How to Fix Negative Zone Volume

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I'm using Rhino + Grasshopper ecosystem for energy modelling, so my case might not help you.

Firstly, I recommend to output all warnings by setting as follows in your idf file.

Output:Diagnostics,
    DisplayAllWarnings;      !- Key 1

I'm not sure if it can be set in OpenStudio...

Secondly, after running simulation, do you see warnings similar to the following in your err file?

   ** Warning ** CheckConvexity: Zone="6F_LOBBY", Surface="6F_LOBBY_SRF007" is non-convex.
   **   ~~~   ** ...vertex 2 to vertex 3 to vertex 4
   **   ~~~   ** ...vertex 2=[29.12,170.22,37.00]
   **   ~~~   ** ...vertex 3=[29.12,170.22,49.00]
   **   ~~~   ** ...vertex 4=[91.15,170.22,49.00]
   ** Warning ** GetVertices: Floor is upside down! Tilt angle=[0.0], should be near 180, Surface="6F_LOBBY_SRF015", in Zone="6F_LOBBY".
   **   ~~~   ** Automatic fix is attempted.
   ** Warning ** CheckConvexity: Zone="6F_LOBBY", Surface="6F_LOBBY_SRF016" is non-convex.
   **   ~~~   ** ...vertex 5 to vertex 6 to vertex 7
   **   ~~~   ** ...vertex 5=[91.15,170.22,37.00]
   **   ~~~   ** ...vertex 6=[91.15,162.47,37.00]
   **   ~~~   ** ...vertex 7=[91.15,162.47,32.00]
   ** Warning ** Indicated Zone Volume <= 0.0 for Zone=6F_LOBBY
   **   ~~~   ** The calculated Zone Volume was=-63155.13
   **   ~~~   ** The simulation will continue with the Zone Volume set to 10.0 m3.

The negative zone volume in my model was fixed by fixing the "upside down" warning and the "non-convex" warning. For example, if the surface with the warning is rectangle and has 4 vertices in your idf file in the followng order:

Vertex1 X,Y,Z -> Vertex2 X,Y,Z -> Vertex3 X,Y,Z -> Vertex4 X,Y,Z,

please try changing the order in your idf file as follows

Vertex4 X,Y,Z -> Vertex3 X,Y,Z -> Vertex2 X,Y,Z -> Vertex 1 X,Y,Z.