renamed polarizability model to pmodel

docs/source/generated/ramannoodle.polarizability.rst

@@ -7,39 +7,39 @@ Subpackages
 .. toctree::
    :maxdepth: 4
 
-   ramannoodle.polarizability.torch
+   ramannoodle.pmodel.torch
 
 Submodules
 ----------
 
-ramannoodle.polarizability.abstract module
+ramannoodle.pmodel.abstract module
 ------------------------------------------
 
-.. automodule:: ramannoodle.polarizability.abstract
+.. automodule:: ramannoodle.pmodel.abstract
    :members:
    :undoc-members:
    :show-inheritance:
 
-ramannoodle.polarizability.art module
+ramannoodle.pmodel.art module
 -------------------------------------
 
-.. automodule:: ramannoodle.polarizability.art
+.. automodule:: ramannoodle.pmodel.art
    :members:
    :undoc-members:
    :show-inheritance:
 
-ramannoodle.polarizability.interpolation module
+ramannoodle.pmodel.interpolation module
 -----------------------------------------------
 
-.. automodule:: ramannoodle.polarizability.interpolation
+.. automodule:: ramannoodle.pmodel.interpolation
    :members:
    :undoc-members:
    :show-inheritance:
 
 Module contents
 ---------------
 
-.. automodule:: ramannoodle.polarizability
+.. automodule:: ramannoodle.pmodel
    :members:
    :undoc-members:
    :show-inheritance:

docs/source/generated/ramannoodle.polarizability.torch.rst

@@ -4,42 +4,42 @@ polarizability.torch
 Submodules
 ----------
 
-ramannoodle.polarizability.torch.dataset module
+ramannoodle.pmodel.torch.dataset module
 -----------------------------------------------
 
-.. automodule:: ramannoodle.polarizability.torch.dataset
+.. automodule:: ramannoodle.pmodel.torch.dataset
    :members:
    :undoc-members:
    :show-inheritance:
 
-ramannoodle.polarizability.torch.gnn module
+ramannoodle.pmodel.torch.gnn module
 -------------------------------------------
 
-.. automodule:: ramannoodle.polarizability.torch.gnn
+.. automodule:: ramannoodle.pmodel.torch.gnn
    :members:
    :undoc-members:
    :show-inheritance:
 
-ramannoodle.polarizability.torch.train module
+ramannoodle.pmodel.torch.train module
 ---------------------------------------------
 
-.. automodule:: ramannoodle.polarizability.torch.train
+.. automodule:: ramannoodle.pmodel.torch.train
    :members:
    :undoc-members:
    :show-inheritance:
 
-ramannoodle.polarizability.torch.utils module
+ramannoodle.pmodel.torch.utils module
 ---------------------------------------------
 
-.. automodule:: ramannoodle.polarizability.torch.utils
+.. automodule:: ramannoodle.pmodel.torch.utils
    :members:
    :undoc-members:
    :show-inheritance:
 
 Module contents
 ---------------
 
-.. automodule:: ramannoodle.polarizability.torch
+.. automodule:: ramannoodle.pmodel.torch
    :members:
    :undoc-members:
    :show-inheritance:

docs/source/generated/ramannoodle.rst

@@ -9,7 +9,7 @@ Subpackages
 
    ramannoodle.dynamics
    ramannoodle.io
-   ramannoodle.polarizability
+   ramannoodle.pmodel
    ramannoodle.spectrum
    ramannoodle.structure
 

docs/source/introduction.rst

@@ -12,7 +12,7 @@ With the atomic dynamics in hand, answering question (2) is conceptually straigh
 
 Unfortunately, the need to calculate so many polarizabilities can make Raman spectrum calculations very computationally costly. These costs can quickly balloon, especially when treating large and/or complex systems. This ultimately makes conventional Raman spectrum calculations impractical for many of the most interesting and technologically relevant materials.
 
-**Ramannoodle's primary purpose is to reduce the computational cost of first principles Raman calculations.** It accomplishes this by providing efficient polarizability models. For example, :class:`~ramannoodle.polarizability.art.ARTModel` and :class:`~ramannoodle.polarizability.interpolation.InterpolationModel` leverage structural symmetries to greatly reduce the number of required first principles polarizability calculations. We hope that current and future versions of this API will make computing Raman spectra simpler and, consequently, make Raman spectroscopy a more powerful characterization tool.
+**Ramannoodle's primary purpose is to reduce the computational cost of first principles Raman calculations.** It accomplishes this by providing efficient polarizability models. For example, :class:`~ramannoodle.pmodel.art.ARTModel` and :class:`~ramannoodle.pmodel.interpolation.InterpolationModel` leverage structural symmetries to greatly reduce the number of required first principles polarizability calculations. We hope that current and future versions of this API will make computing Raman spectra simpler and, consequently, make Raman spectroscopy a more powerful characterization tool.
 
