deploy: 7341d37

_sources/autoapi/lasdi/gp/index.rst.txt

@@ -28,7 +28,6 @@ Module Contents
    We assume each target coefficient is independent with each other.
 
 
-
    -----------------------------------------------------------------------------------------------
    :Parameters: * **X** (*A 2d numpy array of shape (n_train, input_dim), where n_train is the number of training*)
                 * **examples and input_dim is the number of components in each input (e.g., the number of**
@@ -42,12 +41,11 @@ Module Contents
              * *columns of X and whose corresponding target values are the elements of the i'th column of Y.*
 
 
-.. py:function:: eval_gp(gp_list: list[sklearn.gaussian_process.GaussianProcessRegressor], param_grid: numpy.ndarray) -> tuple
+.. py:function:: eval_gp(gp_list: list[sklearn.gaussian_process.GaussianProcessRegressor], param_grid: numpy.ndarray) -> tuple[numpy.ndarray, numpy.ndarray]
 
    Computes the GPs predictive mean and standard deviation for points of the parameter space grid
 
 
-
    -----------------------------------------------------------------------------------------------
    :Parameters: * **gp_list** (*a list of trained GP regressor objects. The number of elements in this list should*)
                 * **match the number of columns in param_grid. The i'th element of this list is a GP regressor**
@@ -74,7 +72,6 @@ Module Contents
    when param is the parameter.
 
 
-
    -----------------------------------------------------------------------------------------------
    :Parameters: * **gp_list** (*a list of trained GP regressor objects. The number of elements in this list should*)
                 * **match the number of columns in param_grid. The i'th element of this list is a GP regressor**

