safety checkin, gergo here!

diff --git a/fluctuation_calc.c b/fluctuation_calc.c
index 0ef0920..469371d 100644 (file)
--- a/fluctuation_calc.c
+++ b/fluctuation_calc.c
@@ -100,7 +100,6 @@ int main(int argc,char **argv) {
                }
        }
 
-printf("  count = %d\n",count);
        de2=e2/count-e*e/(count*count);
        printf("--> fluctuation [eV/atom]: %.20f\n",de2);
        if(argc==8) {

diff --git a/moldyn.c b/moldyn.c
index 16c811e..e0881de 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -218,10 +218,10 @@ int set_potential_params(t_moldyn *moldyn,void *params) {
        return 0;
 }
 
-int set_mean_skip(t_moldyn *moldyn,int skip) {
+int set_avg_skip(t_moldyn *moldyn,int skip) {
 
        printf("[moldyn] skip %d steps before starting average calc\n",skip);
-       moldyn->mean_skip=skip;
+       moldyn->avg_skip=skip;
 
        return 0;
 }
@@ -737,12 +737,6 @@ double temperature_calc(t_moldyn *moldyn) {
 
        moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
 
-       if(moldyn->total_steps<moldyn->mean_skip)
-               return 0;
-
-       moldyn->t_sum+=moldyn->t;
-       moldyn->mean_t=moldyn->t_sum/(moldyn->total_steps+1-moldyn->mean_skip);
-
        return moldyn->t;
 }
 
@@ -824,7 +818,7 @@ double pressure_calc(t_moldyn *moldyn) {
 
        /*
         * PV = NkT + <W>
-        * W = 1/3 sum_i f_i r_i
+        * with W = 1/3 sum_i f_i r_i (- skipped!)
         * virial = sum_i f_i r_i
         * 
         * => P = (2 Ekin + virial) / (3V)
@@ -836,19 +830,16 @@ double pressure_calc(t_moldyn *moldyn) {
                v+=(virial->xx+virial->yy+virial->zz);
        }
 
-       /* virial sum and mean virial */
-       moldyn->virial_sum+=v;
-       if(moldyn->total_steps>=moldyn->mean_skip)
-               moldyn->mean_v=moldyn->virial_sum/
-                              (moldyn->total_steps+1-moldyn->mean_skip);
-
-       /* assume up to date kinetic energy */
-       moldyn->p=2.0*moldyn->ekin+moldyn->mean_v;
-       moldyn->p/=(3.0*moldyn->volume);
-       if(moldyn->total_steps>=moldyn->mean_skip) {
+       /* virial sum and average virial */
+       if(moldyn->total_steps>=moldyn->avg_skip) {
+               moldyn->virial_sum+=v;
+               moldyn->virial_avg=moldyn->virial_sum/
+                                  (moldyn->total_steps+1-moldyn->avg_skip);
+               moldyn->p=2.0*moldyn->k_avg+moldyn->virial_avg;
+               moldyn->p/=(3.0*moldyn->volume);
                moldyn->p_sum+=moldyn->p;
-               moldyn->mean_p=moldyn->p_sum/
-                              (moldyn->total_steps+1-moldyn->mean_skip);
+               moldyn->p_avg=moldyn->p_sum/
+                             (moldyn->total_steps+1-moldyn->avg_skip);
        }
 
        /* pressure from 'absolute coordinates' virial */
@@ -856,37 +847,45 @@ double pressure_calc(t_moldyn *moldyn) {
        v=virial->xx+virial->yy+virial->zz;
        moldyn->gp=2.0*moldyn->ekin+v;
        moldyn->gp/=(3.0*moldyn->volume);
-       if(moldyn->total_steps>=moldyn->mean_skip) {
+       if(moldyn->total_steps>=moldyn->avg_skip) {
                moldyn->gp_sum+=moldyn->gp;
-               moldyn->mean_gp=moldyn->gp_sum/
-                              (moldyn->total_steps+1-moldyn->mean_skip);
+               moldyn->gp_avg=moldyn->gp_sum/
+                              (moldyn->total_steps+1-moldyn->avg_skip);
        }
 
        return moldyn->p;
 }
 
-int energy_fluctuation_calc(t_moldyn *moldyn) {
+int average_and_fluctuation_calc(t_moldyn *moldyn) {
 
