#include "visual/visual.h"
#include "list/list.h"
-int moldyn_usage(char **argv) {
-
- printf("\n%s usage:\n\n",argv[0]);
- printf("--- general options ---\n");
- printf("-E <steps> <file> (log total energy)\n");
- printf("-M <steps> <file> (log total momentum)\n");
- printf("-D <steps> <file> (dump total information)\n");
- printf("-S <steps> <filebase> (single save file)\n");
- printf("-V <steps> <filebase> (rasmol file)\n");
- 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);
- printf(" 0: velocity verlet\n");
- printf(" -- potential --\n");
- printf(" -P <number> <param1 param2 ...>\n");
- printf(" 0: harmonic oscillator\n");
- printf(" param1: spring constant\n");
- printf(" param2: equilibrium distance\n");
- printf(" 1: lennard jones\n");
- printf(" param1: epsilon\n");
- printf(" param2: sigma\n");
- printf("\n");
+
+int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
+
+ //int ret;
+
+ //ret=moldyn_parse_argv(moldyn,argc,argv);
+ //if(ret<0) return ret;
+
+ memset(moldyn,0,sizeof(t_moldyn));
+
+ rand_init(&(moldyn->random),NULL,1);
+ moldyn->random.status|=RAND_STAT_VERBOSE;
return 0;
}
-int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
+int moldyn_shutdown(t_moldyn *moldyn) {
- int i;
- t_ho_params hop;
- t_lj_params ljp;
- t_tersoff_params tp;
- double s,e;
+ printf("[moldyn] shutdown\n");
+ moldyn_log_shutdown(moldyn);
+ link_cell_shutdown(moldyn);
+ rand_close(&(moldyn->random));
+ free(moldyn->atom);
- memset(moldyn,0,sizeof(t_moldyn));
+ return 0;
+}
+
+int set_int_alg(t_moldyn *moldyn,u8 algo) {
- /* default values */
- moldyn->t=MOLDYN_TEMP;
- moldyn->tau=MOLDYN_TAU;
- moldyn->time_steps=MOLDYN_RUNS;
- moldyn->integrate=velocity_verlet;
- moldyn->potential_force_function=lennard_jones;
-
- /* parse argv */
- for(i=1;i<argc;i++) {
- if(argv[i][0]=='-') {
- switch(argv[i][1]){
- case 'E':
- moldyn->ewrite=atoi(argv[++i]);
- strncpy(moldyn->efb,argv[++i],64);
- break;
- case 'M':
- moldyn->mwrite=atoi(argv[++i]);
- strncpy(moldyn->mfb,argv[++i],64);
- break;
- case 'S':
- moldyn->swrite=atoi(argv[++i]);
- strncpy(moldyn->sfb,argv[++i],64);
- break;
- case 'V':
- moldyn->vwrite=atoi(argv[++i]);
- strncpy(moldyn->vfb,argv[++i],64);
- break;
- case 'T':
- moldyn->t=atof(argv[++i]);
- break;
- 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;
- case 'I':
- /* integration algorithm */
- switch(atoi(argv[++i])) {
+ switch(algo) {
case MOLDYN_INTEGRATE_VERLET:
moldyn->integrate=velocity_verlet;
break;
default:
- printf("unknown integration algo %s\n",argv[i]);
- moldyn_usage(argv);
+ printf("unknown integration algorithm: %02x\n",algo);
return -1;
}
- case 'P':
- /* potential + params */
- switch(atoi(argv[++i])) {
- case MOLDYN_POTENTIAL_HO:
- hop.spring_constant=atof(argv[++i]);
- hop.equilibrium_distance=atof(argv[++i]);
- moldyn->pot_params=malloc(sizeof(t_ho_params));
- memcpy(moldyn->pot_params,&hop,sizeof(t_ho_params));
- moldyn->potential_force_function=harmonic_oscillator;
- break;
- case MOLDYN_POTENTIAL_LJ:
- e=atof(argv[++i]);
- s=atof(argv[++i]);
- ljp.epsilon4=4*e;
- ljp.sigma6=s*s*s*s*s*s;
- ljp.sigma12=ljp.sigma6*ljp.sigma6;
- moldyn->pot_params=malloc(sizeof(t_lj_params));
- memcpy(moldyn->pot_params,&ljp,sizeof(t_lj_params));
- moldyn->potential_force_function=lennard_jones;
- break;
- default:
- printf("unknown potential %s\n",argv[i]);
