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I'm running an NVT Equilibration _after a minimization step_. The step size is `0.5*femtoseconds` and every 10 steps the energy and temperature are printed out. There are two issues:
1. Temperatu…
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A large structured hex (eventually mixed) mesh is needed and there are issues getting a mesh generator to easily produce this.
The [`matchedReader` branch](https://github.com/cwsmith/core/tree/matc…
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I'm running simulations of mixed ML/MM systems where part is computed with ANI-2x and part with Amber. As long as I specify `implementation='nnpops'` in the call to `createMixedSystem()` it works wel…
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The adjoint and finite-difference gradients are inconsistent when the `EigenmodeCoefficient` adjoint solver in Meep is applied to a case similar to that in @oskooi's [metagrating-meep.py](https://gith…
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PR #519 introduced tolerances on the evaluation of bsplines in order to avoid issues due to rounding errors near the domain boundaries. However the PR didn't change the evaluation algorithm. As a resu…
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> Hi,
> It means that D(x)=D(x+L), where L is the length of the box along x, so that in the following case:
> data = np.array([[3,3,0,3,3]])
> labels_out = cc3d.connected_components(data, conne…
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Hello!
I think there is a bug in AngleCS and AngleSN in MITgcm. Actually, it concerns the underlying 2D fields angleCosC and angleSinC calculated in s/r CALC_GRID_ANGLES. This s/r is called from in…
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I am unsure if this is the correct place to ask so I will try another channel if this repository is no longer supported!
Currently, I am working on an ASE based implementation of the geodesic inter…
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I am interested in wrapping the real-to-real (at least the discrete sine and discrete cosine) transforms. I set up a branch on my fork of pyFFTW and have written an implementation that appears to work…
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I run this code for proteins solvated in hexane. But some of my structures look like this and are just dispersed in space. no bonds.
my code:
```
from openmm.app import *
from openmm import *
…