int main(int argc,char **argv) {
t_moldyn md;
- t_atom *si;
- t_visual vis;
- t_random random;
+
+ t_lj_params lj;
+ t_ho_params ho;
+ t_tersoff_mult_params tp;
int a,b,c;
- double e,u;
+ double e;
double help;
t_3dvec p;
- int count;
- t_lj_params lj;
- t_ho_params ho;
+ /*
+ * moldyn init
+ *
+ * - parsing argv
+ * - log init
+ * - random init
+ *
+ */
+ a=moldyn_init(&md,argc,argv);
+ if(a<0) return a;
+
+ /*
+ * the following overrides possibly set interaction methods by argv !!
+ */
- /* parse arguments */
- a=moldyn_parse_argv(&md,argc,argv);
- if(a<0) return -1;
+ /* 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;
+ /* assignement */
+ md.potential_force_function=lennard_jones;
+ //md.potential_force_function=harmonic_oscillator;
+ md.pot_params=&lj;
+ //md.pot_params=&ho;
+ /* cutoff radius */
+ md.cutoff=R_CUTOFF*LC_SI;
+
+ /*
+ * testing random numbers
+ */
- /* init */
- moldyn_log_init(&md,&vis);
- rand_init(&random,NULL,1);
- random.status|=RAND_STAT_VERBOSE;
+#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
- /* testing random numbers */
- //for(a=0;a<1000000;a++)
- // printf("%f %f\n",rand_get_gauss(&random),
- // rand_get_gauss(&random));
+ /*
+ * 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;
- /* set for 'bounding atoms' */
- vis.dim.x=a*LC_SI;
- vis.dim.y=b*LC_SI;
- vis.dim.z=c*LC_SI;
-
- /* init lattice
- printf("placing silicon atoms ... ");
- count=create_lattice(DIAMOND,SI,M_SI,LC_SI,a,b,c,&si);
- printf("(%d) ok!\n",count); */
- /* testing purpose */
- count=2;
- si=malloc(2*sizeof(t_atom));
- si[0].r.x=0.35*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.count=count;
- md.atom=si;
- md.potential=potential_lennard_jones;
- md.force=force_lennard_jones;
- //md.potential=potential_harmonic_oscillator;
- //md.force=force_harmonic_oscillator;
- md.cutoff=R_CUTOFF;
- md.cutoff_square=(R_CUTOFF*R_CUTOFF);
- 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;
+ /* (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;
+ md.atom=malloc(md.count*sizeof(t_atom));
+ md.atom[0].r.x=0.23*sqrt(3.0)*LC_SI/2.0;
+ md.atom[0].r.y=0;
+ md.atom[0].r.z=0;
+ md.atom[0].element=SI;
+ md.atom[0].mass=M_SI;
+ md.atom[1].r.x=-md.atom[0].r.x;
+ md.atom[1].r.y=0;
+ md.atom[1].r.z=0;
+ md.atom[1].element=SI;
+ md.atom[1].mass=M_SI;
+
+ //md.atom[2].r.x=0.5*(a-1)*LC_SI;
+ //md.atom[2].r.y=0.5*(b-1)*LC_SI;
+ //md.atom[2].r.z=0;
+ //md.atom[2].element=C;
+ //md.atom[2].mass=M_C;
+
+ //md.atom[3].r.x=0.5*(a-1)*LC_SI;
+ //md.atom[3].r.y=0;
+ //md.atom[3].r.z=0;
+ //md.atom[3].element=SI;
+ //md.atom[3].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,count);
- for(a=0;a<count;a++) v3_zero(&(si[0].v));
- //v3_zero(&(si[0].v));
- //v3_zero(&(si[1].v));
+ thermal_init(&md);
+#else
+ for(a=0;a<md.count;a++) v3_zero(&(md.atom[0].v));
+ md.atom[2].v.x=-320;
+ md.atom[2].v.y=-320;
+#endif
/* check kinetic energy */
-
- e=get_e_kin(si,count);
+ e=get_e_kin(md.atom,md.count);
printf("kinetic energy: %.40f [J]\n",e);
- printf("3/2 N k T = %.40f [J]\n",1.5*count*K_BOLTZMANN*md.t);
+ 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,count);
+ p=get_total_p(md.atom,md.count);
printf("total momentum: %.30f [Ns]\n",v3_norm(&p));
- /* check potential energy */
- 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=0.25*sqrt(3.0)*LC_SI;
- ho.spring_constant=LJ_EPSILON_SI;
-
- 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;
-
+ /* check time step */
printf("estimated accurate time step: %.30f [s]\n",
estimate_time_step(&md,3.0,md.t));
-
/*
* let's do the actual md algorithm now
*
/* close */
- rand_close(&random);
+ link_cell_shutdown(&md);
moldyn_shutdown(&md);
projects / physik / posic.git / blobdiff