printf("--- physics options ---\n");
printf("-T <temperature> [K] (%f)\n",MOLDYN_TEMP);
printf("-t <timestep tau> [s] (%.15f)\n",MOLDYN_TAU);
+ printf("-C <cutoff radius> [m] (%.15f)\n",MOLDYN_CUTOFF);
printf("-R <runs> (%d)\n",MOLDYN_RUNS);
printf(" -- integration algo --\n");
printf(" -I <number> (%d)\n",MOLDYN_INTEGRATE_DEFAULT);
case 't':
moldyn->tau=atof(argv[++i]);
break;
+ case 'C':
+ moldyn->cutoff=atof(argv[++i]);
+ break;
case 'R':
moldyn->time_steps=atoi(argv[++i]);
break;
return 0;
}
-int moldyn_log_init(t_moldyn *moldyn,void *v) {
+int moldyn_log_init(t_moldyn *moldyn) {
moldyn->lvstat=0;
t_visual *vis;
- vis=v;
+ vis=&(moldyn->vis);
if(moldyn->ewrite) {
moldyn->efd=open(moldyn->efb,O_WRONLY|O_CREAT|O_TRUNC);
return 0;
}
-int moldyn_shutdown(t_moldyn *moldyn) {
+int moldyn_log_shutdown(t_moldyn *moldyn) {
if(moldyn->efd) close(moldyn->efd);
if(moldyn->mfd) close(moldyn->efd);
return 0;
}
+int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
+
+ int ret;
+
+ ret=moldyn_parse_argv(moldyn,argc,argv);
+ if(ret<0) return ret;
+
+ ret=moldyn_log_init(moldyn);
+ if(ret<0) return ret;
+
+ rand_init(&(moldyn->random),NULL,1);
+ moldyn->random.status|=RAND_STAT_VERBOSE;
+
+ moldyn->status=0;
+
+ return 0;
+}
+
+int moldyn_shutdown(t_moldyn *moldyn) {
+
+ moldyn_log_shutdown(moldyn);
+ rand_close(&(moldyn->random));
+ free(moldyn->atom);
+
+ return 0;
+}
+
int create_lattice(unsigned char type,int element,double mass,double lc,
int a,int b,int c,t_atom **atom) {
return 0;
}
-int thermal_init(t_moldyn *moldyn,t_random *random) {
+int thermal_init(t_moldyn *moldyn) {
/*
* - gaussian distribution of velocities
double v,sigma;
t_3dvec p_total,delta;
t_atom *atom;
+ t_random *random;
atom=moldyn->atom;
+ random=&(moldyn->random);
/* gaussian distribution of velocities */
v3_zero(&p_total);
int link_cell_init(t_moldyn *moldyn) {
t_linkcell *lc;
+ int i;
lc=&(moldyn->lc);
+ /* list log fd */
+ lc->listfd=open("/dev/null",O_WRONLY);
+
/* partitioning the md cell */
lc->nx=moldyn->dim.x/moldyn->cutoff;
lc->x=moldyn->dim.x/lc->nx;
lc->nz=moldyn->dim.z/moldyn->cutoff;
lc->z=moldyn->dim.z/lc->nz;
- lc->subcell=malloc(lc->nx*lc->ny*lc->nz*sizeof(t_list));
+ lc->cells=lc->nx*lc->ny*lc->nz;
+ lc->subcell=malloc(lc->cells*sizeof(t_list));
+
+ printf("initializing linked cells (%d)\n",lc->cells);
+
+ for(i=0;i<lc->cells;i++)
+ //list_init(&(lc->subcell[i]),1);
+ list_init(&(lc->subcell[i]),lc->listfd);
link_cell_update(moldyn);
lc=&(moldyn->lc);
nx=lc->nx;
ny=lc->ny;
- nx=lc->nz;
+ nz=lc->nz;
count1=1;
count2=27;
a=nx*ny;
for(i=0;i<lc->nx*lc->ny*lc->nz;i++)
list_shutdown(&(moldyn->lc.subcell[i]));
+ if(lc->listfd) close(lc->listfd);
+
return 0;
}
moldyn->tau_square=moldyn->tau*moldyn->tau;
moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
- /* create the neighbour list */
- link_cell_update(moldyn);
-
/* calculate initial forces */
moldyn->potential_force_function(moldyn);
} t_atom;
typedef struct s_linkcell {
+ int listfd;
int nx,ny,nz;
+ int cells;
double x,y,z;
t_list *subcell;
} t_linkcell;
/* energy */
double energy;
/* logging & visualization */
+ t_visual vis;
unsigned char lvstat;
unsigned int ewrite;
char efb[64];
void *visual;
/* moldyn general status */
unsigned char status;
+ /* random */
+ t_random random;
} t_moldyn;
typedef struct s_ho_params {
#define MOLDYN_TEMP 273.0
#define MOLDYN_TAU 1.0e-15
+#define MOLDYN_CUTOFF 10.0e-9
#define MOLDYN_RUNS 1000000
#define MOLDYN_INTEGRATE_VERLET 0x00
int moldyn_usage(char **argv);
int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv);
-int moldyn_log_init(t_moldyn *moldyn,void *v);
+int moldyn_log_init(t_moldyn *moldyn);
+int moldyn_init(t_moldyn *moldyn,int argc,char **argv);
int moldyn_shutdown(t_moldyn *moldyn);
int create_lattice(unsigned char type,int element,double mass,double lc,
int a,int b,int c,t_atom **atom);
int destroy_lattice(t_atom *atom);
-int thermal_init(t_moldyn *moldyn,t_random *random);
+int thermal_init(t_moldyn *moldyn);
int scale_velocity(t_moldyn *moldyn);
double get_e_kin(t_atom *atom,int count);
double get_e_pot(t_moldyn *moldyn);
int main(int argc,char **argv) {
t_moldyn md;
- t_atom *si;
- t_visual vis;
- t_random random;
int a,b,c;
double e;
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
*
link_cell_shutdown(&md);
- rand_close(&random);
-
moldyn_shutdown(&md);
return 0;
projects / physik / posic.git / commitdiff