forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15128 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
78c0df7de2
commit
0f5dcedee1
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@ -38,8 +38,12 @@ possible.
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[Restrictions:]
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The fix {eos/cv} is only available if LAMMPS is built with the
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USER-DPD package.
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This command is part of the USER-DPD package. It is only enabled if
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LAMMPS was built with that package. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info.
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This command also requires use of the "atom_style dpd"_atom_style.html
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command.
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[Related commands:]
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|
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@ -98,13 +98,17 @@ one that matches the specified keyword.
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[Restrictions:]
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The fix {eos/table} is only available if LAMMPS is built with the
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USER-DPD package.
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This command is part of the USER-DPD package. It is only enabled if
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LAMMPS was built with that package. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info.
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This command also requires use of the "atom_style dpd"_atom_style.html
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command.
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The equation of state must be a monotonically increasing function.
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An exit error will occur if the internal temperature or internal
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energies are not within the table cutoffs.
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An error will occur if the internal temperature or internal energies
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are not within the table cutoffs.
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[Related commands:]
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@ -120,13 +120,17 @@ the reactions with the "fix rx"_fix_rx.html command.
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[Restrictions:]
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The fix {eos/table/rx} is only available if LAMMPS is built with the
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USER-DPD package.
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This command is part of the USER-DPD package. It is only enabled if
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LAMMPS was built with that package. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info.
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This command also requires use of the "atom_style dpd"_atom_style.html
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command.
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The equation of state must be a monotonically increasing function.
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An exit error will occur if the internal temperature or internal
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energies are not within the table cutoffs.
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An error will occur if the internal temperature or internal energies
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are not within the table cutoffs.
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[Related commands:]
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@ -38,19 +38,20 @@ the reaction rate equation is defined to be of the form
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:c,image(Eqs/fix_rx_reactionRate.jpg)
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In the current implementation, the exponents are defined to be equal to the
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stoichiometric coefficients. A given reaction set consisting of {n} reaction
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equations will contain a total of {m} species. A set of {m} ordinary
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differential equations (ODEs) that describe the change in concentration of a
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given species as a function of time are then constructed based on the {n}
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reaction rate equations.
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In the current implementation, the exponents are defined to be equal
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to the stoichiometric coefficients. A given reaction set consisting
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of {n} reaction equations will contain a total of {m} species. A set
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of {m} ordinary differential equations (ODEs) that describe the change
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in concentration of a given species as a function of time are then
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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
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Runge-Kutta {rk4} method with a fixed step-size {h}, specified by the
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{lammps_rk4} keyword. The number of ODE steps per DPD timestep for the rk4 method
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is optionally specified immediately after the rk4 keyword. The ODE step-size is set as
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{dt/num_steps}. Smaller step-sizes tend to yield more accurate results but there
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is not control on the error.
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The ODE systems are solved over the full DPD timestep {dt} using a 4th
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order Runge-Kutta {rk4} method with a fixed step-size {h}, specified
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by the {lammps_rk4} keyword. The number of ODE steps per DPD timestep
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for the rk4 method is optionally specified immediately after the rk4
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keyword. The ODE step-size is set as {dt/num_steps}. Smaller
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step-sizes tend to yield more accurate results but there is not
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control on the error.
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:line
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@ -58,27 +59,29 @@ The filename specifies a file that contains the entire set of reaction
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kinetic equations and corresponding Arrhenius parameters. The format of
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this file is described below.
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There is no restriction on the total number or reaction equations that are
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specified. The species names are arbitrary string names that are associated
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with the species concentrations.
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Each species in a given reaction must be preceded by it's stoichiometric
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coefficient. The only delimiters that are recognized between the species are
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either a {+} or {=} character. The {=} character corresponds to an
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irreversible reaction. After specifying the reaction, the reaction rate
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constant is determined through the temperature dependent Arrhenius equation:
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There is no restriction on the total number or reaction equations that
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are specified. The species names are arbitrary string names that are
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associated with the species concentrations. Each species in a given
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reaction must be preceded by it's stoichiometric coefficient. The
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only delimiters that are recognized between the species are either a
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{+} or {=} character. The {=} character corresponds to an
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irreversible reaction. After specifying the reaction, the reaction
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rate constant is determined through the temperature dependent
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Arrhenius equation:
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:c,image(Eqs/fix_rx.jpg)
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where {A} is the Arrhenius factor in time units or concentration/time units,
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{n} is the unitless exponent of the temperature dependence, and {E_a} is the
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activation energy in energy units. The temperature dependence can be removed
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by specifying the exponent as zero.
