*
*/
-#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("-R <runs> (%d)\n",MOLDYN_RUNS);
+ 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;
+
+ /* 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 'D':
+ moldyn->dwrite=atoi(argv[++i]);
+ strncpy(moldyn->dfb,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 'R':
+ moldyn->time_steps=atoi(argv[++i]);
+ break;
+ 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,void *v) {
+
+ moldyn->lvstat=0;
+ t_visual *vis;
+
+ vis=v;
+
+ 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;
+
+ if(moldyn->dwrite) {
+ moldyn->dfd=open(moldyn->dfb,O_WRONLY|O_CREAT|O_TRUNC);
+ if(moldyn->dfd<0) {
+ perror("[moldyn] dfd open");
+ return moldyn->dfd;
+ }
+ write(moldyn->dfd,moldyn,sizeof(t_moldyn));
+ moldyn->lvstat|=MOLDYN_LVSTAT_DUMP;
+ }
+
+ 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_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 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_atom *atom,t_random *random,int count,double t) {
+int thermal_init(t_moldyn *moldyn,t_random *random,int count) {
/*
* - gaussian distribution of velocities
int i;
double v,sigma;
t_3dvec p_total,delta;
+ t_atom *atom;
+
+ atom=moldyn->atom;
/* gaussian distribution of velocities */
v3_zero(&p_total);
for(i=0;i<count;i++) {
- sigma=sqrt(2.0*K_BOLTZMANN*t/atom[i].mass);
+ sigma=sqrt(2.0*K_BOLTZMANN*moldyn->t/atom[i].mass);
/* x direction */
v=sigma*rand_get_gauss(random);
atom[i].v.x=v;
}
/* velocity scaling */
- scale_velocity(atom,count,t);
+ scale_velocity(moldyn,count);
return 0;
}
-int scale_velocity(t_atom *atom,int count,double t) {
+int scale_velocity(t_moldyn *moldyn,int count) {
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++)
e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
- c=sqrt((2.0*e)/(3.0*count*K_BOLTZMANN*t));
+ c=sqrt((2.0*e)/(3.0*count*K_BOLTZMANN*moldyn->t));
for(i=0;i<count;i++)
v3_scale(&(atom[i].v),&(atom[i].v),(1.0/c));
return tau;
}
+/*
+ * numerical tricks
+ */
+
+/* verlet list */
+
+int verlet_list_init(t_moldyn *moldyn) {
+
+ int i,fd;
+
+ fd=open("/dev/null",O_WRONLY);
+
+ for(i=0;i<moldyn->count;i++)
+ list_init(&(moldyn->atom[i].verlet),fd);
+
+ moldyn->r_verlet=1.1*moldyn->cutoff;
+ /* +moldyn->tau*\
+ sqrt(3.0*K_BOLTZMANN*moldyn->t/moldyn->atom[0].mass); */
+
+ printf("debug: r verlet = %.15f\n",moldyn->r_verlet);
+ printf(" r cutoff = %.15f\n",moldyn->cutoff);
+ printf(" dim = %.15f\n",moldyn->dim.x);
+
+ /* make sure to update the list in the beginning */
+ moldyn->dr_max1=moldyn->r_verlet;
+ moldyn->dr_max2=moldyn->r_verlet;
+
+ return 0;
+}
+
+int link_cell_init(t_moldyn *moldyn) {
+
+ t_linkcell *lc;
+
+ lc=&(moldyn->lc);
+
+ /* 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->subcell=malloc(lc->nx*lc->ny*lc->nz*sizeof(t_list));
+
+ link_cell_update(moldyn);
+
+ return 0;
+}
+
+int verlet_list_update(t_moldyn *moldyn) {
+
+ int i,j;
+ t_3dvec d;
+ t_atom *atom;
+
+ atom=moldyn->atom;
+
