feslima · feslima · May 23, 2020 · May 20, 2020 · May 20, 2020 · May 20, 2020
diff --git a/docs/doctrees/bibliography.doctree b/docs/doctrees/bibliography.doctree
diff --git a/docs/doctrees/environment.pickle b/docs/doctrees/environment.pickle
diff --git a/docs/doctrees/examples/c3splitter.doctree b/docs/doctrees/examples/c3splitter.doctree
diff --git a/docs/doctrees/examples/cpu.doctree b/docs/doctrees/examples/cpu.doctree
diff --git a/docs/doctrees/examples/ic4.doctree b/docs/doctrees/examples/ic4.doctree
diff --git a/docs/doctrees/examples/tutorials.doctree b/docs/doctrees/examples/tutorials.doctree
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diff --git a/docs/doctrees/gui/gui_index.doctree b/docs/doctrees/gui/gui_index.doctree
diff --git a/docs/doctrees/gui/load_sim_tab.doctree b/docs/doctrees/gui/load_sim_tab.doctree
diff --git a/docs/doctrees/gui/metamodel_tab.doctree b/docs/doctrees/gui/metamodel_tab.doctree
diff --git a/docs/doctrees/gui/optimization_tab.doctree b/docs/doctrees/gui/optimization_tab.doctree
diff --git a/docs/doctrees/gui/reduced_space_tab.doctree b/docs/doctrees/gui/reduced_space_tab.doctree
diff --git a/docs/doctrees/gui/sampling_tab.doctree b/docs/doctrees/gui/sampling_tab.doctree
diff --git a/docs/doctrees/gui/soc_tab.doctree b/docs/doctrees/gui/soc_tab.doctree
diff --git a/docs/doctrees/index.doctree b/docs/doctrees/index.doctree
diff --git a/docs/doctrees/intro.doctree b/docs/doctrees/intro.doctree
diff --git a/docs/doctrees/overview/mtc.doctree b/docs/doctrees/overview/mtc.doctree
diff --git a/docs/doctrees/overview/z_mtc.doctree b/docs/doctrees/overview/z_mtc.doctree
diff --git a/docs/doctrees/theory/optimization.doctree b/docs/doctrees/theory/optimization.doctree
diff --git a/docs/doctrees/theory/soc.doctree b/docs/doctrees/theory/soc.doctree
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diff --git a/docs/doctrees/theory/theory_index.doctree b/docs/doctrees/theory/theory_index.doctree
diff --git a/docs/doctrees/zbibliography.doctree b/docs/doctrees/zbibliography.doctree
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diff --git a/docs/html/_images/diff_data_dace_function.png b/docs/html/_images/diff_data_dace_function.png
diff --git a/docs/html/_images/diff_data_high_order_data_gen.png b/docs/html/_images/diff_data_high_order_data_gen.png
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diff --git a/docs/html/_images/diff_data_reading_gains.png b/docs/html/_images/diff_data_reading_gains.png
diff --git a/docs/html/_images/diff_data_remove_cvs.png b/docs/html/_images/diff_data_remove_cvs.png
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diff --git a/docs/html/_images/diff_data_training_dialog_window.png b/docs/html/_images/diff_data_training_dialog_window.png
diff --git a/docs/html/_images/plot_soc.svg b/docs/html/_images/plot_soc.svg
diff --git a/docs/html/_images/reduced_cases_config.png b/docs/html/_images/reduced_cases_config.png
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diff --git a/docs/html/_images/soc_condition_number.png b/docs/html/_images/soc_condition_number.png
diff --git a/docs/html/_images/soc_descending_size2.png b/docs/html/_images/soc_descending_size2.png
diff --git a/docs/html/_images/soc_disturbances_magnitude_panel.png b/docs/html/_images/soc_disturbances_magnitude_panel.png
diff --git a/docs/html/_images/soc_f_matrix.png b/docs/html/_images/soc_f_matrix.png
diff --git a/docs/html/_images/soc_h_matrix.png b/docs/html/_images/soc_h_matrix.png
diff --git a/docs/html/_images/soc_main_tab_before_completion.png b/docs/html/_images/soc_main_tab_before_completion.png
diff --git a/docs/html/_images/soc_measurement_error_panel.png b/docs/html/_images/soc_measurement_error_panel.png
diff --git a/docs/html/_images/soc_results_review.png b/docs/html/_images/soc_results_review.png
diff --git a/docs/html/_images/soc_size6.png b/docs/html/_images/soc_size6.png
diff --git a/docs/html/_images/soc_subset_sizing_impossible.png b/docs/html/_images/soc_subset_sizing_impossible.png
diff --git a/docs/html/_images/soc_subset_sizing_options_panel.png b/docs/html/_images/soc_subset_sizing_options_panel.png
diff --git a/docs/html/_sources/bibliography.rst.txt b/docs/html/_sources/bibliography.rst.txt
@@ -0,0 +1,9 @@
+============
+Bibliography
+============
+
+You can found the main literature the allows *Metacontrol* to exist below. 
+For the complete list, go to :ref:`our_papers`.
+
+.. bibliography:: mybibfile.bib
+   :style: plain
diff --git a/docs/html/_sources/gui/diff_data_tab.rst.txt b/docs/html/_sources/gui/diff_data_tab.rst.txt
@@ -2,4 +2,135 @@
 The "Differential Data" tab
 **************************************************
 