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where {A} is the Arrhenius factor in time units or concentration/time
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units, {n} is the unitless exponent of the temperature dependence, and
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{E_a} is the activation energy in energy units. The temperature
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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
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reaction rate constants at every DPD timestep by specifying the keyword {none}.
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Alternatively, the keyword {lucy} can be specified to compute a local-average particle
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internal temperature for use in the reaction rate constant expressions.
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The local-average particle internal temperature is defined as:
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The internal temperature of the coarse-grained particles can be used
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in constructing the reaction rate constants at every DPD timestep by
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specifying the keyword {none}. Alternatively, the keyword {lucy} can
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be specified to compute a local-average particle internal temperature
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for use in the reaction rate constant expressions. The local-average
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particle internal temperature is defined as:
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:c,image(Eqs/fix_rx_localTemp.jpg)
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@ -90,7 +93,8 @@ The self-particle interaction is included in the above equation.
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:line
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The format of a tabulated file is as follows (without the parenthesized comments):
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The format of a tabulated file is as follows (without the
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parenthesized comments):
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# Rxn equations and parameters (one or more comment or blank lines) :pre
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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)
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@ -102,21 +106,23 @@ A section begins with a non-blank line whose 1st character is not a
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"#"; blank lines or lines starting with "#" can be used as comments
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between sections.
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Following a blank line, the next N lines list the N reaction equations.
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Each species within the reaction equation is specified through its
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stoichiometric coefficient and a species tag. Reactant species are specified
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on the left-hand side of the equation and product species are specified on the
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right-hand side of the equation. After specifying the reactant and product
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species, the final three arguments of each line represent the Arrhenius
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parameter {A}, the temperature exponent {n}, and the activation energy {Ea}.
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Following a blank line, the next N lines list the N reaction
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equations. Each species within the reaction equation is specified
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through its stoichiometric coefficient and a species tag. Reactant
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species are specified on the left-hand side of the equation and
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product species are specified on the right-hand side of the equation.
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After specifying the reactant and product species, the final three
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arguments of each line represent the Arrhenius parameter {A}, the
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temperature exponent {n}, and the activation energy {Ea}.
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Note that the species tags that are defined in the reaction equations are
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used by the "fix eos/table/rx"_fix_eos_table_rx.html command to define the
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thermodynamic properties of each species. Furthermore, the number of species
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molecules (i.e., concentration) can be specified either with the "set"_set.html
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command using the "d_" prefix or by reading directly the concentrations from a
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data file. For the latter case, the "read_data"_read_data.html command with the
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fix keyword should be specified, where the fix-ID will be the "fix rx" ID with a
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Note that the species tags that are defined in the reaction equations
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are used by the "fix eos/table/rx"_fix_eos_table_rx.html command to
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define the thermodynamic properties of each species. Furthermore, the
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number of species molecules (i.e., concentration) can be specified
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either with the "set"_set.html command using the "d_" prefix or by
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reading directly the concentrations from a data file. For the latter
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case, the "read_data"_read_data.html command with the fix keyword
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should be specified, where the fix-ID will be the "fix rx" ID with a
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"_SPECIES" suffix, e.g.
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fix foo all rx reaction.file ...
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@ -126,11 +132,15 @@ read_data data.dpd fix foo_SPECIES NULL Species
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[Restrictions:]
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The fix {rx} is only available if LAMMPS is built with the USER-DPD package.
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This command is part of the USER-DPD package. It is only enabled if
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LAMMPS was built with that package. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info.
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The fix {rx} must be used with the "atom_style dpd"_atom_style.html command.
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This command also requires use of the "atom_style dpd"_atom_style.html
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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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This command can only be used with a constant energy or constant
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enthalpy DPD simulation.
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[Related commands:]
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@ -139,5 +149,3 @@ The fix {rx} can only be used with a constant energy or constant enthalpy DPD si
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"pair dpd/fdt/energy"_dpd_fdt_energy.html
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[Default:] none
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:line
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@ -54,9 +54,9 @@ examples/USER/dpd directory.
