Gradient Descent (#181)

* Added ArbitraryDistributionVolumeEmitter

* Updated particle weight calculation

* renamed thermionic_emission test directory to emission

* arbitrary seed from uniform distribution

* Bug fixes and changes to test

* add test for arbitrary seeding

* Changed position sampling, added test

* Removed unused imports and code

* revert traceback printout

* Added comments for binning particle positions

* increased rtol for test

* Allow input of any 2d array, add interpolation of 2d array onto current simulation grid

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* Updated changelog

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* Updated changelog

* update version

* created steady_state_descent.py file

* Added coarsening algorithm

* Added ability to read numpy data and coarsen grid

* Added regression function calculation

* Solve system of equations rather than curve fit

* Use skimage block_reduce

* Hard coded inverse exponential solve

* take mean if exponential equation can't be solved

* Added special cases to use linear regression

* Update docstring

* Added command line arguments

* Modified linear regression logic and added main function

* Added entry point

* Change output file name

* Change output file name

* Fixed interpolate grid

* updated arbitrary distribution emitter test

* Fix interpolation logic

* Changed to take in exact prediction timestep rather than a multiple

* Added ability to specify save directory

* Updated docstrings, removed unneeded files

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* Added gradient descent test, refactored code

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* Changed test parameters

* Increase rtol of arbitrary seed test by 0.01

* Update mewarpx/mewarpx/utils_store/plasma_density_oracle.py

Co-authored-by: Roelof Groenewald <[email protected]>

* Update changelog

* Update version

* Add controller for plasma density oracle

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* WIP oracle control

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* Allow oracle control bins to be overridden

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* Added command line arguments

* Fixed bugs, added info logging

* added ability to modify run_script

* removed unnecessary code

* Cleaned up code

* Refactored code to be clearer

* Update docstrings

* Added test

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* Added documentation about oracle_control

* Updated changelog

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* Fixed TOTAL_TIME calculation

* update wheel in docker build

* change numpy to oldest-supported-numpy for docker

* Updated formatting and documentation

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: KZhu-ME

mewarpx/changelog.csv

@@ -1,5 +1,18 @@
 Version, Physics version, Date,        List of changes
-8.2.1, 2, In progress, "
+8.3.0, 2, In progress, "
+
+**Features**:
+
+- Added
+  :class:`mewarpx.utils_store.plasma_density_oracle.PlasmaDensityOracle` to
+  predict particle densities at a given time point based on 3 input data points.
+- Added :class:`mewarpx.utils_store.oracle_control.OracleControl`
+        as a wrapper to automate calling
+  :class:`mewarpx.utils_store.plasma_density_oracle.PlasmaDensityOracle`
+  by automatically determining the best parameters for it.
+
+"
+8.2.1, 2, 5/31/2022, "
 
 **Other changes**:
 
@@ -8,12 +21,14 @@ Version, Physics version, Date,        List of changes
 "
 8.2.0, 2, 5/11/2022, "
 
+
 **Features**:
 
 - Added :class:`mewarpx.utils_store.json_util.MEWarpXEncoder` to encode a
         runinfo object into a JSON string.
 - Changed runinfo to be saved as JSON file instead of dpkl file.
 
+"
 8.1.1, 2, 5/9/2022, "
 
 **API Changes**:

mewarpx/medocker/docker_shared/python_packages.sh

@@ -16,6 +16,7 @@ INSTALL_CMD="python3 -m pip install --no-build-isolation "
 # internal warnings
 # https://github.com/Nike-Inc/gimme-aws-creds/issues/158
 python3 -m pip install --upgrade pip
+python3 -m pip install --upgrade wheel
 python3 -m pip install --upgrade setuptools keyring keyrings.alt
 
 # Build dependency of cmake
@@ -28,7 +29,7 @@ ${INSTALL_CMD} llvmlite
 
 # The builds of scipy and h5py on aarch64 depends on having these already installed
 ${INSTALL_CMD} cython
-${INSTALL_CMD} numpy
+${INSTALL_CMD} oldest-supported-numpy
 ${INSTALL_CMD} pkgconfig
 
 ${INSTALL_CMD} numba

mewarpx/mewarpx/_version.py

@@ -1,6 +1,6 @@
 # One and only one place to store the version info
 # https://stackoverflow.com/questions/458550/standard-way-to-embed-version-into-python-package
-__version_info__ = (8, 2, 1)
+__version_info__ = (8, 3, 0)
 __version__ = '.'.join([str(x) for x in __version_info__])
 
 # One and only one place to store the Physics version

mewarpx/mewarpx/emission.py

@@ -2067,8 +2067,7 @@ def _get_x_coords(self, npart):
 class ArbitraryDistributionVolumeEmitter(VolumeEmitter):
 
     """Varies density based on given particle density array. NPPC for each
-    species must be an integer greater than or equal to 1. Can only be used
-    with FixedNumberInjector."""
+    species must be an integer greater than or equal to 1."""
 
     geoms = ["XZ"]
 
@@ -2100,15 +2099,21 @@ def _interpolate_grid(input_grid):
             output_grid (np.ndarray): 2d array of current simulation dimensions
                 interpolated values from input_grid
         """
-
         input_shape = input_grid.shape
-        input_x = np.linspace(0.5, input_shape[0] - 0.5, input_shape[0])
-        input_z = np.linspace(0.5, input_shape[1] - 0.5, input_shape[1])
+        # pad edges with current edge values by 1 to avoid NaN when interpolating
+        input_x = np.linspace(-0.5, input_shape[0] + 0.5, input_shape[0] + 2)
+        input_z = np.linspace(-0.5, input_shape[1] + 0.5, input_shape[1] + 2)
+        input_grid = np.pad(input_grid, (1,), "linear_ramp")
+
         input_zz, input_xx = np.meshgrid(input_z, input_x)
+
+        input_xx = input_xx * mwxrun.nx/input_shape[0]
+        input_zz = input_zz * mwxrun.nz/input_shape[1]
         input_coord = np.column_stack([input_xx.flatten(), input_zz.flatten()])
 
-        output_xx = input_xx * mwxrun.nx/input_shape[0]
-        output_zz = input_zz * mwxrun.nz/input_shape[1]
+        output_x = np.linspace(0.5, mwxrun.nx - 0.5, mwxrun.nx)
+        output_z = np.linspace(0.5, mwxrun.nz - 0.5, mwxrun.nz)
+        output_zz, output_xx = np.meshgrid(output_z, output_x)
 
         output_grid = scipy.interpolate.griddata(
             input_coord, input_grid.flatten(), (output_xx, output_zz)