docu & test

changelog.md

@@ -2,6 +2,7 @@
 * Reworked generation methodology for easier shape combination and pattern usage
 * Added new alpha-cristobalite pattern
 * Generalization of connectivity search
+* New Lennard Jones parameter (Coasne, B.; Fourkas, J. T. from 10.1021/jp203831q)
 
 # v0.2.5
 * Add properties output in yaml format

docsrc/conf.py

@@ -119,7 +119,7 @@
     'source_link_position': "",
     'bootswatch_theme': "paper",
     'bootstrap_version': "3",
-    'navbar_links': [("API", "api"), ("Molecule", "molecule"), ("Pore", "pore"), ("Workflow", "workflow"),],
+    'navbar_links': [("API", "api"), ("Molecule", "molecule"), ("Pore", "pore"), ("Workflow", "workflow"), ("Pore shape examples", "shape_examples"),],
 }
 
 html_theme_path = sphinx_bootstrap_theme.get_html_theme_path()

docsrc/shape_examples.rst

@@ -0,0 +1,233 @@
+Complex structure with PoreKit() 
+================================
+.. code:: ipython3
+
+    import porems as pms
+
+Shape 1 (Single Pore)
+---------------------
+
+Create a pore with a diameter of 5 nm, a length of 10 nm, and a
+reservoir length of 5 nm. The silanol on the inner surface is 6.06
+:math:`\mathrm{\mu mol m^{-2}}`. The outer surface is completely
+occupied by TMS molecules with 6.06 :math:`\mathrm{\mu mol m^{-2}}`.
+
+.. code:: ipython3
+
+    # Set pore kit
+    pore = pms.PoreKit()
+    
+    # Set Beta-Cristobalit block witgh (x y z) (11 11 10)
+    pore.structure(pms.BetaCristobalit().generate([11, 11, 10], "z"))
+    pore.build()
+    
+    # Set a reservoir for 5 nm and an outer silanol concentration of 6.06 mumol/m2
+    pore.exterior(5, hydro= 6.06)
+    
+    # Drill a cyclinder in the SiO2 block with a diameter of 5 and a lenght of nm with inner silanol concentration of 6.06 mumol/m2
+    pore.add_shape(pore.shape_cylinder(5, 10, [5.5,5.5,5]), section={"x": [], "y": [], "z": [0,  10]}, hydro= 6.06)
+    pore.prepare()
+    
+    # Replace silanol on the outer surface with TMS 
+    pore.attach(pms.gen.tms(), mount=0, axis=[1, 2], amount=6.06, site_type="ex", inp="molar", scale=0.5)
+    
+    # Create the structure
+    pore.finalize()
+    
+    # Store the structure
+    pore.store("pores/shape1/")
+    
+
+.. figure::  /pics/shapes/shape1.pdf
+      :align: center
+      :width: 70%
+      :name: fig1
+
+Shape 2 (Parallel Pore 5 nm)
+----------------------------
+
+| Create 2 parallel pores with a diameter of 5 nm, a length of 10 nm and
+  a reservoir length of 5 nm.
+| The silanol on the inner surface is 6.06
+  :math:`\mathrm{\mu mol m^{-2}}`.
+| The outer surface is completely occupied by TMS molecules with 6.06
+  :math:`\mathrm{\mu mol m^{-2}}`.
+
+.. code:: ipython3
+
+    # Set pore kit
+    pore = pms.PoreKit()
+    
+    # Set Beta-Cristobalit block with (x y z) (11 11 10)
+    pore.structure(pms.BetaCristobalit().generate([11, 11, 10], "z"))
+    pore.build()
+    
+    # Set a reservoir for 5 nm and an outer silanol concentration of 6.06 mumol/m2
+    pore.exterior(5, hydro= 6.06)
+    
+    # Drill two cyclinder in the SiO2 block with a diameter of 5 and a lenght of nm with inner silanol concentration of 6.06 mumol/m2
