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doc/html/fix_eos_table_rx.html
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@ -154,7 +154,7 @@ of state to relate the concentration-dependent particle internal
energy (u_i) to the particle internal temperature (dpdTheta_i).</p> energy (u_i) to the particle internal temperature (dpdTheta_i).</p>
<p>The concentration-dependent particle internal energy (u_i) is <p>The concentration-dependent particle internal energy (u_i) is
computed according to the following relation:</p> computed according to the following relation:</p>
<img alt="Eqs/fix_eos_table_rx.jpg" class="align-center" src="Eqs/fix_eos_table_rx.jpg" /> <img alt="_images/fix_eos_table_rx.jpg" class="align-center" src="_images/fix_eos_table_rx.jpg" />
<p>where <em>m</em> is the number of species, <em>c_i,j</em> is the concentration of <p>where <em>m</em> is the number of species, <em>c_i,j</em> is the concentration of
species <em>j</em> in particle <em>i</em>, <em>u_j</em> is the internal energy of species j, species <em>j</em> in particle <em>i</em>, <em>u_j</em> is the internal energy of species j,
<em>DeltaH_f,j</em> is the heat of formation of species <em>j</em>, N is the number of <em>DeltaH_f,j</em> is the heat of formation of species <em>j</em>, N is the number of

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doc/html/fix_rx.html
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@ -153,9 +153,9 @@
<p>Fix <em>rx</em> solves the reaction kinetic ODEs for a given reaction set that is <p>Fix <em>rx</em> solves the reaction kinetic ODEs for a given reaction set that is
defined within the file associated with this command.</p> defined within the file associated with this command.</p>
<p>For a general reaction such that</p> <p>For a general reaction such that</p>
<img alt="Eqs/fix_rx_reaction.jpg" class="align-center" src="Eqs/fix_rx_reaction.jpg" /> <img alt="_images/fix_rx_reaction.jpg" class="align-center" src="_images/fix_rx_reaction.jpg" />
<p>the reaction rate equation is defined to be of the form</p> <p>the reaction rate equation is defined to be of the form</p>
<img alt="Eqs/fix_rx_reactionRate.jpg" class="align-center" src="Eqs/fix_rx_reactionRate.jpg" /> <img alt="_images/fix_rx_reactionRate.jpg" class="align-center" src="_images/fix_rx_reactionRate.jpg" />
<p>In the current implementation, the exponents are defined to be equal to the <p>In the current implementation, the exponents are defined to be equal to the
stoichiometric coefficients. A given reaction set consisting of <em>n</em> reaction stoichiometric coefficients. A given reaction set consisting of <em>n</em> reaction
equations will contain a total of <em>m</em> species. A set of <em>m</em> ordinary equations will contain a total of <em>m</em> species. A set of <em>m</em> ordinary
@ -180,7 +180,7 @@ coefficient. The only delimiters that are recognized between the species are
either a <em>+</em> or <em>=</em> character. The <em>=</em> character corresponds to an either a <em>+</em> or <em>=</em> character. The <em>=</em> character corresponds to an
irreversible reaction. After specifying the reaction, the reaction rate irreversible reaction. After specifying the reaction, the reaction rate
constant is determined through the temperature dependent Arrhenius equation:</p> constant is determined through the temperature dependent Arrhenius equation:</p>
<img alt="Eqs/fix_rx.jpg" class="align-center" src="Eqs/fix_rx.jpg" /> <img alt="_images/fix_rx.jpg" class="align-center" src="_images/fix_rx.jpg" />
<p>where <em>A</em> is the Arrhenius factor in time units or concentration/time units, <p>where <em>A</em> is the Arrhenius factor in time units or concentration/time units,
<em>n</em> is the unitless exponent of the temperature dependence, and <em>E_a</em> is the <em>n</em> is the unitless exponent of the temperature dependence, and <em>E_a</em> is the
activation energy in energy units. The temperature dependence can be removed activation energy in energy units. The temperature dependence can be removed
@ -190,9 +190,9 @@ reaction rate constants at every DPD timestep by specifying the keyword <em>none
Alternatively, the keyword <em>lucy</em> can be specified to compute a local-average particle Alternatively, the keyword <em>lucy</em> can be specified to compute a local-average particle
internal temperature for use in the reaction rate constant expressions. internal temperature for use in the reaction rate constant expressions.
