still pressure (+ fixes with cubic lattce and ho potential ...)

diff --git a/moldyn.c b/moldyn.c
index 817a727..f564075 100644 (file)
--- a/moldyn.c
+++ b/moldyn.c
@@ -16,6 +16,7 @@
 #include <math.h>
 
 #include "moldyn.h"
+#include "report/report.h"
 
 int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 
@@ -590,18 +591,9 @@ int thermal_init(t_moldyn *moldyn,u8 equi_init) {
 
 double temperature_calc(t_moldyn *moldyn) {
 
-       double double_ekin;
-       int i;
-       t_atom *atom;
-
-       atom=moldyn->atom;
-
-       double_ekin=0;
-       for(i=0;i<moldyn->count;i++)
-               double_ekin+=atom[i].mass*v3_absolute_square(&(atom[i].v));
+       /* assume up to date kinetic energy, which is 3/2 N k_B T */
 
-       /* kinetic energy = 3/2 N k_B T */
-       moldyn->t=double_ekin/(3.0*K_BOLTZMANN*moldyn->count);
+       moldyn->t=(2.0*moldyn->ekin)/(3.0*K_BOLTZMANN*moldyn->count);
 
        return moldyn->t;
 }
@@ -682,16 +674,21 @@ double pressure_calc(t_moldyn *moldyn) {
        double v;
        t_virial *virial;
 
+       /*
+        * P = 1/(3V) sum_i ( p_i^2 / 2m + f_i r_i )
+        *
+        * virial = f_i r_i
+        */
+
        v=0.0;
        for(i=0;i<moldyn->count;i++) {
                virial=&(moldyn->atom[i].virial);
                v+=(virial->xx+virial->yy+virial->zz);
        }
-       v*=ONE_THIRD;
-printf("kieck mal: %f %f %f\n",v,moldyn->count*K_BOLTZMANN*moldyn->t,v/moldyn->count);
 
-       moldyn->p=moldyn->count*K_BOLTZMANN*moldyn->t+v;
-       moldyn->p/=moldyn->volume;
+       /* assume up to date kinetic energy */
+       moldyn->p=2.0*moldyn->ekin+v;
+       moldyn->p/=(3.0*moldyn->volume);
 
        return moldyn->p;
 }      
@@ -1196,6 +1193,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
                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);
@@ -1203,7 +1201,6 @@ int moldyn_integrate(t_moldyn *moldyn) {
                /* check for log & visualization */
                if(e) {
                        if(!(i%e))
-                               update_e_kin(moldyn);
                                dprintf(moldyn->efd,
                                        "%f %f %f %f\n",
                                        moldyn->time,moldyn->ekin/energy_scale,
@@ -1236,7 +1233,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
                                visual_atoms(&(moldyn->vis),moldyn->time,
                                             moldyn->atom,moldyn->count);
                                printf("\rsched: %d, steps: %d, debug: %f | %f",
-                                      sched->count,i,moldyn->p/ATM,moldyn->debug/ATM);
+                                      sched->count,i,moldyn->p/ATM,moldyn->p/ATM);
                                fflush(stdout);
                        }
                }
@@ -1580,7 +1577,7 @@ int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
                d*=eps;
                v3_scale(&force,&distance,d);
                v3_add(&(aj->f),&(aj->f),&force);
-               v3_scale(&force,&distance,-1.0*d); /* f = - grad E */
+               v3_scale(&force,&force,-1.0); /* f = - grad E */
                v3_add(&(ai->f),&(ai->f),&force);
                virial_calc(ai,&force,&distance);
                virial_calc(aj,&force,&distance); /* f and d signe switched */

diff --git a/moldyn.h b/moldyn.h
index 7329099..69cee96 100644 (file)
--- a/moldyn.h
+++ b/moldyn.h
@@ -12,8 +12,6 @@
 #include "random/random.h"
 #include "list/list.h"
 