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[Restrictions:]
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This fix is only available if LAMMPS is built with the USER-DPD
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package. See the "Making LAMMPS"_Section_start.html#start_3 section
|
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for more info.
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This command is part of the USER-DPD package. It is only enabled if
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LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
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This fix is currently limited to orthogonal simulation cell
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geometries.
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@ -66,7 +66,7 @@ integration, e.g. "fix nve"_fix_nve.html or "fix nph"_fix_nh.html.
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The Shardlow splitting algorithm requires the sizes of the sub-domain
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lengths to be larger than twice the cutoff+skin. Generally, the
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domain decomposition is dependant on the number of processors
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domain decomposition is dependent on the number of processors
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requested.
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[Related commands:]
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|
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@ -110,8 +110,9 @@ specified.
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[Restrictions:]
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Pair styles {dpd/fdt} and {dpd/fdt/energy} are only available if
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LAMMPS is built with the USER-DPD package.
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These commands are part of the USER-DPD package. They are only
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enabled if LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
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Pair styles {dpd/fdt} and {dpd/fdt/energy} require use of the
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"communicate vel yes"_communicate.html option so that velocites are
|
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|
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@ -23,34 +23,37 @@ pair_coeff * * exp6.params 1fluid 1fluid 1.0 1.0 10.0 :pre
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[Description:]
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Style {exp6/rx} is used in reaction DPD simulations, where the coarse-grained (CG)
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particles are composed of {m} species whose reaction rate kinetics are determined
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from a set of {n} reaction rate equations through the "fix rx"_fix_rx.html command.
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The species of one CG particle can interact with a species in a neighboring CG
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particle through a site-site interaction potential model. The {exp6/rx} style
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computes an exponential-6 potential given by
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Style {exp6/rx} is used in reaction DPD simulations, where the
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coarse-grained (CG) particles are composed of {m} species whose
|
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reaction rate kinetics are determined from a set of {n} reaction rate
|
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equations through the "fix rx"_fix_rx.html command. The species of
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one CG particle can interact with a species in a neighboring CG
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particle through a site-site interaction potential model. The
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{exp6/rx} style computes an exponential-6 potential given by
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:c,image(Eqs/pair_exp6_rx.jpg)
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where the {epsilon} parameter determines the depth of the potential
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minimum located at {Rm}, and {alpha} determines the softness of the repulsion.
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The coefficients must be defined for each species in a given particle type
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via the "pair_coeff"_pair_coeff.html command as in the examples above, where
|
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the first argument is the filename that includes the exponential-6 parameters
|
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for each species. The file includes the species tag followed by the {alpha},
|
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{epsilon} and {Rm} parameters. The format of the file is described below.
|
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The coefficients must be defined for each species in a given particle
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type via the "pair_coeff"_pair_coeff.html command as in the examples
|
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above, where the first argument is the filename that includes the
|
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exponential-6 parameters for each species. The file includes the
|
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species tag followed by the {alpha}, {epsilon} and {Rm}
|
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parameters. The format of the file is described below.
|
||||
|
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The second and third arguments specify the site-site interaction
|
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potential between two species contained within two different particles.
|
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The species tags must either correspond to the species defined in the reaction
|
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kinetics files specified with the "fix rx"_fix_rx.html command
|
||||
or they must correspond to the tag "1fluid", signifying interaction
|
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with a product species mixture determined through a one-fluid approximation.
|
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The interaction potential is weighted by the geometric average of the
|
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concentrations of the two species. The coarse-grained potential is
|
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stored before and after the reaction kinetics solver is applied, where the
|
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difference is defined to be the internal chemical energy (uChem).
|
||||
The second and third arguments specify the site-site interaction
|
||||
potential between two species contained within two different
|
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particles. The species tags must either correspond to the species
|
||||
defined in the reaction kinetics files specified with the "fix
|
||||
rx"_fix_rx.html command or they must correspond to the tag "1fluid",
|
||||
signifying interaction with a product species mixture determined
|
||||
through a one-fluid approximation. The interaction potential is
|
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weighted by the geometric average of the concentrations of the two
|
||||
species. The coarse-grained potential is stored before and after the
|
||||
reaction kinetics solver is applied, where the difference is defined
|
||||
to be the internal chemical energy (uChem).
|
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|
||||
The fourth and fifth arguments specify the {Rm} and {epsilon} scaling exponents.