 Installation
 ------------
@@ -44,8 +44,8 @@ The following gives an overview of the modules available in ramannoodle.
         :synopsis:
         :no-index:
 
-4. :mod:`ramannoodle.polarizability`
-    .. automodule:: ramannoodle.polarizability
+4. :mod:`ramannoodle.pmodel`
+    .. automodule:: ramannoodle.pmodel
         :synopsis:
         :no-index:
 

docs/source/notebooks/basics.ipynb

@@ -44,7 +44,7 @@
    "id": "d7da690f-f4db-4509-8c89-014e7a49c83b",
    "metadata": {},
    "source": [
-    "We will be computing TiO2's Raman spectrum using data available in `tests/data/TiO2` (see [Github repo](https://github.com/wolearyc/ramannoodle)). We will be basing this spectrum on frozen phonon calculations and use [InterpolationModel](../generated/ramannoodle.polarizability.html#module-ramannoodle.polarizability.interpolation.InterpolationModel) to estimate polarizabilities.\n",
+    "We will be computing TiO2's Raman spectrum using data available in `tests/data/TiO2` (see [Github repo](https://github.com/wolearyc/ramannoodle)). We will be basing this spectrum on frozen phonon calculations and use [InterpolationModel](../generated/ramannoodle.pmodel.html#module-ramannoodle.pmodel.interpolation.InterpolationModel) to estimate polarizabilities.\n",
     "\n",
     "### Setup\n",
     "\n",
@@ -93,7 +93,7 @@
     }
    ],
    "source": [
-    "from ramannoodle.polarizability.interpolation import InterpolationModel\n",
+    "from ramannoodle.pmodel.interpolation import InterpolationModel\n",
     "\n",
     "# Read a reference (minimum) structure.\n",
     "ref_structure = vasp_io.outcar.read_ref_structure(f\"{data_dir}/ref_eps_OUTCAR\")\n",
@@ -123,7 +123,7 @@
     "\n",
     "Atom 5's displacement along the x-axis is a degree of freedom (DOF) of the system. Convince yourself that TiO2 structure contains many DOFs that are **symmetrically equivalent** to this DOF.\n",
     "\n",
-    " [InterpolationModel](../generated/ramannoodle.polarizability.html#module-ramannoodle.polarizability.interpolation.InterpolationModel)'s key assumption is that every DOF modulates the polarizability independently. The module estimates this modulation using an interpolation around each DOF. We need to \"add\" each DOF to `model`, specifying specific displacements as well as polarizabilities for these displacements (which we calculate using VASP). Internally, the model will handle all symmetry considerations. "
+    " [InterpolationModel](../generated/ramannoodle.pmodel.html#module-ramannoodle.pmodel.interpolation.InterpolationModel)'s key assumption is that every DOF modulates the polarizability independently. The module estimates this modulation using an interpolation around each DOF. We need to \"add\" each DOF to `model`, specifying specific displacements as well as polarizabilities for these displacements (which we calculate using VASP). Internally, the model will handle all symmetry considerations. "
    ]
   },
   {
@@ -441,9 +441,9 @@
    "id": "14cbffbc",
    "metadata": {},
    "source": [
-    "And there you have it! Using ramannoodle's [InterpolationModel](../generated/ramannoodle.polarizability.html#module-ramannoodle.polarizability.interpolation.InterpolationModel), we calculated a full Raman spectrum for TiO2 using data from just a handful of polarizability calculations.\n",
+    "And there you have it! Using ramannoodle's [InterpolationModel](../generated/ramannoodle.pmodel.html#module-ramannoodle.pmodel.interpolation.InterpolationModel), we calculated a full Raman spectrum for TiO2 using data from just a handful of polarizability calculations.\n",
     "\n",
-    "Next, we will introduce [ARTModel](../generated/ramannoodle.polarizability.html#module-ramannoodle.polarizability.art.ARTModel) and give a more complete overview of ramannoodle's workflow: [Full workflow](../notebooks/full-workflow.html)"
+    "Next, we will introduce [ARTModel](../generated/ramannoodle.pmodel.html#module-ramannoodle.pmodel.art.ARTModel) and give a more complete overview of ramannoodle's workflow: [Full workflow](../notebooks/full-workflow.html)"
    ]
   },
   {

