coverage-dependent surface phase thermodynamics

AUTHORS

@@ -7,6 +7,7 @@ tracker.
 Rounak Agarwal (@agarwalrounak)
 David Akinpelu (@DavidAkinpelu), Louisiana State University
 Emil Atz (@EmilAtz)
+Jongyoon Bae (@jongyoonbae), Brown University
 Philip Berndt
 Wolfgang Bessler (@wbessler), Offenburg University of Applied Science
 Paul Blum (@paulblum)

data/covdepsurf.yaml

@@ -0,0 +1,184 @@
+description: |-
+  Coverage-dependent thermodynamic data for CO and O surface species
+  on Pt. NASA polynomial coefficients are extracted from K. Blondal,
+  J. Jelic, E. Mazeau, F. Studt, R.H. West, and C.F. Goldsmith,
+  "Computer-Generated Kinetics for Coupled Heterogeneous/Homogeneous
+  Systems: A Case Study in Catalytic Combustion of Methane on
+  Platinum.", Ind. Eng. Chem. Res. vol. 58, 17682–17691 (2019).
+  Coverage-dependencies data for CO-CO interaction are parametrized
+  from DFT-calculated values. The calculations were done with
+  PBE-D3 xc functional on a 3 x 3 Pt periodic slab. The CO-O
+  interaction parameters is a made-up value for the cross-interaction
+  demonstration purpose.
+
+cantera-version: 3.0.0
+date: Tue, 11 Oct 2022 14:23:01 -0500
+
+phases:
+- name: covdep_lin
+  thermo: coverage-dependent-surface
+  species: [Pt(s), CO(s)_lin]
+  state:
+    T: 300 K
+    P: 1 atm
+    coverages: {Pt(s): 1.0}
+  site-density: 2.72e-09 mol/cm^2
+  reference-state-coverage: 0.11
+
+- name: covdep_pwlin
+  thermo: coverage-dependent-surface
+  species: [Pt(s), CO(s)_pwlin]
+  state:
+    T: 300 K
+    P: 1 atm
+    coverages: {Pt(s): 1.0}
+  site-density: 2.72e-09 mol/cm^2
+  reference-state-coverage: 0.11
+
+- name: covdep_poly
+  thermo: coverage-dependent-surface
+  species: [Pt(s), CO(s)_poly]
+  state:
+    T: 300 K
+    P: 1 atm
+    coverages: {Pt(s): 1.0}
+  site-density: 2.72e-09 mol/cm^2
+  reference-state-coverage: 0.11
+
+- name: covdep_int
+  thermo: coverage-dependent-surface
+  species: [Pt(s), CO(s)_int]
+  state:
+    T: 300 K
+    P: 1 atm
+    coverages: {Pt(s): 1.0}
+  site-density: 2.72e-09 mol/cm^2
+  reference-state-coverage: 0.11
+
+- name: covdep_cross
+  thermo: coverage-dependent-surface
+  species: [Pt(s), CO(s)_cross, O(s)]
+  state:
+    T: 300 K
+    P: 1 atm
+    coverages: {Pt(s): 1.0}
+  site-density: 2.72e-09 mol/cm^2
+  reference-state-coverage: 0.11
+
+species:
+- name: Pt(s)
+  composition: {Pt: 1}
+  thermo:
+    model: NASA7
+    temperature-ranges: [100.0, 1554.81, 5000.0]
+    data:
+    - [7.10129478e-03, -4.25609798e-05, 8.98507278e-08, -7.80169595e-11,
+      2.32458299e-14, -0.876096726, -0.0311207473]
+    - [0.16030291, -2.52239722e-04, 1.14183461e-07, -1.21476333e-11, 3.85825979e-16,
+      -70.8116648, -0.909545048]
+
+- name: CO(s)_lin
+  composition: {Pt: 1, C: 1, O: 1}
+  thermo:
+    model: NASA7
+    temperature-ranges: [100.0, 891.33, 5000.0]
+    data:
+    - [-1.38214121, 0.0375305409, -8.29758476e-05, 8.09701555e-08, -2.85470829e-11,
+      -3.45176032e+04, 4.3544767]
+    - [1.3809066, 8.0571901e-03, -4.6430896e-06, 8.91170699e-10, -5.90048361e-14,
+      -3.43319289e+04, -4.85318015]
+  coverage-dependencies:
+    CO(s)_lin: {model: linear,
+                units: {energy: eV, quantity: molec},
+                enthalpy: 0.845, entropy: -0.051e-3,
+                heat-capacity-a: 0.020e-3, heat-capacity-b: -0.152e-3}
+
+- name: CO(s)_pwlin
+  composition: {Pt: 1, C: 1, O: 1}
+  thermo:
+    model: NASA7
+    temperature-ranges: [100.0, 891.33, 5000.0]
+    data:
+    - [-1.38214121, 0.0375305409, -8.29758476e-05, 8.09701555e-08, -2.85470829e-11,
