-#!/bin/bash
-
rm -f saves/* video/*
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;
+}
+
/*
*
int moldyn_integrate(t_moldyn *moldyn) {
int i;
+ int write;
+
+ write=moldyn->write;
/* calculate initial forces */
moldyn->force(moldyn);
moldyn->integrate(moldyn);
/* check for visualiziation */
- // to be continued ...
- if(!(i%1)) {
+ if(!(i%write)) {
visual_atoms(moldyn->visual,i*moldyn->tau,
moldyn->atom,moldyn->count);
}
/* velocities */
v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
- v3_add(&(atom[i].r),&(atom[i].r),&delta);
+ v3_add(&(atom[i].v),&(atom[i].v),&delta);
}
/* forces depending on chosen potential */
*
*/
+/* 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_3dvec f; /* forces */
int element; /* number of element in pse */
double mass; /* atom mass */
+ //t_list vicinity /* verlet neighbour list */
} t_atom;
typedef struct s_moldyn {
double (*potential)(struct s_moldyn *moldyn);
void *pot_params;
int (*force)(struct s_moldyn *moldyn);
+ double cutoff;
double cutoff_square;
t_3dvec dim;
int (*integrate)(struct s_moldyn *moldyn);
int time_steps;
double tau;
void *visual;
+ int write;
unsigned char status;
} t_moldyn;
+typedef struct s_ho_params {
+ double spring_constant;
+ double equilibrium_distance;
+} t_ho_params;
+
typedef struct s_lj_params {
double sigma6;
double sigma12;
/* phsical values */
-//#define K_BOLTZMANN 1.3807E-23
-#define K_BOLTZMANN 1.0
+#define K_BOLTZMANN 1.3807e-27 /* Nm/K */
+#define AMU 1.660540e-27 /* kg */
#define FCC 0x01
#define DIAMOND 0x02
#define C 0x06
-#define M_C 6.0
+#define M_C (12.011*AMU)
-#define Si 0x0e
-#define M_SI 14.0
-#define LC_SI 5.43105
+#define SI 0x0e
+#define LC_SI 0.543105e-9 /* m */
+#define M_SI (28.085*AMU) /* kg */
+#define LJ_SIGMA_SI ((0.25*sqrt(3.0)*LC_SI)/1.122462) /* m */
+#define LJ_EPSILON_SI (2.1678*1.60e-19) /* Nm */
/* function prototypes */
double get_total_energy(t_moldyn *moldyn);
t_3dvec get_total_p(t_atom *atom,int count);
+double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t);
+
int moldyn_integrate(t_moldyn *moldyn);
int velocity_verlet(t_moldyn *moldyn);
+double potential_harmonic_oscillator(t_moldyn *moldyn);
+int force_harmonic_oscillator(t_moldyn *moldyn);
double potential_lennard_jones(t_moldyn *moldyn);
int force_lennard_jones(t_moldyn *moldyn);
-#!/bin/bash
-
chmod 640 saves/*
/*
* posic.c - precipitation process of silicon carbide in silicon
*
- * author: Frank Zirkelbach <hackbard@hackdaworld.org>
+ * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
*
*/
+
+#include <math.h>
#include "moldyn.h"
#include "math/math.h"
int count;
t_lj_params lj;
+ t_ho_params ho;
- char fb[32]="saves/fcc_test";
+ char fb[32]="saves/lj_test";
/* init */
b=LEN_Y;
c=LEN_Z;
+ vis.dim.x=a*LC_SI;
+ vis.dim.y=b*LC_SI;
+ vis.dim.z=c*LC_SI;
+
t=TEMPERATURE;
printf("placing silicon atoms ... ");
//printf("(%d) ok!\n",count);
count=2;
si=malloc(2*sizeof(t_atom));
- si[0].r.x=2.0;
+ si[0].r.x=0.16e-9;
si[0].r.y=0;
si[0].r.z=0;
- si[0].element=Si;
- si[0].mass=14.0;
- si[1].r.x=-2.0;
+ si[0].element=SI;
+ si[0].mass=M_SI;
+ si[1].r.x=-0.16e-9;
si[1].r.y=0;
si[1].r.z=0;
- si[1].element=Si;
- si[1].mass=14.0;
+ si[1].element=SI;
+ si[1].mass=M_SI;
printf("setting thermal fluctuations\n");
//thermal_init(si,&random,count,t);
/* check kinetic energy */
e=get_e_kin(si,count);
- printf("kinetic energy: %f\n",e);
- printf("3/2 N k T = %f\n",1.5*count*K_BOLTZMANN*t);
+ printf("kinetic energy: %.40f [J]\n",e);
+ printf("3/2 N k T = %.40f [J]\n",1.5*count*K_BOLTZMANN*t);
/* check total momentum */
