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Updating documentation to be more explicit in simulation block #70

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Updating documentation to be more explicit in simulation block
kaeldai Nov 28, 2018
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Updating table
kaeldai Nov 28, 2018
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54 changes: 53 additions & 1 deletion docs/SONATA_DEVELOPER_GUIDE.md
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Expand Up @@ -844,6 +844,59 @@ The "run" block specifies some global parameters of the simulation run, such as
"spike_threshold": -15,
},

<table>
<tr>
<td>Key</td>
<td>Description</td>
<td>Type</td>
<td>Required</td>
<td>Default</td>
</tr>
<tr>
<td>tstart</td>
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@hernando hernando Nov 29, 2018

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rename to start_time for consistency with the reports sections

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@hernando hernando Jan 17, 2019

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@apdavison, @salvadord, @pgleeson, are you OK with the suggested renaming?

<td>Start time of the simulation.</td>
<td>float</td>
<td>False</td>
<td>0.0</td>
</tr>
<tr>
<td>tstop</td>
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@hernando hernando Nov 29, 2018

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rename to end_time for consistency

<td>Stop time of the simulation.</td>
<td>float</td>
<td>True</td>
<td></td>
</tr>
<tr>
<td>dt</td>
<td>Time step size.</td>
<td>float</td>
<td>True</td>
<td></td>
</tr>
<tr>
<td>dL</td>
<td>For compartmental cell models, used to define the minimum segment size of each given section. For a section of length L > dL, the section will be partitioned into 1 + 2 \* int(section.L / (2\*dL)) segments.</td>
<td>float</td>
<td>False</td>
<td> </td>
</tr>
<tr>
<td>spike_threshold</td>
<td>The default membrane potential value at which it can be assumed an action potential can be recorded.</td>
<td>float</td>
<td>False</td>
<td></td>
</tr>
<tr>
<td>block_step_size</td>
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@hernando hernando Nov 29, 2018

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This name is not very clear. If I understand the description correctly I'd rename it to "reporting_skipped_frames" , "skipped_frames", "skip_report_frames", "reporting_start_frame"
I'd also use double for all timestamps, but I think that this is irrelevant for json anyway (isn't number the actual typename in any case?)

<td>Used by the simulator to determine after how many time steps should it save the simulation and results (assume such behavior is available).</td>
<td>int</td>
<td>False</td>
<td></td>
</tr>
</table>


### Conditions Configuration

This block specifies optional global parameters with reserved meaning associated with manipulation of the "in silico preparation".
Expand Down Expand Up @@ -1379,4 +1432,3 @@ Allen folks to fill in
For the case that the model_template follows the *bmtk* schema, the following is the expected structure of the hoc template.

Allen folks to fill in