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Question about '.md2' file.
Date: 2019/12/22 16:30
Name: Liu Jie   <15284076358@163.com>

Dear developer,
I have a question about '.md2' file.This is the structure of my input file:
Atoms.Number 22
Atoms.SpeciesAndCoordinates.Unit FRAC # Ang|AU
<Atoms.SpeciesAndCoordinates
1 B 0.222220004 0.111110002 0.014220000 1.5 1.5 on
2 B 0.555559993 0.111110002 0.014220000 1.5 1.5 on
3 B 0.888890028 0.111110002 0.014220000 1.5 1.5 on
4 B 0.222220004 0.444440007 0.014220000 1.5 1.5 on
5 B 0.555559993 0.444440007 0.014220000 1.5 1.5 on
6 B 0.888890028 0.444440007 0.014220000 1.5 1.5 on
7 B 0.222220004 0.777779996 0.014220000 1.5 1.5 on
8 B 0.555559993 0.777779996 0.014220000 1.5 1.5 on
9 B 0.888890028 0.777779996 0.014220000 1.5 1.5 on
10 N 0.000000000 0.000000000 0.014220000 2.5 2.5 on
11 N 0.333330005 0.000000000 0.014220000 2.5 2.5 on
12 N 0.666670024 0.000000000 0.014220000 2.5 2.5 on
13 N 0.000000000 0.333330005 0.014220000 2.5 2.5 on
14 N 0.333330005 0.333330005 0.014220000 2.5 2.5 on
15 N 0.666670024 0.333330005 0.014220000 2.5 2.5 on
16 N 0.000000000 0.666670024 0.014220000 2.5 2.5 on
17 N 0.333330005 0.666670024 0.014220000 2.5 2.5 on
18 N 0.666670024 0.666670024 0.014220000 2.5 2.5 on
19 Sm 0.444449991 0.055580001 0.161070004 11.0 5.0 on
20 Sm 0.944450021 0.055580001 0.161070004 11.0 5.0 on
21 Sm 0.444440007 0.555559993 0.161070004 11.0 5.0 on
22 Sm 0.944450021 0.555580020 0.161070004 11.0 5.0 on
Atoms.SpeciesAndCoordinates>
After calculation,i obtained a structure ini the '.md2' file:

1 B 1.2327032 0.7218301 0.4843635 1.50000 1.50000
2 B 3.6922667 0.7055417 0.0836378 1.50000 1.50000
3 B 6.1779227 0.7050142 0.0786862 1.50000 1.50000
4 B -0.0000915 2.8462014 0.1469462 1.50000 1.50000
5 B 2.4667656 2.8470084 0.1418826 1.50000 1.50000
6 B 4.9347352 2.8564744 0.0859400 1.50000 1.50000
7 B -1.2250615 4.9789711 0.4438991 1.50000 1.50000
8 B 1.2341684 4.9848423 0.1460543 1.50000 1.50000
9 B 3.6902020 4.9787084 0.4826440 1.50000 1.50000
10 N -0.0088955 0.0048200 0.3348655 2.50000 2.50000
11 N 2.4786263 0.0053291 0.3412420 2.50000 2.50000
12 N 4.9349273 0.0045064 0.1794555 2.50000 2.50000
13 N -1.2356507 2.1314002 0.1826885 2.50000 2.50000
14 N 1.2333783 2.1444666 0.2288946 2.50000 2.50000
15 N 3.7058948 2.1318422 0.1870697 2.50000 2.50000
16 N -2.4648575 4.2578921 0.3435213 2.50000 2.50000
17 N 0.0087106 4.2666033 0.2262765 2.50000 2.50000
18 N 2.4583769 4.2665891 0.2290079 2.50000 2.50000
19 Sm 3.0627337 0.3456863 2.9134885 8.00000 8.00000
20 Sm 6.7973058 0.3474494 2.9077634 8.00000 8.00000
21 Sm 1.2406572 3.5588390 2.7426301 8.00000 8.00000
22 Sm 4.9322851 3.5839998 2.9200082 8.00000 8.00000
I want to know why the up-spin and down-spin of Sm is 8.0 and 8.0 respectively,because the atom Sm have a spin momentum according to the output file.
メンテ
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Re: Question about '.md2' file. ( No.1 )
Date: 2019/12/22 23:26
Name: T. Ozaki

Hi,

In the md2 file, the up-spin and down-spin charge are set to the half of the number of
valence electrons, while the 11th and 12th columns in the md file correspond to
the net charge and spin moment (muB), respectively. Also, the 13th and 14th columns
in the md file are the spin Euler angles.

They are the format of the md2 and md files.