- moldyn_usage(argv);
- return -1;
- }
+ return 0;
+}
- default:
- printf("unknown option %s\n",argv[i]);
- moldyn_usage(argv);
- return -1;
- }
- } else {
- moldyn_usage(argv);
- return -1;
- }
- }
+int set_cutoff(t_moldyn *moldyn,double cutoff) {
+
+ moldyn->cutoff=cutoff;
return 0;
}
-int moldyn_log_init(t_moldyn *moldyn) {
+int set_temperature(t_moldyn *moldyn,double t) {
+
+ moldyn->t=t;
+
+ return 0;
+}
- moldyn->lvstat=0;
- t_visual *vis;
+int set_dim(t_moldyn *moldyn,double x,double y,double z,u8 visualize) {
- vis=&(moldyn->vis);
+ moldyn->dim.x=x;
+ moldyn->dim.y=y;
+ moldyn->dim.z=z;
- if(moldyn->ewrite) {
- moldyn->efd=open(moldyn->efb,O_WRONLY|O_CREAT|O_TRUNC);
- if(moldyn->efd<0) {
- perror("[moldyn] efd open");
- return moldyn->efd;
- }
- dprintf(moldyn->efd,"# moldyn total energy logfile\n");
- moldyn->lvstat|=MOLDYN_LVSTAT_TOTAL_E;
+ if(visualize) {
+ moldyn->vis.dim.x=x;
+ moldyn->vis.dim.y=y;
+ moldyn->vis.dim.z=z;
}
- if(moldyn->mwrite) {
- moldyn->mfd=open(moldyn->mfb,O_WRONLY|O_CREAT|O_TRUNC);
- if(moldyn->mfd<0) {
- perror("[moldyn] mfd open");
- return moldyn->mfd;
- }
- dprintf(moldyn->mfd,"# moldyn total momentum logfile\n");
- moldyn->lvstat|=MOLDYN_LVSTAT_TOTAL_M;
- }
+ return 0;
+}
- if(moldyn->swrite)
- moldyn->lvstat|=MOLDYN_LVSTAT_SAVE;
+int set_pbc(t_moldyn *moldyn,u8 x,u8 y,u8 z) {
- if((moldyn->vwrite)&&(vis)) {
- moldyn->visual=vis;
- visual_init(vis,moldyn->vfb);
- moldyn->lvstat|=MOLDYN_LVSTAT_VISUAL;
- }
+ if(x)
+ moldyn->status|=MOLDYN_STAT_PBX;
+
+ if(y)
+ moldyn->status|=MOLDYN_STAT_PBY;
- moldyn->lvstat|=MOLDYN_LVSTAT_INITIALIZED;
+ if(z)
+ moldyn->status|=MOLDYN_STAT_PBZ;
return 0;
}
-int moldyn_log_shutdown(t_moldyn *moldyn) {
+int set_potential1b(t_moldyn *moldyn,pf_func1b func,void *params) {
- if(moldyn->efd) close(moldyn->efd);
- if(moldyn->mfd) close(moldyn->efd);
- if(moldyn->dfd) close(moldyn->efd);
- if(moldyn->visual) visual_tini(moldyn->visual);
+ moldyn->func1b=func;
+ moldyn->pot1b_params=params;
return 0;
}
-int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
+int set_potential2b(t_moldyn *moldyn,pf_func2b func,void *params) {
- int ret;
+ moldyn->func2b=func;
+ moldyn->pot2b_params=params;
+
+ return 0;
+}
- ret=moldyn_parse_argv(moldyn,argc,argv);
- if(ret<0) return ret;
+int set_potential3b(t_moldyn *moldyn,pf_func3b func,void *params) {
- ret=moldyn_log_init(moldyn);
- if(ret<0) return ret;
+ moldyn->func3b=func;
+ moldyn->pot3b_params=params;
- rand_init(&(moldyn->random),NULL,1);
- moldyn->random.status|=RAND_STAT_VERBOSE;
+ return 0;
+}
+
+int moldyn_set_log(t_moldyn *moldyn,u8 type,char *fb,int timer) {
- moldyn->status=0;
+ switch(type) {
+ case LOG_TOTAL_ENERGY:
+ moldyn->ewrite=timer;
+ moldyn->efd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
+ if(moldyn->efd<0) {
+ perror("[moldyn] efd open");
+ return moldyn->efd;
+ }
+ dprintf(moldyn->efd,"# total energy log file\n");
+ break;
+ case LOG_TOTAL_MOMENTUM:
+ moldyn->mwrite=timer;
+ moldyn->mfd=open(fb,O_WRONLY|O_CREAT|O_TRUNC);
+ if(moldyn->mfd<0) {
+ perror("[moldyn] mfd open");
+ return moldyn->mfd;
+ }
+ dprintf(moldyn->efd,"# total momentum log file\n");
+ break;
+ case SAVE_STEP:
+ moldyn->swrite=timer;
+ strncpy(moldyn->sfb,fb,63);
+ break;
+ case VISUAL_STEP:
+ moldyn->vwrite=timer;
+ strncpy(moldyn->vfb,fb,63);
+ visual_init(&(moldyn->vis),fb);
