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The meaning of Rn in HS.out Date: 2021/05/17 03:13 Name: Mao   <sumao@fudan.edu.cn> Dear OpenMX users, I was trying to obtain the Hamiltonian and overlap matrices from HS.out file: ********** Kohn-Sham Hamiltonian spin=0 global index=1 local index=0 (global=1, Rn=0) -0.7756858 -0.0000098 -0.0000170 0.0129204 -0.0000098 -0.5499314 -0.0000408 0.0000002 -0.0000170 -0.0000408 -0.5499785 0.0000003 0.0129204 0.0000002 0.0000003 -0.3109040 global index=1 local index=1 (global=1, Rn=203) ... ********** I use s1p1 orbitals for the calculation, therefore each pair corresponds to a 4 * 4 matrix. My question is, how can I get the real-space distance of each atom pair? As written in 'analysis_example.c", the global index denotes the atom number in the unit cell, and Rn denotes the cell index. I was confused by the value of Rn, since a vector for the cell index is expected, i.e., Rn = (-1, 2, 0) as in the *.HWR file. It seems like the cell index vector (l, m, n) are given by atv_ijk[Rn]. However, I couldn't find the "atv_ijk[Rn]" data in the output files. Any comments will be appreciated!

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Re: The meaning of Rn in HS.out ( No.1 ) Date: 2021/05/17 14:51 Name: Naoya Yamaguchi Hi, >My question is, how can I get the real-space distance of each atom pair? For example, you can get the distance between atom i and atom j (here, j is a neighboring atom index for atom i) from #include "read_scfout.h" #include <math.h> int main(void){ read_scfout(argv); for (int i=1; i<=atomnum; i++){ for (int j=0; j<=FNAN[i]; j++){ double ix=Gxyz[i][1]; double iy=Gxyz[i][2]; double iz=Gxyz[i][3]; int globalJ=natn[i][j]; int Rn=ncn[i][j]; double jx=atv[Rn][1]+Gxyz[globalJ][1]; double jy=atv[Rn][2]+Gxyz[globalJ][2]; double jz=atv[Rn][3]+Gxyz[globalJ][3]; double jix=jx-ix; double jiy=jy-iy; double jiz=jz-iz; printf("Distance (i = %d, j = %d): %f", i, j, sqrt(jix*jix+jiy*jiy+jiz*jiz)); } } free_scfout(); return 0; } Also, you can refer to "read_scfout.h" or "read_scfout.c" to get information of variables. Regards, Naoya Yamaguchi Re: The meaning of Rn in HS.out ( No.2 ) Date: 2021/05/17 17:14 Name: Mao  <sumao@fudan.edu.cn> Hi Naoya Yamaguchi, Thank you so much! I modified "analysis_example.c" following your suggestion and now it works. Best regards, Mao

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