-       if(moldyn->total_steps<moldyn->mean_skip)
+       if(moldyn->total_steps<moldyn->avg_skip)
                return 0;
 
-       /* assume up to date energies */
+       /* assume up to date energies, temperature, pressure etc */
 
        /* kinetic energy */
        moldyn->k_sum+=moldyn->ekin;
        moldyn->k2_sum+=(moldyn->ekin*moldyn->ekin);
-       moldyn->k_mean=moldyn->k_sum/(moldyn->total_steps+1-moldyn->mean_skip);
-       moldyn->k2_mean=moldyn->k2_sum/
-                       (moldyn->total_steps+1-moldyn->mean_skip);
-       moldyn->dk2_mean=moldyn->k2_mean-(moldyn->k_mean*moldyn->k_mean);
+       moldyn->k_avg=moldyn->k_sum/(moldyn->total_steps+1-moldyn->avg_skip);
+       moldyn->k2_avg=moldyn->k2_sum/(moldyn->total_steps+1-moldyn->avg_skip);
+       moldyn->dk2_avg=moldyn->k2_avg-(moldyn->k_avg*moldyn->k_avg);
 
        /* potential energy */
        moldyn->v_sum+=moldyn->energy;
        moldyn->v2_sum+=(moldyn->energy*moldyn->energy);
-       moldyn->v_mean=moldyn->v_sum/(moldyn->total_steps+1-moldyn->mean_skip);
-       moldyn->v2_mean=moldyn->v2_sum/
-                       (moldyn->total_steps+1-moldyn->mean_skip);
-       moldyn->dv2_mean=moldyn->v2_mean-(moldyn->v_mean*moldyn->v_mean);
+       moldyn->v_avg=moldyn->v_sum/(moldyn->total_steps+1-moldyn->avg_skip);
+       moldyn->v2_avg=moldyn->v2_sum/(moldyn->total_steps+1-moldyn->avg_skip);
+       moldyn->dv2_avg=moldyn->v2_avg-(moldyn->v_avg*moldyn->v_avg);
+
+       /* temperature */
+       moldyn->t_sum+=moldyn->t;
+       moldyn->t_avg=moldyn->t_sum/(moldyn->total_steps+1-moldyn->avg_skip);
+
+       /* virial */
+       
+
+       /* pressure */
+
 
        return 0;
 }
@@ -896,13 +895,13 @@ int get_heat_capacity(t_moldyn *moldyn) {
        double temp2,ighc;
 
        /* averages needed for heat capacity calc */
-       if(moldyn->total_steps<moldyn->mean_skip)
+       if(moldyn->total_steps<moldyn->avg_skip)
                return 0;
 
        /* (temperature average)^2 */
-       temp2=moldyn->mean_t*moldyn->mean_t;
+       temp2=moldyn->t_avg*moldyn->t_avg;
        printf("[moldyn] specific heat capacity for T=%f K [J/(kg K)]\n",
-              moldyn->mean_t);
+              moldyn->t_avg);
 
        /* ideal gas contribution */
        ighc=3.0*moldyn->count*K_BOLTZMANN/2.0;
@@ -910,16 +909,16 @@ int get_heat_capacity(t_moldyn *moldyn) {
               ighc/moldyn->mass*KILOGRAM/JOULE);
 
        /* specific heat for nvt ensemble */
-       moldyn->c_v_nvt=moldyn->dv2_mean/(K_BOLTZMANN*temp2)+ighc;
+       moldyn->c_v_nvt=moldyn->dv2_avg/(K_BOLTZMANN*temp2)+ighc;
        moldyn->c_v_nvt/=moldyn->mass;
 