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@ -58,7 +61,8 @@ The final argument specifies the interaction cutoff.
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:line
|
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|
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The format of a tabulated file is as follows (without the parenthesized comments):
|
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The format of a tabulated file is as follows (without the
|
||||
parenthesized comments):
|
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|
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# exponential-6 parameters for various species (one or more comment or blank lines) :pre
|
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h2o exp6 11.00 0.02 3.50 (species, exp6, alpha, Rm, epsilon)
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@ -68,16 +72,16 @@ co2 exp6 13.00 0.03 3.20 :pre
|
|||
|
||||
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.
|
||||
between sections.
|
||||
|
||||
Following a blank line, the next N lines list the species and their
|
||||
corresponding parameters. The first argument is the species tag,
|
||||
the second argument is the exp6 tag, the 3rd argument is the {alpha}
|
||||
parameter (energy units), the 4th argument is the {epsilon} parameter
|
||||
(energy-distance^6 units), and the 5th argument is the {Rm}
|
||||
parameter (distance units). If a species tag of "1fluid" is listed as a
|
||||
pair coefficient, a one-fluid approximation is specified where a
|
||||
concentration-dependent combination of the parameters is computed
|
||||
Following a blank line, the next N lines list the species and their
|
||||
corresponding parameters. The first argument is the species tag, the
|
||||
second argument is the exp6 tag, the 3rd argument is the {alpha}
|
||||
parameter (energy units), the 4th argument is the {epsilon} parameter
|
||||
(energy-distance^6 units), and the 5th argument is the {Rm} parameter
|
||||
(distance units). If a species tag of "1fluid" is listed as a pair
|
||||
coefficient, a one-fluid approximation is specified where a
|
||||
concentration-dependent combination of the parameters is computed
|
||||
through the following equations:
|
||||
|
||||
:c,image(Eqs/pair_exp6_rx_oneFluid.jpg)
|
||||
|
|
@ -105,7 +109,9 @@ pair interaction.
|
|||
|
||||
[Restrictions:]
|
||||
|
||||
None
|
||||
This command is part of the USER-DPD package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
|
|
|
|||
|
|
@ -22,14 +22,15 @@ pair_coeff * * multibody.table ENTRY1 7.0 :pre
|
|||
|
||||
[Description:]
|
||||
|
||||
Style {multi/lucy} computes a density-dependent force following from the many-body
|
||||
form described in "(Moore)"_#Moore and "(Warren)"_#Warren as
|
||||
Style {multi/lucy} computes a density-dependent force following from
|
||||
the many-body form described in "(Moore)"_#Moore and
|
||||
"(Warren)"_#Warren as
|
||||
|
||||
:c,image(Eqs/pair_multi_lucy.jpg)
|
||||
|
||||
which consists of a density-dependent function, A(rho), and a radial-dependent weight
|
||||
function, omegaDD(rij). The radial-dependent weight function, omegaDD(rij), is taken
|
||||
as the Lucy function:
|
||||
which consists of a density-dependent function, A(rho), and a
|
||||
radial-dependent weight function, omegaDD(rij). The radial-dependent
|
||||
weight function, omegaDD(rij), is taken as the Lucy function:
|
||||
|
||||
:c,image(Eqs/pair_multi_lucy2.jpg)
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|
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|
|
@ -37,24 +38,29 @@ The density-dependent energy for a given particle is given by:
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|||
|
||||
:c,image(Eqs/pair_multi_lucy_energy.jpg)
|
||||
|
||||
See the supporting information of "(Brennan)"_#Brennan or the publication by "(Moore)"_#Moore
|
||||
for more details on the functional form.
|
||||
See the supporting information of "(Brennan)"_#Brennan or the
|
||||
publication by "(Moore)"_#Moore for more details on the functional
|
||||
form.
|
||||
|
||||
An interpolation table is used to evaluate the density-dependent energy (Integral(A(rho)drho) and force (A(rho)).
|
||||
Note that the pre-factor to the energy is computed after the interpolation, thus the Integral(A(rho)drho will
|
||||
have units of energy / length^4.
