Timeline for Minimum image convention for a MD simulation in Python
Current License: CC BY-SA 4.0
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| when toggle format | what | by | license | comment | |
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| Feb 7, 2025 at 18:21 | comment | added | Lana.s | @Slavensky Yes technically it does, but the idea was for it to "disappear" when hitting the upper boundary, and reappear from the lower one as in PBC instead of making this reflection behaviour | |
| Feb 7, 2025 at 18:09 | comment | added | Slavensky | Well, from the position plot above, it looks like it does exactly that: The position of atom 2 becomes larger than $L=8$, so 8 should be retracted from its position, thus the position will jump from 8 to 0. What is the difference between that behaviour and the one you describe? | |
| Feb 7, 2025 at 16:58 | comment | added | Lana.s | @Slavensky I'm trying to implement periodic boundary conditions so that if the atom leaves the boundary of the system it appears from the other side, i.e if it leaves from the bottom boundary it just pops out from the upper one! But that does not seem to be whats actually happening.. | |
| Feb 7, 2025 at 16:21 | comment | added | Slavensky |
Can you elaborate a bit more about what you expect to happen. Right now, you set the position as X_new %= L in update_pos_vel, which means that the position X of the atom will have L subtracted from it if X>L.
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| Feb 7, 2025 at 15:05 | history | asked | Lana.s | CC BY-SA 4.0 |