/*
* 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 "posic.h"
+#include "moldyn.h"
+#include "math/math.h"
+#include "init/init.h"
+#include "visual/visual.h"
-#define RAND(max) (max*(0.5-(1.0*rand()/RAND_MAX+1)));
+#include "posic.h"
int main(int argc,char **argv) {
- t_atom *si;
- //t_si *c;
- int i,j,runs,amount_si;
- double time;
- int fd;
-
- double tau,tau2,m,m2;
- double deltax,deltay,deltaz,distance;
- double deltax2,deltay2,deltaz2,tmp;
- double lj1,lj2,lj;
-
- /* silicon */
- amount_si=AMOUNT_SI;
- printf("simulating %d silicon atoms\n",amount_si);
- si=malloc(amount_si*sizeof(t_atom));
- if(!si) {
- perror("silicon malloc");
- return -1;
- }
- memset(si,0,amount_si*sizeof(t_atom));
- m=SI_M; m2=2.0*m;
-
- /* init */
- printf("placing silicon atoms\n");
- for(i=0;i<amount_si;i++) {
- si[i].x=RAND(LEN_X);
- si[i].y=RAND(LEN_Y);
- si[i].z=RAND(LEN_Z);
- si[i].vx=.0;
- si[i].vy=.0;
- si[i].vz=.0;
- si[i].fx=.0;
- si[i].fy=.0;
- si[i].fz=.0;
- }
-
- /* time */
- time=.0;
- tau=TAU;
- tau2=tau*tau;
-
- /* rasmol */
- printf("opening the rasmol file\n");
- fd=open("rasmol.xyz",O_WRONLY);
- if(fd<0) {
- perror("rasmol file open");
- return -1;
- }
-
- printf("starting velocity verlet: ");
- fflush(stdout);
-
- for(runs=0;runs<RUNS;runs++) {
-
- /*
- * velocity verlet
+ t_moldyn md;
+
+ t_lj_params lj;
+ t_ho_params ho;
+ t_tersoff_mult_params tp;
+
+ int a,b,c;
+ double e;
+ double help;
+ t_3dvec p;
+
+ /*
+ * moldyn init
*
- * 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))
+ * - parsing argv
+ * - log init
+ * - random init
*
*/
- 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);
- }
- 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[i].fx=-lj*deltax;
- si[i].fy=-lj*deltay;
- si[i].fz=-lj*deltaz;
- }
- }
- /* 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);
- }
-
- time+=tau;
-
- /* print out positions in rasmol format */
- dprintf(fd,"%d\nTime %f\n",amount_si,time);
- for(i=0;i<amount_si;i++)
- dprintf(fd,"Si %f %f %f %f\n",
- si[i].x,si[i].y,si[i].z,time);
- printf(".");
- fflush(stdout);
- dprintf(fd,"\n");
-
- }
-
- printf("done\n");
- close(fd);
- free(si);
+ a=moldyn_init(&md,argc,argv);
+ if(a<0) return a;
+
+ /*
+ * the following overrides possibly set interaction methods by argv !!
+ */
+
+ /* params */
+ lj.sigma6=LJ_SIGMA_SI*LJ_SIGMA_SI;
+ help=lj.sigma6*lj.sigma6;
+ lj.sigma6*=help;
+ lj.sigma12=lj.sigma6*lj.sigma6;
+ lj.epsilon4=4.0*LJ_EPSILON_SI;
+ ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
+ ho.spring_constant=1;
+ /* assignement */
+ md.potential_force_function=lennard_jones;
+ //md.potential_force_function=harmonic_oscillator;
+ md.pot_params=&lj;
+ //md.pot_params=&ho;
+ /* cutoff radius */
+ md.cutoff=R_CUTOFF*LC_SI;
+
+ /*
+ * testing random numbers
+ */
+
+#ifdef DEBUG_RANDOM_NUMBER
+ for(a=0;a<1000000;a++)
+ printf("%f %f\n",rand_get_gauss(&(md.random)),
+ rand_get_gauss(&(md.random)));
+ return 0;
+#endif
+
+ /*
+ * geometry & particles
+ */
+
+ /* simulation cell volume in lattice constants */
+ a=LEN_X;
+ b=LEN_Y;
+ c=LEN_Z;
+ md.dim.x=a*LC_SI;
+ md.dim.y=b*LC_SI;
+ md.dim.z=c*LC_SI;
+
+ /* (un)set to (not) get visualized 'bounding atoms' */
+ md.vis.dim.x=a*LC_SI;
+ md.vis.dim.y=b*LC_SI;
+ md.vis.dim.z=c*LC_SI;
+
+ /*
+ * particles
+ */
+
+ /* lattice init */
+
+#ifndef SIMPLE_TESTING
+ md.count=create_lattice(DIAMOND,SI,M_SI,LC_SI,a,b,c,&(md.atom));
+ printf("created silicon lattice (#atoms = %d)\n",md.count);
+#else
+ md.count=2;
+ md.atom=malloc(md.count*sizeof(t_atom));
+ md.atom[0].r.x=0.23*sqrt(3.0)*LC_SI/2.0;
+ md.atom[0].r.y=0;
+ md.atom[0].r.z=0;
+ md.atom[0].element=SI;
+ md.atom[0].mass=M_SI;
+ md.atom[1].r.x=-md.atom[0].r.x;
+ md.atom[1].r.y=0;
+ md.atom[1].r.z=0;
+ md.atom[1].element=SI;
+ md.atom[1].mass=M_SI;
+
+ //md.atom[2].r.x=0.5*(a-1)*LC_SI;
+ //md.atom[2].r.y=0.5*(b-1)*LC_SI;
+ //md.atom[2].r.z=0;
+ //md.atom[2].element=C;
+ //md.atom[2].mass=M_C;
+
+ //md.atom[3].r.x=0.5*(a-1)*LC_SI;
+ //md.atom[3].r.y=0;
+ //md.atom[3].r.z=0;
+ //md.atom[3].element=SI;
+ //md.atom[3].mass=M_SI;
+#endif
+
+ /* initial thermal fluctuations of particles */
+
+#ifndef SIMPLE_TESTING
+ printf("setting thermal fluctuations (T=%f K)\n",md.t);
+ thermal_init(&md);
+#else
+ for(a=0;a<md.count;a++) v3_zero(&(md.atom[0].v));
+ md.atom[2].v.x=-320;
+ md.atom[2].v.y=-320;
+#endif
+
+ /* check kinetic energy */
+ e=get_e_kin(md.atom,md.count);
+ printf("kinetic energy: %.40f [J]\n",e);
+ printf("3/2 N k T = %.40f [J] (T=%f [K])\n",
+ 1.5*md.count*K_BOLTZMANN*md.t,md.t);
+
+ /* check total momentum */
+ p=get_total_p(md.atom,md.count);
+ printf("total momentum: %.30f [Ns]\n",v3_norm(&p));
+
+ /* check time step */
+ printf("estimated accurate time step: %.30f [s]\n",
+ estimate_time_step(&md,3.0,md.t));
+
+ /*
+ * let's do the actual md algorithm now
+ *
+ * integration of newtons equations
+ */
+
+ moldyn_integrate(&md);
+
+ printf("total energy (after integration): %.40f [J]\n",
+ get_total_energy(&md));
+
+ /* close */
+
+ link_cell_shutdown(&md);
+ moldyn_shutdown(&md);
+
return 0;
}
projects / physik / posic.git / blobdiff