*
*/
-#include "moldyn.h"
-
+#define _GNU_SOURCE
#include <stdio.h>
#include <stdlib.h>
+#include <string.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <fcntl.h>
+#include <unistd.h>
#include <math.h>
+#include "moldyn.h"
+
#include "math/math.h"
#include "init/init.h"
#include "random/random.h"
+#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");
+
+ return 0;
+}
+
+int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv) {
+
+ int i;
+
+ memset(moldyn,0,sizeof(t_moldyn));
+
+ /* default values */
+ moldyn->t=MOLDYN_TEMP;
+ moldyn->tau=MOLDYN_TAU;
+ moldyn->time_steps=MOLDYN_RUNS;
+ moldyn->integrate=velocity_verlet;
+
+ /* 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])) {
+ case MOLDYN_INTEGRATE_VERLET:
+ moldyn->integrate=velocity_verlet;
+ break;
+ default:
+ printf("unknown integration algo %s\n",argv[i]);
+ moldyn_usage(argv);
+ 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;
+ }
+
+ default:
+ printf("unknown option %s\n",argv[i]);
+ moldyn_usage(argv);
+ return -1;
+ }
+ } else {
+ moldyn_usage(argv);
+ return -1;
+ }
+ }
+
+ return 0;
+}
+
+int moldyn_log_init(t_moldyn *moldyn) {
+
+ moldyn->lvstat=0;
+ t_visual *vis;
+
+ vis=&(moldyn->vis);
+
+ 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(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;
+ }
+ if(moldyn->swrite)
+ moldyn->lvstat|=MOLDYN_LVSTAT_SAVE;
-int create_lattice(unsigned char type,int element,double mass,double lc,
+ if((moldyn->vwrite)&&(vis)) {
+ moldyn->visual=vis;
+ visual_init(vis,moldyn->vfb);
+ moldyn->lvstat|=MOLDYN_LVSTAT_VISUAL;
+ }
+
+ moldyn->lvstat|=MOLDYN_LVSTAT_INITIALIZED;
+
+ return 0;
+}
+
+int moldyn_log_shutdown(t_moldyn *moldyn) {
+
+ 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);
+
+ 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(u8 type,int element,double mass,double lc,
int a,int b,int c,t_atom **atom) {
int count;
return 0;
}
-int thermal_init(t_atom *atom,t_random *random,int count,double t) {
+int thermal_init(t_moldyn *moldyn) {
/*
* - gaussian distribution of velocities
int i;
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);
- for(i=0;i<count;i++) {
- sigma=sqrt(2.0*K_BOLTZMANN*t/atom[i].mass);
+ for(i=0;i<moldyn->count;i++) {
+ sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t/atom[i].mass);
/* x direction */
v=sigma*rand_get_gauss(random);
atom[i].v.x=v;
}
/* zero total momentum */
- v3_scale(&p_total,&p_total,1.0/count);
- for(i=0;i<count;i++) {
+ v3_scale(&p_total,&p_total,1.0/moldyn->count);
+ for(i=0;i<moldyn->count;i++) {
v3_scale(&delta,&p_total,1.0/atom[i].mass);
v3_sub(&(atom[i].v),&(atom[i].v),&delta);
}
/* velocity scaling */
- scale_velocity(atom,count,t);
+ scale_velocity(moldyn);
return 0;
}
-int scale_velocity(t_atom *atom,int count,double t) {
+int scale_velocity(t_moldyn *moldyn) {
int i;
double e,c;
+ t_atom *atom;
+
+ atom=moldyn->atom;
/*
* - velocity scaling (E = 3/2 N k T), E: kinetic energy
*/
e=0.0;
- for(i=0;i<count;i++)
