average calc moved, more fscking virial testing

diff --git a/moldyn.c b/moldyn.c
index e0881de5db49b1669c5a0b02641e66760dc957a0..992d112622ce35341fa2e3bab745c8b8b683f0e3 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -810,12 +810,29 @@ double ideal_gas_law_pressure(t_moldyn *moldyn) {
        return p;
 }
 
-double pressure_calc(t_moldyn *moldyn) {
+double virial_sum(t_moldyn *moldyn) {
 
        int i;
        double v;
        t_virial *virial;
 
+       /* virial (sum over atom virials) */
+       v=0.0;
+       for(i=0;i<moldyn->count;i++) {
+               virial=&(moldyn->atom[i].virial);
+               v+=(virial->xx+virial->yy+virial->zz);
+       }
+       moldyn->virial=v;
+
+       /* global virial (absolute coordinates) */
+       virial=&(moldyn->gvir);
+       moldyn->gv=virial->xx+virial->yy+virial->zz;
+
+       return moldyn->virial;
+}
+
+double pressure_calc(t_moldyn *moldyn) {
+
        /*
         * PV = NkT + <W>
         * with W = 1/3 sum_i f_i r_i (- skipped!)
@@ -824,34 +841,15 @@ double pressure_calc(t_moldyn *moldyn) {
         * => P = (2 Ekin + virial) / (3V)
         */
 
-       v=0.0;
-       for(i=0;i<moldyn->count;i++) {
-               virial=&(moldyn->atom[i].virial);
-               v+=(virial->xx+virial->yy+virial->zz);
-       }
+       /* assume up to date virial & up to date kinetic energy */
 
-       /* 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->p_avg=moldyn->p_sum/
-                             (moldyn->total_steps+1-moldyn->avg_skip);
-       }
+       /* pressure (atom virials) */
+       moldyn->p=2.0*moldyn->ekin+moldyn->virial;
+       moldyn->p/=(3.0*moldyn->volume);
 
-       /* pressure from 'absolute coordinates' virial */
-       virial=&(moldyn->virial);
-       v=virial->xx+virial->yy+virial->zz;
-       moldyn->gp=2.0*moldyn->ekin+v;
+       /* pressure (absolute coordinates) */
+       moldyn->gp=2.0*moldyn->ekin+moldyn->gv;
        moldyn->gp/=(3.0*moldyn->volume);
-       if(moldyn->total_steps>=moldyn->avg_skip) {
-               moldyn->gp_sum+=moldyn->gp;
-               moldyn->gp_avg=moldyn->gp_sum/
-                              (moldyn->total_steps+1-moldyn->avg_skip);
-       }
 
        return moldyn->p;
 }
@@ -861,31 +859,39 @@ int average_and_fluctuation_calc(t_moldyn *moldyn) {
        if(moldyn->total_steps<moldyn->avg_skip)
                return 0;
 
+       int denom=moldyn->total_steps+1-moldyn->avg_skip;
+
        /* assume up to date energies, temperature, pressure etc */
 
        /* kinetic energy */
        moldyn->k_sum+=moldyn->ekin;
        moldyn->k2_sum+=(moldyn->ekin*moldyn->ekin);
-       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->k_avg=moldyn->k_sum/denom;
+       moldyn->k2_avg=moldyn->k2_sum/denom;
        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_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->v_avg=moldyn->v_sum/denom;
+       moldyn->v2_avg=moldyn->v2_sum/denom;
        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);
+       moldyn->t_avg=moldyn->t_sum/denom;
 
        /* virial */
-       
+       moldyn->virial_sum+=moldyn->virial;
+       moldyn->virial_avg=moldyn->virial_sum/denom;
+       moldyn->gv_sum+=moldyn->gv;
+       moldyn->gv_avg=moldyn->gv_sum/denom;
 
