Tutorial on creating an input format about toml-f

[aslozada]

Common walk-through in gromacs, lammps, tinker, dlpoly

1. Define the box simulation: coordinates, conectivities("topology"), dimensions, format (with/without constrainsts)
2. Define integration time
3. Define ensemble (nvt, npt, grand-canonical, gibbs)
4. Define thermostat
5. Define force field
6. Define types analyses (v.g., pair distribution, normal modes)
7. Define radii-cut
8. Define external field ** uncommon
9. Define type of run ("thermalisation" or sampling)
10. Define frequency for sampling

Common walk-through in stochastic simulation (usually Monte Carlo Methods): Cassandra, MCCCS Towhee, dlmonte

1. Define the box simulation: coordinates, format (with/without constraints)
2. Define number of configurations
3. Define ensemble (nvt, npt, grand-canonical, gibbs)
4. Define type of potential
5. Define radii-cut
6. Define types analyses (v.g., pair distribution)
7. Define type of run ("thermalisation" or sampling)
8. Define frequency for sampling

[aslozada]

Provide a complete walk-through for building a configuration file for an application, discussing advantages and disadvantages of certain data structures, would also be a good choice for a tutorial.

I can help? I work in theoretical/computational chemistry, and I consider that this can be a very useful methodology/tool

[awvwgk]

Exactly the kind of workflows I had in mind, a shorter workflow is probably preferable as the tutorial has to create the input for each step. The more of the actual calculation steps can be put towards a library calls the better, since the main target should be to design the input, running the simulation with the designed input file is the reward for the course in the end.

[aslozada]

a bit of statistics (google trends 2004-2022)

potential public, mainly in gromacs and lammps

maybe, a shorter walk-through: 1 -> 2 -> 3 -> 4 -> 5 -> 7

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Alternatively, for a walk-through test with molecular dynamics (ab initio), I find CP2K or ORCA to be good options. In this case, the most simplified is ORCAMD

A fake "orcadm.toml" :)

name = "calc_name"

[theory] 
level = "MD BLYP D3 def2-SVP"
[directory]
coordinate-file = "coord.xyz"

[md]
initvel ="300"
thermostat =  "berendsen"
run =" 2000"

[awvwgk]

Sure, all contributions are welcome here. You already proposed some nice workflows to encode in a configuration above, which could become a tutorial. I'm undecided on the scope yet, whether it is worth to aim at a beginner tutorial and try for an effortless and surefire setup or go for something more advanced.