+ for(i=0;i<moldyn->count;i++)
e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
- c=sqrt((2.0*e)/(3.0*count*K_BOLTZMANN*t));
- for(i=0;i<count;i++)
+ c=sqrt((2.0*e)/(3.0*moldyn->count*K_BOLTZMANN*moldyn->t));
+ for(i=0;i<moldyn->count;i++)
v3_scale(&(atom[i].v),&(atom[i].v),(1.0/c));
return 0;
double get_e_pot(t_moldyn *moldyn) {
- return(moldyn->potential(moldyn));
+ return moldyn->energy;
}
double get_total_energy(t_moldyn *moldyn) {
return p_total;
}
+double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t) {
+
+ 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);
+
+ return tau;
+}
+
+/*
+ * numerical tricks
+ */
+
+/* linked list / cell method */
+
+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->ny=moldyn->dim.y/moldyn->cutoff;
+ lc->y=moldyn->dim.y/lc->ny;
+ lc->nz=moldyn->dim.z/moldyn->cutoff;
+ lc->z=moldyn->dim.z/lc->nz;
+
+ 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]));
+
+ link_cell_update(moldyn);
+
+ return 0;
+}
+
+int link_cell_update(t_moldyn *moldyn) {
+
+ int count,i,j,k;
+ int nx,ny,nz;
+ t_atom *atom;
+ t_linkcell *lc;
+
+ atom=moldyn->atom;
+ lc=&(moldyn->lc);
+
+ nx=lc->nx;
+ ny=lc->ny;
+ nz=lc->nz;
+
+ for(i=0;i<lc->cells;i++)
+ list_destroy(&(moldyn->lc.subcell[i]));
+
+ for(count=0;count<moedyn->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;
+ list_add_immediate_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
+ &(atom[count]));
+ }
+
+ return 0;
+}
+
+int link_cell_neighbour_index(t_moldyn *moldyn,int i,int j,int k,t_list *cell) {
+
+ t_linkcell *lc;
+ int a;
+ int count1,count2;
+ int ci,cj,ck;
+ int nx,ny,nz;
+ int x,y,z;
+ u8 bx,by,bz;
+
+ lc=&(moldyn->lc);
+ nx=lc->nx;
+ ny=lc->ny;
+ nz=lc->nz;
+ count1=1;
+ count2=27;
+ a=nx*ny;
+
+
+ cell[0]=lc->subcell[i+j*nx+k*a];
+ for(ci=-1;ci<=1;ci++) {
+ bx=0;
+ x=i+ci;
+ if((x<0)||(x>=nx)) {
+ x=(x+nx)%nx;
+ bx=1;
+ }
+ for(cj=-1;cj<=1;cj++) {
+ by=0;
+ y=j+cj;
+ if((y<0)||(y>=ny)) {
+ y=(y+ny)%ny;
+ by=1;
+ }
+ for(ck=-1;ck<=1;ck++) {
+ bz=0;
+ z=k+ck;
+ if((z<0)||(z>=nz)) {
+ z=(z+nz)%nz;
+ bz=1;
+ }
+ if(!(ci|cj|ck)) continue;
+ if(bx|by|bz) {
+ cell[--count2]=lc->subcell[x+y*nx+z*a];
+ }
+ else {
+ cell[count1++]=lc->subcell[x+y*nx+z*a];
+ }
+ }
+ }
+ }
+
+ lc->dnlc=count2;
+ lc->countn=27;
+
+ return count2;
+}
+
+int link_cell_shutdown(t_moldyn *moldyn) {
+
+ int i;
+ t_linkcell *lc;
+
+ lc=&(moldyn->lc);
+
+ 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;
+}
+
+/*
+ *
+ * 'integration of newtons equation' - algorithms
+ *
+ */
+
+/* start the integration */
+
+int moldyn_integrate(t_moldyn *moldyn) {
+
+ int i,sched;
+ unsigned int e,m,s,d,v;
+ t_3dvec p;
+
+ int fd;
+ char fb[128];
+
+ /* initialize linked cell method */
+ link_cell_init(moldyn);
+
+ /* logging & visualization */
+ 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);
+
+ for(sched=0;sched<moldyn->schedule.content_count;sched++) {
+ moldyn->tau=;
+ moldyn->tau_square=;
+
+ // hier weiter ...
