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Dear Developers,
I am encountering an issue while simulating DNA with implicit solvent using OpenMM. My system consists of two DNA strands and several Na ions. I have observed that the Na ions move…
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See https://github.com/MDAnalysis/mdanalysis/pull/1692/commits/8bad42896a16e4ac8662b4886c8b02edc075afeb
The other selections can already choose to use the kdtree option that works also with periodi…
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Defect Description
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**Describe the defect**
##### What did you expect to see happen?
The system should stick to the periodic condition for the defined initial storage level a…
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When restarting a hydro problem with reflecting boundary conditions, non-conservation of mass occurs within 1 timestep. The conservation relative error is of the order 10^{-9}. (Mass is conserved to m…
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We should expect that for non-periodic axis cumsum should start integration with first value as 0 (if using outer or left for the axis being cumsumed to), and increase or decrease accordingly.
Inst…
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Most of the important functions in [``scipy.ndimage``](https://docs.scipy.org/doc/scipy-1.0.0/reference/ndimage.html) support periodic boundary conditions via ``mode="wrap"`` (e.g. [convolve](https://…
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I have modified the [simple 1D diffusion example](https://clima.github.io/OceananigansDocumentation/v0.90.13/literated/one_dimensional_diffusion/) to test how to correct the boundary conditions by usi…
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Improve crack mode in order to
- [x] Work with periodic boundary conditions (PBC)
- [x] Crack floes as a result of a shock
- [x] Crack floes as a result of pressure (= many micro-impulses from L…
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Hi! When I read the code about the Periodic(as following):
`class PeriodicBC(BC):
"""Periodic boundary conditions on component_x."""
def __init__(self, geom, component_x, on_boundary, der…
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### Discussed in https://github.com/idaholab/moose/discussions/23275
Originally posted by **grld** January 30, 2023
Dear community,
I would like to use the MOOSE tensor mechanics module to …