create_lattice fixes, still virial probs ...

diff --git a/moldyn.c b/moldyn.c
index 0d5027c..f6c3c81 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -339,22 +339,24 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
        }
        moldyn->atom=ptr;
        atom=&(moldyn->atom[count]);
-               
-       v3_zero(&origin);
+
+       /* no atoms on the boundaries (only reason: it looks better!) */
+       origin.x=0.5*lc;
+       origin.y=0.5*lc;
+       origin.z=0.5*lc;
 
        switch(type) {
                case CUBIC:
                        set_nn_dist(moldyn,lc);
-                       origin.x=0.5*lc;
-                       origin.y=0.5*lc;
-                       origin.z=0.5*lc;
                        ret=cubic_init(a,b,c,lc,atom,&origin);
                        break;
                case FCC:
+                       v3_scale(&origin,&origin,0.5);
                        set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
-                       ret=fcc_init(a,b,c,lc,atom,NULL);
+                       ret=fcc_init(a,b,c,lc,atom,&origin);
                        break;
                case DIAMOND:
+                       v3_scale(&origin,&origin,0.25);
                        set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
                        ret=diamond_init(a,b,c,lc,atom,&origin);
                        break;
@@ -429,65 +431,55 @@ int cubic_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 int fcc_init(int a,int b,int c,double lc,t_atom *atom,t_3dvec *origin) {
 
        int count;
-       int i,j;
+       int i,j,k,l;
        t_3dvec o,r,n;
        t_3dvec basis[3];
-       double help[3];
-       double x,y,z;
-
-       x=a*lc;
-       y=b*lc;
-       z=c*lc;
 
-       if(origin) v3_copy(&o,origin);
-       else v3_zero(&o);
+       count=0;
+       if(origin)
+               v3_copy(&o,origin);
+       else
+               v3_zero(&o);
 
        /* construct the basis */
-       for(i=0;i<3;i++) {
-               for(j=0;j<3;j++) {
-                       if(i!=j) help[j]=0.5*lc;
-                       else help[j]=.0;
-               }
-               v3_set(&basis[i],help);
-       }
+       memset(basis,0,3*sizeof(t_3dvec));
+       basis[0].x=0.5*lc;
+       basis[0].y=0.5*lc;
+       basis[1].x=0.5*lc;
+       basis[1].z=0.5*lc;
+       basis[2].y=0.5*lc;
+       basis[2].z=0.5*lc;
 
-       v3_zero(&r);
-       count=0;
-       
        /* fill up the room */
        r.x=o.x;
-       while(r.x<x) {
+       for(i=0;i<a;i++) {
                r.y=o.y;
-               while(r.y<y) {
+               for(j=0;j<b;j++) {
                        r.z=o.z;
-                       while(r.z<z) {
+                       for(k=0;k<c;k++) {
+                               /* first atom */
                                v3_copy(&(atom[count].r),&r);
-                               atom[count].element=1;
                                count+=1;
-                               for(i=0;i<3;i++) {
-                                       v3_add(&n,&r,&basis[i]);
-                                       if((n.x<x+o.x)&&
-                                          (n.y<y+o.y)&&
-                                          (n.z<z+o.z)) {
-                                               v3_copy(&(atom[count].r),&n);
-                                               count+=1;
-                                       }
+                               r.z+=lc;
+                               /* the three face centered atoms */
+                               for(l=0;l<3;l++) {
+                                       v3_add(&n,&r,&basis[l]);
+                                       v3_copy(&(atom[count].r),&n);
+                                       count+=1;
                                }
-                               r.z+=lc;        
                        }
                        r.y+=lc;
                }
                r.x+=lc;
        }
-
+                               
        /* coordinate transformation */
-       help[0]=x/2.0;
-       help[1]=y/2.0;
-       help[2]=z/2.0;
-       v3_set(&n,help);
-       for(i=0;i<count;i++)
-               v3_sub(&(atom[i].r),&(atom[i].r),&n);
-               
+       for(i=0;i<count;i++) {
+               atom[i].r.x-=(a*lc)/2.0;
+               atom[i].r.y-=(b*lc)/2.0;
+               atom[i].r.z-=(c*lc)/2.0;
+       }
+
        return count;
 }
 
