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MaginnGroup / PyLAT

GNU General Public License v3.0
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The arrangement of molecule id #17

Closed Yongxiancheng closed 3 years ago

Yongxiancheng commented 3 years ago

In the README.md, there is one sentence-- Also required is the name and number of each molecule type in the system. To do this, use the --mol and --nummol flags. Use the same order as they were entered into the data file. Here is my little question, if the order of type in the data is 1-Na, 2-K, 3-Cl. While the order of molid is disordered, which means the molids are 1-Na, 2-K, 3-Na, 4-Cl, 4-K, 5-Cl, 6-Cl, 7-Cl, 8-Cl. Than I used the code --nummol 2 --nummol 2 --numnol 4 --mol Na --mol K --mol Cl. Woule the calculation automatically identify the molid 1-Na and 3-Na as the input code "--mol Na", or the input code "--mol Na" would appoint the molid 1-Na and 2-K?

mike5603 commented 3 years ago

The code identifies molecule type based on the molecule id, and it assumes that all of the molecules are sequential. So for your example, it would assume that molecules 1 and 2 would be Na, 3 and 4 would be K and 5-8 would be Cl. This is consistent with the output of packmol, which is by far the most widely used initialization code.

Yongxiancheng commented 3 years ago

Thank you for your kind reply. I will try to obey the rule of the program.