int set_int_alg(t_moldyn *moldyn,u8 algo) {
- switch(alg) {
- case 'MOLDYN_INTEGRATE_VERLET':
+ switch(algo) {
+ case MOLDYN_INTEGRATE_VERLET:
moldyn->integrate=velocity_verlet;
break;
default:
- printf("unknown integration algorithm: %02x\",alg);
+ printf("unknown integration algorithm: %02x\n",algo);
return -1;
}
return 0;
}
-int set_potential(t_moldyn *moldyn,u8 type,(int *)(func),void *params) {
+int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params) {
- switch(type) {
- case MOLDYN_1BP:
- moldyn->pf_func1b=func;
- moldyn->pot1b_params=params;
- break;
- case MOLDYN_2BP:
- moldyn->pf_func2b=func;
- moldyn->pot2b_params=params;
- break;
- case MOLDYN_3BP:
- moldyn->pf_func3b=func;
- moldyn->pot3b_params=params;
- break;
- default:
- printf("unknown potential type: %02x\n",type);
- return -1;
- }
+ moldyn->func1b=func;
+ moldyn->pot1b_params=params;
+
+ return 0;
+}
+
+int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) {
+
+ moldyn->func2b=func;
+ moldyn->pot2b_params=params;
+
+ return 0;
+}
+
+int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
+
+ moldyn->func3b=func;
+ moldyn->pot3b_params=params;
return 0;
}
perror("[moldyn] efd open");
return moldyn->efd;
}
- dprintf("# moldyn total energy log file\n");
+ dprintf(moldyn->efd,"# total energy log file\n");
break;
case LOG_TOTAL_MOMENTUM:
moldyn->mwrite=timer;
perror("[moldyn] mfd open");
return moldyn->mfd;
}
- dprintf("# moldyn total momentum log file\n");
+ dprintf(moldyn->efd,"# total momentum log file\n");
break;
case SAVE_STEP:
moldyn->swrite=timer;
return moldyn->energy;
}
+double update_e_kin(t_moldyn *moldyn) {
+
+ return(get_e_kin(moldyn));
+}
+
double get_total_energy(t_moldyn *moldyn) {
- return(get_e_kin(moldyn)+get_e_pot(moldyn));
+ return(moldyn->ekin+moldyn->energy);
}
t_3dvec get_total_p(t_moldyn *moldyn) {
atom=moldyn->atom;
v3_zero(&p_total);
- for(i=0;i<count;i++) {
+ for(i=0;i<moldyn->count;i++) {
v3_scale(&p,&(atom[i].v),atom[i].mass);
v3_add(&p_total,&p_total,&p);
}
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;
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]));
+ list_init(&(lc->subcell[i]),1);
link_cell_update(moldyn);
for(i=0;i<lc->cells;i++)
list_destroy(&(moldyn->lc.subcell[i]));
- for(count=0;count<moedyn->count;count++) {
+ for(count=0;count<moldyn->count;count++) {
i=(atom[count].r.x+(moldyn->dim.x/2))/lc->x;
j=(atom[count].r.y+(moldyn->dim.y/2))/lc->y;
k=(atom[count].r.z+(moldyn->dim.z/2))/lc->z;
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;
}
void *ptr;
t_moldyn_schedule *schedule;
- schedule=moldyn->schedule;
+ schedule=&(moldyn->schedule);
count=++(schedule->content_count);
ptr=realloc(moldyn->schedule.runs,count*sizeof(int));
int moldyn_integrate(t_moldyn *moldyn) {
int i,sched;
- unsigned int e,m,s,d,v;
+ unsigned int e,m,s,v;
t_3dvec p;
+ t_moldyn_schedule *schedule;
int fd;
char fb[128];
+ schedule=&(moldyn->schedule);
+
/* initialize linked cell method */
link_cell_init(moldyn);
e=moldyn->ewrite;
m=moldyn->mwrite;
s=moldyn->swrite;
- d=moldyn->dwrite;