+    pore.add_shape(pore.shape_cylinder(5, 10, [3, 3, 5]), hydro= 6.06)
+    pore.add_shape(pore.shape_cylinder(5, 10, [8, 8, 5]), hydro= 6.06)
+    pore.prepare()
+    
+    # Replace silanol on the outer surface with TMS 
+    pore.attach(pms.gen.tms(), mount=0, axis=[1, 2], amount=6.06, site_type="ex", inp="molar", scale=0.5)
+    
+    # Create the structure
+    pore.finalize()
+    
+    # Store the structure
+    pore.store("pores/shape2/")
+
+
+.. figure::  /pics/shapes/shape2.pdf
+      :align: center
+      :width: 70%
+      :name: fig1
+
+
+Shape 3 (Pore with Connection)
+------------------------------
+
+| Generate a 2 parallel pores with a diameter of 5 nm, a length of 10 nm
+  connected
+| with a 2.5 nm pore and a reservoir length of 5 nm.
+| The silanol on the inner surface is 6.06
+  :math:`\mathrm{\mu mol m^{-2}}`.
+| The outer surface is completely occupied by TMS molecules with 6.06
+  :math:`\mathrm{\mu mol m^{-2}}`.
+
+.. code:: ipython3
+
+    # Set pore kit
+    pore = pms.PoreKit()
+    
+    # Set Beta-Cristobalit block witgh (x y z) (11 11 10)
+    pore.structure(pms.BetaCristobalit().generate([11, 11, 10], "z"))
+    pore.build()
+    
+    # Set a reservoir for 5 nm and an outer silanol concentration of 6.06 mumol/m2
+    pore.exterior(5, hydro= 6.06)
+    
+    # Connect these pores
+    pore.add_shape(pore.shape_cylinder(2.5, 3, [5.5, 5.5, 5], central = [1,1,0]))
+    
+    # Drill two cyclinder in the SiO2 block with a diameter of 5 and a lenght of nm with inner silanol concentration of 6.06 mumol/m2
+    pore.add_shape(pore.shape_cylinder(5, 10, [8, 8, 5]), hydro= 6.06)
+    pore.add_shape(pore.shape_cylinder(5, 10, [3, 3, 5]), hydro= 6.06)
+    
+    # Connect these pores
+    #pore.add_shape(pore.shape_cylinder(2.5, 3, [5.5, 5.5, 5], central = [1,1,0]), hydro= 6.06)
+    pore.prepare()
+    
+    # Replace silanol on the outer surface with TMS 
+    pore.attach(pms.gen.tms(), mount=0, axis=[1, 2], amount=6.06, site_type="ex", inp="molar", scale=0.5)
+    
+    # Create the structure
+    pore.finalize()
+    
+    # Store the structure
+    pore.store("pores/shape3/")
+
+.. note::
+    If there are intersecting shapes, the free Si sites are assigned to the first defined shape. 
+    Keep this in mind if you want to functionalize one of these shapes. 
+
+.. figure::  /pics/shapes/shape3.pdf
+      :align: center
+      :width: 70%
+      :name: fig1
+
+Shape 4 (Pore with different inner surfaces)
+--------------------------------------------
+
+| Generate a 3 pores with a diameter of 5 nm directly adjacent to each
+  other in z-direction.
+| The silanol on the inner surface is 6.06
+  :math:`\mathrm{\mu mol m^{-2}}` in the second pore (shape_01).
+| Shape_00 and shape_02 are occupied by TMS molecules with 6.06
+  :math:`\mathrm{\mu mol m^{-2}}`. The outer surface is completely
+  occupied by TMS molecules with 6.06 :math:`\mathrm{\mu mol m^{-2}}`.
+
+.. code:: ipython3
+
+    # Set pore kit
+    pore = pms.PoreKit()
+    