+      -3.45176032e+04, 4.3544767]
+    - [1.3809066, 8.0571901e-03, -4.6430896e-06, 8.91170699e-10, -5.90048361e-14,
+      -3.43319289e+04, -4.85318015]
+  coverage-dependencies:
+    CO(s)_pwlin: {model: piecewise-linear,
+                  units: {energy: eV, quantity: molec},
+                  enthalpy-low: 0.433, enthalpy-high: 1.512,
+                  enthalpy-change: 0.44,
+                  entropy-low: 0.415e-3, entropy-high: -0.31e-3,
+                  entropy-change: 0.22,
+                  heat-capacity-a: 0.020e-3, heat-capacity-b: -0.152e-3}
+
+- name: CO(s)_poly
+  composition: {Pt: 1, C: 1, O: 1}
+  thermo:
+    model: NASA7
+    temperature-ranges: [100.0, 891.33, 5000.0]
+    data:
+    - [-1.38214121, 0.0375305409, -8.29758476e-05, 8.09701555e-08, -2.85470829e-11,
+      -3.45176032e+04, 4.3544767]
+    - [1.3809066, 8.0571901e-03, -4.6430896e-06, 8.91170699e-10, -5.90048361e-14,
+      -3.43319289e+04, -4.85318015]
+  coverage-dependencies:
+    CO(s)_poly: {model: polynomial,
+                 units: {energy: eV, quantity: molec},
+                 enthalpy-coefficients: [0.129, 0.633, 0.325, 0.],
+                 entropy-coefficients: [0.640e-3, -1.547e-3, 0.798e-3, 0.],
+                 heat-capacity-a: 0.020e-3, heat-capacity-b: -0.152e-3}
+
+- name: CO(s)_int
+  composition: {Pt: 1, C: 1, O: 1}
+  thermo:
+    model: NASA7
+    temperature-ranges: [100.0, 891.33, 5000.0]
+    data:
+    - [-1.38214121, 0.0375305409, -8.29758476e-05, 8.09701555e-08, -2.85470829e-11,
+      -3.45176032e+04, 4.3544767]
+    - [1.3809066, 8.0571901e-03, -4.6430896e-06, 8.91170699e-10, -5.90048361e-14,
+      -3.43319289e+04, -4.85318015]
+  coverage-dependencies:
+    CO(s)_int: {model: interpolative,
+                units: {energy: eV, quantity: molec},
+                enthalpy-coverages: [0.0, 0.11, 0.22, 0.33, 0.44, 0.56,
+                                     0.67, 0.78, 0.89, 1.0],
+                enthalpies: [0., 0., 0.104, 0.182, 0.173, 0.266,
+                             0.413, 0.718, 0.880, 1.05],
+                entropy-coverages: [0.0, 0.11, 0.22, 0.33, 0.44, 0.56,
+                                    0.67, 0.78, 0.89, 1.0],
+                entropies: [0., 0., 0.115e-3, 0.071e-3, 0.059e-3, -0.004e-3,
+                            -0.023e-3, -0.071e-3, -0.074e-3, -0.115e-3],
+                heat-capacity-a: 0.020e-3, heat-capacity-b: -0.152e-3}
+
+- name: CO(s)_cross
+  composition: {Pt: 1, C: 1, O: 1}
+  thermo:
+    model: NASA7
+    temperature-ranges: [100.0, 891.33, 5000.0]
+    data:
+    - [-1.38214121, 0.0375305409, -8.29758476e-05, 8.09701555e-08, -2.85470829e-11,
+      -3.45176032e+04, 4.3544767]
+    - [1.3809066, 8.0571901e-03, -4.6430896e-06, 8.91170699e-10, -5.90048361e-14,
+      -3.43319289e+04, -4.85318015]
+  coverage-dependencies:
+    CO(s)_cross: {model: linear,
+                  units: {energy: eV, quantity: molec},
+                  enthalpy: 0.845, entropy: -0.051e-3,
+                  heat-capacity-a: 0.020e-3, heat-capacity-b: -0.152e-3}
+    O(s): {model: linear,
+           units: {energy: eV, quantity: molec},
+           enthalpy: 0.412}
+
+- name: O(s)
+  composition: {Pt: 1, O: 1}
+  thermo:
+    model: NASA7
+    temperature-ranges: [100.0, 888.26, 5000.0]
+    data:
+    - [-0.759013067, 0.0189868498, -3.82473745e-05, 3.43558395e-08, -1.13974372e-11,
+      -1.72389494e+04, 1.76017396]
+    - [1.89893619, 2.03295425e-03, -1.19976574e-06, 2.32680659e-10, -1.53508282e-14,
+      -1.75144954e+04, -9.6410408]
+