+ puts("debug: list update start");
+
+ for(i=0;i<moldyn->count;i++) {
+ list_destroy(&(atom[i].verlet));
+ for(j=0;j<moldyn->count;j++) {
+ if(i!=j) {
+ v3_sub(&d,&(atom[i].r),&(atom[j].r));
+ v3_per_bound(&d,&(moldyn->dim));
+ if(v3_norm(&d)<=moldyn->r_verlet)
+ list_add_immediate_ptr(&(atom[i].verlet),&(atom[j]));
+ }
+ }
+ }
+
+ moldyn->dr_max1=0.0;
+ moldyn->dr_max2=0.0;
+
+ puts("debug: list update end");
+
+ return 0;
+}
+
+int link_cell_update(t_moldyn *moldyn) {
+
+ int count,i,j,k;
+ int nx,ny,nz;
+ t_atom *atom;
+
+ atom=moldyn->atom;
+ nx=moldyn->lc.nx; ny=moldyn->lc.ny; nz=moldyn->lc.nz;
+
+ for(i=0;i<nx*ny*nz;i++)
+ list_destroy(&(moldyn->lc.subcell[i]));
+
+ for(count=0;count<moldyn->count;count++) {
+ for(i=0;i<nx;i++) {
+ if((atom[count].r.x>=i*moldyn->dim.x) && \
+ (atom[count].r.x<(i+1)*moldyn->dim.x))
+ break;
+ }
+ for(j=0;j<ny;j++) {
+ if((atom[count].r.y>=j*moldyn->dim.y) && \
+ (atom[count].r.y<(j+1)*moldyn->dim.y))
+ break;
+ }
+ for(k=0;k<nz;k++) {
+ if((atom[count].r.z>=k*moldyn->dim.z) && \
+ (atom[count].r.z<(k+1)*moldyn->dim.z))
+ break;
+ }
+ list_add_immediate_ptr(&(moldyn->lc.subcell[i+j*nx+k*nx*ny]),
+ &(atom[count]));
+ }
+
+ return 0;
+}
+
+int verlet_list_shutdown(t_moldyn *moldyn) {
+
+ int i;
+
+ for(i=0;i<moldyn->count;i++)
+ list_shutdown(&(moldyn->atom[i].verlet));
+
+ return 0;
+}
+
+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]));
+
+ return 0;
+}
/*
*
int moldyn_integrate(t_moldyn *moldyn) {
int i;
- int write;
+ unsigned int e,m,s,d,v;
+ t_3dvec p;
+ double rlc;
+
+ int fd;
+ char fb[128];
- write=moldyn->write;
+ /* logging & visualization */
+ e=moldyn->ewrite;
+ m=moldyn->mwrite;
+ s=moldyn->swrite;
+ d=moldyn->dwrite;
+ v=moldyn->vwrite;
+
+ /* verlet list */
+ rlc=moldyn->r_verlet-moldyn->cutoff;
+
+ if(!(moldyn->lvstat&MOLDYN_LVSTAT_INITIALIZED)) {
+ printf("[moldyn] warning, lv system not initialized\n");
+ return -1;
+ }
+
+ /* create the neighbour list */
+ //verlet_list_update(moldyn);
+ link_cell_update(moldyn);
/* calculate initial forces */
moldyn->force(moldyn);
for(i=0;i<moldyn->time_steps;i++) {
+ /* show runs */
+ printf(".");
+
+ /* neighbour list update */
+ link_cell_update(moldyn);
+ //if(moldyn->dr_max1+moldyn->dr_max2>rlc) {
+ // printf("\n");
+ // verlet_list_update(moldyn);
+ //}
+
/* integration step */
moldyn->integrate(moldyn);
- /* check for visualiziation */
- if(!(i%write)) {
- visual_atoms(moldyn->visual,i*moldyn->tau,
- moldyn->atom,moldyn->count);
+ /* check for log & visualiziation */
+ 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));
+ }
+ }
+ }
+ if(d) {
+ if(!(i%d))
+ write(moldyn->dfd,moldyn->atom,
+ moldyn->count*sizeof(t_atom));
+
+ }
+ if(v) {
+ if(!(i%v))
+ visual_atoms(moldyn->visual,i*moldyn->tau,
+ moldyn->atom,moldyn->count);
}
}
int velocity_verlet(t_moldyn *moldyn) {
int i,count;
- double tau,tau_square;
+ double tau,tau_square,dr;
t_3dvec delta;
t_atom *atom;
/* new positions */