+
+ for(i=0;i<moldyn->time_steps;i++) {
+
+ /* integration step */
+ moldyn->integrate(moldyn);
+
+ /* check for log & visualization */
+ if(e) {
+ if(!(i%e))
+ dprintf(moldyn->efd,
+ "%.15f %.45f\n",i*moldyn->tau,
+ get_total_energy(moldyn));
+ }
+ if(m) {
+ if(!(i%m)) {
+ p=get_total_p(moldyn->atom,moldyn->count);
+ dprintf(moldyn->mfd,
+ "%.15f %.45f\n",i*moldyn->tau,
+ v3_norm(&p));
+ }
+ }
+ if(s) {
+ if(!(i%s)) {
+ snprintf(fb,128,"%s-%f-%.15f.save",moldyn->sfb,
+ moldyn->t,i*moldyn->tau);
+ fd=open(fb,O_WRONLY|O_TRUNC|O_CREAT);
+ if(fd<0) perror("[moldyn] save fd open");
+ else {
+ write(fd,moldyn,sizeof(t_moldyn));
+ write(fd,moldyn->atom,
+ moldyn->count*sizeof(t_atom));
+ }
+ close(fd);
+ }
+ }
+ if(v) {
+ if(!(i%v)) {
+ visual_atoms(moldyn->visual,i*moldyn->tau,
+ moldyn->atom,moldyn->count);
+ printf("\rsteps: %d",i);
+ fflush(stdout);
+ }
+ }
+ }
+
+ return 0;
+}
+
+/* velocity verlet */
+
+int velocity_verlet(t_moldyn *moldyn) {
+
+ int i,count;
+ double tau,tau_square;
+ t_3dvec delta;
+ t_atom *atom;
+
+ atom=moldyn->atom;
+ count=moldyn->count;
+ tau=moldyn->tau;
+ tau_square=moldyn->tau_square;
+
+ for(i=0;i<count;i++) {
+ /* new positions */
+ v3_scale(&delta,&(atom[i].v),tau);
+ 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));
+
+ /* velocities */
+ v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
+ v3_add(&(atom[i].v),&(atom[i].v),&delta);
+ }
+
+ /* 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 */
+ v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
+ v3_add(&(atom[i].v),&(atom[i].v),&delta);
+ }
+
+ return 0;
+}
+
/*
*
*
*/
+/* generic potential and force calculation */
+
+int potential_force_calc(t_moldyn *moldyn) {
+
+ int i,count;
+ t_atom *atom;
+ t_linkcell *lc;
+ t_list neighbour[27];
+ t_list *this;
+ double u;
+ u8 bc,bc3;
+ int countn,dnlc;
+
+ count=moldyn->count;
+ atom=moldyn->atom;
+ lc=&(moldyn->lc);
+
+ /* reset energy */
+ moldyn->energy=0.0;
+
+ for(i=0;i<count;i++) {
+
+ /* reset force */
+ v3_zero(&(atom[i].f));
+
+ /* single particle potential/force */
+ if(atom[i].attr&ATOM_ATTR_1BP)
+ moldyn->pf_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,
+ (atom[i].r.z+moldyn->dim.z/2)/lc->z,
+ neighbour);
+
+ countn=lc->countn;
+ dnlc=lc->dnlc;
+
+ for(j=0;j<countn;j++) {
+
+ this=&(neighbour[j]);
+ list_reset(this);
+
+ if(this->start==NULL)
+ continue;
+
+ bc=(j<dnlc)?0:1;
+
+ do {
+ btom=this->current->data;
+
+ if(btom==&(atom[i]))
+ continue;
+
+ if((btom->attr&ATOM_ATTR_2BP)&
+ (atom[i].attr&ATOM_ATTR_2BP))
+ moldyn->pf_func2b(moldyn,
+ &(atom[i]),
+ btom,
+ bc);
+
+ /* 3 body potential/force */
+
+ if(!(atom[i].attr&ATOM_ATTR_3BP)||
+ !(btom->attr&ATOM_ATTR_3BP))
