*
*/
-#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("--- 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 'T':
+ break;
+ moldyn->t=atof(argv[++i]);
+ 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) {
+
+ moldyn->lvstat=0;
+
+ 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->dwrite)
+ moldyn->lvstat|=MOLDYN_LVSTAT_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));
int moldyn_integrate(t_moldyn *moldyn) {
int i;
- int write;
+ unsigned int e,m,s,d,v;
+ unsigned char lvstat;
+ t_3dvec p;
+
+ int fd;
+ char fb[128];
- write=moldyn->write;
+ e=moldyn->ewrite;
+ m=moldyn->mwrite;
+ s=moldyn->swrite;
+ d=moldyn->dwrite;
+ v=moldyn->vwrite;
+
+ if(!(lvstat&MOLDYN_LVSTAT_INITIALIZED)) {
+ printf("[moldyn] warning, lv system not initialized\n");
+ return -1;
+ }
/* calculate initial forces */
moldyn->force(moldyn);
/* integration step */
moldyn->integrate(moldyn);
- /* check for visualiziation */
- if(!(i%write)) {
- visual_atoms(moldyn->visual,i*moldyn->tau,
- moldyn->atom,moldyn->count);
- printf("finished %d / %d\n",i,moldyn->time_steps);
+ /* 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);
}
}
} t_atom;
typedef struct s_moldyn {
+ /* atoms, amount, dimensions */
int count;
t_atom *atom;
+ t_3dvec dim;
+ /* potential, force & parameters */
double (*potential)(struct s_moldyn *moldyn);
- void *pot_params;
int (*force)(struct s_moldyn *moldyn);
+ void *pot_params;
double cutoff;
double cutoff_square;
- t_3dvec dim;
+ /* temperature */
+ double t;
+ /* integration of newtons equations */
int (*integrate)(struct s_moldyn *moldyn);
int time_steps;
double tau;
+ /* logging & visualization */
+ unsigned char lvstat;
+ unsigned int ewrite;
+ char efb[64];
+ int efd;
+ unsigned int mwrite;
+ char mfb[64];
+ int mfd;
+ unsigned int swrite;
+ char sfb[64];
+ int sfd;
+ unsigned int dwrite;
+ char dfb[64];
+ int dfd;
+ unsigned int vwrite;
void *visual;
- int write;
+ /* moldyn general status */
unsigned char status;
} t_moldyn;
/* general defines */
+#define MOLDYN_LVSTAT_TOTAL_E 0x01
+#define MOLDYN_LVSTAT_TOTAL_M 0x02
+#define MOLDYN_LVSTAT_SAVE 0x04
+#define MOLDYN_LVSTAT_DUMP 0x08
+#define MOLDYN_LVSTAT_VISUAL 0x10
+#define MOLDYN_LVSTAT_INITIALIZED 0x80
+
#define MOLDYN_STAT_POTENTIAL 0x01
#define MOLDYN_STAT_FORCE 0x02
+#define MOLDYN_TEMP 273.0
+#define MOLDYN_TAU 1.0e-15
+#define MOLDYN_RUNS 1000000
+
/* phsical values */
#define K_BOLTZMANN 1.3807e-27 /* Nm/K */
/* function prototypes */
+int moldyn_usage(char **argv);
+int moldyn_parse_argv(t_moldyn *moldyn,int argc,char **argv);
+int moldyn_log_init(t_moldyn *moldyn);
+
int create_lattice(unsigned char type,int element,double mass,double lc,
int a,int b,int c,t_atom **atom);