        /* pressure */
-
+       moldyn->p_sum+=moldyn->p;
+       moldyn->p_avg=moldyn->p_sum/denom;
+       moldyn->gp_sum+=moldyn->gp;
+       moldyn->gp_avg=moldyn->gp_sum/denom;
 
        return 0;
 }
@@ -1402,6 +1408,7 @@ return 0;
                /* calculate kinetic energy, temperature and pressure */
                e_kin_calc(moldyn);
                temperature_calc(moldyn);
+               virial_sum(moldyn);
                pressure_calc(moldyn);
                average_and_fluctuation_calc(moldyn);
 
@@ -1467,14 +1474,12 @@ return 0;
 
                /* display progress */
                if(!(i%10)) {
-                       printf("\rsched: %d, steps: %d, T: %f, P: %f %f V: %f",
-                              sched->count,i,
-                              moldyn->t_avg,
-                              //moldyn->p_avg/BAR,
-                              moldyn->p/BAR,
-                              moldyn->gp_avg/BAR,
-                              moldyn->volume);
-                       fflush(stdout);
+       printf("\rsched:%d, steps:%d, T:%3.1f/%3.1f P:%4.1f/%4.1f V:%6.1f",
+              sched->count,i,
+              moldyn->t,moldyn->t_avg,
+              moldyn->p_avg/BAR,moldyn->p/BAR,
+              moldyn->volume);
+       fflush(stdout);
                }
 
                /* increase absolute time */
@@ -1569,7 +1574,7 @@ int potential_force_calc(t_moldyn *moldyn) {
        moldyn->energy=0.0;
 
        /* reset global virial */
-       memset(&(moldyn->virial),0,sizeof(t_virial));
+       memset(&(moldyn->gvir),0,sizeof(t_virial));
 
        /* reset force, site energy and virial of every atom */
        for(i=0;i<count;i++) {
@@ -1795,12 +1800,12 @@ int potential_force_calc(t_moldyn *moldyn) {
 
        /* calculate global virial */
        for(i=0;i<count;i++) {
-               moldyn->virial.xx+=moldyn->atom[i].r.x*moldyn->atom[i].f.x;
-               moldyn->virial.yy+=moldyn->atom[i].r.y*moldyn->atom[i].f.y;
-               moldyn->virial.zz+=moldyn->atom[i].r.z*moldyn->atom[i].f.z;
-               moldyn->virial.xy+=moldyn->atom[i].r.y*moldyn->atom[i].f.x;
-               moldyn->virial.xz+=moldyn->atom[i].r.z*moldyn->atom[i].f.x;
-               moldyn->virial.yz+=moldyn->atom[i].r.z*moldyn->atom[i].f.y;
+               moldyn->gvir.xx+=moldyn->atom[i].r.x*moldyn->atom[i].f.x;
+               moldyn->gvir.yy+=moldyn->atom[i].r.y*moldyn->atom[i].f.y;
+               moldyn->gvir.zz+=moldyn->atom[i].r.z*moldyn->atom[i].f.z;
+               moldyn->gvir.xy+=moldyn->atom[i].r.y*moldyn->atom[i].f.x;
+               moldyn->gvir.xz+=moldyn->atom[i].r.z*moldyn->atom[i].f.x;
+               moldyn->gvir.yz+=moldyn->atom[i].r.z*moldyn->atom[i].f.y;
        }
 
        return 0;

diff --git a/moldyn.h b/moldyn.h
index 212db144cd500c9c578b2b842c596999c564067e..51ad482180fa44ff290109c0118dcb09b0185c09 100644 (file)
--- a/moldyn.h
+++ b/moldyn.h
@@ -109,18 +109,24 @@ typedef struct s_moldyn {
        double t_sum;           /* sum over all t */
        double t_avg;           /* average value of t */
 