|
||||
An interpolation table is used to evaluate the density-dependent
|
||||
energy (Integral(A(rho)drho) and force (A(rho)). Note that the
|
||||
pre-factor to the energy is computed after the interpolation, thus the
|
||||
Integral(A(rho)drho will have units of energy / length^4.
|
||||
|
||||
The interpolation table is created as a pre-computation by fitting cubic splines to
|
||||
the file values and interpolating the density-dependent energy and force at each of {N} densities.
|
||||
During a simulation, the tables are used to interpolate the density-dependent energy and force as
|
||||
needed for each pair of particles separated by a distance {R}. The interpolation is done in
|
||||
one of 2 styles: {lookup} and {linear}.
|
||||
The interpolation table is created as a pre-computation by fitting
|
||||
cubic splines to the file values and interpolating the
|
||||
density-dependent energy and force at each of {N} densities. During a
|
||||
simulation, the tables are used to interpolate the density-dependent
|
||||
energy and force as needed for each pair of particles separated by a
|
||||
distance {R}. The interpolation is done in one of 2 styles: {lookup}
|
||||
and {linear}.
|
||||
|
||||
For the {lookup} style, the density is used to find the nearest table entry, which is the
|
||||
density-dependent energy and force.
|
||||
For the {lookup} style, the density is used to find the nearest table
|
||||
entry, which is the density-dependent energy and force.
|
||||
|
||||
For the {linear} style, the density is used to find the 2 surrounding table values from
|
||||
which the density-dependent energy and force are computed by linear interpolation.
|
||||
For the {linear} style, the density is used to find the 2 surrounding
|
||||
table values from which the density-dependent energy and force are
|
||||
computed by linear interpolation.
|
||||
|
||||
The following coefficients must be defined for each pair of atoms
|
||||
types via the "pair_coeff"_pair_coeff.html command as in the examples
|
||||
|
|
@ -64,13 +70,14 @@ filename
|
|||
keyword
|
||||
cutoff (distance units) :ul
|
||||
|
||||
The filename specifies a file containing the tabulated density-dependent
|
||||
energy and force. The keyword specifies a section of the file.
|
||||
The cutoff is an optional coefficient. If not specified, the outer cutoff in the
|
||||
table itself (see below) will be used to build an interpolation table
|
||||
that extend to the largest tabulated distance. If specified, only
|
||||
file values up to the cutoff are used to create the interpolation
|
||||
table. The format of this file is described below.
|
||||
The filename specifies a file containing the tabulated
|
||||
density-dependent energy and force. The keyword specifies a section
|
||||
of the file. The cutoff is an optional coefficient. If not
|
||||
specified, the outer cutoff in the table itself (see below) will be
|
||||
used to build an interpolation table that extend to the largest
|
||||
tabulated distance. If specified, only file values up to the cutoff
|
||||
are used to create the interpolation table. The format of this file
|
||||
is described below.
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -98,19 +105,19 @@ numeric values.
|
|||
|
||||
The parameter "N" is required and its value is the number of table
|
||||
entries that follow. Note that this may be different than the {N}
|
||||
specified in the "pair_style multi/lucy"_pair_multi_lucy.html command. Let
|
||||
Ntable = {N} in the pair_style command, and Nfile = "N" in the
|
||||
specified in the "pair_style multi/lucy"_pair_multi_lucy.html command.
|
||||
Let Ntable = {N} in the pair_style command, and Nfile = "N" in the
|
||||
tabulated file. What LAMMPS does is a preliminary interpolation by
|
||||
creating splines using the Nfile tabulated values as nodal points. It
|
||||
uses these to interpolate the density-dependent energy and force at Ntable different
|
||||
points. The resulting tables of length Ntable are then used as
|
||||
described above, when computing the density-dependent energy and force.
|
||||
This means that if you want the interpolation tables of
|
||||
length Ntable to match exactly what is in the tabulated file (with
|
||||
effectively no preliminary interpolation), you should set Ntable =
|
||||
Nfile, and use the "RSQ" parameter. This is because the
|
||||
internal table abscissa is always RSQ (separation distance squared),
|
||||
for efficient lookup.