The local-average particle internal temperature is defined as:</p> The local-average particle internal temperature is defined as:</p>
<img alt="Eqs/fix_rx_localTemp.jpg" class="align-center" src="Eqs/fix_rx_localTemp.jpg" /> <img alt="_images/fix_rx_localTemp.jpg" class="align-center" src="_images/fix_rx_localTemp.jpg" />
<p>where the Lucy function is expressed as:</p> <p>where the Lucy function is expressed as:</p>
<img alt="Eqs/fix_rx_localTemp2.jpg" class="align-center" src="Eqs/fix_rx_localTemp2.jpg" /> <img alt="_images/fix_rx_localTemp2.jpg" class="align-center" src="_images/fix_rx_localTemp2.jpg" />
<p>The self-particle interaction is included in the above equation.</p> <p>The self-particle interaction is included in the above equation.</p>
<hr class="docutils" /> <hr class="docutils" />
<p>The format of a tabulated file is as follows (without the parenthesized comments):</p> <p>The format of a tabulated file is as follows (without the parenthesized comments):</p>

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doc/html/pair_exp6_rx.html
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@ -152,7 +152,7 @@ from a set of <em>n</em> reaction rate equations through the <a class="reference
The species of one CG particle can interact with a species in a neighboring CG The species of one CG particle can interact with a species in a neighboring CG
particle through a site-site interaction potential model. The <em>exp6/rx</em> style particle through a site-site interaction potential model. The <em>exp6/rx</em> style
computes an exponential-6 potential given by</p> computes an exponential-6 potential given by</p>
<img alt="Eqs/pair_exp6_rx.jpg" class="align-center" src="Eqs/pair_exp6_rx.jpg" /> <img alt="_images/pair_exp6_rx.jpg" class="align-center" src="_images/pair_exp6_rx.jpg" />
<p>where the <em>epsilon</em> parameter determines the depth of the potential <p>where the <em>epsilon</em> parameter determines the depth of the potential
minimum located at <em>Rm</em>, and <em>alpha</em> determines the softness of the repulsion.</p> minimum located at <em>Rm</em>, and <em>alpha</em> determines the softness of the repulsion.</p>
<p>The coefficients must be defined for each species in a given particle type <p>The coefficients must be defined for each species in a given particle type
@ -195,9 +195,9 @@ parameter (distance units). If a species tag of &#8220;1fluid&#8221; is listed
pair coefficient, a one-fluid approximation is specified where a pair coefficient, a one-fluid approximation is specified where a
concentration-dependent combination of the parameters is computed concentration-dependent combination of the parameters is computed
through the following equations:</p> through the following equations:</p>
<img alt="Eqs/pair_exp6_rx_oneFluid.jpg" class="align-center" src="Eqs/pair_exp6_rx_oneFluid.jpg" /> <img alt="_images/pair_exp6_rx_oneFluid.jpg" class="align-center" src="_images/pair_exp6_rx_oneFluid.jpg" />
<p>where</p> <p>where</p>
<img alt="Eqs/pair_exp6_rx_oneFluid2.jpg" class="align-center" src="Eqs/pair_exp6_rx_oneFluid2.jpg" /> <img alt="_images/pair_exp6_rx_oneFluid2.jpg" class="align-center" src="_images/pair_exp6_rx_oneFluid2.jpg" />
<p>and xa and xb are the mole fractions of a and b, respectively, which <p>and xa and xb are the mole fractions of a and b, respectively, which
comprise the gas mixture.</p> comprise the gas mixture.</p>
<hr class="docutils" /> <hr class="docutils" />