mlwf center positions of the output of AIMD
Posted: Tue Apr 16, 2024 12:05 pm
Hello,
I'd like to ask mlwf center positions of the output of AIMD.
From the output file of AIMD, I performed water molecule-wise classification of "the mlwf center positions" and "O and/or H positions" for molecule-based dipole calculation.
Four mlwf centers positions and one O position and two H position would be taken for each of molecule-wise classifications.
The system consists of 64 water molecules.
For this, at the first mlwf and atomic position output of md.r, I tried to match two H positions and four mlwf center (not spread) positions to each of 64 O atoms.
My questions are as follows.
1. Would the order of atom index be maintained at the time series output of mlwf and/or atomic position (e.g., outputs at every 10 step)? Otherwise, would the atom index order change leading to a random order of atom index?
2. The DO length of D2O would be shorter than that of H2O.
Hence, I made the criterion of the nearest neighboring radius of 1.2 A for each O atom to find nearest neighboring two H atoms and four mlwf centers.
However, my analysis showed that many of mlwf center positions do not follow this while two H atoms are successfully found and listed for each of O atoms as shown below.
O_index:0 len(H_index_list):2 len(mlwf_index_list):3
O_index:1 len(H_index_list):2 len(mlwf_index_list):8
O_index:2 len(H_index_list):2 len(mlwf_index_list):4
O_index:3 len(H_index_list):2 len(mlwf_index_list):3
O_index:4 len(H_index_list):2 len(mlwf_index_list):4
O_index:5 len(H_index_list):2 len(mlwf_index_list):4
O_index:6 len(H_index_list):2 len(mlwf_index_list):3
O_index:7 len(H_index_list):2 len(mlwf_index_list):0
O_index:8 len(H_index_list):2 len(mlwf_index_list):4
O_index:9 len(H_index_list):2 len(mlwf_index_list):3
O_index:10 len(H_index_list):2 len(mlwf_index_list):1
O_index:11 len(H_index_list):2 len(mlwf_index_list):3
O_index:12 len(H_index_list):2 len(mlwf_index_list):3
O_index:13 len(H_index_list):2 len(mlwf_index_list):1
O_index:14 len(H_index_list):2 len(mlwf_index_list):4
O_index:15 len(H_index_list):2 len(mlwf_index_list):0
O_index:16 len(H_index_list):2 len(mlwf_index_list):3
O_index:17 len(H_index_list):2 len(mlwf_index_list):3
O_index:18 len(H_index_list):2 len(mlwf_index_list):4
O_index:19 len(H_index_list):2 len(mlwf_index_list):4
O_index:20 len(H_index_list):2 len(mlwf_index_list):4
O_index:21 len(H_index_list):2 len(mlwf_index_list):4
O_index:22 len(H_index_list):2 len(mlwf_index_list):0
O_index:23 len(H_index_list):2 len(mlwf_index_list):4
O_index:24 len(H_index_list):2 len(mlwf_index_list):4
O_index:25 len(H_index_list):2 len(mlwf_index_list):1
O_index:26 len(H_index_list):2 len(mlwf_index_list):5
O_index:27 len(H_index_list):2 len(mlwf_index_list):4
O_index:28 len(H_index_list):2 len(mlwf_index_list):4
O_index:29 len(H_index_list):2 len(mlwf_index_list):5
O_index:30 len(H_index_list):2 len(mlwf_index_list):5
O_index:31 len(H_index_list):2 len(mlwf_index_list):4
O_index:32 len(H_index_list):2 len(mlwf_index_list):4
O_index:33 len(H_index_list):2 len(mlwf_index_list):4