int destroy_lattice(t_atom *atom);
-int thermal_init(t_atom *atom,t_random *random,int count,double t);
-int scale_velocity(t_atom *atom,int count,double t);
+int thermal_init(t_moldyn *moldyn,t_random *random,int count);
+int scale_velocity(t_moldyn *moldyn,int count);
double get_e_kin(t_atom *atom,int count);
double get_e_pot(t_moldyn *moldyn);
double get_total_energy(t_moldyn *moldyn);
int count;
t_lj_params lj;
- t_ho_params ho;
char fb[32]="saves/lj_test";
b=LEN_Y;
c=LEN_Z;
- vis.dim.x=a*LC_SI;
- vis.dim.y=b*LC_SI;
- vis.dim.z=c*LC_SI;
+ /* set for 'bounding atoms' */
+ //vis.dim.x=a*LC_SI;
+ //vis.dim.y=b*LC_SI;
+ //vis.dim.z=c*LC_SI;
t=TEMPERATURE;
printf("placing silicon atoms ... ");
- //count=create_lattice(DIAMOND,Si,M_SI,LC_SI,a,b,c,&si);
- //printf("(%d) ok!\n",count);
+ count=create_lattice(DIAMOND,SI,M_SI,LC_SI,a,b,c,&si);
+ printf("(%d) ok!\n",count);
+
+ /* testing purpose
count=2;
si=malloc(2*sizeof(t_atom));
si[0].r.x=0.16e-9;
si[1].r.z=0;
si[1].element=SI;
si[1].mass=M_SI;
+ */
printf("setting thermal fluctuations\n");
- //thermal_init(si,&random,count,t);
- v3_zero(&(si[0].v));
- v3_zero(&(si[1].v));
+ thermal_init(si,&random,count,t);
+ //v3_zero(&(si[0].v));
+ //v3_zero(&(si[1].v));
/* check kinetic energy */
md.count=count;
md.atom=si;
md.potential=potential_lennard_jones;
- //md.potential=potential_harmonic_oscillator;
md.force=force_lennard_jones;
- //md.force=force_harmonic_oscillator;
- //md.cutoff_square=((LC_SI/4.0)*(LC_SI/4.0));
- md.cutoff=(0.4e-9);
- md.cutoff_square=(0.6e-9*0.6e-9);
+ md.cutoff=R_CUTOFF;
+ md.cutoff_square=(R_CUTOFF*R_CUTOFF);
md.pot_params=&lj;
- //md.pot_params=&ho;
md.integrate=velocity_verlet;
md.time_steps=RUNS;
md.tau=TAU;
lj.sigma12=lj.sigma6*lj.sigma6;
lj.epsilon=LJ_EPSILON_SI;
- ho.equilibrium_distance=0.3e-9;
- ho.spring_constant=1.0e-9;
-
u=get_e_pot(&md);
printf("potential energy: %.40f [J]\n",u);
rand_close(&random);
-
- //printf("starting velocity verlet: ");
- //fflush(stdout);
-
- //for(runs=0;runs<RUNS;runs++) {
-
- /*
- * velocity verlet
- *
- * r(t+h) = r(t) + h * dr/dt|t + h^2/2m * F(t)
- * dr/dt|(t+h) = dr/dt|t + h/2m * (F(t) + F(t+h))
- *
- */
- //for(i=0;i<amount_si;i++) {
-// /* calculation of new positions r(t+h) */
-// si[i].x+=si[i].vx*tau;
-// si[i].y+=si[i].vy*tau;
-// si[i].z+=si[i].vz*tau;
-// si[i].x+=(tau2*si[i].fx/m2);
-// if(si[i].x>LX) si[i].x-=LEN_X;
-// else if(si[i].x<-LX) si[i].x+=LEN_X;
-// si[i].y+=(tau2*si[i].fy/m2);
-// if(si[i].y>LY) si[i].y-=LEN_Y;
-// else if(si[i].y<-LY) si[i].y+=LEN_Y;
-// si[i].z+=(tau2*si[i].fz/m2);
-// if(si[i].z>LZ) si[i].z-=LEN_Z;
-// else if(si[i].z<-LZ) si[i].z+=LEN_Z;
-// /* calculation of velocities v(t+h/2) */
-// si[i].vx+=(tau*si[i].fx/m2);