doc/sphinx/yaml/phases.rst

@@ -86,6 +86,7 @@ and optionally reactions that can take place in that phase. The fields of a
     - :ref:`ideal-condensed <sec-yaml-ideal-condensed>`
     - :ref:`ideal-solution-VPSS <sec-yaml-ideal-solution-VPSS>`
     - :ref:`ideal-surface <sec-yaml-ideal-surface>`
+    - :ref:`coverage-dependent-surface <sec-yaml-coverage-dependent-surface>`
     - :ref:`ions-from-neutral-molecule <sec-yaml-ions-from-neutral-molecule>`
     - :ref:`lattice <sec-yaml-lattice>`
     - :ref:`liquid-water-IAPWS95 <sec-yaml-liquid-water-IAPWS95>`
@@ -656,6 +657,41 @@ Example::
       site-density: 2.7063e-09
 
 
+.. _sec-yaml-coverage-dependent-surface:
+
+``coverage-dependent-surface``
+------------------------------
+
+A coverage-dependent surface phase. That is, a surface phase where the enthalpy,
+entropy, and heat capacity of each species may depend on its coverage and the
+coverage of other species in the phase.
+Full details are
+`described here <https://cantera.org/documentation/dev/doxygen/html/db/d25/classCantera_1_1CoverageDependentSurfPhase.html#details>`__.
+Majority of coverage dependency parameters are provided in the species entry as
+`described here <https://cantera.org/documentation/dev/sphinx/html/yaml/species.html#coverage-dependent-surface>`__.
+
+Additional fields:
+
+``site-density``
+    The molar density of surface sites.
+
+``reference-state-coverage``
+    The reference state coverage denoting the low-coverage limit (ideal-surface)
+    thermodynamic properties.
+
+Example::
+
+    - name: covdep
+      thermo: coverage-dependent-surface
+      species: [Pt, OC_Pt, CO2_Pt, C_Pt, O_Pt]
+      state:
+        T: 500.0
+        P: 1.01325e+05
+        coverages: {Pt: 0.5, OC_Pt: 0.5, CO2_Pt: 0.0, C_Pt: 0.0, O_Pt: 0.0}
+      site-density: 2.72e-09
+      reference-state-coverage: 0.22
+
+
 .. _sec-yaml-ions-from-neutral-molecule:
 
 ``ions-from-neutral-molecule``

doc/sphinx/yaml/species.rst

@@ -483,6 +483,99 @@ Additional fields:
     coefficients for binary interactions between the two species.
 