O_index:34 len(H_index_list):2 len(mlwf_index_list):6
O_index:35 len(H_index_list):2 len(mlwf_index_list):5
O_index:36 len(H_index_list):2 len(mlwf_index_list):4
O_index:37 len(H_index_list):2 len(mlwf_index_list):0
O_index:38 len(H_index_list):2 len(mlwf_index_list):0
O_index:39 len(H_index_list):2 len(mlwf_index_list):0
O_index:40 len(H_index_list):2 len(mlwf_index_list):4
O_index:41 len(H_index_list):2 len(mlwf_index_list):0
O_index:42 len(H_index_list):2 len(mlwf_index_list):1
O_index:43 len(H_index_list):2 len(mlwf_index_list):0
O_index:44 len(H_index_list):2 len(mlwf_index_list):3
O_index:45 len(H_index_list):2 len(mlwf_index_list):3
O_index:46 len(H_index_list):2 len(mlwf_index_list):3
O_index:47 len(H_index_list):2 len(mlwf_index_list):6
O_index:48 len(H_index_list):2 len(mlwf_index_list):6
O_index:49 len(H_index_list):2 len(mlwf_index_list):1
O_index:50 len(H_index_list):2 len(mlwf_index_list):4
O_index:51 len(H_index_list):2 len(mlwf_index_list):4
O_index:52 len(H_index_list):2 len(mlwf_index_list):0
O_index:53 len(H_index_list):2 len(mlwf_index_list):0
O_index:54 len(H_index_list):2 len(mlwf_index_list):5
O_index:55 len(H_index_list):2 len(mlwf_index_list):0
O_index:56 len(H_index_list):2 len(mlwf_index_list):4
O_index:57 len(H_index_list):2 len(mlwf_index_list):5
O_index:58 len(H_index_list):2 len(mlwf_index_list):4
O_index:59 len(H_index_list):2 len(mlwf_index_list):0
O_index:60 len(H_index_list):2 len(mlwf_index_list):5
O_index:61 len(H_index_list):2 len(mlwf_index_list):0
O_index:62 len(H_index_list):2 len(mlwf_index_list):1
O_index:63 len(H_index_list):2 len(mlwf_index_list):1
I use the length conversion from Bohr to Angstrom when the results was taken from md.r.
I think that the unit of mlwf center positions should be the same as that of atomic positions (i.e., Bohr). Is it right?
I attached the file of the first output named md_first_output.r.
Would you let me know what would be wrong with it?
Best regards,
Young
I'd like to ask mlwf center positions of the output of AIMD.
From the output file of AIMD, I performed water molecule-wise classification of "the mlwf center positions" and "O and/or H positions" for molecule-based dipole calculation.
Four mlwf centers positions and one O position and two H position would be taken for each of molecule-wise classifications.
The system consists of 64 water molecules.
For this, at the first mlwf and atomic position output of md.r, I tried to match two H positions and four mlwf center (not spread) positions to each of 64 O atoms.
My questions are as follows.
1. Would the order of atom index be maintained at the time series output of mlwf and/or atomic position (e.g., outputs at every 10 step)? Otherwise, would the atom index order change leading to a random order of atom index?
2. The DO length of D2O would be shorter than that of H2O.
Hence, I made the criterion of the nearest neighboring radius of 1.2 A for each O atom to find nearest neighboring two H atoms and four mlwf centers.
However, my analysis showed that many of mlwf center positions do not follow this while two H atoms are successfully found and listed for each of O atoms as shown below.
