# processEigenModesDampedPara

Computes damped eigenmodes for every packing `.mat` file in a directory. For
each file and each damping constant it: removes rattlers (`cleanRats`), builds
the system matrices (`matSpringDampMass`), and solves the quadratic eigenvalue
problem with `polyeig`. Uses a parallel pool, and chooses the `parfor` loop
dimension (files vs. damping values) automatically so more workers stay busy.
Input files must contain `x`, `y`, `Dn`, `K`, `Ly`, `Lx`, `P`, `N` (old packing
format).

## Default Syntax

```matlab
inPath = "path/to/packings/2d/hooke"      % string, directory of packing .mat files
outPath = "path/to/output"                % string, where results are saved
gammas = [0.001 0.01 0.03]                % double vector, damping constants
processEigenModesDampedPara(inPath, outPath, gammas)
```

Runs the full file x damping sweep in parallel and saves one combined
`2D_damped_eigenstuff_N*_*by*_K*_M*.mat` file containing `outData` (cells:
`eigenVectors`, `eigenValues`, `radii`, `positions`; columns: `pressure`,
`damping`, `Lx`, `Ly`, `springConstant`).

## Options

```matlab
opts.periodic    = true;    % logical, periodic boundary conditions in matSpringDampMass
opts.serial      = false;   % logical, run on the base MATLAB process instead of parpool
opts.singleFiles = false;   % logical, save one .mat per (file, damping) combination
                            %         (2D_eigenData_*by*_P*_damp*_K*_M*.mat) instead of one combined file
processEigenModesDampedPara(inPath, outPath, gammas, opts)
```

Note: in `opts.serial` mode only the last (file, damping) combination is kept
in the combined output — use `opts.singleFiles = true` with `opts.serial` to
save every combination individually.

## Examples

```matlab
% Parallel sweep over three dampings for all packings in a directory
processEigenModesDampedPara('data/packings/2d/hooke', 'data/junkyard/', [0.001 0.01 0.03]);

% Periodic boundary conditions
opts.periodic = true;
processEigenModesDampedPara('data/packings/2d/hooke', 'data/junkyard/', [0.01], opts);

% Serial run, saving one file per (packing, damping) pair
opts.serial     = true;
opts.singleFiles = true;
processEigenModesDampedPara('data/packings/2d/hooke', 'data/junkyard/', [0.01], opts);

% Single damping, no parallel overhead (one file x one gamma)
opts.serial = true;
processEigenModesDampedPara('data/packings/2d/hooke', 'data/junkyard/', [0.01], opts);
```

The combined output is the `outData` struct consumed by
`simEigenmode(..., loadPolyData = true)` and by `eigenWavespeed`.