_sources/autoapi/lasdi/gplasdi/index.rst.txt

@@ -26,33 +26,132 @@ Functions
 Module Contents
 ---------------
 
-.. py:function:: average_rom(autoencoder, physics, latent_dynamics, gp_dictionary, param_grid)
+.. py:function:: average_rom(autoencoder: lasdi.latent_space.Autoencoder, physics: lasdi.physics.Physics, latent_dynamics: lasdi.latent_dynamics.LatentDynamics, gp_list: list[sklearn.gaussian_process.GaussianProcessRegressor], param_grid: numpy.ndarray)
+
+   This function simulates the latent dynamics for a collection of testing parameters by using
+   the mean of the posterior distribution for each coefficient's posterior distribution.
+   Specifically, for each parameter combination, we determine the mean of the posterior
+   distribution for each coefficient. We then use this mean to simulate the latent dynamics
+   forward in time (starting from the latent encoding of the fom initial condition for that
+   combination of coefficients).
+
+
+   -----------------------------------------------------------------------------------------------
+   :Parameters: * **autoencoder** (*The actual autoencoder object that we use to map the ICs into the latent space.*)
+                * **physics** (*A "Physics" object that stores the datasets for each parameter combination.*)
+                * **latent_dynamics** (*A LatentDynamics object which describes how we specify the dynamics in the*)
+                * **Autoencoder's latent space.**
+                * **gp_list** (*a list of trained GP regressor objects. The number of elements in this list should*)
+                * **match the number of columns in param_grid. The i'th element of this list is a GP regressor**
+                * **object that predicts the i'th coefficient.**
+                * **param_grid** (*A 2d numpy.ndarray object of shape (number of parameter combination) x (number of*)
+                * **parameters). The i,j element of this array holds the value of the j'th parameter in the i'th**
+                * **combination of parameters.**
+
+   -----------------------------------------------------------------------------------------------
+   :returns: * *A 3d numpy ndarray whose i, j, k element holds the k'th component of the j'th time step of*
+             * *the solution to the latent dynamics when we use the latent encoding of the initial condition*
+             * *from the i'th combination of parameter values*
+
+
+.. py:function:: sample_roms(autoencoder: lasdi.latent_space.Autoencoder, physics: lasdi.physics.Physics, latent_dynamics: lasdi.latent_dynamics.LatentDynamics, gp_list: list[sklearn.gaussian_process.GaussianProcessRegressor], param_grid: numpy.ndarray, n_samples: int) -> numpy.ndarray
+
+   This function samples the latent coefficients, solves the corresponding latent dynamics, and
+   then returns the resulting latent solutions.
+
+   Specifically, for each combination of parameter values in the param_grid, we draw n_samples
+   samples of the latent coefficients (from the coefficient posterior distributions evaluated at
+   that parameter value). This gives us a set of n_samples latent dynamics coefficients. For each
+   set of coefficients, we solve the corresponding latent dynamics forward in time and store the
+   resulting solution frames. We do this for each sample and each combination of parameter values,
+   resulting in an (n_param, n_sample, n_t, n_z) array of solution frames, which is what we
+   return.
+
+
+   -----------------------------------------------------------------------------------------------
+   :Parameters: * **autoencoder** (*An autoencoder. We use this to map the fom IC's (stored in Physics) to the*)
+                * **latent space using the autoencoder's encoder.**
+                * **physics** (*A "Physics" object that stores the ICs for each parameter combination.*)
+                * **latent_dynamics** (*A LatentDynamics object which describes how we specify the dynamics in the*)
+                * **Autoencoder's latent space. We use this to simulate the latent dynamics forward in time.**
+                * **gp_list** (*a list of trained GP regressor objects. The number of elements in this list should*)
+                * **match the number of columns in param_grid. The i'th element of this list is a GP regressor**
+                * **object that predicts the i'th coefficient.**
+                * **param_grid** (*A 2d numpy.ndarray object of shape (number of parameter combination) x (number of*)
+                * **parameters). The i,j element of this array holds the value of the j'th parameter in the i'th**
+                * **combination of parameters.**
+                * **n_samples** (*The number of samples we want to draw from each posterior distribution for each*)
+                * **coefficient evaluated at each combination of parameter values.**
+
+   -----------------------------------------------------------------------------------------------
+   :returns: * *A np.array of size [n_test, n_samples, physics.nt, autoencoder.n_z]. The i, j, k, l element*
+             * *holds the l'th component of the k'th frame of the solution to the latent dynamics when we use*
+             * *the j'th sample of latent coefficients drawn from the posterior distribution for the i'th*
+             * *combination of parameter values (i'th row of param_grid).*
+
+
+.. py:function:: get_fom_max_std(autoencoder: lasdi.latent_space.Autoencoder, Zis: numpy.ndarray) -> int
+
+   Computes the maximum standard deviation across the trajectories in Zis and returns the
+   corresponding parameter index. Specifically, Zis is a 4d tensor of shape (n_test, n_samples,
+   n_t, n_z). The first axis specifies which parameter combination we're using. For each
+   combination of parameters, we assume that we drew n_samples of the posterior distribution of
+   the coefficients at that parameter value, simulated the corresponding dynamics for n_t time
+   steps, and then recorded the results in Zis[i]. Thus, Zis[i, j, k, :] represents the k'th
+   time step of the solution to the latent dynamics when we use the coefficients from the j'th
+   sample of the posterior distribution for the i'th set of parameters.
+
+   Let i \in {1, 2, ... , n_test} and k \in {1, 2, ... , n_t}. For each j, we map the k'th frame
+   of the j'th solution trajectory for the i'th parameter combination (Zi[i, j, k, :]) to a fom
+   frame. We do this for each j (the set of samples), which gives us a collection of n_sample
+   fom frames, representing samples of the distribution of fom frames at the k'th time step
+   when we use the posterior distribution for the i'th set of parameters. For each l \in {1, 2,
+   ... , n_fom}, we compute the STD of the set of l'th components of these n_sample fom frames.
+   We do this for each i and k and then figure out which i, k, l combination gives the largest
+   STD. We return the corresponding i index.
+
+
+   -----------------------------------------------------------------------------------------------
+   :Parameters: * **autoencoder** (*The autoencoder. We assume the solved dynamics (whose frames are stored in Zis)*)
+                * **take place in the autoencoder's latent space. We use this to decode the solution frames.**
+                * **Zis** (*A 4d numpy array of shape (n_test, n_samples, n_t, n_z) whose i, j, k, l element holds*)
+                * **the l'th component of the k'th frame of the solution to the latent dynamics when we use the**
+                * **j'th sample of latent coefficients drawn from the posterior distribution for the i'th testing**
+                * **parameter.**
+
+   -----------------------------------------------------------------------------------------------
+   Returns:
+   -----------------------------------------------------------------------------------------------
+
+   An integer. The index of the testing parameter that gives the largest standard deviation.
+   Specifically, for each testing parameter, we compute the STD of each component of the fom
+   solution at each frame generated by samples from the posterior coefficient distribution for
+   that parameter. We compute the maximum of these STDs and pair that number with the parameter.
+   We then return the index of the parameter whose corresponding maximum std (the number we pair
+   with it) is greatest.
+
+
+.. py:function:: optimizer_to(optim: torch.optim.Optimizer, device: str) -> None
+
+   This function moves an optimizer object to a specific device.
+
+
+   -----------------------------------------------------------------------------------------------
+   :Parameters: * **optim** (*The optimizer whose device we want to change.*)
+                * **device** (*The device we want to move optim onto.*)
+
+   -----------------------------------------------------------------------------------------------
+   :rtype: Nothing.
+
 