v=moldyn->vwrite;
if(!(moldyn->lvstat&MOLDYN_LVSTAT_INITIALIZED)) {
moldyn->cutoff_square=moldyn->cutoff*moldyn->cutoff;
/* calculate initial forces */
- moldyn->potential_force_function(moldyn);
+ potential_force_calc(moldyn);
+
+ /* zero absolute time */
+ moldyn->time=0.0;
for(sched=0;sched<moldyn->schedule.content_count;sched++) {
- /* setting amont of runs and finite time step size */
+ /* setting amount of runs and finite time step size */
moldyn->tau=schedule->tau[sched];
moldyn->tau_square=moldyn->tau*moldyn->tau;
- moldyn->timesteps=schedule->runs[sched];
+ moldyn->time_steps=schedule->runs[sched];
/* integration according to schedule */
/* integration step */
moldyn->integrate(moldyn);
+ /* increase absolute time */
+ moldyn->time+=moldyn->tau;
+
/* check for log & visualization */
if(e) {
if(!(i%e))
dprintf(moldyn->efd,
- "%.15f %.45f\n",i*moldyn->tau,
+ "%.15f %.45f %.45f %.45f\n",
+ moldyn->time,update_e_kin(moldyn),
+ moldyn->energy,
get_total_energy(moldyn));
}
if(m) {
if(!(i%m)) {
- p=get_total_p(moldyn->atom,moldyn->count);
+ p=get_total_p(moldyn);
dprintf(moldyn->mfd,
- "%.15f %.45f\n",i*moldyn->tau,
+ "%.15f %.45f\n",moldyn->time,
v3_norm(&p));
}
}
int potential_force_calc(t_moldyn *moldyn) {
- int i,count;
- t_atom *atom;
+ int i,j,k,count;
+ t_atom *atom,*btom,*ktom;
t_linkcell *lc;
t_list neighbour[27];
- t_list *this;
- double u;
- u8 bc,bc3;
+ t_list *this,*thisk,*neighbourk;
+ u8 bc,bck;
int countn,dnlc;
count=moldyn->count;
/* single particle potential/force */
if(atom[i].attr&ATOM_ATTR_1BP)
- moldyn->pf_func1b(moldyn,&(atom[i]));
+ moldyn->func1b(moldyn,&(atom[i]));
/* 2 body pair potential/force */
if(atom[i].attr&(ATOM_ATTR_2BP|ATOM_ATTR_3BP)) {
if((btom->attr&ATOM_ATTR_2BP)&
(atom[i].attr&ATOM_ATTR_2BP))
- moldyn->pf_func2b(moldyn,
- &(atom[i]),
- btom,
- bc);
+ moldyn->func2b(moldyn,
+ &(atom[i]),
+ btom,
+ bc);
/* 3 body potential/force */
if(ktom==&(atom[i]))
continue;
- moldyn->pf_func3b(moldyn,&(atom[i]),btom,ktom,bck);
+ moldyn->func3b(moldyn,&(atom[i]),btom,ktom,bck);
} while(list_next(thisk)!=\
L_NO_NEXT_ELEMENT);
+
+ }
} while(list_next(this)!=L_NO_NEXT_ELEMENT);
}
int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
double x,y,z;
+ t_3dvec *dim;
+
+ dim=&(moldyn->dim);
x=0.5*dim->x;
y=0.5*dim->y;
z=0.5*dim->z;
- if(moldyn->MOLDYN_ATTR_PBX)
+ if(moldyn->status&MOLDYN_STAT_PBX) {
if(a->x>=x) a->x-=dim->x;
else if(-a->x>x) a->x+=dim->x;
- if(moldyn->MOLDYN_ATTR_PBY)
+ }
+ if(moldyn->status&MOLDYN_STAT_PBY) {
if(a->y>=y) a->y-=dim->y;
else if(-a->y>y) a->y+=dim->y;
- if(moldyn->MOLDYN_ATTR_PBZ)
+ }
+ if(moldyn->status&MOLDYN_STAT_PBZ) {
if(a->z>=z) a->z-=dim->z;
else if(-a->z>z) a->z+=dim->z;
+ }
return 0;
}
/* harmonic oscillator potential and force */
-int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc)) {
+int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
t_ho_params *params;
t_3dvec force,distance;
sc=params->spring_constant;
equi_dist=params->equilibrium_distance;
- v3_sub(&distance,&(ai->r),&(aj->r);
