X-Git-Url: https://www.hackdaworld.org/gitweb/?a=blobdiff_plain;f=sic.c;h=714710b579257452f2600517ad897c7e614d4d12;hb=7fcb896467bdf236f60c4c3784a9d51214737fcb;hp=f97ffe872b2938523f5dc1259f56cd240643a270;hpb=cb177e7c208a85b45d77b09fcada23b62d0248b5;p=physik%2Fposic.git diff --git a/sic.c b/sic.c index f97ffe8..714710b 100644 --- a/sic.c +++ b/sic.c @@ -8,23 +8,59 @@ #include #include "moldyn.h" - #include "posic.h" +/* potential */ +#include "potentials/harmonic_oscillator.h" +#include "potentials/lennard_jones.h" +#include "potentials/tersoff.h" +//#include "potentials/tersoff_orig.h" + +#define INJECT 1 +#define NR_ATOMS 4 + int hook(void *moldyn,void *hook_params) { t_moldyn *md; + t_3dvec r,v,dist; + double d; + unsigned char run; + int i,j; + t_atom *atom; md=moldyn; - /* switch to direct scaling in first hook */ - if(md->schedule.count==0) + printf("\nschedule hook: "); + + if(!(md->schedule.count%2)) { + /* add carbon at random place, and enable t scaling */ + for(j=0;jrandom))*md->dim.x; + r.y=rand_get_double(&(md->random))*md->dim.y; + r.z=rand_get_double(&(md->random))*md->dim.z; + for(i=0;icount;i++) { + atom=&(md->atom[i]); + v3_sub(&dist,&(atom->r),&r); + d=v3_absolute_square(&dist); + if(d>TM_R_C) + run=0; + } + } + v.x=0; v.y=0; v.z=0; + add_atom(md,C,M_C,1, + ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB, + &r,&v); + } + printf("adding atoms & enable t scaling\n"); set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0); - /* switch off temp scaling in second hook */ - if(md->schedule.count==1) + } + else { + /* disable t scaling */ + printf("disabling t scaling\n"); set_pt_scale(md,0,0,0,0); - - //set_temperature(md,md->t_ref-100.0); + } return 0; } @@ -45,8 +81,13 @@ int main(int argc,char **argv) { t_ho_params ho; t_tersoff_mult_params tp; + /* atom injection counter */ + int inject; + /* testing location & velocity vector */ t_3dvec r,v; + memset(&r,0,sizeof(t_3dvec)); + memset(&v,0,sizeof(t_3dvec)); /* initialize moldyn */ moldyn_init(&md,argc,argv); @@ -55,17 +96,25 @@ int main(int argc,char **argv) { set_int_alg(&md,MOLDYN_INTEGRATE_VERLET); /* choose potential */ - //set_potential1b(&md,tersoff_mult_1bp,&tp); - //set_potential2b(&md,tersoff_mult_2bp,&tp); - //set_potential2b_post(&md,tersoff_mult_post_2bp,&tp); - //set_potential3b(&md,tersoff_mult_3bp,&tp); - set_potential2b(&md,lennard_jones,&lj); - //set_potential2b(&md,harmonic_oscillator,&ho); + set_potential1b(&md,tersoff_mult_1bp); + set_potential2b(&md,tersoff_mult_2bp); + //set_potential3b_j1(&md,tersoff_mult_2bp); + //set_potential3b_k1(&md,tersoff_mult_3bp); + //set_potential3b_j3(&md,tersoff_mult_post_2bp); + set_potential3b_j1(&md,tersoff_mult_3bp_j1); + set_potential3b_k1(&md,tersoff_mult_3bp_k1); + set_potential3b_j2(&md,tersoff_mult_3bp_j2); + set_potential3b_k2(&md,tersoff_mult_3bp_k2); + //set_potential2b(&md,lennard_jones); + //set_potential2b(&md,harmonic_oscillator); + set_potential_params(&md,&tp); + //set_potential_params(&md,&lj); + //set_potential_params(&md,&ho); /* cutoff radius */ - //set_cutoff(&md,TM_S_SI); - //set_cutoff(&md,2*LC_SI*0.5*sqrt(1.5)); - set_cutoff(&md,2.0*LC_SI); + set_cutoff(&md,TM_S_SI); + //set_cutoff(&md,LC_SI*sqrt(3.0)); + //set_cutoff(&md,2.0*LC_SI); /* * potential parameters @@ -79,8 +128,8 @@ int main(int argc,char **argv) { lj.uc=lj.epsilon4*(lj.sigma12/pow(md.cutoff,12.0)-lj.sigma6/pow(md.cutoff,6)); /* harmonic oscillator */ - //ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI; - ho.equilibrium_distance=LC_SI; + ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI; + //ho.equilibrium_distance=LC_SI; ho.spring_constant=LJ_EPSILON_SI; /* @@ -122,16 +171,16 @@ int main(int argc,char **argv) { /* create the lattice / place atoms */ //create_lattice(&md,CUBIC,LC_SI,SI,M_SI, - create_lattice(&md,FCC,LC_SI,SI,M_SI, - //create_lattice(&md,DIAMOND,LC_SI,SI,M_SI, - // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB, - ATOM_ATTR_2BP|ATOM_ATTR_HB, + //create_lattice(&md,FCC,LC_SI,SI,M_SI, + create_lattice(&md,DIAMOND,LC_SI,SI,M_SI, + ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB, + // ATOM_ATTR_2BP|ATOM_ATTR_HB, 0,6,6,6); moldyn_bc_check(&md); /* testing configuration */ - //r.x=0.28*sqrt(3)*LC_SI/2; v.x=0; - //r.x=1.75*LC_SI; v.x=-0.01; + //r.x=0.27*sqrt(3.0)*LC_SI/2.0; v.x=0; + //r.x=(TM_S_SI+TM_R_SI)/4.0; v.x=0; //r.y=0; v.y=0; //r.z=0; v.z=0; //add_atom(&md,SI,M_SI,0, @@ -145,10 +194,25 @@ int main(int argc,char **argv) { // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB, // ATOM_ATTR_2BP|ATOM_ATTR_HB, // &r,&v); + //r.z=0.27*sqrt(3.0)*LC_SI/2.0; v.z=0; + //r.x=(TM_S_SI+TM_R_SI)/4.0; v.x=0; + //r.y=0; v.y=0; + //r.x=0; v.x=0; + //add_atom(&md,SI,M_SI,0, + // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB, + // ATOM_ATTR_2BP|ATOM_ATTR_HB, + // &r,&v); + //r.z=-r.z; v.z=-v.z; + //r.y=0; v.y=0; + //r.x=0; v.x=0; + //add_atom(&md,SI,M_SI,0, + // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB, + // ATOM_ATTR_2BP|ATOM_ATTR_HB, + // &r,&v); /* set temperature & pressure */ set_temperature(&md,atof(argv[2])+273.0); - set_pressure(&md,ATM); + set_pressure(&md,BAR); /* set p/t scaling */ //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001, @@ -160,18 +224,27 @@ int main(int argc,char **argv) { thermal_init(&md,TRUE); /* create the simulation schedule */ - moldyn_add_schedule(&md,101,1.0); - //moldyn_add_schedule(&md,501,1.0); - //moldyn_add_schedule(&md,501,1.0); + /* initial configuration */ + moldyn_add_schedule(&md,10000,1.0); + /* adding atoms */ + //for(inject=0;inject