Analyzing objects and geometries with buff-analyze

The buff-em suite comes with a simple standalone utility named buff-analyze that you can use to gather some quick statistics on meshed objects and scattering geometries described by mesh files and geometry files.

There are several situations in which this can be useful:

You want to know how much memory will be occupied by the VIE matrix for a geometry described by a .buffgeo file.
Your .buffgeo file contains multiple OBJECTs, each described by separate volume meshes and possibly displaced and/or rotated, and you want to visualize the full geometry to make sure the file you wrote actually describes what you want.
You have created a .trans file describing a list of geometrical transformations to be applied to your geometry, and before running a full calculation you want to do a quick sanity check by visualizing the geometry under each of your transformations to make sure they are what you intended.
Your geometry involves one or more spatially inhomogeneous permittivities, and you want a plot of permittivity vs. space to double-check that the permittivity you got is the one you wanted.
You have created a new volume mesh and you want to do a preliminary calculation to compute the buff-em cache before you start any actual calculations.

Table of Contents

buff-analyze Command-Line Options
buff-analyze console output
- Running buff-analyze on a geometry file
Running buff-analyze to precompute the buff-em cache

buff-analyze Command-Line Options

Options specifying the file to analyze

--geometry MyGeometry.buffgeo

Analyze a full geometry described by a buff-em geometry.

--mesh MyObject.vmsh

--meshFile MyObject.vmsh

Analyze a single object described by a volume mesh. (The two options are synonymous.)

Option specifying a list of geometrical transformations

--TransFile MyTransFile.trans

Specify a list of geometrical transformations to be applied to a geometry. This is useful for (a) checking that your transformation file can be properly parsed by buff-em, and (b) producing a visualization output file to confirm that the transformations you got are the ones you wanted.

Options controlling the generation of visualization files

--WriteGMSHFiles

Append visualization data to gmsh visualization files that provides information on how the geometry is represented internally within buff-em.

--PlotPermittivity

Produces a visualization file showing the spatial variation of the dielectric permittivity in your geometry. This is useful if you specified any .SVTensor files and want to doublecheck that your specification was interpreted correctly by buff-em.

Options controlling the generation of cache files

--WriteCache

buff-analyze console output

Running buff-analyze on a geometry file

Running buff-analyze on a typical buff-em geometry file yields console output that looks like this:

% buff-analyze --geometry ThinPinwheel_N7_2190.buffgeo

*
* Geometry file MESH__ThinPinwheel_N7_2190__MAT__Gold.buffgeo: 1 objects 
*

**************************************************
* Object 0: 
**************************************************
Volume ThinPinwheel_N7_2190 (file ThinPinwheel_N7_2190.vmsh): 
 878 vertices 
 2190 tetrahedra 
 3568 interior faces 
 1624 exterior faces 

 Volume:          8.682680e-01 
 Surface area:    1.479837e+01 

 Moment of inertia: {+8.91e-01,+8.91e-01,+1.78e+00}

 Min/Max/Avg Quality factor: 1.376158e-01 / 9.928907e-01 / 7.479818e-01 

Thank you for your support.

Running buff-analyze to precompute the buff-em cache

As discussed here, the first calculation performed by buff-em on a given volume mesh is considerably slower than all subsequent calculations, because on this first calculation the code computes and certain frequency- and material-independent quantities needed to assemble the system matrix, which it then writes to a binary data file named Mesh.cache (where Mesh.vmsh is the name of the mesh file as specified using the MESHFILE keyword in a .buffgeo file). In some case it is convenient to generate the .cache file before running any actual scattering or non-equilibrium Casimir calculations. (For example, if you are planning to launch a bunch of parallel buff-em jobs that will refer to the same .vmsh files---even if the corresponding objects have different material properties!---you will want to precompute the .cache file so that the jobs don't all repeat the same calculation when they start up).

You can use buff-analyze to precompute the cache file for a given volume mesh like this:

 % buff-analyze --mesh MyObject.vmsh --WriteCache

This will produce a file named MyObject.cache. If the environment variable BUFF_CACHE_DIR is set, then this file will be written to the directory it specifies; otherwise, the file will be written to the current working directory.

Then all subsequent calculations that refer to MyObject.vmsh (including calculations performed by buff-scatter, buff-neq, or API codes) will automatically read in the MyObject.cache file (assuming they can find it either in their current working directory or in the directory specified by BUFF_CACHE_DIR), thus bypassing the costly cache-computation step and significantly accelerating calculations.