|
||||
uses these to interpolate the density-dependent energy and force at
|
||||
Ntable different points. The resulting tables of length Ntable are
|
||||
then used as described above, when computing the density-dependent
|
||||
energy and force. This means that if you want the interpolation
|
||||
tables of length Ntable to match exactly what is in the tabulated file
|
||||
(with effectively no preliminary interpolation), you should set Ntable
|
||||
= Nfile, and use the "RSQ" parameter. This is because the internal
|
||||
table abscissa is always RSQ (separation distance squared), for
|
||||
efficient lookup.
|
||||
|
||||
All other parameters are optional. If "R" or "RSQ" does
|
||||
not appear, then the distances in each line of the table are used
|
||||
|
|
@ -167,7 +174,11 @@ This pair style can only be used via the {pair} keyword of the
|
|||
|
||||
:line
|
||||
|
||||
[Restrictions:] none
|
||||
[Restrictions:]
|
||||
|
||||
This command is part of the USER-DPD package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
|
|
|
|||
|
|
@ -23,19 +23,21 @@ pair_coeff * * multibody.table ENTRY1 h2o 1fluid 7.0 :pre
|
|||
|
||||
[Description:]
|
||||
|
||||
Style {multi/lucy/rx} is used in reaction DPD simulations, where the coarse-grained
|
||||
(CG) particles are composed of {m} species whose reaction rate kinetics are determined
|
||||
from a set of {n} reaction rate equations through the "fix rx"_fix_rx.html command.
|
||||
The species of one CG particle can interact with a species in a neighboring CG particle
|
||||
through a site-site interaction potential model. Style {multi/lucy/rx} computes the
|
||||
site-site density-dependent force following from the many-body form described in
|
||||
"(Moore)"_#Moore and "(Warren)"_#Warren as
|
||||
Style {multi/lucy/rx} is used in reaction DPD simulations, where the
|
||||
coarse-grained (CG) particles are composed of {m} species whose
|
||||
reaction rate kinetics are determined from a set of {n} reaction rate
|
||||
equations through the "fix rx"_fix_rx.html command. The species of
|
||||
one CG particle can interact with a species in a neighboring CG
|
||||
particle through a site-site interaction potential model. Style
|
||||
{multi/lucy/rx} computes the site-site density-dependent force
|
||||
following from the many-body form described in "(Moore)"_#Moore and
|
||||
"(Warren)"_#Warren as
|
||||
|
||||
:c,image(Eqs/pair_multi_lucy.jpg)
|
||||
|
||||
which consists of a density-dependent function, A(rho), and a radial-dependent weight
|
||||
function, omegaDD(rij). The radial-dependent weight function, omegaDD(rij), is taken
|
||||
as the Lucy function:
|
||||
which consists of a density-dependent function, A(rho), and a
|
||||
radial-dependent weight function, omegaDD(rij). The radial-dependent
|
||||
weight function, omegaDD(rij), is taken as the Lucy function:
|
||||
|
||||
:c,image(Eqs/pair_multi_lucy2.jpg)
|
||||
|
||||
|
|
@ -43,24 +45,29 @@ The density-dependent energy for a given particle is given by:
|
|||
|
||||
:c,image(Eqs/pair_multi_lucy_energy.jpg)
|
||||
|
||||
See the supporting information of "(Brennan)"_#Brennan or the publication by "(Moore)"_#Moore
|
||||
for more details on the functional form.
|
||||
See the supporting information of "(Brennan)"_#Brennan or the
|
||||
publication by "(Moore)"_#Moore for more details on the functional
|
||||
form.
|
||||
|
||||
An interpolation table is used to evaluate the density-dependent energy (Integral(A(rho)drho) and force (A(rho)).
|
||||
Note that the pre-factor to the energy is computed after the interpolation, thus the Integral(A(rho)drho will
|
||||
have units of energy / length^4.
|
||||
An interpolation table is used to evaluate the density-dependent
|
||||
energy (Integral(A(rho)drho) and force (A(rho)). Note that the
|
||||
pre-factor to the energy is computed after the interpolation, thus the
|
||||
Integral(A(rho)drho will have units of energy / length^4.
|
||||
|
||||
The interpolation table is created as a pre-computation by fitting cubic splines to
|
||||
the file values and interpolating the density-dependent energy and force at each of {N} densities.