+ continue;
+
+ link_cell_neighbour_index(moldyn,
+ (btom->r.x+moldyn->dim.x/2)/lc->x,
+ (btom->r.y+moldyn->dim.y/2)/lc->y,
+ (btom->r.z+moldyn->dim.z/2)/lc->z,
+ neighbourk);
+
+ for(k=0;k<lc->countn;k++) {
+
+ thisk=&(neighbourk[k]);
+ list_reset(thisk);
+
+ if(thisk->start==NULL)
+ continue;
+
+ bck=(k<lc->dnlc)?0:1;
+
+ do {
+
+ ktom=thisk->current->data;
+
+ if(!(ktom->attr&ATOM_ATTR_3BP))
+ continue;
+
+ if(ktom==btom)
+ continue;
+
+ if(ktom==&(atom[i]))
+ continue;
+
+ moldyn->pf_func3b(moldyn,&(atom[i]),btom,ktom,bck);
+
+ } while(list_next(thisk)!=\
+ L_NO_NEXT_ELEMENT);
+
+ } while(list_next(this)!=L_NO_NEXT_ELEMENT);
+ }
+ }
+ }
+
+ return 0;
+}
+
+/*
+ * periodic boundayr checking
+ */
+
+int check_per_bound(t_moldyn *moldyn,t_3dvec *a) {
+
+ double x,y,z;
+
+ x=0.5*dim->x;
+ y=0.5*dim->y;
+ z=0.5*dim->z;
+
+ if(moldyn->MOLDYN_ATTR_PBX)
+ if(a->x>=x) a->x-=dim->x;
+ else if(-a->x>x) a->x+=dim->x;
+ if(moldyn->MOLDYN_ATTR_PBY)
+ if(a->y>=y) a->y-=dim->y;
+ else if(-a->y>y) a->y+=dim->y;
+ if(moldyn->MOLDYN_ATTR_PBZ)
+ if(a->z>=z) a->z-=dim->z;
+ else if(-a->z>z) a->z+=dim->z;
+
+ return 0;
+}
+
+
+/*
+ * example potentials
+ */
+
+/* harmonic oscillator potential and force */
+
+int harmonic_oscillator(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc)) {
+
+ t_ho_params *params;
+ t_3dvec force,distance;
+ double d;
+ double sc,equi_dist;
+
+ params=moldyn->pot2b_params;
+ sc=params->spring_constant;
+ equi_dist=params->equilibrium_distance;
+
+ 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) {
+ /* energy is 1/2 (d-d0)^2, but we will add this twice ... */
+ moldyn->energy+=(0.25*sc*(d-equi_dist)*(d-equi_dist));
+ v3_scale(&force,&distance,-sc*(1.0-(equi_dist/d)));
+ v3_add(&(ai->f),&(ai->f),&force);
+ }
+
+ return 0;
+}
+
/* lennard jones potential & force for one sort of atoms */
-double potential_lennard_jones(t_moldyn *moldyn) {
+int lennard_jones(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
t_lj_params *params;
- t_atom *atom;
- int i,j;
- int count;
- t_3dvec distance;
- double d,help;
- double u;
+ t_3dvec force,distance;
+ double d,h1,h2,u;
double eps,sig6,sig12;
params=moldyn->pot_params;
- atom=moldyn->atom;
- count=moldyn->count;
- eps=params->epsilon;
+ eps=params->epsilon4;
sig6=params->sigma6;
sig12=params->sigma12;
- u=0.0;
- for(i=0;i<count;i++) {
- for(j=0;j<i;j++) {
- v3_sub(&distance,&(atom[j].r),&(atom[i].r));
- d=1.0/v3_absolute_square(&distance); /* 1/r^2 */
- help=d*d; /* 1/r^4 */
- help*=d; /* 1/r^6 */
- d=help*help; /* 1/r^12 */
- u+=eps*(sig12*d-sig6*help);
- }
+ v3_sub(&distance,&(ai->r),&(aj->r));
+ if(bc) check_per_bound(moldyn,&distance);