+ break;
+ default:
+ printf("unknown log mechanism: %02x\n",type);
+ return -1;
+ }
return 0;
}
-int moldyn_shutdown(t_moldyn *moldyn) {
+int moldyn_log_shutdown(t_moldyn *moldyn) {
- moldyn_log_shutdown(moldyn);
- rand_close(&(moldyn->random));
- free(moldyn->atom);
+ printf("[moldyn] log shutdown\n");
+ if(moldyn->efd) close(moldyn->efd);
+ if(moldyn->mfd) close(moldyn->mfd);
+ if(&(moldyn->vis)) visual_tini(&(moldyn->vis));
return 0;
}
-int create_lattice(u8 type,int element,double mass,double lc,
- int a,int b,int c,t_atom **atom) {
+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 count;
int ret;
count=a*b*c;
if(type==FCC) count*=4;
+
if(type==DIAMOND) count*=8;
- *atom=malloc(count*sizeof(t_atom));
- if(*atom==NULL) {
+ moldyn->atom=malloc(count*sizeof(t_atom));
+ if(moldyn->atom==NULL) {
perror("malloc (atoms)");
return -1;
}
switch(type) {
case FCC:
- ret=fcc_init(a,b,c,lc,*atom,&origin);
+ ret=fcc_init(a,b,c,lc,moldyn->atom,&origin);
break;
case DIAMOND:
- ret=diamond_init(a,b,c,lc,*atom,&origin);
+ ret=diamond_init(a,b,c,lc,moldyn->atom,&origin);
break;
default:
printf("unknown lattice type (%02x)\n",type);
return -1;
}
+ moldyn->count=count;
+
while(count) {
- (*atom)[count-1].element=element;
- (*atom)[count-1].mass=mass;
+ moldyn->atom[count-1].element=element;
+ moldyn->atom[count-1].mass=mass;
+ moldyn->atom[count-1].attr=attr;
+ moldyn->atom[count-1].bnum=bnum;
count-=1;
}
return ret;
}
-int destroy_lattice(t_atom *atom) {
+int add_atom(t_moldyn *moldyn,int element,double mass,u8 bnum,u8 attr,
+ t_3dvec *r,t_3dvec *v) {
- if(atom) free(atom);
+ t_atom *atom;
+ void *ptr;
+ int count;
+
+ atom=moldyn->atom;
+ count=++(moldyn->count);
+
+ ptr=realloc(atom,count*sizeof(t_atom));
+ if(!ptr) {
+ perror("[moldyn] realloc (add atom)");
+ return -1;
+ }
+ moldyn->atom=ptr;
+
+ atom=moldyn->atom;
+ atom[count-1].r=*r;
+ atom[count-1].v=*v;
+ atom[count-1].element=element;
+ atom[count-1].mass=mass;
+ atom[count-1].bnum=bnum;
+ atom[count-1].attr=attr;
+
+ return 0;
+}
+
+int destroy_atoms(t_moldyn *moldyn) {
+
+ if(moldyn->atom) free(moldyn->atom);
return 0;
}
/*
* - velocity scaling (E = 3/2 N k T), E: kinetic energy
*/
+
+ if(moldyn->t==0.0) {
+ printf("[moldyn] no velocity scaling for T = 0 K\n");
+ return -1;
+ }
+
e=0.0;
for(i=0;i<moldyn->count;i++)
e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
return 0;
}
-double get_e_kin(t_atom *atom,int count) {
+double get_e_kin(t_moldyn *moldyn) {
int i;
- double e;
+ t_atom *atom;
- e=0.0;
+ atom=moldyn->atom;
+ moldyn->ekin=0.0;
- for(i=0;i<count;i++) {
- e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
- }
+ for(i=0;i<moldyn->count;i++)
+ moldyn->ekin+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
- return e;
+ return moldyn->ekin;
}
double get_e_pot(t_moldyn *moldyn) {
return moldyn->energy;
}
-double get_total_energy(t_moldyn *moldyn) {
+double update_e_kin(t_moldyn *moldyn) {
- double e;
+ return(get_e_kin(moldyn));
+}
- e=get_e_kin(moldyn->atom,moldyn->count);
- e+=get_e_pot(moldyn);
+double get_total_energy(t_moldyn *moldyn) {
- return e;
+ return(moldyn->ekin+moldyn->energy);
}
-t_3dvec get_total_p(t_atom *atom, int count) {
+t_3dvec get_total_p(t_moldyn *moldyn) {
t_3dvec p,p_total;
int i;
+ t_atom *atom;
+
+ 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);
}
return p_total;
}