 
+.. _sec-yaml-coverage-dependent-surface-species:
+
+Coverage-dependent Surface
+--------------------------
+
+A model where species thermodynamic properties are calculated as a function
+coverage as
+`described here <https://cantera.org/documentation/dev/doxygen/html/db/d25/classCantera_1_1CoverageDependentSurfPhase.html#details>`__.
+
+Additional fields:
+
+``coverage-dependencies``
+    Mapping where keys are the name of species whose coverage affects
+    thermodynamic properties of the node-owner species. The map values are
+    the dependency entries including ``model``, model-specific parameters,
+    ``heat-capacity-a``, and ``heat-capacity-b`` that correspond
+    to an individual dependency between the node-owner species and keyed species.
+
+``model``
+    Dependency model for coverage-dependent enthalpy or entropy. It should be
+    one of the four: ``linear``, ``polynomial``, ``piecewise-linear``
+    or ``interpolative``. The ``model`` and model-specific parameters are grouped
+    as follow.
+
+    ``linear``: ``enthalpy``, ``entropy``
+
+    ``polynomial``: ``enthalpy-coefficients``, ``entropy-coefficients``
+
+    ``piecewise-linear``: ``enthalpy-low``, ``enthalpy-high``, ``enthalpy-change``,
+    ``entropy-low``, ``entropy-high``, ``entropy-change``
+
+    ``interpolative``: ``enthalpy-coverages``, ``enthalpies``, ``entropy-coverages``,
+    ``entropies``
+
+``enthalpy`` or ``entropy``
+    Slope of the coverage-dependent enthalpy or entropy used in the ``linear``
+    model.
+
+``enthalpy-coefficients`` or ``entropy-coefficients``
+    Array of polynomial coefficients in order of 1st, 2nd, 3rd, and 4th-order
+    used in coverage-dependent enthalpy or entropy calculation with the ``polynomial``
+    model.
+
+``enthalpy-low`` or ``entropy-low``
+    Slope of the coverage-dependent enthalpy or entropy for the lower coverage
+    region used in the ``piecewise-linear`` model.
+
+``enthalpy-high`` or ``entropy-high``
+    Slope of the coverage-dependent enthalpy or entropy for the higher coverage
+    region used in the ``piecewise-linear`` model.
+
+``enthalpy-change`` or ``entropy-change``
+    Coverage that separates the lower and higher coverage regions of the
+    coverage-dependent enthalpy or entropy used in the ``piecewise-linear`` model.
+
+``enthalpy-coverages`` or ``entropy-coverages``
+    Array of discrete coverage values used in coverage-dependent enthalpy
+    or entropy used in the ``interpolative`` model.
+
+``enthalpies`` or ``entropies``
+    Array of discrete enthalpy or entropy values corresponding to the coverages
+    in ``enthalpy-coverages`` or ``entropy-coverages``, respectively, used in the
+    ``interpolative`` model.
+
+``heat-capacity-a`` or ``heat-capacity-b``
+    Coefficient :math:`c^{(a)}` or :math:`c^{(b)}` used in the coverage-dependent
+    ``heat capacity`` model.
+
+Example::
+
+    coverage-dependencies:
+      OC_Pt: {model: linear,
+              units: {energy: eV, quantity: molec},
+              enthalpy: 0.48, entropy: -0.031}
+      C_Pt: {model: polynomial,
+             units: {energy: J, quantity: mol},
+             enthalpy-coefficients: [0.0, -3.86e4, 0.0, 4.2e5],
+             entropy-coefficients: [0.8e3, 0.0, -1.26e4, 0.0]}
+      CO2_Pt: {model: piecewise-linear,
+               units: {energy: kJ, quantity: mol},
+               enthalpy-low: 0.5e2, enthalpy-high: 1.0e2,
+               enthalpy-change: 0.4,
+               entropy-low: 0.1e2, entropy-high: -0.2e2,
+               entropy-change: 0.4,
+               heat-capacity-a: 0.02e-1, heat-capacity-b: -0.156e-1}
+      O_Pt: {model: interpolative,
+             units: {energy: kcal, quantity: mol},
+             enthalpy-coverages: [0.0, 0.2, 0.4, 0.7, 0.9, 1.0],
+             enthalpies: [0.0, 0.5, 1.0, 2.7, 3.5, 4.0],
+             entropy-coverages: [0.0, 0.5, 1.0],
+             entropies: [0.0, -0.7, -2.0]}
+
+
 .. _sec-yaml-species-transport:
 
 Species transport models