O_index:0 len(H_index_list):2 len(mlwf_index_list):3
O_index:1 len(H_index_list):2 len(mlwf_index_list):8
O_index:2 len(H_index_list):2 len(mlwf_index_list):4
O_index:3 len(H_index_list):2 len(mlwf_index_list):3
O_index:4 len(H_index_list):2 len(mlwf_index_list):4
O_index:5 len(H_index_list):2 len(mlwf_index_list):4
O_index:6 len(H_index_list):2 len(mlwf_index_list):3
O_index:7 len(H_index_list):2 len(mlwf_index_list):0
O_index:8 len(H_index_list):2 len(mlwf_index_list):4
O_index:9 len(H_index_list):2 len(mlwf_index_list):3
O_index:10 len(H_index_list):2 len(mlwf_index_list):1
O_index:11 len(H_index_list):2 len(mlwf_index_list):3
O_index:12 len(H_index_list):2 len(mlwf_index_list):3
O_index:13 len(H_index_list):2 len(mlwf_index_list):1
O_index:14 len(H_index_list):2 len(mlwf_index_list):4
O_index:15 len(H_index_list):2 len(mlwf_index_list):0
O_index:16 len(H_index_list):2 len(mlwf_index_list):3
O_index:17 len(H_index_list):2 len(mlwf_index_list):3
O_index:18 len(H_index_list):2 len(mlwf_index_list):4
O_index:19 len(H_index_list):2 len(mlwf_index_list):4
O_index:20 len(H_index_list):2 len(mlwf_index_list):4
O_index:21 len(H_index_list):2 len(mlwf_index_list):4
O_index:22 len(H_index_list):2 len(mlwf_index_list):0
O_index:23 len(H_index_list):2 len(mlwf_index_list):4
O_index:24 len(H_index_list):2 len(mlwf_index_list):4
O_index:25 len(H_index_list):2 len(mlwf_index_list):1
O_index:26 len(H_index_list):2 len(mlwf_index_list):5
O_index:27 len(H_index_list):2 len(mlwf_index_list):4
O_index:28 len(H_index_list):2 len(mlwf_index_list):4
O_index:29 len(H_index_list):2 len(mlwf_index_list):5
O_index:30 len(H_index_list):2 len(mlwf_index_list):5
O_index:31 len(H_index_list):2 len(mlwf_index_list):4
O_index:32 len(H_index_list):2 len(mlwf_index_list):4
O_index:33 len(H_index_list):2 len(mlwf_index_list):4
O_index:34 len(H_index_list):2 len(mlwf_index_list):6
O_index:35 len(H_index_list):2 len(mlwf_index_list):5
O_index:36 len(H_index_list):2 len(mlwf_index_list):4
O_index:37 len(H_index_list):2 len(mlwf_index_list):0
O_index:38 len(H_index_list):2 len(mlwf_index_list):0
O_index:39 len(H_index_list):2 len(mlwf_index_list):0
O_index:40 len(H_index_list):2 len(mlwf_index_list):4
O_index:41 len(H_index_list):2 len(mlwf_index_list):0
O_index:42 len(H_index_list):2 len(mlwf_index_list):1
O_index:43 len(H_index_list):2 len(mlwf_index_list):0
O_index:44 len(H_index_list):2 len(mlwf_index_list):3
O_index:45 len(H_index_list):2 len(mlwf_index_list):3
O_index:46 len(H_index_list):2 len(mlwf_index_list):3
O_index:47 len(H_index_list):2 len(mlwf_index_list):6
O_index:48 len(H_index_list):2 len(mlwf_index_list):6
O_index:49 len(H_index_list):2 len(mlwf_index_list):1
O_index:50 len(H_index_list):2 len(mlwf_index_list):4
O_index:51 len(H_index_list):2 len(mlwf_index_list):4
O_index:52 len(H_index_list):2 len(mlwf_index_list):0
O_index:53 len(H_index_list):2 len(mlwf_index_list):0
O_index:54 len(H_index_list):2 len(mlwf_index_list):5
O_index:55 len(H_index_list):2 len(mlwf_index_list):0
O_index:56 len(H_index_list):2 len(mlwf_index_list):4
O_index:57 len(H_index_list):2 len(mlwf_index_list):5
O_index:58 len(H_index_list):2 len(mlwf_index_list):4
O_index:59 len(H_index_list):2 len(mlwf_index_list):0
O_index:60 len(H_index_list):2 len(mlwf_index_list):5
O_index:61 len(H_index_list):2 len(mlwf_index_list):0
O_index:62 len(H_index_list):2 len(mlwf_index_list):1
O_index:63 len(H_index_list):2 len(mlwf_index_list):1
I use the length conversion from Bohr to Angstrom when the results was taken from md.r.
I think that the unit of mlwf center positions should be the same as that of atomic positions (i.e., Bohr). Is it right?
I attached the file of the first output named md_first_output.r.
Would you let me know what would be wrong with it?
Best regards,
Young