-Placeholder text...
+
+At this tab you will extract the high-order data (Gradients and Hessians)
+that are necessary in order to calculate the self-optimizing control structures using
+the exact local method from :cite:`alstad09`. 
+
+The high-order data is calculated with
+analytical expressions derived by :cite:`DACE` and :cite:`alves2018`, using the kriging 
+metamodel built for the reduced space problem.
+
+
+The aforementioned procedure is encapsulated in this tab. You will be able to:
+
+* Generate the gradients and hessians, and inspect them.
+* Remove any CV candidate from the list of candidates if you want.
+
+Here is an overview of this tab, before you start using it:
+
+
+.. figure:: ../images/diff_data_main.png
+   :align: center
+
+   Differential Data tab.
+
+
+
+There are four main panels on this tab
+
+* Reduced space metamodel training *Panel*
+* Gradient and Hessian estimation *Panel*
+* Gradient results *panel* and Hessian results *panel*
+
+Reduced space metamodel training *Panel*
+========================================
+
+Under this panel, you are able to click on "Open training dialog" in order to
+configure your reduced-space kriging metamodel.
+
+
+Configuring your kriging metamodel
+-----------------------------------
+
+Click on "Open training dialog":
+
+
+.. figure:: ../images/diff_data_training_dialog.png
+   :align: center
+
+   Opening the kriging training dialog window.
+
+
+You will notice that the window that appears to you is exactly the same from
+:ref:`metamodel_tab`. Therefore the process of configuring your reduced-space 
+kriging metamodel is essentially the same.
+
+.. figure:: ../images/diff_data_training_dialog_window.png
+   :align: center
+
+   Training dialog window.
+
+.. IMPORTANT::
+    At the training dialog window, you will notice that only the Candidates that
+    were not active constraints are considered now. This happens because *Metacontrol*
+    automatically removes the variables that are nominally active (MVs and CVs) based on the
+    previous tab (Reduced Space tab). In addition, you can remove any of the remaining CVs, if you
+    want. Just *de-select* the box of the variable you want to remove:
+
+    .. figure:: ../images/diff_data_remove_cvs.png
+        :align: center
+
+        Removing one variable from the CV candidates list (*fco2out* in this example).
+
+
+After configuring the hyperparameters estimates, choosing which CVs will be taken into acount in your
+metamodel, you can click on "Generate metamodel" in order to inspect the validation metrics of your metamodel.
+
+
+Acessing performance of your reduced-space metamodel
+-----------------------------------------------------
+
+For the reduced-space metamodel, one additional metric has been added in order to help you to evaluate the
+robustness of the metamodel generated. It corresponds to the objective function of the maximum likelihood estimation
+from the work of :cite:`DACE`. Values under 1e-5 will give robust estimation of the gradients and hessians. (Check :ref:`our_papers`
+and the :ref:`theory_tab` section where we give some examples and discuss the theoretical background in detail)
+
+.. figure:: ../images/diff_data_dace_function.png
+   :align: center
+
+   Evaluating reduced space kriging metamodel estimation capabilities. Highlighted in blue,
+   the value of the optimized objective function value, that results in the optimal hyperparameters estimation.
+
+Gradient and Hessian estimation *Panel*
+==========================================
+
+After configuring the kriging metamodel options under the training 
+dialog window, you can click on "Estimate Gradient and Hessian", to generate the
+high-order data.
+
+
+.. figure:: ../images/diff_data_high_order_data_gen.png
+   :align: center
+
+   Generating high-order data.
+
+
+Gradient results *panel* and Hessian results *panel*
+=====================================================
+
+After performing the previous step, you will notice that the panels for Gradients and Hessians are now
+completed:
+
+.. figure:: ../images/diff_data_completed.png
+   :align: center
+
+   Generating high-order data.
+
+If you take a closer look, you will notice that the matrices are in a Dataframe format, making them easy to ready
+and to understand each element of the matrices generated. Note that the elements are indexed using the aliases that you
+created. For example, the gain between the unconstrained degree of freedom (*mccp*) and one CV candidate (*co2rrcv*) is easily
+read:
+
+
+.. figure:: ../images/diff_data_reading_gains.png
+   :align: center
+
+   Generating high-order data.
+
+
+The same is true for every element of the gradients and hessians calculated.
+
+After the procedure here described, you can go to the last tab: Self-Optimizing Control.
+
+
diff --git a/docs/html/_sources/gui/load_sim_tab.rst.txt b/docs/html/_sources/gui/load_sim_tab.rst.txt
@@ -102,12 +102,12 @@ you entered. Giving proper (non-repeated) aliases and correctly classifying your
 .. figure:: ../images/var_tree_class_input.png
    :align: center
 
