Comments (4)
Also for the input file spec:
Mjolnir allows to split an input file to several toml files to avoid too long input file. Currently, adding table name to the splitted input file is discouraged.
# input.toml
[[systems]]
file_name = "system1.toml"
The above input file requires a toml file like the following.
# system1.toml
# [system] <- currently discouraged because
# it is already clear that
# this file is dedicated to a system.
particles = [
# ...
]
But now I think it is better to have a tabl in the splitted input files to show explicitly what does the file define. Of course one can guess what is defined in the file because each table requires different values, but it takes time to understand what is the content (and also requires knowledge about the input file). With a table name, we can easily see what is defined in the file. Users will be enforced to write the information explicitly in the file by requiring table, but I think it is better than to write comments manually.
So, here I propose changing the requirements for the splitted input files. It also introduce an extra complexity to read_*
because the current implementation also allows to define a table. To simplify the code, we also need to decide the way to split an input file.
The splitted input files correspond to one element of arrays of tables, [[systems]]
, [[forcefields]]
or something like that, so it is good to require a table for each file (e.g. [system]
for a file that defines an element of [[systems]]
).
from mjolnir.
ExcludedVolumePotential
that is used with a global interaction requires radius
for all the particles. But ExcludedVolumeWallPotential
that is used with an external interaction (it acts as a wall!) requires sigma
.
It should be fixed. I think radius
is better because it's clearer.
from mjolnir.
Finally I found that it is not clear to use different name and data type for the same table defined in a different file (like, [forcefield.global]
for an individual file and [[forcefields.global]]
in a separated file).
For now, I decided to use the same name, [[systems]]
and [[forcefields.global]]
for separated input files.
from mjolnir.
done.
from mjolnir.
Related Issues (20)
- enable to set positions of data points in FlexibleLocalAngle HOT 1
- remove deprecated features HOT 1
- simplify input for 3SPN2 HOT 1
- enable to generate initial velocities HOT 1
- energy calculation mode HOT 1
- support PDNS interaction HOT 1
- support PWMcos interaction
- documents in English HOT 1
- Multiple Basin Forcefield HOT 2
- update toml11 HOT 1
- try mdbook or docsify for docs HOT 2
- cmake option to skip tests
- pass string to Interactions.dump_energy() HOT 1
- Change MultipleBasin input format
- update sample input files HOT 1
- Add combination-rule class and simplify implementation in global potential HOT 2
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- DCD Header HOT 2
- merge calc_force and calc_energy via boolean template parameter HOT 1
- add `calc_force_and_virial` HOT 1
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from mjolnir.