pt scaling tests, though pressure estimation still a mess!

diff --git a/moldyn.c b/moldyn.c
index 881f0b6..0d5027c 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -73,7 +73,7 @@ int set_temperature(t_moldyn *moldyn,double t_ref) {
 
        moldyn->t_ref=t_ref;
 
-       printf("[moldyn] temperature: %f\n",moldyn->t_ref);
+       printf("[moldyn] temperature [K]: %f\n",moldyn->t_ref);
 
        return 0;
 }
@@ -82,7 +82,7 @@ int set_pressure(t_moldyn *moldyn,double p_ref) {
 
        moldyn->p_ref=p_ref;
 
-       printf("[moldyn] pressure: %f\n",moldyn->p_ref);
+       printf("[moldyn] pressure [atm]: %f\n",moldyn->p_ref/ATM);
 
        return 0;
 }
@@ -344,15 +344,18 @@ int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
 
        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:
+                       set_nn_dist(moldyn,0.5*sqrt(2.0)*lc);
                        ret=fcc_init(a,b,c,lc,atom,NULL);
                        break;
                case DIAMOND:
+                       set_nn_dist(moldyn,0.25*sqrt(3.0)*lc);
                        ret=diamond_init(a,b,c,lc,atom,&origin);
                        break;
                default:
@@ -720,7 +723,7 @@ double thermodynamic_pressure_calc(t_moldyn *moldyn) {
        scale_dim(moldyn,scale,TRUE,0,0);
        scale_atoms(moldyn,scale,TRUE,0,0);
        link_cell_shutdown(moldyn);
-       link_cell_init(moldyn);
+       link_cell_init(moldyn,QUIET);
        potential_force_calc(moldyn);
        tp->x=(moldyn->energy-u)/moldyn->dv;
        p=tp->x*tp->x;
@@ -734,7 +737,7 @@ double thermodynamic_pressure_calc(t_moldyn *moldyn) {
        scale_dim(moldyn,scale,0,TRUE,0);
        scale_atoms(moldyn,scale,0,TRUE,0);
        link_cell_shutdown(moldyn);
-       link_cell_init(moldyn);
+       link_cell_init(moldyn,QUIET);
        potential_force_calc(moldyn);
        tp->y=(moldyn->energy-u)/moldyn->dv;
        p+=tp->y*tp->y;
@@ -748,7 +751,7 @@ double thermodynamic_pressure_calc(t_moldyn *moldyn) {
        scale_dim(moldyn,scale,0,0,TRUE);
        scale_atoms(moldyn,scale,0,0,TRUE);
        link_cell_shutdown(moldyn);
-       link_cell_init(moldyn);
+       link_cell_init(moldyn,QUIET);
        potential_force_calc(moldyn);
        tp->z=(moldyn->energy-u)/moldyn->dv;
        p+=tp->z*tp->z;
@@ -765,7 +768,7 @@ printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x);
        scale_dim(moldyn,scale,1,1,1);
        scale_atoms(moldyn,scale,1,1,1);
        link_cell_shutdown(moldyn);
-       link_cell_init(moldyn);
+       link_cell_init(moldyn,QUIET);
        potential_force_calc(moldyn);
 printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x);
 
@@ -779,7 +782,7 @@ printf("debug: %f %f\n",moldyn->atom[0].r.x,moldyn->dim.x);
        moldyn->energy=u;
 
        link_cell_shutdown(moldyn);
-       link_cell_init(moldyn);
+       link_cell_init(moldyn,QUIET);
 
        return sqrt(p);
 }
@@ -820,61 +823,48 @@ int scale_atoms(t_moldyn *moldyn,double scale,u8 x,u8 y,u8 z) {
 
 int scale_volume(t_moldyn *moldyn) {
 
-       t_atom *atom;
        t_3dvec *dim,*vdim;
-       double scale,v;
-       t_virial virial;
+       double scale;
        t_linkcell *lc;
-       int i;
 
-       atom=moldyn->atom;
-       dim=&(moldyn->dim);
        vdim=&(moldyn->vis.dim);
+       dim=&(moldyn->dim);
        lc=&(moldyn->lc);
 