|
||||
During a simulation, the tables are used to interpolate the density-dependent energy and force as
|
||||
needed for each pair of particles separated by a distance {R}. The interpolation is done in
|
||||
one of 2 styles: {lookup} and {linear}.
|
||||
The interpolation table is created as a pre-computation by fitting
|
||||
cubic splines to the file values and interpolating the
|
||||
density-dependent energy and force at each of {N} densities. During a
|
||||
simulation, the tables are used to interpolate the density-dependent
|
||||
energy and force as needed for each pair of particles separated by a
|
||||
distance {R}. The interpolation is done in one of 2 styles: {lookup}
|
||||
and {linear}.
|
||||
|
||||
For the {lookup} style, the density is used to find the nearest table entry, which is the
|
||||
density-dependent energy and force.
|
||||
For the {lookup} style, the density is used to find the nearest table
|
||||
entry, which is the density-dependent energy and force.
|
||||
|
||||
For the {linear} style, the density is used to find the 2 surrounding table values from
|
||||
which the density-dependent energy and force are computed by linear interpolation.
|
||||
For the {linear} style, the density is used to find the 2 surrounding
|
||||
table values from which the density-dependent energy and force are
|
||||
computed by linear interpolation.
|
||||
|
||||
The following coefficients must be defined for each pair of atoms
|
||||
types via the "pair_coeff"_pair_coeff.html command as in the examples
|
||||
|
|
@ -72,23 +79,24 @@ species1
|
|||
species2
|
||||
cutoff (distance units) :ul
|
||||
|
||||
The filename specifies a file containing the tabulated density-dependent
|
||||
energy and force. The keyword specifies a section of the file.
|
||||
The cutoff is an optional coefficient. If not specified, the outer cutoff in the
|
||||
table itself (see below) will be used to build an interpolation table
|
||||
that extend to the largest tabulated distance. If specified, only
|
||||
file values up to the cutoff are used to create the interpolation
|
||||
table. The format of this file is described below.
|
||||
The filename specifies a file containing the tabulated
|
||||
density-dependent energy and force. The keyword specifies a section
|
||||
of the file. The cutoff is an optional coefficient. If not
|
||||
specified, the outer cutoff in the table itself (see below) will be
|
||||
used to build an interpolation table that extend to the largest
|
||||
tabulated distance. If specified, only file values up to the cutoff
|
||||
are used to create the interpolation table. The format of this file
|
||||
is described below.
|
||||
|
||||
The species tags define the site-site interaction potential between two
|
||||
species contained within two different particles.
|
||||
The species tags must either correspond to the species defined in the reaction
|
||||
kinetics files specified with the "fix rx"_fix_rx.html command
|
||||
or they must correspond to the tag "1fluid", signifying interaction
|
||||
with a product species mixture determined through a one-fluid approximation.
|
||||
The interaction potential is weighted by the geometric average of the
|
||||
concentrations of the two species. The coarse-grained potential
|
||||
is stored before and after the reaction kinetics solver is applied, where
|
||||
The species tags define the site-site interaction potential between
|
||||
two species contained within two different particles. The species
|
||||
tags must either correspond to the species defined in the reaction
|
||||
kinetics files specified with the "fix rx"_fix_rx.html command or they
|
||||
must correspond to the tag "1fluid", signifying interaction with a
|
||||
product species mixture determined through a one-fluid approximation.
|
||||
The interaction potential is weighted by the geometric average of the
|
||||
concentrations of the two species. The coarse-grained potential is
|
||||
stored before and after the reaction kinetics solver is applied, where
|
||||
the difference is defined to be the internal chemical energy (uChem).
|
||||
|
||||
:line
|
||||
|
|
@ -117,47 +125,48 @@ numeric values.
|
|||
|
||||
The parameter "N" is required and its value is the number of table
|
||||
entries that follow. Note that this may be different than the {N}
|
||||
specified in the "pair_style multi/lucy/rx"_pair_multi_lucy_rx.html command. Let
|
||||
Ntable = {N} in the pair_style command, and Nfile = "N" in the
|
||||
tabulated file. What LAMMPS does is a preliminary interpolation by
|
||||
creating splines using the Nfile tabulated values as nodal points. It
|
||||
uses these to interpolate the density-dependent energy and force at Ntable different
|
||||
points. The resulting tables of length Ntable are then used as
|
||||
described above, when computing the density-dependent energy and force.