-.. py:function:: sample_roms(autoencoder, physics, latent_dynamics, gp_dictionary, param_grid, n_samples)
-
-   Collect n_samples of ROM trajectories on param_grid.
-   gp_dictionary: list of Gaussian process regressors (size of n_test)
-   param_grid: numpy 2d array
-   n_samples: integer
-   assert(len(gp_dictionnary) == param_grid.shape[0])
-
-   output: np.array of size [n_test, n_samples, physics.nt, autoencoder.n_z]
-
-
-.. py:function:: get_fom_max_std(autoencoder, Zis)
-
-   Computes the maximum standard deviation accross the parameter space grid and finds the corresponding parameter location
-
-
-
-.. py:function:: optimizer_to(optim, device)
-
-.. py:class:: BayesianGLaSDI(physics, autoencoder, latent_dynamics, param_space, config)
+.. py:class:: BayesianGLaSDI(physics: lasdi.physics.Physics, autoencoder: lasdi.latent_space.Autoencoder, latent_dynamics: lasdi.latent_dynamics.LatentDynamics, param_space: lasdi.param.ParameterSpace, config: dict)
 
    .. py:attribute:: X_train
+      :type:  torch.Tensor
 
 
    .. py:attribute:: X_test
+      :type:  torch.Tensor
 
 
    .. py:attribute:: autoencoder
@@ -71,60 +170,119 @@ Module Contents
 
 
    .. py:attribute:: n_samples
+      :type:  int
 
 
    .. py:attribute:: lr
+      :type:  float
 
 
    .. py:attribute:: n_iter
+      :type:  int
 
 
    .. py:attribute:: max_iter
+      :type:  int
 
 
    .. py:attribute:: max_greedy_iter
+      :type:  int
 
 
    .. py:attribute:: ld_weight
+      :type:  float
 
 
    .. py:attribute:: coef_weight
+      :type:  float
 
 
    .. py:attribute:: optimizer
+      :type:  torch.optim.Optimizer
 
 
    .. py:attribute:: MSE
 
 
    .. py:attribute:: path_checkpoint
+      :type:  str
 
 
    .. py:attribute:: path_results
+      :type:  str
 
 
    .. py:attribute:: best_loss
+      :type:  float
 
 
    .. py:attribute:: best_coefs
+      :type:  numpy.ndarray
       :value: None
 
 
 
    .. py:attribute:: restart_iter
+      :type:  int
       :value: 0
 
 
 
-   .. py:method:: train()
+   .. py:method:: train() -> None
+
+      Runs a round of training on the autoencoder.
+
+      -------------------------------------------------------------------------------------------
+      :Parameters: **None!**
+
+      -------------------------------------------------------------------------------------------
+      :rtype: Nothing!
+
+
+
+   .. py:method:: get_new_sample_point() -> numpy.ndarray
+
+      This function uses a greedy process to sample a new parameter value. Specifically, it runs
+      through each combination of parameters in in self.param_space. For the i'th combination of
+      parameters, we generate a collection of samples of the coefficients in the latent dynamics.
+      We draw the k'th sample of the j'th coefficient from the posterior distribution for the
+      j'th coefficient at the i'th combination of parameters. We map the resulting solution back
+      into the real space and evaluate the standard deviation of the fom frames. We return the
+      combination of parameters which engenders the largest standard deviation (see the function
+      get_fom_max_std).
+
+
+      -------------------------------------------------------------------------------------------
+      :Parameters: **None!**
+
+      -------------------------------------------------------------------------------------------
+      :returns: * *a 2d numpy ndarray object of shape (1, n_param) whose (0, j) element holds the value of*
+                * *the j'th parameter in the new sample.*
+
+
+
+   .. py:method:: export() -> dict
+
+      -------------------------------------------------------------------------------------------
+      :returns: * *A dictionary housing most of the internal variables in self. You can pass this dictionary*
+                * *to self (after initializing it using ParameterSpace, Autoencoder, and LatentDynamics*
+                * *objects) to make a GLaSDI object whose internal state matches that of self.*
+
+
 