-       memset(&virial,0,sizeof(t_virial));
+       /* scaling factor */
+       if(moldyn->pt_scale&P_SCALE_BERENDSEN) {
+               scale=1.0-(moldyn->p_ref-moldyn->p)/moldyn->p_tc;
+               scale=pow(scale,ONE_THIRD);
+       }
+       else {
+               scale=pow(moldyn->p/moldyn->p_ref,ONE_THIRD);
+       }
+moldyn->debug=scale;
 
-       for(i=0;i<moldyn->count;i++) {
-               virial.xx+=atom[i].virial.xx;
-               virial.yy+=atom[i].virial.yy;
-               virial.zz+=atom[i].virial.zz;
-               virial.xy+=atom[i].virial.xy;
-               virial.xz+=atom[i].virial.xz;
-               virial.yz+=atom[i].virial.yz;
+       /* scale the atoms and dimensions */
+       scale_atoms(moldyn,scale,TRUE,TRUE,TRUE);
+       scale_dim(moldyn,scale,TRUE,TRUE,TRUE);
+
+       /* visualize dimensions */
+       if(vdim->x!=0) {
+               vdim->x=dim->x;
+               vdim->y=dim->y;
+               vdim->z=dim->z;
        }
 
-       /* just a guess so far ... */
-       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->volume;
-printf("%f | %f\n",moldyn->p/(ATM),moldyn->p_ref/ATM);
-
-       /* scale factor */
-       if(moldyn->pt_scale&P_SCALE_BERENDSEN)
-               scale=3*sqrt(1-(moldyn->p_ref-moldyn->p)/moldyn->p_tc);
-       else 
-               /* should actually never be used */
-               scale=pow(moldyn->p/moldyn->p_ref,1.0/3.0);
-
-printf("scale = %f\n",scale);
-       /* actual scaling */
-       dim->x*=scale;
-       dim->y*=scale;
-       dim->z*=scale;
-       if(vdim->x) vdim->x=dim->x;
-       if(vdim->y) vdim->y=dim->y;
-       if(vdim->z) vdim->z=dim->z;
-       moldyn->volume*=(scale*scale*scale);
-
-       /* check whether we need a new linkcell init */
-       if((dim->x/moldyn->cutoff!=lc->nx)||
-          (dim->y/moldyn->cutoff!=lc->ny)||
-          (dim->z/moldyn->cutoff!=lc->nx)) {
+       /* recalculate scaled volume */
+       moldyn->volume=dim->x*dim->y*dim->z;
+
+       /* adjust/reinit linkcell */
+       if(((int)(dim->x/moldyn->cutoff)!=lc->nx)||
+          ((int)(dim->y/moldyn->cutoff)!=lc->ny)||
+          ((int)(dim->z/moldyn->cutoff)!=lc->nx)) {
                link_cell_shutdown(moldyn);
-               link_cell_init(moldyn);
+               link_cell_init(moldyn,QUIET);
+       } else {
+               lc->x*=scale;
+               lc->y*=scale;
+               lc->z*=scale;
        }
 
        return 0;
@@ -939,7 +929,7 @@ double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
 
 /* linked list / cell method */
 
-int link_cell_init(t_moldyn *moldyn) {
+int link_cell_init(t_moldyn *moldyn,u8 vol) {
 
        t_linkcell *lc;
        int i;
@@ -960,7 +950,7 @@ int link_cell_init(t_moldyn *moldyn) {
        if(lc->cells<27)
                printf("[moldyn] FATAL: less then 27 subcells!\n");
 
-       printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
+       if(vol) printf("[moldyn] initializing linked cells (%d)\n",lc->cells);
 
        for(i=0;i<lc->cells;i++)
                list_init_f(&(lc->subcell[i]));
@@ -1137,7 +1127,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
        atom=moldyn->atom;
 
        /* initialize linked cell method */
-       link_cell_init(moldyn);
+       link_cell_init(moldyn,VERBOSE);
 
        /* logging & visualization */
        e=moldyn->ewrite;
@@ -1152,10 +1142,8 @@ int moldyn_integrate(t_moldyn *moldyn) {
        /* energy scaling factor */
        energy_scale=moldyn->count*EV;
 