docs/source/notebooks/full-workflow.ipynb

@@ -15,17 +15,17 @@
    "source": [
     "This notebook outlines a complete ramannoodle workflow and is, as always, available on [Github](https://github.com/wolearyc/ramannoodle/blob/main/docs/source/notebooks/full-workflow.ipynb).  \n",
     "\n",
-    "Here, we will use [ARTModel](../generated/ramannoodle.polarizability.html#module-ramannoodle.polarizability.art.ARTModel), a flavor of [InterpolationModel](../generated/ramannoodle.polarizability.html#module-ramannoodle.polarizability.interpolation.InterpolationModel), to again calculate TiO2's Raman spectrum. ARTModel uses \"atomic Raman tensors\" to predict polarizabilities, but is ultimately an InterpolationModel where\n",
+    "Here, we will use [ARTModel](../generated/ramannoodle.pmodel.html#module-ramannoodle.pmodel.art.ARTModel), a flavor of [InterpolationModel](../generated/ramannoodle.pmodel.html#module-ramannoodle.pmodel.interpolation.InterpolationModel), to again calculate TiO2's Raman spectrum. ARTModel uses \"atomic Raman tensors\" to predict polarizabilities, but is ultimately an InterpolationModel where\n",
     "\n",
     "1. All degrees of freedom (DOFs) are single atom displacements.\n",
     "2. All interpolations are first-order.\n",
     "3. Only two polarizabilities are used to construct each interpolation.\n",
     "\n",
     "Under these conditions, we dub each DOF polarizability interpolation (or more precisely, the derivative of the interpolation) as an **atomic Raman tensor**, or ART.\n",
     "\n",
-    "Although [ARTModel](../generated/ramannoodle.polarizability.html#module-ramannoodle.polarizability.art.ARTModel) dictates that each DOF is a single atom displacement, we are free to choose the three orthogonal directions of the atom displacements. This means there are an infinite number of valid DOFs! Ultimately, the chosen atomic DOFs depends on user preference as well as the research question at hand. Still, wise choice of atomic DOFs can significantly reduce the cost of Raman calculations. \n",
+    "Although [ARTModel](../generated/ramannoodle.pmodel.html#module-ramannoodle.pmodel.art.ARTModel) dictates that each DOF is a single atom displacement, we are free to choose the three orthogonal directions of the atom displacements. This means there are an infinite number of valid DOFs! Ultimately, the chosen atomic DOFs depends on user preference as well as the research question at hand. Still, wise choice of atomic DOFs can significantly reduce the cost of Raman calculations. \n",
     "\n",
-    "Regardless of how we choose our DOFs, we want to be sure that our DOFs are **valid** before carrying out expensive polarizability calculations and feeding the results into [ARTModel](../generated/ramannoodle.polarizability.html#module-ramannoodle.polarizability.art.ARTModel). To check our DOFs, we use **dummy models**. Essentially, we will build up a polarizability model in the usual way, except we instruct the model to internally generate \"dummy polarizabilities\". Although a dummy model cannot be used to predict polarizabilities (and therefore cannot be used to compute Raman spectra), it allows us to perform a dry run before we expend our valuable computational resources.\n",
+    "Regardless of how we choose our DOFs, we want to be sure that our DOFs are **valid** before carrying out expensive polarizability calculations and feeding the results into [ARTModel](../generated/ramannoodle.pmodel.html#module-ramannoodle.pmodel.art.ARTModel). To check our DOFs, we use **dummy models**. Essentially, we will build up a polarizability model in the usual way, except we instruct the model to internally generate \"dummy polarizabilities\". Although a dummy model cannot be used to predict polarizabilities (and therefore cannot be used to compute Raman spectra), it allows us to perform a dry run before we expend our valuable computational resources.\n",
     "\n",
     "We'll begin with some imports and some customizations to matplotlib. "
    ]
@@ -106,7 +106,7 @@
     }
    ],
    "source": [
-    "from ramannoodle.polarizability.art import ARTModel\n",
+    "from ramannoodle.pmodel.art import ARTModel\n",
     "\n",
     "model = ARTModel(ref_structure=ref_structure, \n",
     "                 ref_polarizability = np.zeros((3,3)), \n",

