added harmonic potntial + bugfixes + boundings

[physik/posic.git] / posic.c

diff --git a/posic.c b/posic.c
index 6d1256f..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"
@@ -14,29 +16,138 @@
 
 int main(int argc,char **argv) {
 
-       t_atom *si;
-       int a,b,c;
+       t_moldyn md;
 
-       char fb[32]="saves/fcc_test";
+       t_atom *si;
 
        t_visual vis;
 
+       t_random random;
+
+       int a,b,c;
+       double t,e,u;
+       double help;
+       t_3dvec p;
        int count;
 
+       t_lj_params lj;
+       t_ho_params ho;
+
+       char fb[32]="saves/lj_test";
+
+       /* init */
+
+       rand_init(&random,NULL,1);
+       random.status|=RAND_STAT_VERBOSE;
+
+       /* testing random numbers */
+       //for(a=0;a<1000000;a++)
+       //      printf("%f %f\n",rand_get_gauss(&random),
+       //                       rand_get_gauss(&random));
+
+       visual_init(&vis,fb);
+
        a=LEN_X;
        b=LEN_Y;
        c=LEN_Z;
-       
-       visual_init(&vis,fb);
 
-       /* init */
-       printf("placing silicon atoms\n");
-       count=create_lattice(FCC,Si,M_SI,LC_SI,a,b,c,&si);
+       vis.dim.x=a*LC_SI;
+       vis.dim.y=b*LC_SI;
+       vis.dim.z=c*LC_SI;
+
+       t=TEMPERATURE;
+
+       printf("placing silicon atoms ... ");
+       //count=create_lattice(DIAMOND,Si,M_SI,LC_SI,a,b,c,&si);
+       //printf("(%d) ok!\n",count);
+       count=2;
+       si=malloc(2*sizeof(t_atom));
+       si[0].r.x=0.16e-9;
+       si[0].r.y=0;
+       si[0].r.z=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=M_SI;
 
-       visual_atoms(&vis,0.0,si,count);
+       printf("setting thermal fluctuations\n");
+       //thermal_init(si,&random,count,t);
+       v3_zero(&(si[0].v));
+       v3_zero(&(si[1].v));
+
+       /* check kinetic energy */
+
+       e=get_e_kin(si,count);
+       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: %.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=(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=LJ_SIGMA_SI*LJ_SIGMA_SI;
+       help=lj.sigma6*lj.sigma6;
+       lj.sigma6*=help;
+       lj.sigma12=lj.sigma6*lj.sigma6;
+       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: %.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
+        */
+
+       moldyn_integrate(&md);
+
+       printf("total energy (after integration): %.40f [J]\n",
+              get_total_energy(&md));
+
+       /* close */
 
        visual_tini(&vis);
 
+       rand_close(&random);
+       
+
        //printf("starting velocity verlet: ");
        //fflush(stdout);