-       t_virial virial;        /* global virial (absolute coordinates) */
+       t_virial gvir;          /* global virial (absolute coordinates) */
+       double gv;
+       double gv_sum;
+       double gv_avg;
+
        double gp;              /* pressure computed from global virial */
        double gp_sum;          /* sum over all gp */
        double gp_avg;          /* average value of gp */
 
-       double virial_avg;      /* average of virial */
+       double virial;          /* actual virial */
        double virial_sum;      /* sum over all calculated virials */
+       double virial_avg;      /* average of virial */
 
        double p_ref;           /* reference pressure */
        double p;               /* actual pressure (computed by virial) */
        double p_sum;           /* sum over all p */
        double p_avg;           /* average value of p */
+
        t_3dvec tp;             /* thermodynamic pressure dU/dV */
        double dv;              /* dV for thermodynamic pressure calc */
 
@@ -416,6 +422,7 @@ double total_mass_calc(t_moldyn *moldyn);
 double temperature_calc(t_moldyn *moldyn);
 double get_temperature(t_moldyn *moldyn);
 int scale_velocity(t_moldyn *moldyn,u8 equi_init);
+double virial_sum(t_moldyn *moldyn);
 double pressure_calc(t_moldyn *moldyn);
 int energy_fluctuation_calc(t_moldyn *moldyn);
 int get_heat_capacity(t_moldyn *moldyn);

diff --git a/potentials/albe.c b/potentials/albe.c
index 338fb0374439cafb7fd87a42570ef1da6244f98a..c0a5fe4aba2b7c42280d9bc68f6b87c52677a380 100644 (file)
--- a/potentials/albe.c
+++ b/potentials/albe.c
@@ -380,13 +380,13 @@ int albe_mult_3bp_k2(t_moldyn *moldyn,
 
        /* cos_theta derivatives wrt i,j,k */
        dijdik_inv=1.0/(d_ij*d_ik);
-       v3_scale(&dcosdrj,&dist_ik,dijdik_inv);
+       v3_scale(&dcosdrj,&dist_ik,dijdik_inv);         // j
        v3_scale(&tmp,&dist_ij,-cos_theta/d_ij2);
        v3_add(&dcosdrj,&dcosdrj,&tmp);
-       v3_scale(&dcosdrk,&dist_ij,dijdik_inv);
+       v3_scale(&dcosdrk,&dist_ij,dijdik_inv);         // k
        v3_scale(&tmp,&dist_ik,-cos_theta/d_ik2);
        v3_add(&dcosdrk,&dcosdrk,&tmp);
-       v3_add(&dcosdri,&dcosdrj,&dcosdrk);
+       v3_add(&dcosdri,&dcosdrj,&dcosdrk);             // i
        v3_scale(&dcosdri,&dcosdri,-1.0);
 
        /* f_c_ik * dg, df_c_ik * g */
@@ -428,8 +428,8 @@ int albe_mult_3bp_k2(t_moldyn *moldyn,
 #endif
 
        /* virial */
-       //v3_scale(&force,&force,-1.0);
-       //virial_calc(ai,&force,&dist_ij);
+       v3_scale(&force,&force,-1.0);
+       virial_calc(ai,&force,&dist_ij);
 
        /* derivative wrt k */
        v3_scale(&force,&dist_ik,-1.0*dfcg); // dri rik = - drk rik
@@ -449,7 +449,7 @@ int albe_mult_3bp_k2(t_moldyn *moldyn,
 #endif
 
        /* virial */
-       //v3_scale(&force,&force,-1.0);
+       v3_scale(&force,&force,-1.0);
        virial_calc(ai,&force,&dist_ik);
        
        /* increase k counter */

diff --git a/sic.c b/sic.c
index f8e6ce1cb367b75535deaf676c1fab10b5c45a6b..ba7de3d27c0f3ca64b12c0cfb881f302a477a608 100644 (file)
--- a/sic.c
+++ b/sic.c
@@ -289,7 +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,1000);
+       set_avg_skip(&md,1000);
 
        /* set p/t scaling */
        //set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);