+ d=v3_absolute_square(&distance); /* 1/r^2 */
+ if(d<=moldyn->cutoff_square) {
+ d=1.0/d; /* 1/r^2 */
+ h2=d*d; /* 1/r^4 */
+ h2*=d; /* 1/r^6 */
+ h1=h2*h2; /* 1/r^12 */
+ /* energy is eps*..., but we will add this twice ... */
+ moldyn->energy+=0.5*eps*(sig12*h1-sig6*h2);
+ h2*=d; /* 1/r^8 */
+ h1*=d; /* 1/r^14 */
+ h2*=6*sig6;
+ h1*=12*sig12;
+ d=+h1-h2;
+ d*=eps;
+ v3_scale(&force,&distance,d);
+ v3_add(&(ai->f),&(aj->f),&force);
}
+
+ return 0;
+}
+
+/*
+ * tersoff potential & force for 2 sorts of atoms
+ */
+
+/* tersoff 1 body part */
+int tersoff_mult_1bp(t_moldyn *moldyn,t_atom *ai) {
+
+ int num;
+ t_tersoff_mult_params *params;
+ t_tersoff_exchange *exchange;
- return u;
+ num=ai->bnum;
+ params=moldyn->pot1b_params;
+ exchange=&(params->exchange);
+
+ /*
+ * simple: point constant parameters only depending on atom i to
+ * their right values
+ */
+
+ exchange->beta=&(params->beta[num]);
+ exchange->n=&(params->n[num]);
+ exchange->c=&(params->c[num]);
+ 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;
+
+ return 0;
}
+
+/* tersoff 2 body part */
+int tersoff_mult_2bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,u8 bc) {
-int force_lennard_jones(t_moldyn *moldyn) {
+ t_tersoff_mult_params *params;
+ t_tersoff_exchange *exchange;
+ t_3dvec dist_ij;
+ double d_ij;
+ double A,B,R,S,lambda;
+ int num;
- t_lj_params *params;
- int i,j,count;
- t_atom *atom;
- t_3dvec distance;
- t_3dvec force;
- double d,h1,h2;
+ params=moldyn->pot_params;
+ num=ai->bnum;
+ exchange=&(params->exchange);
+
+ exchange->run3bp=0;
+
+ /*
+ * we need: f_c, df_c, f_r, df_r
+ *
+ * therefore we need: R, S, A, lambda
+ */
+
+ v3_sub(&dist_ij,&(ai->r),&(aj->r));
+
+ if(bc) check_per_bound(moldyn,&dist_ij);
+
+ /* save for use in 3bp */ /* REALLY ?!?!?! */
+ exchange->dist_ij=dist_ij;
+
+ /* constants */
+ if(num==aj->bnum) {
+ S=params->S[num];
+ R=params->R[num];
+ A=params->A[num];
+ 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.chi=1.0;
+ }
+ else {
+ S=params->Smixed;
+ R=params->Rmixed;
+ A=params->Amixed;
+ lambda=params->lambda_m;
+ /* more constants depending of atoms i and j, needed in 3bp */
+ params->exchange.B=&(params->Bmixed);
+ params->exchange.mu=&(params->mu_m);
+ params->exchange.chi=params->chi;
+ }
+
+ d_ij=v3_norm(&dist_ij);
+
+ /* save for use in 3bp */
+ exchange->d_ij=d_ij;
+
+ if(d_ij>S)
+ return 0;
+
+ f_r=A*exp(-lamda*d_ij);
+ df_r=-lambda*f_r/d_ij;
+
+ /* f_a, df_a calc + save for 3bp use */
+ exchange->f_a=-B*exp(-mu*d_ij);
+ exchange->df_a=-mu*exchange->f_a/d_ij;
+
+ if(d_ij<R) {
+ /* f_c = 1, df_c = 0 */
+ f_c=1.0;
+ df_c=0.0;
+ v3_scale(&force,&dist_ij,df_r);
+ }
+ else {
+ s_r=S-R;