        /* specific heat for nve ensemble */
-       moldyn->c_v_nve=ighc/(1.0-(moldyn->dv2_mean/(ighc*K_BOLTZMANN*temp2)));
+       moldyn->c_v_nve=ighc/(1.0-(moldyn->dv2_avg/(ighc*K_BOLTZMANN*temp2)));
        moldyn->c_v_nve/=moldyn->mass;
 
        printf("  NVE: %f\n",moldyn->c_v_nve*KILOGRAM/JOULE);
        printf("  NVT: %f\n",moldyn->c_v_nvt*KILOGRAM/JOULE);
-printf("  --> <dV2> sim: %f experimental: %f\n",moldyn->dv2_mean,1.5*moldyn->count*K_B2*moldyn->mean_t*moldyn->mean_t*(1.0-1.5*moldyn->count*K_BOLTZMANN/(700*moldyn->mass*JOULE/KILOGRAM)));
+printf("  --> <dV2> sim: %f experimental: %f\n",moldyn->dv2_avg,1.5*moldyn->count*K_B2*moldyn->t_avg*moldyn->t_avg*(1.0-1.5*moldyn->count*K_BOLTZMANN/(700*moldyn->mass*JOULE/KILOGRAM)));
 
        return 0;
 }
@@ -1404,9 +1403,7 @@ return 0;
                e_kin_calc(moldyn);
                temperature_calc(moldyn);
                pressure_calc(moldyn);
-               energy_fluctuation_calc(moldyn);
-               //tp=thermodynamic_pressure_calc(moldyn);
-//printf("thermodynamic p: %f\n",thermodynamic_pressure_calc(moldyn)/BAR);
+               average_and_fluctuation_calc(moldyn);
 
                /* p/t scaling */
                if(moldyn->pt_scale&(T_SCALE_BERENDSEN|T_SCALE_DIRECT))
@@ -1436,15 +1433,15 @@ return 0;
                        if(!(i%p)) {
                                dprintf(moldyn->pfd,
                                        "%f %f %f %f %f\n",moldyn->time,
-                                        moldyn->p/BAR,moldyn->mean_p/BAR,
-                                        moldyn->gp/BAR,moldyn->mean_gp/BAR);
+                                        moldyn->p/BAR,moldyn->p_avg/BAR,
+                                        moldyn->gp/BAR,moldyn->gp_avg/BAR);
                        }
                }
                if(t) {
                        if(!(i%t)) {
                                dprintf(moldyn->tfd,
                                        "%f %f %f\n",
-                                       moldyn->time,moldyn->t,moldyn->mean_t);
+                                       moldyn->time,moldyn->t,moldyn->t_avg);
                        }
                }
                if(s) {
@@ -1472,13 +1469,12 @@ return 0;
                if(!(i%10)) {
                        printf("\rsched: %d, steps: %d, T: %f, P: %f %f V: %f",
                               sched->count,i,
-                              moldyn->mean_t,
-                              moldyn->mean_p/BAR,
-                              moldyn->mean_gp/BAR,
+                              moldyn->t_avg,
+                              //moldyn->p_avg/BAR,
+                              moldyn->p/BAR,
+                              moldyn->gp_avg/BAR,
                               moldyn->volume);
                        fflush(stdout);
-printf("\n");
-get_heat_capacity(moldyn);
                }
 
                /* increase absolute time */
@@ -1489,11 +1485,12 @@ get_heat_capacity(moldyn);
 
                /* check for hooks */
                if(sched->count+1<sched->total_sched)
-                       if(sched->hook)
+                       if(sched->hook) {
+                               printf("\n ## schedule hook %d/%d start ##\n",
+                                      sched->count+1,sched->total_sched);
                                sched->hook(moldyn,sched->hook_params);
-
-               /* get a new info line */
-               printf("\n");
+                               printf(" ## schedule hook end ##\n");
+                       }
 