-printf("debug: %f\n",moldyn->atom[0].f.x);
        /* calculate initial forces */
        potential_force_calc(moldyn);
-printf("debug: %f\n",moldyn->atom[0].f.x);
 
        /* some stupid checks before we actually start calculating bullshit */
        if(moldyn->cutoff>0.5*moldyn->dim.x)
@@ -1192,17 +1180,18 @@ printf("debug: %f\n",moldyn->atom[0].f.x);
                /* integration step */
                moldyn->integrate(moldyn);
 
+               /* calculate kinetic energy, temperature and pressure */
+               update_e_kin(moldyn);
+               temperature_calc(moldyn);
+               pressure_calc(moldyn);
+               //thermodynamic_pressure_calc(moldyn);
+
                /* p/t scaling */
                if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
                        scale_velocity(moldyn,FALSE);
                if(moldyn->pt_scale&(P_SCALE_BERENDSEN|P_SCALE_DIRECT))
                        scale_volume(moldyn);
 
-               update_e_kin(moldyn);
-               temperature_calc(moldyn);
-               pressure_calc(moldyn);
-               //thermodynamic_pressure_calc(moldyn);
-
                /* check for log & visualization */
                if(e) {
                        if(!(i%e))
@@ -1237,8 +1226,9 @@ printf("debug: %f\n",moldyn->atom[0].f.x);
                        if(!(i%v)) {
                                visual_atoms(&(moldyn->vis),moldyn->time,
                                             moldyn->atom,moldyn->count);
-                               printf("\rsched: %d, steps: %d, debug: %f",
-                                      sched->count,i,moldyn->p/ATM);
+                               printf("\rsched: %d, steps: %d, T: %f, P: %f V: %f",
+                                      sched->count,i,
+                                      moldyn->t,moldyn->p/ATM,moldyn->volume);
                                fflush(stdout);
                        }
                }

diff --git a/moldyn.h b/moldyn.h
index 0dbc1f9..f2ccdb5 100644 (file)
--- a/moldyn.h
+++ b/moldyn.h
@@ -313,6 +313,9 @@ typedef struct s_tersoff_mult_params {
 #define TRUE                           1
 #define FALSE                          0
 
+#define VERBOSE                                1
+#define QUIET                          0
+
 /*
  *
  * phsical values / constants
@@ -428,7 +431,7 @@ t_3dvec get_total_p(t_moldyn *moldyn);
 
 double estimate_time_step(t_moldyn *moldyn,double nn_dist);
 
-int link_cell_init(t_moldyn *moldyn);
+int link_cell_init(t_moldyn *moldyn,u8 vol);
 int link_cell_update(t_moldyn *moldyn);
 int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell);
 int link_cell_shutdown(t_moldyn *moldyn);

diff --git a/sic.c b/sic.c
index 7e1249c..2a2c7bc 100644 (file)
--- a/sic.c
+++ b/sic.c
@@ -146,26 +146,15 @@ int main(int argc,char **argv) {
        //           ATOM_ATTR_2BP|ATOM_ATTR_HB,
        //           &r,&v);
 
-       /* setting a nearest neighbour distance for the moldyn checks */
-       //set_nn_dist(&md,0.25*sqrt(3.0)*LC_SI); /* diamond ! */
-       set_nn_dist(&md,LC_SI);
-
-       /* set temperature */
-       //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);
+       /* set temperature & pressure */
        set_temperature(&md,atof(argv[2])+273.0);
-
-       /* set pressure */
        set_pressure(&md,ATM);
 
        /* set p/t scaling */
-       //set_pt_scale(&md,P_SCALE_BERENDSEN,100.0,
-       //                 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,100.0,0,0);
+       //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
        
        /* initial thermal fluctuations of particles (in equilibrium) */
        thermal_init(&md,TRUE);

diff --git a/visual/visual.c b/visual/visual.c
index a76c608..d6ce369 100644 (file)
--- a/visual/visual.c
+++ b/visual/visual.c
@@ -87,7 +87,8 @@ 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 100\n");
+       dprintf(v->fd,"spacefill\n");
+       //dprintf(v->fd,"spacefill 100\n");
        dprintf(v->fd,"rotate x 100\n");
        dprintf(v->fd,"rotate y 10\n");
        dprintf(v->fd,"set ambient 20\n");