Alon Grinberg Dana

While generating a model, I got the following trace: ``` Traceback (most recent call last): File "/home/alongd/anaconda3/envs/rmg_env/lib/python3.7/site-packages/julia/pseudo_python_cli.py", line 308, in main python(**vars(ns)) File "/home/alongd/anaconda3/envs/rmg_env/lib/python3.7/site-packages/julia/pseudo_python_cli.py", line 59, in python scope =...

We should consider improving our sigma, epsilon and Delta-E_down estimations using Jasper's method: [A. W. Jasper, Int. J. Chem. Kinet., 2020, 52, 387–402](https://onlinelibrary.wiley.com/doi/epdf/10.1002/kin.21358)

We should consider improving our L-J and parameter estimations based on the strategy and formulas discussed in A.W. Jasper 2020, [10.1002/kin.21358](https://doi.org/10.1002/kin.21358).

Unsuccessful atom mapping attempts

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**Describe the bug** The `Molecule.align()` method for atom mapping could not successfully map some (relatively simple?) examples. The problem seems to be in mapping H atoms. ## Example 1: ```...

[WIP] [draft] Add a TS search module

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## Description This PR enhances fractal with reaction transition state search capabilities. Methods which will be implemented are: AutoTST, DE-GSM, brute-force heuristics, KinBot, ML, NEB via ASE, NEB via TeraChem,...

Added a species constraint for the max number of rings fused together

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### Motivation or Problem Sometimes users know they are not interested in ring growth in their model, yet RMG spends significant time on suggesting species with complex fused rings. Using...

Solution phase models might include PDep rates from libraries

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### Bug Description If a kinetic library has pressure-dependent rates, and this library is used in a simulation involving a LiquidReactor, some of these rates end up in the core,...

A question regarding this awesome tool: I'm trying to represent a chemical reaction in 3D with atom indices. I'd like the 2nd reactant, for example, to have consecutive atom indices...

Rate coefficient plot isn't being diplayed when many sources are available

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Searching for reaction kinetics for [CH3] + [CH3] gives 66 results (most are R_reccombination/NIST), and the plot shows only the long legend, and is unreadable. 

Searching for a reaction with only two or more library sources that report identical rates may result in a weird-looking averaged rate:  At a first glance it looks as...