*
*/
-#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"
+
+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] (%f)\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) {
ret=diamond_init(a,b,c,lc,*atom,&origin);
break;
default:
- ret=-1;
printf("unknown lattice type (%02x)\n",type);
+ return -1;
}
/* debug */
printf("ok, there is something wrong ...\n");
printf("calculated -> %d atoms\n",count);
printf("created -> %d atoms\n",ret);
+ return -1;
}
while(count) {
return ret;
}
+int destroy_lattice(t_atom *atom) {
+
+ if(atom) free(atom);
+
+ return 0;
+}
+
+int thermal_init(t_moldyn *moldyn,t_random *random,int count) {
+
+ /*
+ * - gaussian distribution of velocities
+ * - zero total momentum
+ * - velocity scaling (E = 3/2 N k T), E: kinetic energy
+ */
+
+ 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*moldyn->t/atom[i].mass);
+ /* x direction */
+ v=sigma*rand_get_gauss(random);
+ atom[i].v.x=v;
+ p_total.x+=atom[i].mass*v;
+ /* y direction */
+ v=sigma*rand_get_gauss(random);
+ atom[i].v.y=v;
+ p_total.y+=atom[i].mass*v;
+ /* z direction */
+ v=sigma*rand_get_gauss(random);
+ atom[i].v.z=v;
+ p_total.z+=atom[i].mass*v;
+ }
+
+ /* zero total momentum */
+ v3_scale(&p_total,&p_total,1.0/count);
+ for(i=0;i<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(moldyn,count);
+
+ return 0;
+}
+
+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*moldyn->t));
+ for(i=0;i<count;i++)
+ v3_scale(&(atom[i].v),&(atom[i].v),(1.0/c));
+
+ return 0;
+}
+
+double get_e_kin(t_atom *atom,int count) {
+
+ int i;
+ double e;
+
+ e=0.0;
+
+ for(i=0;i<count;i++) {
+ e+=0.5*atom[i].mass*v3_absolute_square(&(atom[i].v));
+ }
+
+ return e;
+}
+
+double get_e_pot(t_moldyn *moldyn) {
+
+ return(moldyn->potential(moldyn));
+}
+
+double get_total_energy(t_moldyn *moldyn) {
+
+ double e;
+
+ e=get_e_kin(moldyn->atom,moldyn->count);
+ e+=get_e_pot(moldyn);
+
+ return e;
+}
+
+t_3dvec get_total_p(t_atom *atom, int count) {
+
+ t_3dvec p,p_total;
+ int i;
+
+ v3_zero(&p_total);
+ for(i=0;i<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 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;
+}
+
+
+/*
+ *
+ * 'integration of newtons equation' - algorithms
+ *
+ */
+
+/* start the integration */
+
+int moldyn_integrate(t_moldyn *moldyn) {
+
+ int i;
+ unsigned int e,m,s,d,v;
+ t_3dvec p;
+
+ int fd;
+ char fb[128];
+
+ 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;
+ }
+
+ /* calculate initial forces */
+ moldyn->force(moldyn);
+
+ for(i=0;i<moldyn->time_steps;i++) {
+ /* integration step */
+ moldyn->integrate(moldyn);
+
+ /* 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);
+ }
+ }
+
+ 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=tau*tau;
+
+ 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);
+ }
+
+ /* forces depending on chosen potential */
+ moldyn->force(moldyn);
+
+ 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;
+}
+
+
+/*
+ *
+ * potentials & corresponding forces
+ *
+ */
+
+/* harmonic oscillator potential and force */
+
+double potential_harmonic_oscillator(t_moldyn *moldyn) {
+
+ t_ho_params *params;
+ t_atom *atom;
+ int i,j;
+ int count;
+ t_3dvec distance;
+ double d,u;
+ double sc,equi_dist;
+
+ params=moldyn->pot_params;
+ atom=moldyn->atom;
+ sc=params->spring_constant;
+ equi_dist=params->equilibrium_distance;
+ count=moldyn->count;
+
+ u=0.0;
+ for(i=0;i<count;i++) {
+ for(j=0;j<i;j++) {
+ v3_sub(&distance,&(atom[i].r),&(atom[j].r));
+ d=v3_norm(&distance);
+ u+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
+ }
+ }
+
+ return u;
+}
+
+int force_harmonic_oscillator(t_moldyn *moldyn) {
+
+ t_ho_params *params;
+ int i,j,count;
+ t_atom *atom;
+ t_3dvec distance;
+ t_3dvec force;
+ double d;
+ double sc,equi_dist;
+
+ atom=moldyn->atom;
+ count=moldyn->count;
+ params=moldyn->pot_params;
+ sc=params->spring_constant;
+ equi_dist=params->equilibrium_distance;
+
+ 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[i].r),&(atom[j].r));
+ v3_per_bound(&distance,&(moldyn->dim));
+ d=v3_norm(&distance);
+ if(d<=moldyn->cutoff) {
+ v3_scale(&force,&distance,
+ (-sc*(1.0-(equi_dist/d))));
+ v3_add(&(atom[i].f),&(atom[i].f),&force);
+ v3_sub(&(atom[j].f),&(atom[j].f),&force);
+ }
+ }
+ }
+
+ return 0;
+}
+
+
+/* lennard jones potential & force for one sort of atoms */
+
+double potential_lennard_jones(t_moldyn *moldyn) {
+
+ t_lj_params *params;
+ t_atom *atom;
+ int i,j;
+ int count;
+ t_3dvec distance;
+ double d,help;
+ double u;
+ double eps,sig6,sig12;
+
+ params=moldyn->pot_params;
+ atom=moldyn->atom;
+ count=moldyn->count;
+ eps=params->epsilon;
+ 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);
+ }
+ }
+
+ return u;
+}
+
+int force_lennard_jones(t_moldyn *moldyn) {
+
+ t_lj_params *params;
+ int i,j,count;
+ t_atom *atom;
+ t_3dvec distance;
+ t_3dvec force;
+ double d,h1,h2;
+ double eps,sig6,sig12;
+
+ atom=moldyn->atom;
+ count=moldyn->count;
+ params=moldyn->pot_params;
+ eps=params->epsilon;
+ sig6=params->sigma6;
+ sig12=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));
+ 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 */
+ h1*=sig12;
+ h2*=sig6;
+ d=12.0*h1-6.0*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);
+ }
+ }
+ }
+
+ return 0;
+}
+
projects / physik / posic.git / blobdiff