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+

fix rx command

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Syntax

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fix ID group-ID rx file localTemp solver ...
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  • ID, group-ID are documented in fix command
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  • rx = style name of this fix command
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  • file = filename containing the reaction kinetic equations and Arrhenius parameters
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  • localTemp = none,lucy = no local temperature averaging or local temperature defined through Lucy weighting function
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  • solver = lammps_rk4 = Explicit 4th order Runge-Kutta method
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  • minSteps = # of steps for rk4 solver
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Examples

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fix 1 all rx kinetics.rx none lammps_rk4
+fix 1 all rx kinetics.rx none lammps_rk4 1
+fix 1 all rx kinetics.rx lucy lammps_rk4 10
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Description

+

Fix rx solves the reaction kinetic ODEs for a given reaction set that is +defined within the file associated with this command.

+

For a general reaction such that

+Eqs/fix_rx_reaction.jpg +

the reaction rate equation is defined to be of the form

+Eqs/fix_rx_reactionRate.jpg +

In the current implementation, the exponents are defined to be equal to the +stoichiometric coefficients. A given reaction set consisting of n reaction +equations will contain a total of m species. A set of m ordinary +differential equations (ODEs) that describe the change in concentration of a +given species as a function of time are then constructed based on the n +reaction rate equations.

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The ODE systems are solved over the full DPD timestep dt using a 4th order +Runge-Kutta rk4 method with a fixed step-size h, specified by the +lammps_rk4 keyword. The number of ODE steps per DPD timestep for the rk4 method +is optionally specified immediately after the rk4 keyword. The ODE step-size is set as +dt/num_steps. Smaller step-sizes tend to yield more accurate results but there +is not control on the error.

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The filename specifies a file that contains the entire set of reaction +kinetic equations and corresponding Arrhenius parameters. The format of +this file is described below.

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There is no restriction on the total number or reaction equations that are +specified. The species names are arbitrary string names that are associated +with the species concentrations. +Each species in a given reaction must be preceded by it’s stoichiometric +coefficient. The only delimiters that are recognized between the species are +either a + or = character. The = character corresponds to an +irreversible reaction. After specifying the reaction, the reaction rate +constant is determined through the temperature dependent Arrhenius equation:

+Eqs/fix_rx.jpg +

where A is the Arrhenius factor in time units or concentration/time units, +n is the unitless exponent of the temperature dependence, and E_a is the +activation energy in energy units. The temperature dependence can be removed +by specifying the exponent as zero.

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The internal temperature of the coarse-grained particles can be used in constructing the +reaction rate constants at every DPD timestep by specifying the keyword none. +Alternatively, the keyword lucy 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:

+Eqs/fix_rx_localTemp.jpg +

where the Lucy function is expressed as:

+Eqs/fix_rx_localTemp2.jpg +

The self-particle interaction is included in the above equation.

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The format of a tabulated file is as follows (without the parenthesized comments):

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# Rxn equations and parameters                                               (one or more comment or blank lines)
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1.0 hcn + 1.0 no2 = 1.0  no + 0.5 n2  + 0.5 h2 + 1.0 co   2.49E+01 0.0 1.34  (rxn equation, A, n, Ea)
+1.0 hcn + 1.0  no = 1.0  co + 1.0 n2  + 0.5 h2            2.16E+00 0.0 1.52
+...
+1.0  no + 1.0  co = 0.5  n2 + 1.0 co2                     1.66E+06 0.0 0.69
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+
+

A section begins with a non-blank line whose 1st character is not a +“#”; blank lines or lines starting with “#” can be used as comments +between sections.

+

Following a blank line, the next N lines list the N reaction equations. +Each species within the reaction equation is specified through its +stoichiometric coefficient and a species tag. Reactant species are specified +on the left-hand side of the equation and product species are specified on the +right-hand side of the equation. After specifying the reactant and product +species, the final three arguments of each line represent the Arrhenius +parameter A, the temperature exponent n, and the activation energy Ea.

+

Note that the species tags that are defined in the reaction equations are +used by the fix eos/table/rx command to define the +thermodynamic properties of each species. Furthermore, the number of species +molecules (i.e., concentration) can be specified either with the set +command using the “d_” prefix or by reading directly the concentrations from a +data file. For the latter case, the read_data command with the +fix keyword should be specified, where the fix-ID will be the “fix rx`ID with a <SPECIES”>`_ suffix, e.g.

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fix foo all rx reaction.file ... +read_data data.dpd fix foo_SPECIES NULL Species

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Restrictions

+

The fix rx is only available if LAMMPS is built with the USER-DPD package.

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The fix rx must be used with the atom_style dpd command.

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The fix rx can only be used with a constant energy or constant enthalpy DPD simulation.

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