added post proc stuff

diff --git a/moldyn.c b/moldyn.c
index aebd604..c130ef4 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -404,11 +404,14 @@ int moldyn_log_shutdown(t_moldyn *moldyn) {
        if(moldyn->rfd) {
                dprintf(moldyn->rfd,report_end);
                close(moldyn->rfd);
-               snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
+               snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
+                        moldyn->vlsdir);
                system(sc);
-               snprintf(sc,255,"cd %s && pdflatex report",moldyn->vlsdir);
+               snprintf(sc,255,"cd %s && pdflatex report >/dev/null 2>&1",
+                        moldyn->vlsdir);
                system(sc);
-               snprintf(sc,255,"cd %s && dvipdf report",moldyn->vlsdir);
+               snprintf(sc,255,"cd %s && dvipdf report >/dev/null 2>&1",
+                        moldyn->vlsdir);
                system(sc);
        }
        if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
@@ -1385,8 +1388,9 @@ return 0;
        }
 
                /* check for hooks */
-               if(sched->hook)
-                       sched->hook(moldyn,sched->hook_params);
+               if(sched->count+1<sched->total_sched)
+                       if(sched->hook)
+                               sched->hook(moldyn,sched->hook_params);
 
                /* get a new info line */
                printf("\n");
@@ -1809,17 +1813,17 @@ int moldyn_bc_check(t_moldyn *moldyn) {
 /*
  * postprocessing functions
  */
-#define LINE_MAX 128
-int read_line(int fd,char *line) {
+
+int get_line(int fd,char *line,int max) {
 
        int count,ret;
 
        count=0;
 
        while(1) {
-               if(count==LINE_MAX) return count;
+               if(count==max) return count;
                ret=read(fd,line+count,1);
-               if(ret<0) return ret;
+               if(ret<=0) return ret;
                if(line[count]=='\n') {
                        line[count]='\0';
                        return count+1;
@@ -1828,19 +1832,21 @@ int read_line(int fd,char *line) {
        }
 }
 
-int calc_fluctuations(double start,double end,char *file) {
+int calc_fluctuations(double start,double end,t_moldyn *moldyn) {
 
        int fd;
        int count,ret;
        double time,pot,kin,tot;
-       double p_m,k_m,t_m;
-       double p2_m,k2_m,t2_m;
        double p_sum,k_sum,t_sum;
-       char buf[LINE_MAX];
+       char buf[64];
+       char file[128+7];
+
+       printf("[moldyn] calculating energy fluctuations [eV]:\n");
 
+       snprintf(file,128+7,"%s/energy",moldyn->vlsdir);
        fd=open(file,O_RDONLY);
        if(fd<0) {
-               perror("[moldyn] post proc open");
+               perror("[moldyn] post proc energy open");
                return fd;
        }
 
@@ -1850,24 +1856,21 @@ int calc_fluctuations(double start,double end,char *file) {
        t_sum=0.0;
        count=0;
        while(1) {
-               ret=read_line(fd,buf);
-               if(ret<0) break;
-printf("%d\n",ret);
+               ret=get_line(fd,buf,63);
+               if(ret<=0) break;
                if(buf[0]=='#') continue;
                sscanf(buf,"%lf %lf %lf %lf",&time,&kin,&pot,&tot);
-printf("%f %f %f %f\n",time,pot,kin,tot);
-               //if(time>end) break;
-               if((time>=start)&(time<=end)) {
-                       p_sum+=pot;
-                       k_sum+=kin;
-                       t_sum+=tot;
-                       count+=1;
-               }
+               if(time<start) continue;
+               if(time>end) break;
+               p_sum+=pot;
+               k_sum+=kin;
+               t_sum+=tot;
+               count+=1;
        }
 
-       p_m=p_sum/count;
-       k_m=k_sum/count;
-       t_m=t_sum/count;
+       moldyn->p_m=p_sum/count;
+       moldyn->k_m=k_sum/count;
+       moldyn->t_m=t_sum/count;
 
        /* mean square fluctuations */
        if(lseek(fd,SEEK_SET,0)<0) {
@@ -1879,28 +1882,60 @@ printf("%f %f %f %f\n",time,pot,kin,tot);
        k_sum=0.0;
        t_sum=0.0;
        while(1) {
-               ret=read_line(fd,buf);
-               if(ret<0) break;
+               ret=get_line(fd,buf,63);
+               if(ret<=0) break;
                if(buf[0]=='#') continue;
                sscanf(buf,"%lf %lf %lf %lf",&time,&kin,&pot,&tot);
+               if(time<start) continue;
                if(time>end) break;
-               if((time>=start)&(time<=end)) {
-                       p_sum+=((pot-p_m)*(pot-p_m));
-                       k_sum+=((kin-k_m)*(kin-k_m));
-                       t_sum+=((tot-t_m)*(tot-t_m));
-                       count+=1;
-               }
+               k_sum+=((kin-moldyn->k_m)*(kin-moldyn->k_m));
+               p_sum+=((pot-moldyn->p_m)*(pot-moldyn->p_m));
+               t_sum+=((tot-moldyn->t_m)*(tot-moldyn->t_m));
+               count+=1;
        }
 