-// si[i].vy+=(tau*si[i].fy/m2);
-// si[i].vz+=(tau*si[i].fz/m2);
-// /* reset of forces */
-// si[i].fx=.0;
-// si[i].fy=.0;
-// si[i].fz=.0;
-// }
-// for(i=0;i<amount_si;i++) {
-// /* calculation of forces at new positions r(t+h) */
-// for(j=0;j<i;j++) {
-// deltax=si[i].x-si[j].x;
-// if(deltax>LX) deltax-=LEN_X;
-// else if(-deltax>LX) deltax+=LEN_X;
-// deltax2=deltax*deltax;
-// deltay=si[i].y-si[j].y;
-// if(deltay>LY) deltay-=LEN_Y;
-// else if(-deltay>LY) deltay+=LEN_Y;
-// deltay2=deltay*deltay;
-// deltaz=si[i].z-si[j].z;
-// if(deltaz>LZ) deltaz-=LEN_Z;
-// else if(-deltaz>LZ) deltaz+=LEN_Z;
-// deltaz2=deltaz*deltaz;
-// distance=deltax2+deltay2+deltaz2;
-// if(distance<=R2_CUTOFF) {
-// tmp=1.0/distance; // 1/r^2
-// lj1=tmp; // 1/r^2
-// tmp*=tmp; // 1/r^4
-// lj1*=tmp; // 1/r^6
-// tmp*=tmp; // 1/r^8
-// lj2=tmp; // 1/r^8
-// lj1*=tmp; // 1/r^14
-// lj1*=LJ_SIGMA_12;
-// lj2*=LJ_SIGMA_06;
-// lj=-2*lj1+lj2;
-// si[i].fx-=lj*deltax;
-// si[i].fy-=lj*deltay;
-// si[i].fz-=lj*deltaz;
-// si[j].fx+=lj*deltax;
-// si[j].fy+=lj*deltay;
-// si[j].fz+=lj*deltaz;
-// }
-// }
-// }
-// for(i=0;i<amount_si;i++) {
-// /* calculation of new velocities v(t+h) */
-// si[i].vx+=(tau*si[i].fx/m2);
-// si[i].vy+=(tau*si[i].fy/m2);
-// si[i].vz+=(tau*si[i].fz/m2);
-// }
-//
-// if(!(runs%150)) {
-//
-// /* rasmol script & xyz file */
-// sprintf(xyz,"./saves/si-%.15f.xyz",time);
-// sprintf(ppm,"./video/si-%.15f.ppm",time);
-// fd1=open(xyz,O_WRONLY|O_CREAT|O_TRUNC);
-// if(fd1<0) {
-// perror("rasmol xyz file open");
-// return -1;
-// }
-// dprintf(fd2,"load xyz %s\n",xyz);
-// dprintf(fd2,"spacefill 200\n");
-// dprintf(fd2,"rotate x 11\n");
-// dprintf(fd2,"rotate y 13\n");
-// dprintf(fd2,"set ambient 20\n");
-// dprintf(fd2,"set specular on\n");
-// dprintf(fd2,"zoom 400\n");
-// dprintf(fd2,"write ppm %s\n",ppm);
-// dprintf(fd2,"zap\n");
-// dprintf(fd1,"%d\nsilicon\n",amount_si+9);
-// for(i=0;i<amount_si;i++)
-// dprintf(fd1,"Si %f %f %f %f\n",
-// si[i].x,si[i].y,si[i].z,time);
-// dprintf(fd1,"H 0.0 0.0 0.0 %f\n",time);
-// dprintf(fd1,"He %f %f %f %f\n",LX,LY,LZ,time);
-// dprintf(fd1,"He %f %f %f %f\n",-LX,LY,LZ,time);
-// dprintf(fd1,"He %f %f %f %f\n",LX,-LY,LZ,time);
-// dprintf(fd1,"He %f %f %f %f\n",LX,LY,-LZ,time);
-// dprintf(fd1,"He %f %f %f %f\n",-LX,-LY,LZ,time);
-// dprintf(fd1,"He %f %f %f %f\n",-LX,LY,-LZ,time);
-// dprintf(fd1,"He %f %f %f %f\n",LX,-LY,-LZ,time);
-// dprintf(fd1,"He %f %f %f %f\n",-LX,-LY,-LZ,time);
-// close(fd1);
-//
-// }
-//
-// /* increase time */
-// time+=tau;
-// printf(".");
-// fflush(stdout);
-//
-// }
-//
-// printf(" done\n");
-// close(fd2);
-// free(si);
-//
-
return 0;
}
projects / physik / posic.git / commitdiff