From 047fd9ec0cfef1138f661cee95fa63edd3ce3ef4 Mon Sep 17 00:00:00 2001
From: Ludger Paehler <ludger.paehler@tum.de>
Date: Sat, 16 Mar 2024 01:05:14 -0700
Subject: [PATCH] Yank modred from the package as it is unused.

---
 hydrogym/firedrake/utils/linalg.py           | 83 --------------------
 hydrogym/firedrake/utils/modred_interface.py | 44 -----------
 pyproject.toml                               |  1 -
 3 files changed, 128 deletions(-)
 delete mode 100644 hydrogym/firedrake/utils/modred_interface.py

diff --git a/hydrogym/firedrake/utils/linalg.py b/hydrogym/firedrake/utils/linalg.py
index 54df8e3..a7fdd2d 100644
--- a/hydrogym/firedrake/utils/linalg.py
+++ b/hydrogym/firedrake/utils/linalg.py
@@ -4,7 +4,6 @@
 import numpy as np
 import ufl
 from firedrake import logging
-from modred import PODHandles, VectorSpaceHandles
 from scipy import sparse
 
 # Type suggestions
@@ -91,88 +90,6 @@ def inner_product(u, v):
     return inner_product
 
 
-def pod(
-    flow: FlowConfig,
-    snapshot_handles: Iterable[Snapshot],
-    r: int,
-    mass_matrix,
-    decomp_indices=None,
-    remove_mean=True,
-    mean_dest="mean",
-    atol=1e-13,
-    rtol=None,
-    max_vecs_per_node=None,
-    verbosity=1,
-    output_dir=".",
-    modes_dest="pod",
-    eigvals_dest="eigvals.dat",
-    pvd_dest=None,
-    coeffs_dest="coeffs.dat",
-    field_name="q",
-):
-    """
-    Args:
-        ``flow``: ``FlowConfig`` for the POD (used for weighted inner product)
-
-        ``snapshots``: List of Snapshot handles
-
-        ``r``: Number of modes to compute
-
-    Kwargs:
-        ``decomp_indices``: Indices to use in method of snapshots (defaults to ``range(r)``)
-
-    NOTE: could actually take the "flow" dependence out if we replaced the PVD with a postprocessing callback...
-    """
-    if fd.COMM_WORLD.size > 1:
-        raise NotImplementedError("Not yet supported in parallel")
-
-    # Compute actual POD
-    if decomp_indices is None:
-        decomp_indices = range(r)
-
-    inner_product = define_inner_product(mass_matrix)
-
-    if remove_mean:
-        base_vec_handle = Snapshot(f"{output_dir}/{mean_dest}")
-        base_vec_handle.put(vec_handle_mean(snapshot_handles))
-
-        # Redefine snapshots with mean subtraction
-        snapshot_handles = [
-            Snapshot(snap.filename, base_vec_handle=base_vec_handle)
-            for snap in snapshot_handles
-        ]
-        logging.log(logging.DEBUG, "Mean subtracted")
-
-    logging.log(logging.DEBUG, "Computing POD")
-    POD = PODHandles(
-        inner_product=inner_product,
-        max_vecs_per_node=max_vecs_per_node,
-        verbosity=verbosity,
-    )
-    POD.compute_decomp(snapshot_handles, atol=atol, rtol=rtol)
-
-    # Vector handles for storing snapshots
-    mode_handles = [
-        Snapshot(filename=f"{output_dir}/{modes_dest}{i}") for i in range(r)
-    ]
-    POD.compute_modes(range(r), mode_handles)
-
-    POD.put_eigvals(f"{output_dir}/{eigvals_dest}")
-
-    # Save for visualization
-    if pvd_dest is not None:
-        pvd = fd.File(f"{output_dir}/{pvd_dest}", "w")
-        for i, mode in enumerate(mode_handles):
-            u, p = mode.get().as_function().subfunctions
-            pvd.write(u, p, flow.vorticity(u))
-
-    # Compute temporal coefficients
-    coeffs = POD.compute_proj_coeffs().T  # If all snapshots used for POD
-    np.savetxt(f"{output_dir}/{coeffs_dest}", coeffs, fmt="%0.6f", delimiter="\t")
-
-    return coeffs, mode_handles
-
-
 def project(basis_handles, data_handles, mass_matrix):
     inner_product = define_inner_product(mass_matrix)
     vec_space = VectorSpaceHandles(inner_product)
diff --git a/hydrogym/firedrake/utils/modred_interface.py b/hydrogym/firedrake/utils/modred_interface.py
deleted file mode 100644
index 3e365aa..0000000
--- a/hydrogym/firedrake/utils/modred_interface.py
+++ /dev/null
@@ -1,44 +0,0 @@
-import firedrake as fd
-import modred as mr
-import numpy as np
-
-from .utils import set_from_array
-
-
-class Snapshot(mr.VecHandle):
-    """Interface between time series in numpy binaries and modred"""
-
-    def __init__(self, filename: str, base_vec_handle=None, scale=None):
-        super().__init__(base_vec_handle=base_vec_handle, scale=scale)
-
-        if filename[-4:] != ".npy":
-            filename += ".npy"
-        self.filename = filename
-
-    def _get(self, filename=None):
-        # with fd.CheckpointFile(self.filename, 'r') as chk:
-        #     q = chk.load_function(self.flow.mesh, name=self.name, idx=self.idx)
-        if filename is None:
-            filename = self.filename
-        return np.load(filename)
-
-    def _put(self, q, filename=None):
-        if filename is None:
-            filename = self.filename
-        np.save(filename, q)
-
-    def as_function(self, flow):
-        if fd.COMM_WORLD.size > 1:
-            raise NotImplementedError
-
-        q = fd.Function(flow.mixed_space)
-        set_from_array(q, self.get())
-        return q
-
-
-def vec_handle_mean(vec_handles):
-    """Compute the mean of the vector handles and return as SnapshotVector"""
-    from functools import reduce
-
-    data = [h.get() for h in vec_handles]
-    return reduce(lambda x1, x2: x1 + x2, data) * (1 / len(data))
diff --git a/pyproject.toml b/pyproject.toml
index 656be1e..cdff794 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -45,7 +45,6 @@ control = "^0.9.2"
 dmsuite = "^0.1.1"
 gmsh = "^4.11.1"
 gym = "^0.26.2"
-modred = "^2.1.0"
 python = "^3.10"
 torch = "^2.0"