Questions tagged [software]

For questions about matter modeling software. Questions can be about usage or recommendations.

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13
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Empirically determining thermostat damping factor

Is there a way to determine an appropriate thermostat damping factor given a timestep size and a numerical integration method? I am computing a set of simulations in LAMMPS, using ReaxFF, tracking ...
9
votes
0answers
82 views

Is there any code that runs WHAM starting from histograms rather than time series?

I'm looking for a way to run the Weighted Histogram Analsys Method, but I don't have a time series to feed to the code as usually happens, but rather I have histograms coming from the debiasing of a ...
6
votes
0answers
35 views

What could be the possible causes of the energy difference in the following calculating using Octopus (TDDFT) code?

I am trying to do a simple ground state energy calculation of methane molecule using the Octopus (TDDFT) code. The example is already available in the octopus manual. ...
6
votes
0answers
96 views

Fix deposit and USER-REAXC: pre-allocating memory for atoms when using LAMMPS with ReaxFF

I would like to use "fix deposit" with ReaxFF to add atoms to a simulation in which I deposit molecules on a surface. I have built working scripts for my system with other force fields. ...
5
votes
0answers
28 views

Interpreting Critic2 charge analysis in metallic systems

I'm using Critic2 software to perform post-processing of the charge density of metallic alloys. With the charge density obtained from the Self-Consistent-Field calculation (for that I'm using Quantum ...
3
votes
0answers
15 views

How can I calculate the exchange energy for a molecule in PySCF?

I am trying to generate exchange energy separately in pyscf but didn't see a way to do that. For correlation energy, it's fairly simple but do you have any idea how to calculate exchange energy?