[1].r.x);
-       printf("[sic] check: atoms x vel: %.15f %.15f\n",md.atom[0].v.x,md.atom[1].v.x);
 
        /* create the simulation schedule */
        printf("[sic] adding schedule\n");
-       moldyn_add_schedule(&md,10000,1.0e-12);
+       moldyn_add_schedule(&md,10000,1.0e-15);
 
        /* activate logging */
        printf("[sic] activate logging\n");
-       moldyn_set_log(&md,LOG_TOTAL_ENERGY,"saves/test-energy",1);
-       moldyn_set_log(&md,VISUAL_STEP,"saves/test-visual",1);
+       moldyn_set_log(&md,LOG_TOTAL_ENERGY,"saves/test-energy",100);
+       moldyn_set_log(&md,VISUAL_STEP,"saves/test-visual",100);
 
        /*
         * let's do the actual md algorithm now

diff --git a/visual/visual.c b/visual/visual.c
index d675c5d..427e765 100644 (file)
--- a/visual/visual.c
+++ b/visual/visual.c
@@ -55,8 +55,6 @@ int visual_init(t_visual *v,char *filebase) {
        }
        dprintf(v->fd,"set write on\n");
 
-       memset(&(v->dim),0,sizeof(t_3dvec));
-
        return 0;
 }