+ v3_sub(&distance,&(ai->r),&(aj->r));
v3_per_bound(&distance,&(moldyn->dim));
if(bc) check_per_bound(moldyn,&distance);
t_lj_params *params;
t_3dvec force,distance;
- double d,h1,h2,u;
+ double d,h1,h2;
double eps,sig6,sig12;
- params=moldyn->pot_params;
+ params=moldyn->pot2b_params;
eps=params->epsilon4;
sig6=params->sigma6;
sig12=params->sigma12;
t_tersoff_mult_params *params;
t_tersoff_exchange *exchange;
- t_3dvec dist_ij;
+ t_3dvec dist_ij,force;
double d_ij;
- double A,B,R,S,lambda;
+ double A,B,R,S,lambda,mu;
+ double f_r,df_r;
+ double f_c,df_c;
int num;
+ double s_r;
+ double arg;
+ double scale;
- params=moldyn->pot_params;
+ params=moldyn->pot2b_params;
num=ai->bnum;
exchange=&(params->exchange);
lambda=params->lambda[num];
/* more constants depending of atoms i and j, needed in 3bp */
params->exchange.B=&(params->B[num]);
- params->exchange.mu=params->mu[num];
+ params->exchange.mu=&(params->mu[num]);
+ mu=params->mu[num];
params->exchange.chi=1.0;
}
else {
/* more constants depending of atoms i and j, needed in 3bp */
params->exchange.B=&(params->Bmixed);
params->exchange.mu=&(params->mu_m);
+ mu=params->mu_m;
params->exchange.chi=params->chi;
}
if(d_ij>S)
return 0;
- f_r=A*exp(-lamda*d_ij);
+ f_r=A*exp(-lambda*d_ij);
df_r=-lambda*f_r/d_ij;
/* f_a, df_a calc + save for 3bp use */
}
else {
s_r=S-R;
- arg=PI*(d_ij-R)/s_r;
+ arg=M_PI*(d_ij-R)/s_r;
f_c=0.5+0.5*cos(arg);
- df_c=-0.5*sin(arg)*(PI/(s_r*d_ij));
+ df_c=-0.5*sin(arg)*(M_PI/(s_r*d_ij));
scale=df_c*f_r+df_r*f_c;
v3_scale(&force,&dist_ij,scale);
}
t_3dvec dist_ij,dist_ik,dist_jk;
t_3dvec temp,force;
double R,S,s_r;
- double d_ij,d_ik,d_jk;
+ double d_ij,d_ij2,d_ik,d_jk;
double f_c,df_c,b_ij,f_a,df_a;
- double n,c,d,h,neta,betan,betan_1;
+ double f_c_ik,df_c_ik,arg;
+ double scale;
+ double chi;
+ double n,c,d,h,beta,betan;
+ double c2,d2,c2d2;
+ double numer,denom;
double theta,cos_theta,sin_theta;
+ double d_theta,d_theta1,d_theta2;
+ double h_cos,h_cos2,d2_h_cos2;
+ double frac1,bracket1,bracket2,bracket2_n_1,bracket2_n;
+ double bracket3,bracket3_pow_1,bracket3_pow;
int num;
- params=moldyn->pot_params;
+ params=moldyn->pot3b_params;
num=ai->bnum;
- exchange=params->exchange;
+ exchange=&(params->exchange);
if(!(exchange->run3bp))
return 0;
*/
- v3_sub(&dist_ik,&(aj->i),&(ak->r));
+ v3_sub(&dist_ik,&(ai->r),&(ak->r));
if(bc) check_per_bound(moldyn,&dist_ik);
d_ik=v3_norm(&dist_ik);
}
else {
s_r=S-R;
- arg=PI*(d_ik-R)/s_r;
+ arg=M_PI*(d_ik-R)/s_r;
f_c_ik=0.5+0.5*cos(arg);
- df_c_ik=-0.5*sin(arg)*(PI/(s_r*d_ik));
+ df_c_ik=-0.5*sin(arg)*(M_PI/(s_r*d_ik));
}
v3_sub(&dist_jk,&(aj->r),&(ak->r));
denom=2*d_ij*d_ik;
cos_theta=numer/denom;
sin_theta=sqrt(1.0-(cos_theta*cos_theta));
- theta=arccos(cos_theta);
+ theta=acos(cos_theta);
d_theta=(-1.0/sqrt(1.0-cos_theta*cos_theta))/(denom*denom);
d_theta1=2*denom-numer*2*d_ik/d_ij;
d_theta2=2*denom-numer*2*d_ij/d_ik;
b_ij=chi*bracket3_pow;
/* derivation of theta */
- v3_scale(&force,&dist_ij,d1_theta);
+ v3_scale(&force,&dist_ij,d_theta1);
v3_scale(&temp,&dist_ik,d_theta2);
