- 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);
-
- /* 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=0.27*sqrt(3.0)*LC_SI/2.0; v.x=0;
+ //r.x=(TM_S_SI+TM_R_SI)/4.0; 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,
+ // 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);
+ //r.x=0; v.x=0;
+ //r.y=0; v.y=0;
+ //r.z=sin(M_PI*60.0/180.0)*(TM_S_SI+TM_R_SI)/4.0; 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,BAR);
+
+ /* 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);