-#include "report/report.h"
-
 /*
  * 
  * datatypes

diff --git a/report/report.h b/report/report.h
index 7fd3180..3868515 100644 (file)
--- a/report/report.h
+++ b/report/report.h
@@ -37,7 +37,7 @@ static char report_start[]="\
 static char report_end[]="\
 \\begin{figure}[!h]\n\
 \\begin{center}\n\
-\\includegraphics[width=10cm]{energy.eps}\n\
+\\includegraphics[width=16cm]{energy.eps}\n\
 \\caption{Kinetic, potential and total energy over time}\n\
 \\end{center}\n\
 \\end{figure}\n\
@@ -50,15 +50,12 @@ unset log \n\
 unset label \n\
 set xtic auto \n\
 set ytic auto \n\
-set title 'Energy vs. time' \n\
+set title 'Energy per atom vs. time' \n\
 set xlabel 'Time [fs]' \n\
-set ylabel 'Energy [eV]' \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 \n\
-#set size 1.0, 0.6 \n\
+set ylabel 'Energy per atom [eV]' \n\
 set terminal postscript eps enhanced color dashed lw 1 'Helvetica' 14 \n\
 set output 'energy.eps' \n\
-replot\
+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\
 ";
 
-
 #endif

diff --git a/sic.c b/sic.c
index b5d4596..999d860 100644 (file)
--- a/sic.c
+++ b/sic.c
@@ -59,12 +59,13 @@ int main(int argc,char **argv) {
        //set_potential2b(&md,tersoff_mult_2bp,&tp);
        //set_potential2b_post(&md,tersoff_mult_post_2bp,&tp);
        //set_potential3b(&md,tersoff_mult_3bp,&tp);
-       set_potential2b(&md,lennard_jones,&lj);
-       //set_potential2b(&md,harmonic_oscillator,&ho);
+       //set_potential2b(&md,lennard_jones,&lj);
+       set_potential2b(&md,harmonic_oscillator,&ho);
 
        /* cutoff radius */
        //set_cutoff(&md,TM_S_SI);
-       set_cutoff(&md,2*LC_SI*0.5*sqrt(1.5));
+       //set_cutoff(&md,2*LC_SI*0.5*sqrt(1.5));
+       set_cutoff(&md,1.1*LC_SI);
 
        /*
         * potential parameters
@@ -78,7 +79,8 @@ int main(int argc,char **argv) {
        lj.uc=lj.epsilon4*(lj.sigma12/pow(md.cutoff,12.0)-lj.sigma6/pow(md.cutoff,6));
 
        /* harmonic oscillator */
-       ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
+       //ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
+       ho.equilibrium_distance=LC_SI;
        ho.spring_constant=.1;
 
        /*
@@ -113,13 +115,14 @@ int main(int argc,char **argv) {
        tersoff_mult_complete_params(&tp);
 
        /* set (initial) dimensions of simulation volume */
-       set_dim(&md,8*LC_SI*0.5*sqrt(1.5),8*LC_SI*0.5*sqrt(1.5),8*LC_SI*0.5*sqrt(1.5),TRUE);
+       //set_dim(&md,8*LC_SI*0.5*sqrt(1.5),8*LC_SI*0.5*sqrt(1.5),8*LC_SI*0.5*sqrt(1.5),TRUE);
+       set_dim(&md,8*LC_SI,8*LC_SI,8*LC_SI,TRUE);
 
        /* set periodic boundary conditions in all directions */
        set_pbc(&md,TRUE,TRUE,TRUE);
 
        /* create the lattice / place atoms */
-       create_lattice(&md,FCC,LC_SI*0.5*sqrt(1.5),SI,M_SI,
+       create_lattice(&md,CUBIC,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,
@@ -144,7 +147,8 @@ int main(int argc,char **argv) {
        //           &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,0.25*sqrt(3.0)*LC_SI); /* diamond ! */
+       set_nn_dist(&md,LC_SI);
 
        /* set temperature */
        //set_temperature(&md,273.0+1410.0);