v3_add(&force,&force,&temp);
/* part 1 of derivation of b_ij */
- v3_scale(&force,sin_theta*2*h_cos*f_c_ik*frac1);
+ v3_scale(&force,&force,sin_theta*2*h_cos*f_c_ik*frac1);
/* part 2 of derivation of b_ij */
v3_scale(&temp,&dist_ik,df_c_ik*bracket1);
t_3dvec dim; /* dimensions of the simulation volume */
/* potential force function and parameter pointers */
- int (*pf_func1b)(struct s_moldyn *,t_atom *);
+ int (*func1b)(struct s_moldyn *moldyn,t_atom *ai);
void *pot1b_params;
- int (*pf_func2b)(struct s_moldyn *,t_atom *,t_atom *);
+ int (*func2b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
void *pot2b_params;
- int (*pf_func3b)(struct s_moldyn *,t_atom *,t_atom *,t_atom *);
+ int (*func3b)(struct s_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,
+ u8 bck);
void *pot3b_params;
//int (*potential_force_function)(struct s_moldyn *moldyn);
int (*integrate)(struct s_moldyn *moldyn);
int time_steps; /* amount of iterations */
double tau; /* delta t */
+ double time; /* absolute time */
double tau_square; /* delta t squared */
double elapsed; /* total elapsed time */
/* tersoff exchange structure to exchange 2bp and 3bp calculated values */
typedef struct s_tersoff_exchange {
double f_c,df_c;
+ double f_a,df_a;
t_3dvec dist_ij;
double d_ij;
double h[2];
t_tersoff_exchange exchange; /* exchange between 2bp and 3bp calc */
-} t_tersoff_params;
+} t_tersoff_mult_params;
#define MOLDYN_POTENTIAL_LJ 0x01
#define MOLDYN_POTENTIAL_TM 0x02
-#define MOLDYN_SET_POTENTIAL 0x00
-#define MOLDYN_SET_TEMPERATURE 0x01
-#define MOLDYN_SET_
-#define MOLDYN_SET_
+#define LOG_TOTAL_ENERGY 0x01
+#define LOG_TOTAL_MOMENTUM 0x02
+#define SAVE_STEP 0x04
+#define VISUAL_STEP 0x08
#define TRUE 1
#define FALSE 0
*
*/
+typedef int (*pf_func1b)(t_moldyn *,t_atom *ai);
+typedef int (*pf_func2b)(t_moldyn *,t_atom *,t_atom *,u8 bc);
+typedef int (*pf_func3b)(t_moldyn *,t_atom *,t_atom *,t_atom *,u8 bc);
+
int moldyn_init(t_moldyn *moldyn,int argc,char **argv);
int moldyn_shutdown(t_moldyn *moldyn);
int set_temperature(t_moldyn *moldyn,double t);
int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize);
int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z);
-int set_potential(t_moldyn *moldyn,u8 type,(int *)(func),void *params);
+int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params);
+int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params);
+int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params);
int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer);
-nt moldyn_log_shutdown(t_moldyn *moldyn);
+int moldyn_log_shutdown(t_moldyn *moldyn);
int create_lattice(t_moldyn *moldyn,u8 type,double lc,int element,double mass,
u8 attr,u8 bnum,int a,int b,int c);
int potential_force_calc(t_moldyn *moldyn);
int check_per_bound(t_moldyn *moldyn,t_3dvec *a);
-int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_Atom *aj,u8 bc);
+int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai);
int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc);
projects / physik / posic.git / commitdiff