p=get_total_p(si,count);
- printf("total momentum: %f\n",v3_norm(&p));
+ printf("total momentum: %.30f [Ns]\n",v3_norm(&p));
/* check potential 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_square=36.0;
+ md.cutoff=(0.4e-9);
+ md.cutoff_square=(0.6e-9*0.6e-9);
md.pot_params=&lj;
+ //md.pot_params=&ho;
md.integrate=velocity_verlet;
md.time_steps=RUNS;
md.tau=TAU;
md.status=0;
md.visual=&vis;
+ md.write=WRITE_FILE;
- lj.sigma6=3.0/16.0*LC_SI*LC_SI;
+ lj.sigma6=LJ_SIGMA_SI*LJ_SIGMA_SI;
help=lj.sigma6*lj.sigma6;
lj.sigma6*=help;
lj.sigma12=lj.sigma6*lj.sigma6;
- lj.epsilon=10000;
+ 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: %f\n",u);
- printf("total energy (1): %f\n",e+u);
- printf("total energy (2): %f\n",get_total_energy(&md));
+ printf("potential energy: %.40f [J]\n",u);
+ printf("total energy (1): %.40f [J]\n",e+u);
+ printf("total energy (2): %.40f [J]\n",get_total_energy(&md));
md.dim.x=a*LC_SI;
md.dim.y=b*LC_SI;
md.dim.z=c*LC_SI;
+ printf("estimated accurate time step: %.30f [s]\n",
+ estimate_time_step(&md,3.0,t));
+
+
/*
* let's do the actual md algorithm now
*
* integration of newtons equations
*/
- /* visualize */
- //visual_atoms(&vis,0.0,si,count);
-
-
moldyn_integrate(&md);
- printf("total energy (after integration): %f\n",get_total_energy(&md));
+ printf("total energy (after integration): %.40f [J]\n",
+ get_total_energy(&md));
/* close */
#ifndef POSIC_H
#define POSIC_H
-#define RUNS 200
-#define TAU 0.001
+#define RUNS 10000000
+#define TAU 0.000000000000001
+#define WRITE_FILE 100000
#define TEMPERATURE 273.0
-#define LEN_X 15
-#define LEN_Y 15
-#define LEN_Z 15
+#define LEN_X 3
+#define LEN_Y 3
+#define LEN_Z 3
-#define R_CUTOFF 20
+#define R_CUTOFF (0.25*LEN_Z)
#endif
return -1;
}
+ memset(&(v->dim),0,sizeof(t_3dvec));
+
return 0;
}
int i,fd;
char file[128+64];
+ t_3dvec dim;
+
+ dim.x=10e9*v->dim.x;
+ dim.y=10e9*v->dim.y;
+ dim.z=10e9*v->dim.z;
char pse[19][4]={
- "foo",
+ "*",
"H",
"He",
"Li",
/* script file update */
dprintf(v->fd,"load xyz %s\n",file);
- dprintf(v->fd,"spacefill 200\n");
- //dprintf(v->fd,"rotate x 100\n");
- //dprintf(v->fd,"rotate y 10\n");
+ dprintf(v->fd,"spacefill 300\n");
+ dprintf(v->fd,"rotate x 100\n");
+ dprintf(v->fd,"rotate y 10\n");
dprintf(v->fd,"set ambient 20\n");
dprintf(v->fd,"set specular on\n");
sprintf(file,"%s-%.15f.ppm",v->fb,time);
dprintf(v->fd,"zap\n");
/* write the actual data file */
- dprintf(fd,"%d\n",n);
+ dprintf(fd,"%d\n",(dim.x==0)?n:n+8);
dprintf(fd,"atoms at time %.15f\n",time);
for(i=0;i<n;i++)
dprintf(fd,"%s %f %f %f\n",pse[atom[i].element],
- atom[i].r.x,atom[i].r.y,atom[i].r.z);
+ 10e9*atom[i].r.x,
+ 10e9*atom[i].r.y,
+ 10e9*atom[i].r.z);
+ if(dim.x) {
+ dprintf(fd,"%s %f %f %f\n",pse[0],dim.x/2,dim.y/2,dim.z/2);
+ dprintf(fd,"%s %f %f %f\n",pse[0],-dim.x/2,dim.y/2,dim.z/2);
+ dprintf(fd,"%s %f %f %f\n",pse[0],dim.x/2,-dim.y/2,dim.z/2);
+ dprintf(fd,"%s %f %f %f\n",pse[0],dim.x/2,dim.y/2,-dim.z/2);
+ dprintf(fd,"%s %f %f %f\n",pse[0],-dim.x/2,-dim.y/2,dim.z/2);
+ dprintf(fd,"%s %f %f %f\n",pse[0],dim.x/2,-dim.y/2,-dim.z/2);
+ dprintf(fd,"%s %f %f %f\n",pse[0],-dim.x/2,dim.y/2,-dim.z/2);
+ dprintf(fd,"%s %f %f %f\n",pse[0],-dim.x/2,-dim.y/2,-dim.z/2);
+ }
close(fd);
return 0;
#define VISUAL_H
#include "../moldyn.h"
+#include "../math/math.h"
typedef struct s_visual {
int fd; /* rasmol script file descriptor */
char fb[128]; /* basename of the save files */
+ t_3dvec dim; /* dimensions of the simulation cell */
} t_visual;
projects / physik / posic.git / commitdiff