foo

diff --git a/Makefile b/Makefile
index 42ff2bd..39457f7 100644 (file)
--- a/Makefile
+++ b/Makefile
@@ -2,8 +2,9 @@ CC=gcc-3.4
 #CC=gcc
 CFLAGS=-Wall
 CFLAGS+=-O3
-CFLAGS+=-g
 CFLAGS+=-ffloat-store
+CFLAGS+=-g
+CFLAGS+=-DDEBUG
 LDFLAGS=-lm
 
 OBJS=visual/visual.o random/random.o

diff --git a/moldyn.c b/moldyn.c
index db91859..faa6b7c 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -541,13 +541,13 @@ int scale_volume(t_moldyn *moldyn) {
        }
 
        /* just a guess so far ... */
-       v=sqrt(virial.xx*virial.xx+virial.yy*virial.yy+virial.zz+virial.zz);
+       v=virial.xx+virial.yy+virial.zz;
 
 printf("%f\n",v);
        /* get pressure from virial */
-       moldyn->p=moldyn->count*K_BOLTZMANN*moldyn->t-ONE_THIRD*v;
+       moldyn->p=moldyn->count*K_BOLTZMANN*moldyn->t+ONE_THIRD*v;
        moldyn->p/=moldyn->volume;
-printf("%f\n",moldyn->p/(ATM));
+printf("%f | %f\n",moldyn->p/(ATM),moldyn->p_ref/ATM);
 
        /* scale factor */
        if(moldyn->pt_scale&P_SCALE_BERENDSEN)
@@ -1427,6 +1427,15 @@ int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
        /* add forces of 2bp (ij, ji) contribution
         * dVij = dVji and we sum up both: no 1/2) */
        v3_add(&(ai->f),&(ai->f),&force);
+
+       /* virial */
+       ai->virial.xx-=force.x*dist_ij.x;
+       ai->virial.yy-=force.y*dist_ij.y;
+       ai->virial.zz-=force.z*dist_ij.z;
+       ai->virial.xy-=force.x*dist_ij.y;
+       ai->virial.xz-=force.x*dist_ij.z;
+       ai->virial.yz-=force.y*dist_ij.z;
+
 #ifdef DEBUG
 if(ai==&(moldyn->atom[0])) {
        printf("dVij, dVji (2bp) contrib:\n");
@@ -1526,6 +1535,15 @@ int tersoff_mult_post_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
 
        /* add force */
        v3_add(&(ai->f),&(ai->f),&force);
+
+       /* virial */
+       ai->virial.xx-=force.x*dist_ij->x;
+       ai->virial.yy-=force.y*dist_ij->y;
+       ai->virial.zz-=force.z*dist_ij->z;
+       ai->virial.xy-=force.x*dist_ij->y;
+       ai->virial.xz-=force.x*dist_ij->z;
+       ai->virial.yz-=force.y*dist_ij->z;
+
 #ifdef DEBUG
 if(ai==&(moldyn->atom[0])) {
        printf("dVij (3bp) contrib:\n");
@@ -1562,6 +1580,15 @@ if(ai==&(moldyn->atom[0])) {
 
        /* add force */
        v3_add(&(ai->f),&(ai->f),&force);
+
+       /* virial - plus sign, as dist_ij = - dist_ji - (really??) */
+       ai->virial.xx+=force.x*dist_ij->x;
+       ai->virial.yy+=force.y*dist_ij->y;
+       ai->virial.zz+=force.z*dist_ij->z;
+       ai->virial.xy+=force.x*dist_ij->y;
+       ai->virial.xz+=force.x*dist_ij->z;
+       ai->virial.yz+=force.y*dist_ij->z;
+
 #ifdef DEBUG
 if(ai==&(moldyn->atom[0])) {
        printf("dVji (3bp) contrib:\n");
@@ -1830,6 +1857,15 @@ int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
                v3_scale(&temp2,&temp2,tmp*B*exp(-mu*d_jk)*f_c_jk*0.5);
                v3_add(&(ai->f),&(ai->f),&temp2); /* -1 skipped in f_a calc ^ */
                                                  /* scaled with 0.5 ^ */
+
+               /* virial */
+               ai->virial.xx-=temp2.x*dist_jk.x;
+               ai->virial.yy-=temp2.y*dist_jk.y;
+               ai->virial.zz-=temp2.z*dist_jk.z;
+               ai->virial.xy-=temp2.x*dist_jk.y;
+               ai->virial.xz-=temp2.x*dist_jk.z;
+               ai->virial.yz-=temp2.y*dist_jk.z;
+
 #ifdef DEBUG
 if(ai==&(moldyn->atom[0])) {
        printf("dVjk (3bp) contrib:\n");

diff --git a/sic.c b/sic.c
index c4355b3..aabb79c 100644 (file)
--- a/sic.c
+++ b/sic.c
@@ -112,26 +112,26 @@ int main(int argc,char **argv) {
 
        /* 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_HB,
-       //               0,5,5,5);
-       //moldyn_bc_check(&md);
+       create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
+                      ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+                      0,5,5,5);
+       moldyn_bc_check(&md);
 
        /* testing configuration */
-       r.x=2.8/2;      v.x=0;
-       r.y=0;          v.y=0;
-       r.z=0;          v.z=0;
-       add_atom(&md,SI,M_SI,0,
-                  ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP,//|ATOM_ATTR_HB,
+       //r.x=2.8/2;    v.x=0;
+       //r.y=0;                v.y=0;
+       //r.z=0;                v.z=0;
+       //add_atom(&md,SI,M_SI,0,
+       //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
        //           ATOM_ATTR_2BP,
-                  &r,&v);
-       r.x=-2.8/2;     v.x=0;
-       r.y=0;          v.y=0;
-       r.z=0;          v.z=0;
-       add_atom(&md,SI,M_SI,0,
-                  ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP,//|ATOM_ATTR_HB,
+       //           &r,&v);
+       //r.x=-2.8/2;   v.x=0;
+       //r.y=0;                v.y=0;
+       //r.z=0;                v.z=0;
+       //add_atom(&md,SI,M_SI,0,
+       //           ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
        //           ATOM_ATTR_2BP,
-                  &r,&v);
+       //           &r,&v);
 
        /* setting a nearest neighbour distance for the moldyn checks */
        set_nn_dist(&md,0.25*sqrt(3.0)*LC_SI); /* diamond ! */
@@ -153,7 +153,7 @@ int main(int argc,char **argv) {
        printf("[sic] set p/t scaling\n");
        //set_pt_scale(&md,P_SCALE_BERENDSEN,100.0,
        //                 T_SCALE_BERENDSEN,100.0);
-       //set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);
+       set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);
        
        /* initial thermal fluctuations of particles (in equilibrium) */
        printf("[sic] thermal init\n");
@@ -161,13 +161,13 @@ int main(int argc,char **argv) {
 
        /* create the simulation schedule */
        printf("[sic] adding schedule\n");
-       moldyn_add_schedule(&md,10000,.1);
+       moldyn_add_schedule(&md,100,1.0);
 
        /* activate logging */
        printf("[sic] activate logging\n");
        moldyn_set_log_dir(&md,argv[1]);
        moldyn_set_log(&md,LOG_TOTAL_ENERGY,1);
-       moldyn_set_log(&md,VISUAL_STEP,20);
+       moldyn_set_log(&md,VISUAL_STEP,1);
 
        /*
         * let's do the actual md algorithm now