-       p2_m=p_sum/count;
-       k2_m=k_sum/count;
-       t2_m=t_sum/count;
+       moldyn->dp2_m=p_sum/count;
+       moldyn->dk2_m=k_sum/count;
+       moldyn->dt2_m=t_sum/count;
 
-       printf("[moldyn] fluctuations (%f - %f):\n",start,end);
-       printf("  - averages   : %f %f %f\n",k_m,p_m,t_m);
-       printf("  - mean square: %f %f %f\n",k2_m,p2_m,t2_m);
+       printf("  averages   : %f %f %f\n",moldyn->k_m,
+                                       moldyn->p_m,
+                                       moldyn->t_m);
+       printf("  mean square: %f %f %f\n",moldyn->dk2_m,
+                                          moldyn->dp2_m,
+                                          moldyn->dt2_m);
 
        close(fd);
 
        return 0;
 }
+
+int get_heat_capacity(t_moldyn *moldyn) {
+
+       double temp2,mass,ighc;
+       int i;
+
+       /* (temperature average)^2 */
+       temp2=2.0*moldyn->k_m*EV/(3.0*K_BOLTZMANN);
+       printf("[moldyn] specific heat capacity for T=%f K [J/(kg K)]\n",temp2);
+       temp2*=temp2;
+
+       /* total mass */
+       mass=0.0;
+       for(i=0;i<moldyn->count;i++)
+               mass+=moldyn->atom[i].mass;
+
+       /* ideal gas contribution */
+       ighc=3.0*moldyn->count*K_BOLTZMANN/2.0;
+       printf("  ideal gas contribution: %f\n",ighc/mass*KILOGRAM/JOULE);
+
+       moldyn->c_v_nvt=moldyn->dp2_m*moldyn->count*moldyn->count*EV/(K_BOLTZMANN*temp2)+ighc;
+       moldyn->c_v_nvt/=mass;
+       moldyn->c_v_nve=ighc/(1.0-(moldyn->dp2_m*moldyn->count*moldyn->count*EV/(ighc*K_BOLTZMANN*temp2)));
+       moldyn->c_v_nve/=mass;
+
+       printf("  NVE: %f\n",moldyn->c_v_nve*KILOGRAM/JOULE);
+       printf("  NVT: %f\n",moldyn->c_v_nvt*KILOGRAM/JOULE);
+
+       return 0;
+}

diff --git a/moldyn.h b/moldyn.h
index fc9bce7..484c456 100644 (file)
--- a/moldyn.h
+++ b/moldyn.h
@@ -139,9 +139,22 @@ typedef struct s_moldyn {
        double tau_square;      /* delta t squared */
        int total_steps;        /* total steps */
 
+       /* energy */
        double energy;          /* potential energy */
        double ekin;            /* kinetic energy */
 
+       /* energy averages & fluctuations */
+       double k_m;
+       double p_m;
+       double t_m;
+       double dk2_m;           /* mean square kinetic energy fluctuations */
+       double dp2_m;           /* mean square potential energy fluctuations */
+       double dt2_m;           /* mean square fluctuations in total energy */
+       
+       /* response functions */
+       double c_v_nve;         /* constant volume heat capacity (nve) */
+       double c_v_nvt;         /* constant volume heat capacity (nvt) */
+
        char vlsdir[128];       /* visualization/log/save directory */
        t_visual vis;           /* visualization interface structure */
        u8 vlsprop;             /* log/vis/save properties */
@@ -209,7 +222,9 @@ typedef struct s_moldyn {
 #define PASCAL (NEWTON/(METER*METER))                  /* N / A^2 */
 #define BAR    ((1.0e5*PASCAL))                        /* N / A^2 */
 #define K_BOLTZMANN    (1.380650524e-23*METER*NEWTON)  /* NA/K */
+#define K_B2           (K_BOLTZMANN*K_BOLTZMANN)       /* (NA)^2/K^2 */
 #define EV             (1.6021765314e-19*METER*NEWTON) /* NA */
+#define JOULE          (NEWTON*METER)                  /* NA */
 
 #define MOLDYN_TEMP                    273.0
 #define MOLDYN_TAU                     1.0
@@ -427,7 +442,8 @@ int check_per_bound(t_moldyn *moldyn,t_3dvec *a);
 
 int moldyn_bc_check(t_moldyn *moldyn);
 