v3_scale(&delta,&(atom[i].v),tau);
v3_add(&(atom[i].r),&(atom[i].r),&delta);
+ v3_add(&(atom[i].dr),&(atom[i].dr),&delta);
v3_scale(&delta,&(atom[i].f),0.5*tau_square/atom[i].mass);
v3_add(&(atom[i].r),&(atom[i].r),&delta);
+ v3_add(&(atom[i].dr),&(atom[i].dr),&delta);
v3_per_bound(&(atom[i].r),&(moldyn->dim));
+ /* set maximum dr (possible list update) [obsolete] */
+ //dr=v3_norm(&(atom[i].dr));
+ //if(dr>moldyn->dr_max1) {
+ // moldyn->dr_max2=moldyn->dr_max1;
+ // moldyn->dr_max1=dr;
+ //}
+ //else if(dr>moldyn->dr_max2) moldyn->dr_max2=dr;
+
/* velocities */
v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
v3_add(&(atom[i].v),&(atom[i].v),&delta);
d=v3_norm(&distance);
if(d<=moldyn->cutoff) {
v3_scale(&force,&distance,
- (-sc*(1.0-(equi_dist/d))));
+ -sc*(1.0-(equi_dist/d)));
v3_add(&(atom[i].f),&(atom[i].f),&force);
v3_sub(&(atom[j].f),&(atom[j].f),&force);
}
double potential_lennard_jones(t_moldyn *moldyn) {
t_lj_params *params;
- t_atom *atom;
- int i,j;
+ t_atom *atom,*btom;
+ t_linkcell *lc;
+ int i;
int count;
t_3dvec distance;
double d,help;
double u;
double eps,sig6,sig12;
+ int i,j,k;
+ int ni,nj,nk;
params=moldyn->pot_params;
atom=moldyn->atom;
+ lc=&(moldyn->lc);
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));
+ /* verlet list [obsolete] */
+ //list_reset(&(atom[i].verlet));
+ //if(atom[i].verlet.current==NULL) continue;
+
+ /* determine cell */
+ ni=atom[i].r.x/lc->x;
+ nj=atom[i].r.y/lc->y;
+ nk=atom[i].r.z/lc->z;
+
+ while(1) {
+ btom=atom[i].verlet.current->data;
+ v3_sub(&distance,&(atom[i].r),&(btom->r));
+ v3_per_bound(&distance,&(moldyn->dim));
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);
+ if(list_next(&(atom[i].verlet))==L_NO_NEXT_ELEMENT)
+ break;
}
}
int force_lennard_jones(t_moldyn *moldyn) {
t_lj_params *params;
- int i,j,count;
- t_atom *atom;
+ int i,count;
+ t_atom *atom,*btom;
t_3dvec distance;
t_3dvec force;
double d,h1,h2;
atom=moldyn->atom;
count=moldyn->count;
params=moldyn->pot_params;
- eps=params->epsilon;
- sig6=params->sigma6;
- sig12=params->sigma12;
+ eps=params->epsilon4;
+ sig6=6*params->sigma6;
+ sig12=12*params->sigma12;
for(i=0;i<count;i++) v3_zero(&(atom[i].f));
for(i=0;i<count;i++) {
- for(j=0;j<i;j++) {
- v3_sub(&distance,&(atom[j].r),&(atom[i].r));
+ list_reset(&(atom[i].verlet));
+ if(atom[i].verlet.current==NULL) continue;
+ while(1) {
+ btom=atom[i].verlet.current->data;
+ v3_sub(&distance,&(atom[i].r),&(btom->r));
v3_per_bound(&distance,&(moldyn->dim));
d=v3_absolute_square(&distance);
if(d<=moldyn->cutoff_square) {
h1*=h2; /* 1/r^14 */
h1*=sig12;
h2*=sig6;
- d=12.0*h1-6.0*h2;
+ /* actually there would be a '-', *
+ * but f=-d/dr potential */
+ d=h1+h2;
d*=eps;
v3_scale(&force,&distance,d);
- v3_add(&(atom[j].f),&(atom[j].f),&force);
- v3_sub(&(atom[i].f),&(atom[i].f),&force);
+ v3_add(&(atom[i].f),&(atom[i].f),&force);
+ //v3_sub(&(atom[j].f),&(atom[j].f),&force);
}
+ if(list_next(&(atom[i].verlet))==L_NO_NEXT_ELEMENT)
+ break;
}
}