linked cell list updates (not well working by now!)

[physik/posic.git] / posic.c

diff --git a/posic.c b/posic.c
index 236e208..2b18c79 100644 (file)
--- a/posic.c
+++ b/posic.c
@@ -17,9 +17,6 @@
 int main(int argc,char **argv) {
 
        t_moldyn md;
-       t_atom *si;
-       t_visual vis;
-       t_random random;
 
        int a,b,c;
        double e;
@@ -29,90 +26,115 @@ int main(int argc,char **argv) {
        t_lj_params lj;
        t_ho_params ho;
 
-       /* parse arguments */
-       a=moldyn_parse_argv(&md,argc,argv);
-       if(a<0) return -1;
-
-       /* init */
-       moldyn_log_init(&md,&vis);
-       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));
-
-       a=LEN_X;
-       b=LEN_Y;
-       c=LEN_Z;
+       /*
+        *  moldyn init
+        *
+        * - parsing argv
+        * - log init
+        * - random init
+        *
+        */
+       moldyn_init(&md,argc,argv);
 
-       /* set for 'bounding atoms' */
-       vis.dim.x=a*LC_SI;
-       vis.dim.y=b*LC_SI;
-       vis.dim.z=c*LC_SI;
+       /*
+        * the following overrides possibly set interaction methods by argv !!
+        */
 
-       /* init lattice
-       printf("placing silicon atoms ... ");
-       md.count=create_lattice(DIAMOND,SI,M_SI,LC_SI,a,b,c,&si);
-       printf("(%d) ok!\n",md.count);
-       testing purpose */
-       md.count=2;
-       si=malloc(2*sizeof(t_atom));
-       si[0].r.x=0.13*sqrt(3.0)*LC_SI/2.0;
-       si[0].r.y=0;
-       si[0].r.z=0;
-       si[0].element=SI;
-       si[0].mass=M_SI;
-       si[1].r.x=-si[0].r.x;
-       si[1].r.y=0;
-       si[1].r.z=0;
-       si[1].element=SI;
-       si[1].mass=M_SI;
-       /* */
-
-       /* moldyn init (now si is a valid address) */
-       md.atom=si;
+       /* params */
+       lj.sigma6=LJ_SIGMA_SI*LJ_SIGMA_SI;
+       help=lj.sigma6*lj.sigma6;
+       lj.sigma6*=help;
+       lj.sigma12=lj.sigma6*lj.sigma6;
+       lj.epsilon4=4.0*LJ_EPSILON_SI;
+       ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
+       ho.spring_constant=1.0;
+       /* assignement */
        md.potential_force_function=lennard_jones;
        //md.potential_force_function=harmonic_oscillator;
-       md.cutoff=R_CUTOFF*LC_SI;
        md.pot_params=&lj;
        //md.pot_params=&ho;
-       md.status=0;
-       md.visual=&vis;
-       /* dimensions of the simulation cell */
+       /* cutoff radius */
+       md.cutoff=R_CUTOFF*LC_SI;
+
+       /*
+        * testing random numbers
+        */
+
+#ifdef DEBUG_RANDOM_NUMBER
+       for(a=0;a<1000000;a++)
+               printf("%f %f\n",rand_get_gauss(&(md.random)),
+                                rand_get_gauss(&(md.random)));
+       return 0;
+#endif
+
+       /*
+        * geometry & particles
+        */
+
+       /* simulation cell volume in lattice constants */
+       a=LEN_X;
+       b=LEN_Y;
+       c=LEN_Z;
        md.dim.x=a*LC_SI;
        md.dim.y=b*LC_SI;
        md.dim.z=c*LC_SI;
 
+       /* (un)set to (not) get visualized 'bounding atoms' */
+       md.vis.dim.x=a*LC_SI;
+       md.vis.dim.y=b*LC_SI;
+       md.vis.dim.z=c*LC_SI;
+
+       /*
+        * particles
+        */
+
+       /* lattice init */
+
+#ifndef SIMPLE_TESTING
+       md.count=create_lattice(DIAMOND,SI,M_SI,LC_SI,a,b,c,&(md.atom));
+       printf("created silicon lattice (#atoms = %d)\n",md.count);
+#else
+       md.count=2;
+       moldyn->atom=malloc(2*sizeof(t_atom));
+       moldyn->atom[0].r.x=0.13*sqrt(3.0)*LC_SI/2.0;
+       moldyn->atom[0].r.y=0;
+       moldyn->atom[0].r.z=0;
+       moldyn->atom[0].element=SI;
+       moldyn->atom[0].mass=M_SI;
+       moldyn->atom[1].r.x=-si[0].r.x;
+       moldyn->atom[1].r.y=0;
+       moldyn->atom[1].r.z=0;
+       moldyn->atom[1].element=SI;
+       moldyn->atom[1].mass=M_SI;
+#endif
+
+       /* initial thermal fluctuations of particles */
+
+#ifndef SIMPLE_TESTING
        printf("setting thermal fluctuations (T=%f K)\n",md.t);
-       // thermal_init(&md,&random);
+       thermal_init(&md);
+#else
        for(a=0;a<md.count;a++) v3_zero(&(si[0].v));
+#endif
 
        /* check kinetic energy */
-
-       e=get_e_kin(si,md.count);
+       e=get_e_kin(md.atom,md.count);
        printf("kinetic energy: %.40f [J]\n",e);
        printf("3/2 N k T = %.40f [J] (T=%f [K])\n",
               1.5*md.count*K_BOLTZMANN*md.t,md.t);
 
        /* check total momentum */
-       p=get_total_p(si,md.count);
+       p=get_total_p(md.atom,md.count);
        printf("total momentum: %.30f [Ns]\n",v3_norm(&p));
 
-       /* potential paramters */
-       lj.sigma6=LJ_SIGMA_SI*LJ_SIGMA_SI;
-       help=lj.sigma6*lj.sigma6;
-       lj.sigma6*=help;
-       lj.sigma12=lj.sigma6*lj.sigma6;
-       lj.epsilon4=4.0*LJ_EPSILON_SI;
-
-       ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
-       ho.spring_constant=1.0;
-
+       /* check time step */
        printf("estimated accurate time step: %.30f [s]\n",
               estimate_time_step(&md,3.0,md.t));
 
+       /* initialize linked list / cell method */
+       printf("initializing linked cells\n");
+       link_cell_init(&md);
+
        /*
         * let's do the actual md algorithm now
         *
@@ -128,8 +150,6 @@ int main(int argc,char **argv) {
 
        link_cell_shutdown(&md);
 
-       rand_close(&random);
-
        moldyn_shutdown(&md);
        
        return 0;