#include <math.h>
#include "moldyn.h"
-#include "math/math.h"
-#include "init/init.h"
-#include "visual/visual.h"
#include "posic.h"
-#define TRUE 1
-#define FALSE 0
+int hook(void *moldyn,void *hook_params) {
+
+ t_moldyn *md;
+
+ md=moldyn;
+
+ /* switch to direct scaling in first hook */
+ if(md->schedule.count==0)
+ set_pt_scale(md,0,0,T_SCALE_BERENDSEN,100.0);
+ /* switch off temp scaling in second hook */
+ if(md->schedule.count==1)
+ set_pt_scale(md,0,0,0,0);
+
+ //set_temperature(md,md->t_ref-100.0);
+
+ return 0;
+}
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 */
+ /* testing location & velocity vector */
t_3dvec r,v;
- /* temperature */
- double t;
-
/* initialize moldyn */
- printf("[sic] moldyn init\n");
moldyn_init(&md,argc,argv);
/* choose integration algorithm */
- printf("[sic] setting integration algorithm\n");
set_int_alg(&md,MOLDYN_INTEGRATE_VERLET);
/* choose potential */
- printf("[sic] selecting potential\n");
//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);
+ //set_potential2b(&md,harmonic_oscillator,&ho);
+
+ /* cutoff radius */
+ //set_cutoff(&md,TM_S_SI);
+ //set_cutoff(&md,2*LC_SI*0.5*sqrt(1.5));
+ set_cutoff(&md,2.0*LC_SI);
/*
* potential parameters
lj.sigma6*=lj.sigma6;
lj.sigma12=lj.sigma6*lj.sigma6;
lj.epsilon4=4.0*LJ_EPSILON_SI;
+ lj.uc=lj.epsilon4*(lj.sigma12/pow(md.cutoff,12.0)-lj.sigma6/pow(md.cutoff,6));
/* harmonic oscillator */
- ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
- ho.spring_constant=1;
+ //ho.equilibrium_distance=0.25*sqrt(3.0)*LC_SI;
+ ho.equilibrium_distance=LC_SI;
+ ho.spring_constant=LJ_EPSILON_SI;
- /* cutoff radius */
- printf("[sic] setting cutoff radius\n");
- set_cutoff(&md,LC_SI);
+ /*
+ * 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);
/* set (initial) dimensions of simulation volume */
- printf("[sic] setting dimensions\n");
- set_dim(&md,10*LC_SI,10*LC_SI,10*LC_SI,TRUE);
+ set_dim(&md,6*LC_SI,6*LC_SI,6*LC_SI,TRUE);
/* set periodic boundary conditions in all directions */
- printf("[sic] setting periodic boundary conditions\n");
set_pbc(&md,TRUE,TRUE,TRUE);
/* 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);
- printf("[sic] check: there are %d atoms\n",md.count);
- printf("[sic] check: atoms x pos: %.15f %.15f\n",md.atom[0].r.x,md.atom[1].r.x);
- printf("[sic] check: atoms x vel: %.15f %.15f\n",md.atom[0].v.x,md.atom[1].v.x);
- printf("[sic] check: atoms mass: %.35f %.35f\n",md.atom[0].mass,md.atom[1].mass);
-
- /* set temperature */
- printf("[sic] setting temperature\n");
- set_temperature(&md,0.0);
+ create_lattice(&md,CUBIC,LC_SI,SI,M_SI,
+ //create_lattice(&md,FCC,LC_SI,SI,M_SI,
+ //create_lattice(&md,DIAMOND,LC_SI,SI,M_SI,
+ // ATOM_ATTR_1BP|ATOM_ATTR_2BP|ATOM_ATTR_3BP|ATOM_ATTR_HB,
+ ATOM_ATTR_2BP|ATOM_ATTR_HB,
+ 0,6,6,6);
+ moldyn_bc_check(&md);
+
+ /* testing configuration */
+ //r.x=0.28*sqrt(3)*LC_SI/2; v.x=0;
+ //r.x=1.75*LC_SI; v.x=-0.01;
+ //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,
+ // ATOM_ATTR_2BP|ATOM_ATTR_HB,
+ // &r,&v);
+ //r.x=-r.x; v.x=-v.x;
+ //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,
+ // ATOM_ATTR_2BP|ATOM_ATTR_HB,
+ // &r,&v);
+
+ /* set temperature & pressure */
+ set_temperature(&md,atof(argv[2])+273.0);
+ set_pressure(&md,ATM);
+
+ /* set p/t scaling */
+ set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,
+ T_SCALE_BERENDSEN,100.0);
+ //set_pt_scale(&md,0,0,T_SCALE_DIRECT,1.0);
+ //set_pt_scale(&md,P_SCALE_BERENDSEN,0.001,0,0);
- /* initial thermal fluctuations of particles */
- printf("[sic] thermal init\n");
- thermal_init(&md);
- printf("[sic] check: there are %d atoms\n",md.count);
- printf("[sic] check: atoms x pos: %.15f %.15f\n",md.atom[0].r.x,md.atom[1].r.x);
- printf("[sic] check: atoms x vel: %.15f %.15f\n",md.atom[0].v.x,md.atom[1].v.x);
+ /* initial thermal fluctuations of particles (in equilibrium) */
+ thermal_init(&md,TRUE);
/* create the simulation schedule */
- printf("[sic] adding schedule\n");
- moldyn_add_schedule(&md,10000,1.0e-12);
+ moldyn_add_schedule(&md,100001,1.0);
+ //moldyn_add_schedule(&md,501,1.0);
+ //moldyn_add_schedule(&md,501,1.0);
+
+ /* schedule hook function */
+ //moldyn_set_schedule_hook(&md,&hook,NULL);
/* activate logging */
- printf("[sic] activate logging\n");
- moldyn_set_log(&md,LOG_TOTAL_ENERGY,"saves/test-energy",1);
- moldyn_set_log(&md,VISUAL_STEP,"saves/test-visual",1);
+ moldyn_set_log_dir(&md,argv[1]);
+ moldyn_set_report(&md,"Frank Zirkelbach","Test 1");
+ moldyn_set_log(&md,LOG_TOTAL_ENERGY,1);
+ moldyn_set_log(&md,VISUAL_STEP,1000);
+ moldyn_set_log(&md,CREATE_REPORT,0);
/*
* let's do the actual md algorithm now
*
* integration of newtons equations
*/
-
- printf("[sic] integration start, go get a coffee ...\n");
moldyn_integrate(&md);
/* close */
-
- printf("[sic] shutdown\n");
moldyn_shutdown(&md);
return 0;