+   .. py:method:: load(dict_: dict) -> None
 
-   .. py:method:: get_new_sample_point()
+      Modifies self's internal state to match the one whose export method generated the dict_
+      dictionary.
 
 
-   .. py:method:: export()
+      -------------------------------------------------------------------------------------------
+      :Parameters: * **dict_** (*This should be a dictionary returned by calling the export method on another*)
+                   * **GLaSDI object. We use this to make self hav the same internal state as the object that**
+                   * **generated dict_.**
 
+      -------------------------------------------------------------------------------------------
+      :rtype: Nothing!
 
-   .. py:method:: load(dict_)
 
 

_sources/autoapi/lasdi/latent_space/index.rst.txt

@@ -45,8 +45,10 @@ Module Contents
 
    -----------------------------------------------------------------------------------------------
    :Parameters: * **param_grid** (*A 2d numpy.ndarray object of shape (number of parameter combination) x (number of*)
-                * **parameters).**
-                * **physics** (*A "Physics" object that stores the datasets for each parameter combination.*)
+                * **parameters). The i,j element of this array holds the value of the j'th parameter in the i'th**
+                * **combination of parameters.**
+                * **physics** (*A "Physics" object that, among other things, stores the IC for each combination of*)
+                * **parameters.**
                 * **autoencoder** (*The actual autoencoder object that we use to map the ICs into the latent space.*)
 
    -----------------------------------------------------------------------------------------------
@@ -105,14 +107,8 @@ Module Contents
 
    .. py:method:: init_weight() -> None
 
-      This function initializes the weight matrices and bias vectors in self's layers.
-
-
-      -------------------------------------------------------------------------------------------
-      :Parameters: **None!**
-
-      -------------------------------------------------------------------------------------------
-      :rtype: Nothing!
+      This function initializes the weight matrices and bias vectors in self's layers. It takes
+      no arguments and returns nothing!
 
 
 
@@ -155,14 +151,11 @@ Module Contents
 
    .. py:method:: export() -> dict
 
-      This function extracts self's parameters and returns them in a dictionary.
-
-
-      -------------------------------------------------------------------------------------------
-      :Parameters: **None!**
-
       -------------------------------------------------------------------------------------------
-      :rtype: The A dictionary housing self's state dictionary.
+      :returns: * *This function extracts self's parameters and returns them in a dictionary. You can pass*
+                * *the dictionary returned by this function to the load method of another Autoencoder object*
+                * *(that you initialized to have the same architecture as self) to make the other autoencoder*
+                * *identical to self.*
 
 
 

_sources/autoapi/lasdi/param/index.rst.txt

@@ -289,7 +289,7 @@ Module Contents
    .. py:method:: load(dict_: dict) -> None
 
       This function builds a parameter space object from a dictionary. This dictionary should
-      be one that was returned by th export method, or a loaded copy of a dictionary that was
+      be one that was returned by the export method, or a loaded copy of a dictionary that was
       returned by the export method.
 
 

_sources/autoapi/lasdi/physics/burgers1d/index.rst.txt

@@ -55,12 +55,15 @@ Module Contents
 
 
    .. py:attribute:: nt
+      :type:  int
 
 
    .. py:attribute:: grid_size
+      :type:  list[int]
 
 
    .. py:attribute:: qgrid_size
+      :type:  list[int]
 
       numpy nd-array, assuming the shape of:
       - 1d: (space_dim[0],)