Regards,

TO
メンテ
Re: Question about '.md2' file. ( No.2 )
Date: 2019/12/23 11:27
Name: Liu Jie  <15284076358@163.com>

Thank you T. Ozaki!This is my md file:
B 1.23301 0.72303 0.49656 -0.00087 0.00081 0.00296 0.00000 0.00000 0.00000 0.36167 0.01196 0.00000 0.00000
B 3.69136 0.70566 0.08261 -0.00017 0.00039 -0.00196 0.00000 0.00000 0.00000 0.47835 0.01557 0.00000 0.00000
B 6.17906 0.70418 0.07690 0.00016 0.00024 -0.00143 0.00000 0.00000 0.00000 0.48142 0.01741 0.00000 0.00000
B 0.00055 2.84566 0.13910 0.00095 0.00180 -0.00173 0.00000 0.00000 0.00000 0.47714 0.00332 0.00000 0.00000
B 2.46726 2.84686 0.13514 -0.00049 0.00063 -0.00130 0.00000 0.00000 0.00000 0.48009 0.00623 0.00000 0.00000
B 4.93399 2.85759 0.08561 -0.00025 0.00033 -0.00256 0.00000 0.00000 0.00000 0.47762 0.01944 0.00000 0.00000
B -1.22467 4.97824 0.45024 0.00150 -0.00105 0.00091 0.00000 0.00000 0.00000 0.39014 0.01050 0.00000 0.00000
B 1.23504 4.98435 0.13776 -0.00074 -0.00195 -0.00197 0.00000 0.00000 0.00000 0.47485 0.00227 0.00000 0.00000
B 3.68945 4.97750 0.49418 -0.00088 -0.00004 0.00504 0.00000 0.00000 0.00000 0.35970 0.00829 0.00000 0.00000
N -0.00923 0.00471 0.34555 0.00166 -0.00036 0.00311 0.00000 0.00000 0.00000 -0.60985 -0.00755 0.00000 0.00000
N 2.47880 0.00582 0.35212 -0.00066 -0.00040 0.00533 0.00000 0.00000 0.00000 -0.61317 0.00016 0.00000 0.00000
N 4.93432 0.00433 0.17184 0.00055 0.00062 -0.00332 0.00000 0.00000 0.00000 -0.62704 0.00561 0.00000 0.00000
N -1.23590 2.13197 0.17514 -0.00077 -0.00026 -0.00148 0.00000 0.00000 0.00000 -0.62646 0.00505 0.00000 0.00000
N 1.23406 2.14326 0.22350 0.00021 -0.00141 -0.00266 0.00000 0.00000 0.00000 -0.60900 -0.00087 0.00000 0.00000
N 3.70505 2.13227 0.18124 0.00007 0.00070 -0.00186 0.00000 0.00000 0.00000 -0.62513 0.00627 0.00000 0.00000
N -2.46541 4.25774 0.35425 0.00047 -0.00003 0.00541 0.00000 0.00000 0.00000 -0.61237 -0.00765 0.00000 0.00000
N 0.00794 4.26718 0.21995 -0.00093 -0.00008 -0.00283 0.00000 0.00000 0.00000 -0.61128 0.00253 0.00000 0.00000
N 2.45963 4.26661 0.22360 0.00101 -0.00018 -0.00296 0.00000 0.00000 0.00000 -0.60920 0.00115 0.00000 0.00000
Sm 3.06064 0.34575 2.91690 0.00325 0.00178 0.00482 0.00000 0.00000 0.00000 0.35052 3.48309 0.00000 0.00000
Sm 6.79957 0.34693 2.91012 -0.00341 0.00176 0.00335 0.00000 0.00000 0.00000 0.39359 6.67146 0.00000 0.00000
Sm 1.24137 3.55823 2.73432 -0.00009 0.00015 -0.00575 0.00000 0.00000 0.00000 0.47225 6.75363 0.00000 0.00000
Sm 4.93176 3.58589 2.92407 -0.00038 -0.00332 0.00051 0.00000 0.00000 0.00000 0.34615 5.93299 0.00000 0.00000
I have learned the 2nd,3rd and 4th are flags for the x-,y- and z-coordinates,respectively.And i guess the 5th,6th and 7th are the force coordinates,is it true?Then,the 12th column has minus value,is it means that it indicates the down-spin momentum.Finally,i don't know what the 8th,9th and 10th mean.Would you please tell me that?Thank you very much.
メンテ
Re: Question about '.md2' file. ( No.3 )
Date: 2019/12/23 20:19
Name: T. Ozaki

Hi,

Each column in the md file stores the following information:

1: atomic symbol
2: x-coordinate in Angstrom
3: y-coordinate in Angstrom
4: z-coordinate in Angstrom
5: x-component of force in Hartree/Bohr
6: y-component of force in Hartree/Bohr
7: z-component of force in Hartree/Bohr
8: x-component of velocity in m/sec.
9: y-component of velocity in m/sec.
10: z-component of velocity in m/sec.
11: net charge
12: spin moment in muB
13: Euler angle, theta, for spin in deg.
14: Euler angle, phi, for spin in deg.

Also, in each block of data, the first line is the number of atoms, and
the second line contains the lattice vectors.

You can confirm them by looking at iterout.c.

Regards,

TO
メンテ
Re: Question about '.md2' file. ( No.4 )
Date: 2019/12/23 15:30
Name: Liu Jie  <15284076358@163.com>

Oh!Thank you T. Ozaki.

Best wishes!
メンテ

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