just foo

diff --git a/moldyn.c b/moldyn.c
index c25fed3ae9d4c21587336bc2cf321d0bd96b5bbb..551e07a89ea47bde8a3ad8439308f9a94a6f93e8 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -1001,6 +1001,9 @@ int potential_force_calc(t_moldyn *moldyn) {
                /* reset viral of atom i */
                v3_zero(&(itom[i].virial));
 
+               /* reset site energy */
+               itom[i].e=0.0;
+
                /* single particle potential/force */
                if(itom[i].attr&ATOM_ATTR_1BP)
                        moldyn->func1b(moldyn,&(itom[i]));

diff --git a/moldyn.h b/moldyn.h
index c01bc9f6e5e81da8cca4ca56c8206ea21e4aed81..b4f71d6be65e157a247fd7581e17cc3ed94c42f5 100644 (file)
--- a/moldyn.h
+++ b/moldyn.h
@@ -28,6 +28,7 @@ typedef struct s_atom {
        t_3dvec v;              /* velocity */
        t_3dvec f;              /* force */
        t_3dvec virial;         /* virial */
+       double e;               /* site energy */
        int element;            /* number of element in pse */
        double mass;            /* atom mass */
        u8 bnum;                /* brand number */

diff --git a/run b/run
index 2110d438fbc821f5b98ab122062cac7d9dfacc2e..3a155433e7452906f3ff329cfa6a969ecb863c10 100755 (executable)
--- a/run
+++ b/run
@@ -4,7 +4,7 @@ mkdir -p saves video
 if [ "$?" == "0" ]; then
        #./perms
        if [ "$1" ] ; then
-               rasmol -nodisplay < $1/visualize.scr > /dev/null 2>&1
+               rasmol -32 -nodisplay < $1/visualize.scr > /dev/null 2>&1
                ./ppm2avi $1
        fi
 fi

diff --git a/sic.c b/sic.c
index 7ab3dc92d979eadfec8a148d4757fa21fe3a6ab8..a105987ee32d845c5aa08103547f09fa3f3017ba 100644 (file)
--- a/sic.c
+++ b/sic.c
@@ -137,8 +137,8 @@ int main(int argc,char **argv) {
 
        /* set temperature */
        printf("[sic] setting temperature\n");
-       //set_temperature(&md,273.0+1410.0);
-       set_temperature(&md,273.0+450.0);
+       set_temperature(&md,273.0+1410.0);
+       //set_temperature(&md,273.0+450.0);
        //set_temperature(&md,273.0);
        //set_temperature(&md,1.0);
        //set_temperature(&md,0.0);
@@ -158,7 +158,7 @@ int main(int argc,char **argv) {
 
        /* create the simulation schedule */
        printf("[sic] adding schedule\n");
-       moldyn_add_schedule(&md,30001,1.0);
+       moldyn_add_schedule(&md,20001,1.0);
 
        /* activate logging */
        printf("[sic] activate logging\n");