#include <math.h>
#include "moldyn.h"
-#include "math/math.h"
-#include "init/init.h"
-#include "visual/visual.h"
#include "posic.h"
int main(int argc,char **argv) {
+ /* check argv */
+ if(argc!=3) {
+ printf("[sic] usage: %s <logdir> <temperatur>\n",argv[0]);
+ return -1;
+ }
+
/* main moldyn structure */
t_moldyn md;
t_ho_params ho;
t_tersoff_mult_params tp;
- /* misc variables, mainly to initialize stuff */
+ /* misc parameters */
+ double tau;
+
+ /* testing location & velocity vector */
t_3dvec r,v;
- /* temperature */
- double t;
+ /* values */
+ tau=1.0e-15; /* delta t = 1 fs */
/* initialize moldyn */
printf("[sic] moldyn init\n");
/* choose potential */
printf("[sic] selecting potential\n");
- //set_potential1b(&md,tersoff_mult_1bp,&tp);
- //set_potential2b(&md,tersoff_mult_2bp,&tp);
- //set_potential3b(&md,tersoff_mult_3bp,&tp);
- set_potential2b(&md,lennard_jones,&lj);
+ set_potential1b(&md,tersoff_mult_1bp,&tp);
+ set_potential2b(&md,tersoff_mult_2bp,&tp);
+ set_potential2b_post(&md,tersoff_mult_post_2bp,&tp);
+ set_potential3b(&md,tersoff_mult_3bp,&tp);
+ //set_potential2b(&md,lennard_jones,&lj);
/*
* potential parameters
ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
ho.spring_constant=1;
+ /*
+ * tersoff mult potential parameters for SiC
+ */
+ tp.S[0]=TM_S_SI;
+ tp.R[0]=TM_R_SI;
+ tp.A[0]=TM_A_SI;
+ tp.B[0]=TM_B_SI;
+ tp.lambda[0]=TM_LAMBDA_SI;
+ tp.mu[0]=TM_MU_SI;
+ tp.beta[0]=TM_BETA_SI;
+ tp.n[0]=TM_N_SI;
+ tp.c[0]=TM_C_SI;
+ tp.d[0]=TM_D_SI;
+ tp.h[0]=TM_H_SI;
+
+ tp.S[1]=TM_S_C;
+ tp.R[1]=TM_R_C;
+ tp.A[1]=TM_A_C;
+ tp.B[1]=TM_B_C;
+ tp.lambda[1]=TM_LAMBDA_C;
+ tp.mu[1]=TM_MU_C;
+ tp.beta[1]=TM_BETA_C;
+ tp.n[1]=TM_N_C;
+ tp.c[1]=TM_C_C;
+ tp.d[1]=TM_D_C;
+ tp.h[1]=TM_H_C;
+
+ tp.chi=TM_CHI_SIC;
+
+ tersoff_mult_complete_params(&tp);
+
/* cutoff radius */
printf("[sic] setting cutoff radius\n");
- set_cutoff(&md,1*LC_SI);
+ set_cutoff(&md,TM_S_SI);
+ //set_cutoff(&md,2*LC_SI);
/* set (initial) dimensions of simulation volume */
printf("[sic] setting dimensions\n");
- set_dim(&md,4*LC_SI,4*LC_SI,4*LC_SI,TRUE);
+ set_dim(&md,5*LC_SI,5*LC_SI,5*LC_SI,TRUE);
/* set periodic boundary conditions in all directions */
printf("[sic] setting periodic boundary conditions\n");
/* create the lattice / place atoms */
printf("[sic] creating atoms\n");
- //memset(&v,0,sizeof(t_3dvec));
- //r.y=0;
- //r.z=0;
- //r.x=0.23*sqrt(3.0)*LC_SI/2.0;
- //add_atom(&md,SI,M_SI,0,ATOM_ATTR_2BP,&r,&v);
- //r.x=-r.x;
- //add_atom(&md,SI,M_SI,0,ATOM_ATTR_2BP,&r,&v);
- create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,ATOM_ATTR_2BP,0,4,4,4);
+ create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
+ ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+ 0,5,5,5);
+ moldyn_bc_check(&md);
+
+ /* testing configuration */
+ //r.x=2.95/2; v.x=0;
+ //r.y=0; v.y=0;
+ //r.z=0; v.z=0;
+ //add_atom(&md,SI,M_SI,0,
+ // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP,//|ATOM_ATTR_HB,
+ // &r,&v);
+ //r.x=-2.95/2; v.x=0;
+ //r.y=0; v.y=0;
+ //r.z=0; v.z=0;
+ //add_atom(&md,SI,M_SI,0,
+ // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP,//|ATOM_ATTR_HB,
+ // &r,&v);
/* setting a nearest neighbour distance for the moldyn checks */
- set_nn_dist(&md,sqrt(3.0)*LC_SI/4.0); /* diamond ! */
+ set_nn_dist(&md,0.25*sqrt(3.0)*LC_SI); /* diamond ! */
/* set temperature */
- printf("[sic] setting temperature\n");
- set_temperature(&md,273.0);
+ printf("[sic] setting temperature -> %f\n",273+atof(argv[2]));
+ //set_temperature(&md,273.0+1410.0);
+ //set_temperature(&md,273.0+450.0);
+ //set_temperature(&md,273.0);
+ //set_temperature(&md,1.0);
+ //set_temperature(&md,0.0);
+ set_temperature(&md,atof(argv[2])+273.0);
+
+ /* set pressure */
+ printf("[sic] setting pressure\n");
+ set_pressure(&md,ATM);
+
+ /* set p/t scaling */
+ printf("[sic] set p/t scaling\n");
+ //set_pt_scale(&md,P_SCALE_BERENDSEN,100.0,
+ // T_SCALE_BERENDSEN,100.0);
+ set_pt_scale(&md,0,0,T_SCALE_BERENDSEN,100.0);
- /* initial thermal fluctuations of particles */
+ /* initial thermal fluctuations of particles (in equilibrium) */
printf("[sic] thermal init\n");
- thermal_init(&md);
+ thermal_init(&md,TRUE);
/* create the simulation schedule */
printf("[sic] adding schedule\n");
- moldyn_add_schedule(&md,10000,1.0e-15);
+ moldyn_add_schedule(&md,20000,.1);
+ moldyn_add_schedule(&md,10000,.2);
+ moldyn_add_schedule(&md,6667,.3);
+ moldyn_add_schedule(&md,5000,.4);
+ moldyn_add_schedule(&md,4001,.5);
/* activate logging */
printf("[sic] activate logging\n");
- moldyn_set_log(&md,LOG_TOTAL_ENERGY,"saves/test-energy",100);
- moldyn_set_log(&md,VISUAL_STEP,"saves/test-visual",100);
+ moldyn_set_log_dir(&md,argv[1]);
+ moldyn_set_log(&md,LOG_TOTAL_ENERGY,100);
+ moldyn_set_log(&md,VISUAL_STEP,100);
/*
* let's do the actual md algorithm now