This set of tools uses python to deal with POSCAR5 Direct.
SCRIPTDIR : '/home/zkdsnbzx/src/pypos' list element[:] : ['La','Mn','O','O','O'] np.float64 cell[0:2][0:3] : [a1,a2,a3],[b1,b2,b3],[c1,c2,c3]] (POSCAR) np.float64 base[0:2][0:3] : [[rx1,ry1,rz1],[rx2,ry2,rz2],...,[rx10,ry10,rz10]] (0<rx,ry,rz<1, Direct) np.float64 rpos_imaged[:][0:3] : [[rx1-1,ry1-1,rz1-1],...,[rx10+1,ry10+1,rz10+1]] (Direct) np.float64 pos_original[:][0:3] : [[rx1,ry1,rz1],[rx2,ry2,rz2],...,[rx10,ry10,rz10]] * [a\,b\,c] (Cartesian) np.float64 pos_imaged[:][0:3] : [[rx1-1,ry1-1,rz1-1],...,[rx10+1,ry10+1,rz10+1]] * [a\,b\,c] (Cartesian) np.float64 dist_qui[:][0:5] : [id_imaged1,id_imaged2,atomid1,atomid2,|r1-r2|] ele_* : element of homogeneous list * id_* : id of homogeneous list * (starting from 0) tmp_??? : tmp physical quantity with meaning ???
- : really physical (core) quantity with meaning * master_data_structure:{'quantity':quantity}, used for passing&using in functions in modules
truncate_dist_at integer exclude_pair[:][0:1] list exclude_ele_pair[:][0:1] list exclude_dist[:][0] np.float64
##calculate_mag_j np.float64 dist_noindex_nonrep[0:?][0] np.float64 all dis_truncated[:][2] 1E-3 ? row * [dis] np.float64 dist_qui_ex_tr[:][0:5] : dis_qui exclude-ed and truncated np.float64 effective_magnetic_pair[:][0:2] : effective magnetic pairs a.k.a. pairs in dist_qui_tr_ex
##genposcar_using_radius np.float64 dist_noindex_nonrep[0:?][0] np.float64 all dis_truncated[:][2] 1E-3 ? row * [dis] np.float64 dist_qui_ex_tr[:][0:5] : dis_qui exclude-ed and truncated np.float64 target_pair[:][0:2] : effective magnetic pairs a.k.a. pairs[id0_imaged:id1_imaged] in dist_qui_tr_ex