+    # Set Beta-Cristobalit block with (x y z) (11 11 25)
+    pore.structure(pms.BetaCristobalit().generate([11, 11, 25], "z"))
+    pore.build()
+    
+    # Set a reservoir for 5 nm and an outer silanol concentration of 6.06 mumol/m2
+    pore.exterior(5, hydro= 6.06)
+    
+    # Drill three cyclinder with the same central in x,y direction in the SiO2 block with a diameter of 5 nm and a inner silanol concentration of 6.06 mumol/m2
+    pore.add_shape(pore.shape_cylinder(5.0, 10, [5.5,5.5,5]), hydro= 6.06)   #shape_00
+    pore.add_shape(pore.shape_cylinder(5.0, 5, [5.5,5.5,12.5]), hydro= 6.06) #shape_01
+    pore.add_shape(pore.shape_cylinder(5.0, 10, [5.5,5.5,20]), hydro= 6.06)  #shape_02
+    pore.prepare()
+    
+    # Replace silanol on the outer surface with TMS 
+    pore.attach(pms.gen.tms(), mount=0, axis=[1, 2], amount=6.06, site_type="ex", inp="molar", scale=0.5)
+    
+    # Replace silanol on the inner surface with TMS for shape 0 and shape 2
+    pore.attach(pms.gen.tms(), mount=0, axis=[1, 2], amount=6.06, shape="shape_00", site_type="in", inp="molar", scale=0.5)
+    pore.attach(pms.gen.tms(), mount=0, axis=[1, 2], amount=6.06, shape="shape_02", site_type="in", inp="molar", scale=0.5)
+    
+    
+    # Create the structure
+    pore.finalize()
+    
+    # Store the structure
+    pore.store("pores/shape4/")
+
+
+.. figure::  /pics/shapes/shape4.pdf
+      :align: center
+      :width: 100%
+      :name: fig1
+
+
+Shape 5 (Pore with different inner surfaces)
+--------------------------------------------
+
+| Generate a 3 pores with a diameter of 5, 2.5 and 5 nm directly adjacent to each
+  other in z-direction connected with a cone shape.
+| The outer surface is completely
+  occupied by TMS molecules with 6.06 :math:`\mathrm{\mu mol m^{-2}}`.
+
+.. code:: ipython3
+
+    # Set pore kit
+    pore = pms.PoreKit()
+    
+    # Set Beta-Cristobalit block with (x y z) (11 11 30)
+    pore.structure(pms.BetaCristobalit().generate([11, 11, 30], "z"))
+    pore.build()
+    
+    # Set a reservoir for 5 nm and an outer silanol concentration of 6.06 mumol/m2
+    pore.exterior(5, hydro= 6.06)
+    
+    # Drill three cyclinder with the same central in x,y direction in the SiO2 block with a diameter of 5 nm and a inner silanol concentration of 6.06 mumol/m2
+    pore.add_shape(pore.shape_cylinder(5, 8, [5.5,5.5, 4]), hydro=6.06)
+    pore.add_shape(pore.shape_cone(4, 3, 2,  [5.5,5.5, 9]), hydro=6.06)
+    pore.add_shape(pore.shape_cylinder(2.5, 10, [5.5,5.5, 15]),  hydro=6.06)
+    pore.add_shape(pore.shape_cone(3.4, 4.1, 2,  [5.5,5.5, 21]),  hydro=6.06)
+    pore.add_shape(pore.shape_cylinder(5, 8, [5.5,5.5, 26]), hydro=6.06)
+    pore.prepare()
+    
+    # Replace silanol on the outer surface with TMS 
+    pore.attach(pms.gen.tms(), mount=0, axis=[1, 2], amount=6.06, site_type="ex", inp="molar", scale=0.5)
+    
+    # Create the structure
+    pore.finalize()
+    
+    # Store the structure
+    pore.store("pores/shape5/")
+
+
+.. figure::  /pics/shapes/shape5.pdf
+      :align: center
+      :width: 100%
+      :name: fig1
+