Dear all,
I have a two elementary questions about the dump atom and similar dump commands:
1- What is the rationale behind outputting the scaled atoms coordinates as the default setting for the dump atom command? Is it computationally better?
2- If the scaled or unsealed coordinates are out of the simulation box size, how I need to fix them in the data analyzing step (I know there is a dump_modify pbc on/off command but it is computationally expensive in the case of my simulations)?
Thanks in advance for your help,
Amir Sadeghi
Dear all,
I have a two elementary questions about the dump atom and similar dump commands:
1- What is the rationale behind outputting the scaled atoms coordinates as the default setting for the dump atom command? Is it computationally better?
no. it is just an arbitrary choice. some people prefer fractional coordinates.
2- If the scaled or unsealed coordinates are out of the simulation box size, how I need to fix them in the data analyzing step (I know there is a dump_modify pbc on/off command but it is computationally expensive in the case of my simulations)?
no, it is not expensive compared to the force computation or time needed for i/o. please note, that you will usually only output coordinates every 1000th step of fewer, so it won’t really matter much, even if it were more expensive.
axel.