docs/source/notebooks/machine-learning.ipynb

@@ -178,7 +178,7 @@
    "outputs": [],
    "source": [
     "import torch\n",
-    "from ramannoodle.polarizability.torch.gnn import PotGNN\n",
+    "from ramannoodle.pmodel.torch.gnn import PotGNN\n",
     "ref_structure = vasp_io.poscar.read_ref_structure(\"../../../test/data/TiO2/POSCAR\")\n",
     "\n",
     "model = PotGNN(\n",
@@ -228,7 +228,7 @@
     }
    ],
    "source": [
-    "from ramannoodle.polarizability.torch.train import train_single_epoch\n",
+    "from ramannoodle.pmodel.torch.train import train_single_epoch\n",
     "\n",
     "loss_function = torch.nn.MSELoss()\n",
     "optimizer = torch.optim.Adam(model.parameters(), lr=0.02)\n",
@@ -271,7 +271,7 @@
     }
    ],
    "source": [
-    "from ramannoodle.polarizability.torch.train import train_single_epoch\n",
+    "from ramannoodle.pmodel.torch.train import train_single_epoch\n",
     "\n",
     "loss_function = torch.nn.MSELoss()\n",
     "optimizer = torch.optim.Adam(model.parameters(), lr=0.0001)\n",

docs/source/notebooks/masking.ipynb

@@ -15,7 +15,7 @@
    "source": [
     "This tutorial explores some of ramannoodle's masking features. These features are useful when analyzing simulated Raman spectra. \n",
     "\n",
-    " [InterpolationModel](../generated/ramannoodle.polarizability.html#module-ramannoodle.polarizability.interpolation.InterpolationModel), as well it's subclasses (such as [ARTModel](../generated/ramannoodle.polarizability.html#module-ramannoodle.polarizability.art.ARTModel)), can be modified by \"masking\" specified degrees of freedom (DOFs). When a DOF is masked, it is excluded when calculating polarizabilities and therefore will not be accounted for when calculating Raman spectra. Raman spectra computed with masking should be regarded as *partial Raman spectra*. By choosing the masks wisely, quite a bit can be learned about which atom (or groups of atoms) correspond to which features in the simulated Raman spectra."
+    " [InterpolationModel](../generated/ramannoodle.pmodel.html#module-ramannoodle.pmodel.interpolation.InterpolationModel), as well it's subclasses (such as [ARTModel](../generated/ramannoodle.pmodel.html#module-ramannoodle.pmodel.art.ARTModel)), can be modified by \"masking\" specified degrees of freedom (DOFs). When a DOF is masked, it is excluded when calculating polarizabilities and therefore will not be accounted for when calculating Raman spectra. Raman spectra computed with masking should be regarded as *partial Raman spectra*. By choosing the masks wisely, quite a bit can be learned about which atom (or groups of atoms) correspond to which features in the simulated Raman spectra."
    ]
   },
   {
@@ -54,7 +54,7 @@
    "source": [
     "### Setup of model\n",
     "\n",
-    "We will be computing TiO2's Raman spectrum using data available in `tests/data/TiO2` (see [Github repo](https://github.com/wolearyc/ramannoodle)). We will be basing this spectrum on frozen phonon calculations and use [ARTModel](../generated/ramannoodle.polarizability.html#module-ramannoodle.polarizability.art.ARTModel) to estimate polarizabilities."
+    "We will be computing TiO2's Raman spectrum using data available in `tests/data/TiO2` (see [Github repo](https://github.com/wolearyc/ramannoodle)). We will be basing this spectrum on frozen phonon calculations and use [ARTModel](../generated/ramannoodle.pmodel.html#module-ramannoodle.pmodel.art.ARTModel) to estimate polarizabilities."
    ]
   },
   {
@@ -65,7 +65,7 @@
    "outputs": [],
    "source": [
     "import ramannoodle.io.vasp as vasp_io\n",
-    "from ramannoodle.polarizability.art import ARTModel\n",
+    "from ramannoodle.pmodel.art import ARTModel\n",
     "\n",
     "data_dir = \"../../../test/data/TiO2\"\n",
     "# phonon_OUTCAR contains phonons (duh) as well as the reference TiO2 structure.\n",

docs/source/notebooks/molecular-dynamics.ipynb

@@ -76,7 +76,7 @@
    ],
    "source": [
     "import ramannoodle.io.vasp as vasp_io\n",
-    "from ramannoodle.polarizability.interpolation import InterpolationModel\n",
+    "from ramannoodle.pmodel.interpolation import InterpolationModel\n",
     "\n",
     "data_dir = \"../../../test/data/TiO2\"\n",
     "ref_structure = vasp_io.poscar.read_ref_structure(f\"{data_dir}/POSCAR\")\n",

ramannoodle/dynamics/abstract.py

@@ -2,7 +2,7 @@
 
 from abc import ABC, abstractmethod
 
-from ramannoodle.polarizability.abstract import PolarizabilityModel
+from ramannoodle.pmodel.abstract import PolarizabilityModel
 from ramannoodle.spectrum.abstract import RamanSpectrum
 