-int read_line(int fd,char *line);
-int calc_fluctuations(double start,double end,char *file);
+int get_line(int fd,char *line,int max);
+int calc_fluctuations(double start,double end,t_moldyn *moldyn);
+int get_heat_capacity(t_moldyn *moldyn);
 
 #endif

diff --git a/ppm2avi b/ppm2avi
index 74e65cf..fec403e 100755 (executable)
--- a/ppm2avi
+++ b/ppm2avi
@@ -2,4 +2,4 @@ for i in $1/*.ppm; do
        convert $i $1/$(basename $i ppm)png
 done
 
-mencoder mf://$1/*.png -ovc copy -o $1/md.avi
+mencoder mf://$1/*.png -ovc copy -o $1/md.avi >/dev/null 2>&1

diff --git a/sic.c b/sic.c
index cea2644..d50c35e 100644 (file)
--- a/sic.c
+++ b/sic.c
@@ -35,6 +35,12 @@ int hook(void *moldyn,void *hook_params) {
 
        md=moldyn;
 
+// vortrag
+set_temperature(moldyn,(4-md->schedule.count)*1000.0);
+set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
+
+return 0;
+
        printf("\nschedule hook: ");
 
        if(!(md->schedule.count%2)) {
@@ -203,11 +209,11 @@ int main(int argc,char **argv) {
        albe_mult_complete_params(&ap);
 
        /* set (initial) dimensions of simulation volume */
-       //set_dim(&md,6*LC_SI_ALBE,6*LC_SI_ALBE,6*LC_SI_ALBE,TRUE);
+       set_dim(&md,6*LC_SI_ALBE,6*LC_SI_ALBE,6*LC_SI_ALBE,TRUE);
        //set_dim(&md,6*LC_SI,6*LC_SI,6*LC_SI,TRUE);
        //set_dim(&md,6*LC_C_ALBE,6*LC_C_ALBE,6*LC_C_ALBE,TRUE);
        //set_dim(&md,6*LC_C,6*LC_C,6*LC_C,TRUE);
-       set_dim(&md,6*LC_SIC_ALBE,6*LC_SIC_ALBE,6*LC_SIC_ALBE,TRUE);
+       //set_dim(&md,6*LC_SIC_ALBE,6*LC_SIC_ALBE,6*LC_SIC_ALBE,TRUE);
 
        /* set periodic boundary conditions in all directions */
        set_pbc(&md,TRUE,TRUE,TRUE);
@@ -215,14 +221,14 @@ int main(int argc,char **argv) {
        /* create the lattice / place atoms */
        //create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
        //create_lattice(&md,DIAMOND,LC_C_ALBE,C,M_C,
-       //create_lattice(&md,DIAMOND,LC_SI_ALBE,SI,M_SI,
-       //               ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+       create_lattice(&md,DIAMOND,LC_SI_ALBE,SI,M_SI,
+                      ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
        //               ATOM_ATTR_2BP|ATOM_ATTR_HB,
-       //               0,6,6,6,NULL);
+                      0,6,6,6,NULL);
        //               1,6,6,6,NULL);
 
        /* create centered zinc blende lattice */
-       /**/
+       /*
        r.x=0.5*0.25*LC_SIC_ALBE; r.y=r.x; r.z=r.x;
        create_lattice(&md,FCC,LC_SIC_ALBE,SI,M_SI,
                       ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
@@ -231,7 +237,7 @@ int main(int argc,char **argv) {
        create_lattice(&md,FCC,LC_SIC_ALBE,C,M_C,
                       ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
                       1,6,6,6,&r);
-       /**/
+       */
 
        moldyn_bc_check(&md);
 
@@ -283,6 +289,11 @@ int main(int argc,char **argv) {
        /* create the simulation schedule */
        /* initial configuration */
        moldyn_add_schedule(&md,10000,1.0);
+       //moldyn_add_schedule(&md,1000,1.0);
+       //moldyn_add_schedule(&md,1000,1.0);
+       //moldyn_add_schedule(&md,1000,1.0);
+       //moldyn_add_schedule(&md,1000,1.0);
+       //moldyn_add_schedule(&md,1000,1.0);
        /* adding atoms */
        //for(inject=0;inject<INJECT;inject++) {
        //      /* injecting atom and run with enabled t scaling */
@@ -291,6 +302,7 @@ int main(int argc,char **argv) {
        //      moldyn_add_schedule(&md,1100,1.0);
        //}
 
+
        /* schedule hook function */
        moldyn_set_schedule_hook(&md,&hook,NULL);
 
@@ -314,6 +326,14 @@ int main(int argc,char **argv) {
 return 0;
 #endif
 
+       /*
+        * post processing the data
+        */
+
+       /* response functions expressed by energy fluctuations */
+       calc_fluctuations(1000.0,9999.0,&md);
+       get_heat_capacity(&md);
+
        /* close */
        moldyn_shutdown(&md);