-double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t) {
+double estimate_time_step(t_moldyn *moldyn,double nn_dist) {
double tau;
- tau=0.05*nn_dist/(sqrt(3.0*K_BOLTZMANN*t/moldyn->atom[0].mass));
- tau*=1.0E-9;
- if(tau<moldyn->tau)
- printf("[moldyn] warning: time step (%f > %.15f)\n",
- moldyn->tau,tau);
+ /* nn_dist is the nearest neighbour distance */
+
+ if(moldyn->t==5.0) {
+ printf("[moldyn] i do not estimate timesteps below %f K!\n",
+ MOLDYN_CRITICAL_EST_TEMP);
+ return 23.42;
+ }
+
+ tau=(0.05*nn_dist*moldyn->atom[0].mass)/sqrt(3.0*K_BOLTZMANN*moldyn->t);
return tau;
}
t_linkcell *lc;
int i;
+ int fd;
- lc=&(moldyn->lc);
+ fd=open("/dev/null",O_WRONLY);
- /* list log fd */
- lc->listfd=open("/dev/null",O_WRONLY);
+ lc=&(moldyn->lc);
/* partitioning the md cell */
lc->nx=moldyn->dim.x/moldyn->cutoff;
lc->cells=lc->nx*lc->ny*lc->nz;
lc->subcell=malloc(lc->cells*sizeof(t_list));
- printf("initializing linked cells (%d)\n",lc->cells);
+ printf("[moldyn] 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]),fd);
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;
+}
+
+int moldyn_add_schedule(t_moldyn *moldyn,int runs,double tau) {
+
+ int count;
+ void *ptr;
+ t_moldyn_schedule *schedule;
+
+ schedule=&(moldyn->schedule);
+ count=++(schedule->content_count);
+
+ ptr=realloc(moldyn->schedule.runs,count*sizeof(int));
+ if(!ptr) {
+ perror("[moldyn] realloc (runs)");
+ return -1;
+ }
+ moldyn->schedule.runs=ptr;
+ moldyn->schedule.runs[count-1]=runs;
+
+ ptr=realloc(schedule->tau,count*sizeof(double));
+ if(!ptr) {
+ perror("[moldyn] realloc (tau)");
+ return -1;
+ }
+ moldyn->schedule.tau=ptr;
+ moldyn->schedule.tau[count-1]=tau;
+
+ return 0;
+}
+
+int moldyn_set_schedule_hook(t_moldyn *moldyn,void *hook,void *hook_params) {
+ moldyn->schedule.hook=hook;
+ moldyn->schedule.hook_params=hook_params;
+
return 0;
}
int moldyn_integrate(t_moldyn *moldyn) {
- int i;
- unsigned int e,m,s,d,v;
+ int i,sched;
+ unsigned int e,m,s,v;
t_3dvec p;
+ t_moldyn_schedule *schedule;
+ t_atom *atom;
int fd;
char fb[128];
+ schedule=&(moldyn->schedule);
+ atom=moldyn->atom;
+
/* 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)) {
- printf("[moldyn] warning, lv system not initialized\n");
- return -1;
- }
-
/* sqaure of some variables */
moldyn->tau_square=moldyn->tau*moldyn->tau;
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 amount of runs and finite time step size */
+ moldyn->tau=schedule->tau[sched];
+ moldyn->tau_square=moldyn->tau*moldyn->tau;
+ moldyn->time_steps=schedule->runs[sched];
+
+ /* integration according to schedule */
for(i=0;i<moldyn->time_steps;i++) {
/* 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));
}
}
}
if(v) {
if(!(i%v)) {
- visual_atoms(moldyn->visual,i*moldyn->tau,
+ visual_atoms(&(moldyn->vis),moldyn->time,
moldyn->atom,moldyn->count);
- printf("\rsteps: %d",i);
+ printf("\rsched: %d, steps: %d",sched,i);
fflush(stdout);
}
}
+
+ }
+
+ /* check for hooks */
+ if(schedule->hook)
+ schedule->hook(moldyn,schedule->hook_params);
+
}
return 0;
v3_add(&(atom[i].r),&(atom[i].r),&delta);
v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
v3_add(&(atom[i].r),&(atom[i].r),&delta);
- v3_per_bound(&(atom[i].r),&(moldyn->dim));
+ check_per_bound(moldyn,&(atom[i].r));
/* velocities */
v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
}