-   classifying your variables in *Metacontrol* - Input Variables.
+   Classifying your variables in *Metacontrol* - Input Variables.
 
 .. figure:: ../images/var_tree_class_output.png
    :align: center
 
-   classifying your variables in *Metacontrol* - Output Variables.
+   Classifying your variables in *Metacontrol* - Output Variables.
 
 .. IMPORTANT::
     To create aliases in *Metacontrol*, only lower case alphanumeric characters are allowed.
@@ -265,7 +265,7 @@ Creating a Constraint function
 -------------------------------
 
 It is very common to have process constraints in the processes that you
-want to study in a plantwide (Self-Optimizing) Perspective. *Metacontrol* supports the
+want to study in a plantwide (Self-Optimizing) perspective. *Metacontrol* supports the
 creation of constraints that are added to the optimization problem solved using metamodels.
 The constraints are always written in the form:
 
@@ -307,13 +307,13 @@ Simulation info *panel*
 =======================
 
 This panel serves as a "At a glance" simulation data info panel: After you load your Aspen Plus simulation,
-You can inspect the following information:
+it is possible to inspect the following information:
 
 * Number and name of components
 * Thermodynamic Package used in your model
 * Number and name of blocks used
 * Number and name of streams in your flowsheet
-* Chemical Reactions modelled
+* Chemical Reactions modeled
 * If there are any sensitivity analysis, optimizations, calculators and/or Design Specifications Within your model.
 
 .. ATTENTION::

diff --git a/docs/html/_sources/gui/metamodel_tab.rst.txt b/docs/html/_sources/gui/metamodel_tab.rst.txt
@@ -1,9 +1,11 @@
-**************************************************
+.. _metamodel_tab:
+
+===================
 The "Metamodel" tab
-**************************************************
+===================
 
 At this tab you will use the Design of Experiments (DOE) generated previously to
-generate kriging metamodels of the initial Sampling. The main idea here is to inspect if
+generate kriging metamodels of the initial sampling. The main idea here is to inspect if
 the initial sampling providing is capable of predicting the basic form of the functions that you
 chose/created on the first step (Objective Function, CV candidates and constraints). If the kriging generated 
 by the initial sampling is good enough, you are able to optimize it and refine it on the next step.
@@ -12,7 +14,7 @@ On this tab you will be able to:
 * Define the lower and upper bounds for the hyperparameters that will be adjusted to give the
   best kriging prediction
 * Define the regression and correlation (kernel) model for your kriging interpolator
-* Define which variables will have their model built
+* Define which variables will have their kriging metamodel built
 * Inspect several validation metrics in order to conclude if your model is a good representation
 * Perform k-fold or hold-out validation. On the latter, you will be able to also inspect graphically
   your model.
@@ -196,6 +198,7 @@ They allow you to:
 
 
 
+
 Validation metrics *panel*
 ===========================
 

diff --git a/docs/html/_sources/gui/optimization_tab.rst.txt b/docs/html/_sources/gui/optimization_tab.rst.txt
@@ -88,15 +88,15 @@ panel the iterations in real time, and each step performed by the algorithm.
 Control *panel*
 ================
 
-This is how the control *panel* looks like during an optimization run in *Metacontrol*
+This is how the control *panel* looks like during an optimization run in *Metacontrol*:
 
 
 .. figure:: ../images/opt_control_panel.png
    :align: center
 
    Control *panel* output.
 
-The control panel shows the operations performed by the adaptive sampling algorithm, the decision variables values (MVs) at each
+The control panel shows (being updated in real time) the operations performed by the adaptive sampling algorithm, the decision variables values (MVs) at each
 iteration, the actual and predicted objective function values, and the largest infeasiblity (constraint) violation for that iteration.
 At the end of the optimization run, *Metacontrol* will inform you how many points are within the trust-region.