 

ramannoodle/dynamics/phonon.py

@@ -5,7 +5,7 @@
 
 from ramannoodle.dynamics.abstract import Dynamics
 from ramannoodle.constants import RAMAN_TENSOR_CENTRAL_DIFFERENCE
-from ramannoodle.polarizability.abstract import PolarizabilityModel
+from ramannoodle.pmodel.abstract import PolarizabilityModel
 from ramannoodle.spectrum.raman import PhononRamanSpectrum
 from ramannoodle.exceptions import verify_ndarray_shape
 

ramannoodle/dynamics/trajectory.py

@@ -7,7 +7,7 @@
 from numpy.typing import NDArray
 
 from ramannoodle.dynamics.abstract import Dynamics
-from ramannoodle.polarizability.abstract import PolarizabilityModel
+from ramannoodle.pmodel.abstract import PolarizabilityModel
 from ramannoodle.exceptions import verify_ndarray_shape, get_type_error
 from ramannoodle.spectrum.raman import MDRamanSpectrum
 from ramannoodle.structure.utils import apply_pbc

ramannoodle/io/generic.py

@@ -21,7 +21,7 @@
 
 TORCH_PRESENT = True
 try:
-    from ramannoodle.polarizability.torch.dataset import PolarizabilityDataset
+    from ramannoodle.pmodel.torch.dataset import PolarizabilityDataset
 except UserError:
     TORCH_PRESENT = False
 

ramannoodle/io/utils.py

@@ -20,7 +20,7 @@
 
 TORCH_PRESENT = True
 try:
-    from ramannoodle.polarizability.torch.dataset import PolarizabilityDataset
+    from ramannoodle.pmodel.torch.dataset import PolarizabilityDataset
 except UserError:
     TORCH_PRESENT = False
 

ramannoodle/io/vasp/outcar.py

@@ -18,7 +18,7 @@
 from ramannoodle.structure.reference import ReferenceStructure
 
 try:
-    from ramannoodle.polarizability.torch.dataset import PolarizabilityDataset
+    from ramannoodle.pmodel.torch.dataset import PolarizabilityDataset
 except UserError:
     pass
 

ramannoodle/io/vasp/vasprun.py

@@ -16,7 +16,7 @@
 from ramannoodle.structure.reference import ReferenceStructure
 
 try:
-    from ramannoodle.polarizability.torch.dataset import PolarizabilityDataset
+    from ramannoodle.pmodel.torch.dataset import PolarizabilityDataset
 except UserError:
     pass
 

ramannoodle/polarizability/art.py → ramannoodle/pmodel/art.py

@@ -9,7 +9,7 @@
 from tabulate import tabulate
 
 from ramannoodle.constants import ANSICOLORS
-from ramannoodle.polarizability.interpolation import InterpolationModel
+from ramannoodle.pmodel.interpolation import InterpolationModel
 from ramannoodle.exceptions import (
     get_type_error,
     get_shape_error,

ramannoodle/polarizability/interpolation.py → ramannoodle/pmodel/interpolation.py

@@ -15,7 +15,7 @@
 from scipy.interpolate import make_interp_spline, BSpline
 
 from ramannoodle.constants import ANSICOLORS
-from ramannoodle.polarizability.abstract import PolarizabilityModel
+from ramannoodle.pmodel.abstract import PolarizabilityModel
 from ramannoodle.structure.utils import calc_displacement
 from ramannoodle.structure.symmetry_utils import (
     is_orthogonal_to_all,

ramannoodle/polarizability/torch/dataset.py → ramannoodle/pmodel/torch/dataset.py

@@ -13,7 +13,7 @@
     import torch
     from torch import Tensor
     from torch.utils.data import Dataset
-    import ramannoodle.polarizability.torch.utils as rn_torch_utils
+    import ramannoodle.pmodel.torch.utils as rn_torch_utils
 except ModuleNotFoundError as exc:
     raise get_torch_missing_error() from exc