/* neighbour list update */
-printf("list update ...\n");
link_cell_update(moldyn);
-printf("done\n");
/* forces depending on chosen potential */
-printf("calc potential/force ...\n");
potential_force_calc(moldyn);
//moldyn->potential_force_function(moldyn);
-printf("done\n");
for(i=0;i<count;i++) {
/* again velocities */
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;
moldyn->energy=0.0;
for(i=0;i<count;i++) {
+printf("BAR %d %d\n",i,count);
/* reset force */
v3_zero(&(atom[i].f));
/* 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)) {
-
+
link_cell_neighbour_index(moldyn,
(atom[i].r.x+moldyn->dim.x/2)/lc->x,
(atom[i].r.y+moldyn->dim.y/2)/lc->y,
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);
d=v3_norm(&distance);
if(d<=moldyn->cutoff) {
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;
d=+h1-h2;
d*=eps;
v3_scale(&force,&distance,d);
- v3_add(&(ai->f),&(aj->f),&force);
+ v3_add(&(ai->f),&(ai->f),&force);
}
return 0;
exchange->d=&(params->d[num]);
exchange->h=&(params->h[num]);
+ exchange->betan=pow(*(exchange->beta),*(exchange->n));
exchange->c2=params->c[num]*params->c[num];
exchange->d2=params->d[num]*params->d[num];
exchange->c2d2=exchange->c2/exchange->d2;
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_tersoff_mult_params *params;
t_tersoff_exchange *exchange;
t_3dvec dist_ij,dist_ik,dist_jk;
- t_3dvec db_ij,temp,force;
+ 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 B,mu;
+ 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;
d_ij=exchange->d_ij;
d_ij2=exchange->d_ij2;
- B=*(params->exchange.B);
- mu=*(params->exchange.mu);
-
f_a=params->exchange.f_a;
df_a=params->exchange.df_a;
*/
- 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));
if(bc) check_per_bound(moldyn,&dist_jk);
d_jk=v3_norm(&dist_jk);
-
- // GO ON HERE !!!
-
- cos_theta=(d_ij2+d_ik*d_ik-d_jk*d_jk)/(2*d_ij*d_ik);
+ beta=*(exchange->beta);
+ betan=exchange->betan;
+ n=*(exchange->n);
+ c=*(exchange->c);
+ d=*(exchange->d);
+ h=*(exchange->h);
+ c2=exchange->c2;
+ d2=exchange->d2;
+ c2d2=exchange->c2d2;
+
+ numer=d_ij2+d_ik*d_ik-d_jk*d_jk;
+ 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;
+ d_theta1*=d_theta;
+ d_theta2*=d_theta;
h_cos=(h-cos_theta);
h_cos2=h_cos*h_cos;
d2_h_cos2=d2-h_cos2;
+ /* some usefull expressions */
+ frac1=c2/(d2-h_cos2);
+ bracket1=1+c2d2-frac1;
+ bracket2=f_c_ik*bracket1;
+ bracket2_n_1=pow(bracket2,n-1.0);
+ bracket2_n=bracket2_n_1*bracket2;
+ bracket3=1+betan*bracket2_n;
+ bracket3_pow_1=pow(bracket3,(-1.0/(2.0*n))-1.0);
+ bracket3_pow=bracket3_pow_1*bracket3;
+
+ /* now go on with calc of b_ij and derivation of b_ij */
+ b_ij=chi*bracket3_pow;
+
+ /* derivation of 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,&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);
+
+ /* sum up and scale ... */
+ v3_add(&temp,&temp,&force);
+ scale=bracket2_n_1*n*betan*(1+betan*bracket3_pow_1)*chi*(1.0/(2.0*n));
+ v3_scale(&temp,&temp,scale);
+
+ /* now construct an energy and a force out of that */
+ v3_scale(&temp,&temp,f_a);
+ v3_scale(&force,&dist_ij,df_a*b_ij);
+ v3_add(&temp,&temp,&force);
+ v3_scale(&temp,&temp,f_c);
+ v3_scale(&force,&dist_ij,df_c*b_ij*f_a);
+ v3_add(&force,&force,&temp);
+
/* add forces */
v3_add(&(ai->f),&(ai->f),&force);
/* energy is 0.5 f_r f_c, but we will sum it up twice ... */
projects / physik / posic.git / blobdiff