poly_info.md - Opengist

poly_info.md · 2.7 KiB · Markdown 原始檔案

The `neighbour_list` program only works with the old format of the supercell configuration. These days we almost always use the `rmc6f` format, but before this format, there was an old version of the configuration in the `rmc3` format. The `data2config` program can be used to convert from `rmc6f` to `rmc3` (with the extension of `cfg`). For the conversion, we basically want to generate a `1x1x1` 'supercell' from the input `rmc6f` configuration, so nothing is really happening except from the format conversion. The `neighbour_list` command can then be run with the created `cfg` file from previous step, and we just need to follow the prompt to provide answers to those questions about the center and surrounding atoms, the maximum distance between them and the output file. Multiple files can be generated by answer `y` to the question `Produce another file (y/<n>)`. Then we need to manually prepare a `.poly` file containing the information about the expected bond lengths regarding the polyhedron. The input lines are specific to each type of supported polyhedron -- see section 4.9 in the manual. Apart from the expected bond length is each line, two entries are also expected in each line, to specify the weight for bond and angle constraint, respectively. The weight is applied in the positive way, i.e., the larger of the number, the stronger weight to be applied. > For the `get_poly_gapo4` command involved in `ex_6`, it is just a bash script that goes over all the mentioned steps here in a single shot. The contents of the script are pasted below. Basically, the first two lines run the `data2config` for the format conversion. The following lines are for preparing the input file for running `neighbour_list` and then running the program. Then we prepare the `.poly` file by filling in the necessary contents, which is, again, specific to the type of polyhedron for `ex_6`. ```bash echo $1 > .rmc_tempy data2config -rmc3 -order [Ga P O] -supercell [1 1 1] $1.rmc6f < .rmc_tempy > .delete_me echo $1.cfg > .rmc_tempy echo 1 >> .rmc_tempy echo 3 >> .rmc_tempy echo 2.5 >> .rmc_tempy echo $1.alo >> .rmc_tempy echo y >> .rmc_tempy echo 3 >> .rmc_tempy echo 1 >> .rmc_tempy echo 2.5 >> .rmc_tempy echo $1.oal >> .rmc_tempy echo y >> .rmc_tempy echo 2 >> .rmc_tempy echo 3 >> .rmc_tempy echo 2.5 >> .rmc_tempy echo $1.po >> .rmc_tempy echo y >> .rmc_tempy echo 3 >> .rmc_tempy echo 2 >> .rmc_tempy echo 2.5 >> .rmc_tempy echo $1.op >> .rmc_tempy echo n >> .rmc_tempy neighbour_list < .rmc_tempy >> .delete_me echo Bondlength Bondweight Angleweight > $1.poly echo 1.820 8000 2400 >> $1.poly echo 1.538 16000 4800 >> $1.poly rm .rmc_tempy rm .delete_me rm $1.cfg ``` --- Yuanpeng Zhang @ 07/29/2025 09:36:18 EST SNS-HFIR, ORNL ---

The neighbour_list program only works with the old format of the supercell configuration. These days we almost always use the rmc6f format, but before this format, there was an old version of the configuration in the rmc3 format. The data2config program can be used to convert from rmc6f to rmc3 (with the extension of cfg). For the conversion, we basically want to generate a 1x1x1 'supercell' from the input rmc6f configuration, so nothing is really happening except from the format conversion.

The neighbour_list command can then be run with the created cfg file from previous step, and we just need to follow the prompt to provide answers to those questions about the center and surrounding atoms, the maximum distance between them and the output file. Multiple files can be generated by answer y to the question Produce another file (y/<n>).

Then we need to manually prepare a .poly file containing the information about the expected bond lengths regarding the polyhedron. The input lines are specific to each type of supported polyhedron -- see section 4.9 in the manual. Apart from the expected bond length is each line, two entries are also expected in each line, to specify the weight for bond and angle constraint, respectively. The weight is applied in the positive way, i.e., the larger of the number, the stronger weight to be applied.

For the get_poly_gapo4 command involved in ex_6, it is just a bash script that goes over all the mentioned steps here in a single shot. The contents of the script are pasted below. Basically, the first two lines run the data2config for the format conversion. The following lines are for preparing the input file for running neighbour_list and then running the program. Then we prepare the .poly file by filling in the necessary contents, which is, again, specific to the type of polyhedron for ex_6.

echo $1 > .rmc_tempy
data2config -rmc3 -order [Ga P O] -supercell [1 1 1] $1.rmc6f < .rmc_tempy > .delete_me
echo $1.cfg > .rmc_tempy
echo 1 >> .rmc_tempy
echo 3 >> .rmc_tempy
echo 2.5 >> .rmc_tempy
echo $1.alo >> .rmc_tempy
echo y >> .rmc_tempy
echo 3 >> .rmc_tempy
echo 1 >> .rmc_tempy
echo 2.5 >> .rmc_tempy
echo $1.oal >> .rmc_tempy
echo y >> .rmc_tempy
echo 2 >> .rmc_tempy
echo 3 >> .rmc_tempy
echo 2.5 >> .rmc_tempy
echo $1.po >> .rmc_tempy
echo y >> .rmc_tempy
echo 3 >> .rmc_tempy
echo 2 >> .rmc_tempy
echo 2.5 >> .rmc_tempy
echo $1.op >> .rmc_tempy
echo n >> .rmc_tempy
neighbour_list < .rmc_tempy >> .delete_me
echo Bondlength  Bondweight  Angleweight > $1.poly
echo 1.820       8000        2400 >> $1.poly
echo 1.538       16000       4800 >> $1.poly
rm .rmc_tempy
rm .delete_me
rm $1.cfg

Yuanpeng Zhang @ 07/29/2025 09:36:18 EST

SNS-HFIR, ORNL