t_random random;
int a,b,c;
- double e,u;
+ double e;
double help;
t_3dvec p;
- int count;
t_lj_params lj;
t_ho_params ho;
vis.dim.y=b*LC_SI;
vis.dim.z=c*LC_SI;
- /* init lattice */
+ /* 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;
+ 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=0.23*sqrt(3.0)*LC_SI/2.0;
+ 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[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.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.integrate=velocity_verlet;
- //md.time_steps=RUNS;
- //md.tau=TAU;
md.status=0;
md.visual=&vis;
+ /* dimensions of the simulation cell */
+ md.dim.x=a*LC_SI;
+ md.dim.y=b*LC_SI;
+ md.dim.z=c*LC_SI;
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));
+ // thermal_init(&md,&random);
+ for(a=0;a<md.count;a++) v3_zero(&(si[0].v));
/* check kinetic energy */
- e=get_e_kin(si,count);
+ e=get_e_kin(si,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(si,md.count);
printf("total momentum: %.30f [Ns]\n",v3_norm(&p));
- /* check potential energy */
+ /* potential paramters */
lj.sigma6=LJ_SIGMA_SI*LJ_SIGMA_SI;
help=lj.sigma6*lj.sigma6;
lj.sigma6*=help;
lj.epsilon4=4.0*LJ_EPSILON_SI;
ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
- ho.spring_constant=4.0*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;
+ ho.spring_constant=1.0;
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 */
+ link_cell_shutdown(&md);
+
rand_close(&random);
moldyn_shutdown(&md);