        }
 

diff --git a/moldyn.h b/moldyn.h
index 868db62..212db14 100644 (file)
--- a/moldyn.h
+++ b/moldyn.h
@@ -102,25 +102,25 @@ typedef struct s_moldyn {
 
        t_linkcell lc;          /* linked cell list interface */
 
-       int mean_skip;          /* amount of steps without average calc */
+       int avg_skip;           /* amount of steps without average calc */
 
        double t_ref;           /* reference temperature */
        double t;               /* actual temperature */
        double t_sum;           /* sum over all t */
-       double mean_t;          /* mean value of t */
+       double t_avg;           /* average value of t */
 
        t_virial virial;        /* global virial (absolute coordinates) */
        double gp;              /* pressure computed from global virial */
        double gp_sum;          /* sum over all gp */
-       double mean_gp;         /* mean value of gp */
+       double gp_avg;          /* average value of gp */
 
-       double mean_v;          /* mean of virial */
+       double virial_avg;      /* average of virial */
        double virial_sum;      /* sum over all calculated virials */
 
        double p_ref;           /* reference pressure */
        double p;               /* actual pressure (computed by virial) */
        double p_sum;           /* sum over all p */
-       double mean_p;          /* mean value of p */
+       double p_avg;           /* average value of p */
        t_3dvec tp;             /* thermodynamic pressure dU/dV */
        double dv;              /* dV for thermodynamic pressure calc */
 
@@ -149,14 +149,14 @@ typedef struct s_moldyn {
        /* energy averages & fluctuations */
        double k_sum;           /* sum of kinetic energy */
        double v_sum;           /* sum of potential energy */
-       double k_mean;          /* average of kinetic energy */
-       double v_mean;          /* average of potential energy */
+       double k_avg;           /* average of kinetic energy */
+       double v_avg;           /* average of potential energy */
        double k2_sum;          /* sum of kinetic energy squared */
        double v2_sum;          /* sum of potential energy squared */
-       double k2_mean;         /* average of kinetic energy squared */
-       double v2_mean;         /* average of potential energy squared */
-       double dk2_mean;        /* mean square kinetic energy fluctuations */
-       double dv2_mean;        /* mean square potential energy fluctuations */
+       double k2_avg;          /* average of kinetic energy squared */
+       double v2_avg;          /* average of potential energy squared */
+       double dk2_avg;         /* mean square kinetic energy fluctuations */
+       double dv2_avg;         /* mean square potential energy fluctuations */
        
        /* response functions */
        double c_v_nve;         /* constant volume heat capacity (nve) */
@@ -395,7 +395,7 @@ int set_potential3b_k1(t_moldyn *moldyn,pf_func3b func);
 int set_potential3b_k2(t_moldyn *moldyn,pf_func3b func);
 int set_potential_params(t_moldyn *moldyn,void *params);
 
-int set_mean_skip(t_moldyn *moldyn,int skip);
+int set_avg_skip(t_moldyn *moldyn,int skip);
 
 int moldyn_set_log_dir(t_moldyn *moldyn,char *dir);
 int moldyn_set_report(t_moldyn *moldyn,char *author,char *title);

diff --git a/potentials/albe.c b/potentials/albe.c
index a79f58d..338fb03 100644 (file)
--- a/potentials/albe.c
+++ b/potentials/albe.c
@@ -450,7 +450,7 @@ int albe_mult_3bp_k2(t_moldyn *moldyn,
 
        /* virial */
        //v3_scale(&force,&force,-1.0);
-       //virial_calc(ai,&force,&dist_ik);
+       virial_calc(ai,&force,&dist_ik);
        
        /* increase k counter */
        exchange->kcount++;     

diff --git a/sic.c b/sic.c
index 5bdfeea..f8e6ce1 100644 (file)
--- a/sic.c
+++ b/sic.c
@@ -35,14 +35,6 @@ 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)) {
                /* add carbon at random place, and enable t scaling */
                for(j=0;j<NR_ATOMS;j++) {
@@ -297,7 +289,7 @@ int main(int argc,char **argv) {
        set_pressure(&md,BAR);
 
        /* set amount of steps to skip before average calc */
-       set_mean_skip(&md,500);
+       set_mean_skip(&md,1000);
 
        /* set p/t scaling */
        //set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);