+ arg=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));
+ scale=df_c*f_r+df_r*f_c;
+ v3_scale(&force,&dist_ij,scale);
+ }
+
+ /* add forces */
+ v3_add(&(ai->f),&(ai->f),&force);
+ /* energy is 0.5 f_r f_c, but we will sum it up twice ... */
+ moldyn->energy+=(0.25*f_r*f_c);
+
+ /* save for use in 3bp */
+ exchange->f_c=f_c;
+ exchange->df_c=df_c;
+
+ /* enable the run of 3bp function */
+ exchange->run3bp=1;
+
+ return 0;
+}
+
+/* tersoff 3 body part */
+
+int tersoff_mult_3bp(t_moldyn *moldyn,t_atom *ai,t_atom *aj,t_atom *ak,u8 bc) {
+
+ t_tersoff_mult_params *params;
+ t_tersoff_exchange *exchange;
+ 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 f_c,df_c,b_ij,f_a,df_a;
+ double n,c,d,h,neta,betan,betan_1;
+ double theta,cos_theta,sin_theta;
+ int num;
- atom=moldyn->atom;
- count=moldyn->count;
params=moldyn->pot_params;
+ num=ai->bnum;
+ exchange=params->exchange;
- for(i=0;i<count;i++) {
- for(j=0;j<i;j++) {
- v3_sub(&distance,&(atom[j].r),&(atom[i].r));
- v3_per_bound(&distance,&(moldyn->dim));
- d=v3_absolute_square(&distance);
- if(d<=moldyn->cutoff_square) {
- h1=1.0/d; /* 1/r^2 */
- d=h1*h1; /* 1/r^4 */
- h2=d*d; /* 1/r^8 */
- h1*=d; /* 1/r^6 */
- h1*=h2; /* 1/r^14 */
- }
- }
+ if(!(exchange->run3bp))
+ return 0;
+
+ /*
+ * we need: f_c, d_fc, b_ij, db_ij, f_a, df_a
+ *
+ * we got f_c, df_c, f_a, df_a from 2bp calculation
+ */
+
+ d_ij=exchange->d_ij;
+ d_ij2=exchange->d_ij2;
+
+ f_a=params->exchange.f_a;
+ df_a=params->exchange.df_a;
+
+ /* d_ij is <= S, as we didn't return so far! */
+
+ /*
+ * calc of b_ij (scalar) and db_ij (vector)
+ *
+ * - for b_ij: chi, beta, f_c_ik, w(=1), c, d, h, n, cos_theta
+ *
+ * - for db_ij: d_theta, sin_theta, cos_theta, f_c_ik, df_c_ik,
+ * w_ik,
+ *
+ */
+
+
+ v3_sub(&dist_ik,&(aj->i),&(ak->r));
+ if(bc) check_per_bound(moldyn,&dist_ik);
+ d_ik=v3_norm(&dist_ik);
+
+ /* constants for f_c_ik calc */
+ if(num==ak->bnum) {
+ R=params->R[num];
+ S=params->S[num];
+ }
+ else {
+ R=params->Rmixed;
+ S=params->Smixed;
}
+ /* calc of f_c_ik */
+ if(d_ik>S)
+ return 0;
+
+ if(d_ik<R) {
+ /* f_c_ik = 1, df_c_ik = 0 */
+ f_c_ik=1.0;
+ df_c_ik=0.0;
+ }
+ else {
+ s_r=S-R;
+ arg=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));
+ }
+
+ v3_sub(&dist_jk,&(aj->r),&(ak->r));
+ if(bc) check_per_bound(moldyn,&dist_jk);
+ d_jk=v3_norm(&dist_jk);
+
+ 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);
+ 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,d1_theta);
+ 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);
+
+ /* 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 ... */
+ moldyn->energy+=(0.25*f_a*b_ij*f_c);
+
return 0;
}
projects / physik / posic.git / blobdiff