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sjplimp 2016-06-07 15:41:19 +00:00
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2
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>
<p>The concentration-dependent particle internal energy (u_i) is
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
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

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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
defined within the file associated with this command.</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>
<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
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
@ -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
irreversible reaction. After specifying the reaction, the reaction rate
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,
<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
@ -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
internal temperature for use in the reaction rate constant expressions.
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>
<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>
<hr class="docutils" />
<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
particle through a site-site interaction potential model. The <em>exp6/rx</em> style
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
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
@ -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
concentration-dependent combination of the parameters is computed
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>
<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
comprise the gas mixture.</p>
<hr class="docutils" />