added harmonic potntial + bugfixes + boundings

[physik/posic.git] / posic.c

diff --git a/posic.c b/posic.c
index 926e20c..5ff3bc1 100644 (file)
--- a/posic.c
+++ b/posic.c
@@ -1,9 +1,11 @@
 /*
  * posic.c - precipitation process of silicon carbide in silicon
  *
- * author: Frank Zirkelbach <hackbard@hackdaworld.org>
+ * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
  *
  */
+
+#include <math.h>
  
 #include "moldyn.h"
 #include "math/math.h"
@@ -29,8 +31,9 @@ int main(int argc,char **argv) {
        int count;
 
        t_lj_params lj;
+       t_ho_params ho;
 
-       char fb[32]="saves/fcc_test";
+       char fb[32]="saves/lj_test";
 
        /* init */
 
@@ -48,6 +51,10 @@ int main(int argc,char **argv) {
        b=LEN_Y;
        c=LEN_Z;
 
+       vis.dim.x=a*LC_SI;
+       vis.dim.y=b*LC_SI;
+       vis.dim.z=c*LC_SI;
+
        t=TEMPERATURE;
 
        printf("placing silicon atoms ... ");
@@ -55,16 +62,16 @@ int main(int argc,char **argv) {
        //printf("(%d) ok!\n",count);
        count=2;
        si=malloc(2*sizeof(t_atom));
-       si[0].r.x=2.0;
+       si[0].r.x=0.16e-9;
        si[0].r.y=0;
        si[0].r.z=0;
-       si[0].element=Si;
-       si[0].mass=14.0;
-       si[1].r.x=-2.0;
+       si[0].element=SI;
+       si[0].mass=M_SI;
+       si[1].r.x=-0.16e-9;
        si[1].r.y=0;
        si[1].r.z=0;
-       si[1].element=Si;
-       si[1].mass=14.0;
+       si[1].element=SI;
+       si[1].mass=M_SI;
 
        printf("setting thermal fluctuations\n");
        //thermal_init(si,&random,count,t);
@@ -74,56 +81,65 @@ int main(int argc,char **argv) {
        /* check kinetic energy */
 
        e=get_e_kin(si,count);
-       printf("kinetic energy: %f\n",e);
-       printf("3/2 N k T = %f\n",1.5*count*K_BOLTZMANN*t);
+       printf("kinetic energy: %.40f [J]\n",e);
+       printf("3/2 N k T = %.40f [J]\n",1.5*count*K_BOLTZMANN*t);
 
        /* check total momentum */
        p=get_total_p(si,count);
-       printf("total momentum: %f\n",v3_norm(&p));
+       printf("total momentum: %.30f [Ns]\n",v3_norm(&p));
 
        /* check potential energy */
        md.count=count;
        md.atom=si;
        md.potential=potential_lennard_jones;
+       //md.potential=potential_harmonic_oscillator;
        md.force=force_lennard_jones;
+       //md.force=force_harmonic_oscillator;
        //md.cutoff_square=((LC_SI/4.0)*(LC_SI/4.0));
-       md.cutoff_square=36.0;
+       md.cutoff=(0.4e-9);
+       md.cutoff_square=(0.6e-9*0.6e-9);
        md.pot_params=&lj;
+       //md.pot_params=&ho;
        md.integrate=velocity_verlet;
        md.time_steps=RUNS;
        md.tau=TAU;
        md.status=0;
        md.visual=&vis;
+       md.write=WRITE_FILE;
 
-       lj.sigma6=3.0/16.0*LC_SI*LC_SI;
+       lj.sigma6=LJ_SIGMA_SI*LJ_SIGMA_SI;
        help=lj.sigma6*lj.sigma6;
        lj.sigma6*=help;
        lj.sigma12=lj.sigma6*lj.sigma6;
-       lj.epsilon=10000;
+       lj.epsilon=LJ_EPSILON_SI;
+
+       ho.equilibrium_distance=0.3e-9;
+       ho.spring_constant=1.0e-9;
 
        u=get_e_pot(&md);
 
-       printf("potential energy: %f\n",u);
-       printf("total energy (1): %f\n",e+u);
-       printf("total energy (2): %f\n",get_total_energy(&md));
+       printf("potential energy: %.40f [J]\n",u);
+       printf("total energy (1): %.40f [J]\n",e+u);
+       printf("total energy (2): %.40f [J]\n",get_total_energy(&md));
 
        md.dim.x=a*LC_SI;
        md.dim.y=b*LC_SI;
        md.dim.z=c*LC_SI;
 
+       printf("estimated accurate time step: %.30f [s]\n",
+              estimate_time_step(&md,3.0,t));
+
+
        /*
         * let's do the actual md algorithm now
         *
         * integration of newtons equations
         */
 
-       /* visualize */
-       //visual_atoms(&vis,0.0,si,count);
-       
-
        moldyn_integrate(&md);
 
-       printf("total energy (after integration): %f\n",get_total_energy(&md));
+       printf("total energy (after integration): %.40f [J]\n",
+              get_total_energy(&md));
 
        /* close */