@@ -1575,6 +1567,7 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
                v3_scale(&force,&force,-1.0); /* f = - grad E */
                v3_add(&(ai->f),&(ai->f),&force);
                virial_calc(ai,&force,&distance);
+if(force.x*distance.x<=0) printf("virial xx: %.15f -> %f %f %f\n",force.x*distance.x,distance.x,distance.y,distance.z);
                virial_calc(aj,&force,&distance); /* f and d signe switched */
        }
 

diff --git a/moldyn.h b/moldyn.h
index f2ccdb5..3c53a86 100644 (file)
--- a/moldyn.h
+++ b/moldyn.h
@@ -334,7 +334,8 @@ typedef struct s_tersoff_mult_params {
 #define M_SI                   28.08553                        /* amu */
 
 //#define LJ_SIGMA_SI          ((0.25*sqrt(3.0)*LC_SI)/1.122462)       /* A */
-#define LJ_SIGMA_SI            (LC_SI/1.122462)                        /* A */
+//#define LJ_SIGMA_SI          (LC_SI/1.122462)                        /* A */
+#define LJ_SIGMA_SI            (0.5*sqrt(2.0)*LC_SI/1.122462)                  /* A */
 #define LJ_EPSILON_SI          (2.1678*EV)                             /* NA */
 
 #define TM_R_SI                        (2.7e-10*METER)                 /* A */

diff --git a/report/report.h b/report/report.h
index 3868515..e46ff2a 100644 (file)
--- a/report/report.h
+++ b/report/report.h
@@ -53,7 +53,7 @@ set ytic auto \n\
 set title 'Energy per atom vs. time' \n\
 set xlabel 'Time [fs]' \n\
 set ylabel 'Energy per atom [eV]' \n\
-set terminal postscript eps enhanced color dashed lw 1 'Helvetica' 14 \n\
+set terminal postscript eps enhanced color solid lw 1 'Helvetica' 14 \n\
 set output 'energy.eps' \n\
 plot \"energy\" using 1:2 title 'Kinetic energy' with lines , \"energy\" using 1:3 title 'Potential energy' with lines , \"energy\" using 1:4 title 'Total energy' with lines\
 ";

diff --git a/sic.c b/sic.c
index 2a2c7bc..f97ffe8 100644 (file)
--- a/sic.c
+++ b/sic.c
@@ -121,8 +121,8 @@ int main(int argc,char **argv) {
        set_pbc(&md,TRUE,TRUE,TRUE);
 
        /* create the lattice / place atoms */
-       create_lattice(&md,CUBIC,LC_SI,SI,M_SI,
-       //create_lattice(&md,FCC,LC_SI,SI,M_SI,
+       //create_lattice(&md,CUBIC,LC_SI,SI,M_SI,
+       create_lattice(&md,FCC,LC_SI,SI,M_SI,
        //create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
        //               ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
                       ATOM_ATTR_2BP|ATOM_ATTR_HB,
@@ -151,8 +151,8 @@ int main(int argc,char **argv) {
        set_pressure(&md,ATM);
 
        /* set p/t scaling */
-       set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
-                        T_SCALE_BERENDSEN,100.0);
+       //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
+       //                 T_SCALE_BERENDSEN,100.0);
        //set_pt_scale(&md,0,0,T_SCALE_DIRECT,1.0);
        //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
        
@@ -160,7 +160,7 @@ int main(int argc,char **argv) {
        thermal_init(&md,TRUE);
 
        /* create the simulation schedule */
-       moldyn_add_schedule(&md,100001,1.0);
+       moldyn_add_schedule(&md,101,1.0);
        //moldyn_add_schedule(&md,501,1.0);
        //moldyn_add_schedule(&md,501,1.0);
 
@@ -171,7 +171,7 @@ int main(int argc,char **argv) {
        moldyn_set_log_dir(&md,argv[1]);
        moldyn_set_report(&md,"Frank Zirkelbach","Test 1");
        moldyn_set_log(&md,LOG_TOTAL_ENERGY,1);
-       moldyn_set_log(&md,VISUAL_STEP,1000);
+       moldyn_set_log(&md,VISUAL_STEP,1);
        moldyn_set_log(&md,CREATE_REPORT,0);
 
        /*

diff --git a/visual/visual.c b/visual/visual.c
index d6ce369..573ac4f 100644 (file)
--- a/visual/visual.c
+++ b/visual/visual.c
@@ -87,8 +87,7 @@ int visual_atoms(t_visual *v,double time,t_atom *atom,int n) {
 
        /* script file update */
        dprintf(v->fd,"load xyz %s\n",file);
-       dprintf(v->fd,"spacefill\n");
-       //dprintf(v->fd,"spacefill 100\n");
+       dprintf(v->fd,"spacefill 200\n");
        dprintf(v->fd,"rotate x 100\n");
        dprintf(v->fd,"rotate y 10\n");
        dprintf(v->fd,"set ambient 20\n");