|
||||
This means that if you want the interpolation tables of
|
||||
length Ntable to match exactly what is in the tabulated file (with
|
||||
effectively no preliminary interpolation), you should set Ntable =
|
||||
Nfile, and use the "RSQ" parameter. This is because the
|
||||
internal table abscissa is always RSQ (separation distance squared),
|
||||
for efficient lookup.
|
||||
specified in the "pair_style multi/lucy/rx"_pair_multi_lucy_rx.html
|
||||
command. Let Ntable = {N} in the pair_style command, and Nfile = "N"
|
||||
in the tabulated file. What LAMMPS does is a preliminary
|
||||
interpolation by creating splines using the Nfile tabulated values as
|
||||
nodal points. It uses these to interpolate the density-dependent
|
||||
energy and force at Ntable different points. The resulting tables of
|
||||
length Ntable are then used as described above, when computing the
|
||||
density-dependent energy and force. This means that if you want the
|
||||
interpolation tables of length Ntable to match exactly what is in the
|
||||
tabulated file (with effectively no preliminary interpolation), you
|
||||
should set Ntable = Nfile, and use the "RSQ" parameter. This is
|
||||
because the internal table abscissa is always RSQ (separation distance
|
||||
squared), for efficient lookup.
|
||||
|
||||
All other parameters are optional. If "R" or "RSQ" does
|
||||
not appear, then the distances in each line of the table are used
|
||||
as-is to perform spline interpolation. In this case, the table values
|
||||
can be spaced in {density} uniformly or however you wish to position table
|
||||
values in regions of large gradients.
|
||||
All other parameters are optional. If "R" or "RSQ" does not appear,
|
||||
then the distances in each line of the table are used as-is to perform
|
||||
spline interpolation. In this case, the table values can be spaced in
|
||||
{density} uniformly or however you wish to position table values in
|
||||
regions of large gradients.
|
||||
|
||||
If used, the parameters "R" or "RSQ" are followed by 2 values {rlo}
|
||||
and {rhi}. If specified, the density associated with each density-dependent
|
||||
energy and force value is computed from these 2 values (at high accuracy), rather
|
||||
than using the (low-accuracy) value listed in each line of the table.
|
||||
The density values in the table file are ignored in this case.
|
||||
For "R", distances uniformly spaced between {rlo} and {rhi} are
|
||||
computed; for "RSQ", squared distances uniformly spaced between
|
||||
{rlo*rlo} and {rhi*rhi} are computed.
|
||||
and {rhi}. If specified, the density associated with each
|
||||
density-dependent energy and force value is computed from these 2
|
||||
values (at high accuracy), rather than using the (low-accuracy) value
|
||||
listed in each line of the table. The density values in the table
|
||||
file are ignored in this case. For "R", distances uniformly spaced
|
||||
between {rlo} and {rhi} are computed; for "RSQ", squared distances
|
||||
uniformly spaced between {rlo*rlo} and {rhi*rhi} are computed.
|
||||
|
||||
NOTE: If you use "R" or "RSQ", the tabulated distance values in the
|
||||
file are effectively ignored, and replaced by new values as described
|
||||
in the previous paragraph. If the density value in the table is not
|
||||
very close to the new value (i.e. round-off difference), then you will
|
||||
be assigning density-dependent energy and force values to a different density,
|
||||
which is probably not what you want. LAMMPS will warn if this is occurring.
|
||||
be assigning density-dependent energy and force values to a different
|
||||
density, which is probably not what you want. LAMMPS will warn if
|
||||
this is occurring.
|
||||
|
||||
Following a blank line, the next N lines list the tabulated values.
|
||||
On each line, the 1st value is the index from 1 to N, the 2nd value is
|
||||
r (in density units), the 3rd value is the density-dependent function value
|
||||
(in energy units / length^4), and the 4th is the force (in force units). The
|
||||
density values must increase from one line to the next.
|
||||
r (in density units), the 3rd value is the density-dependent function
|
||||
value (in energy units / length^4), and the 4th is the force (in force
|
||||
units). The density values must increase from one line to the next.
|
||||
|
||||
Note that one file can contain many sections, each with a tabulated
|
||||
potential. LAMMPS reads the file section by section until it finds
|
||||
|
|
@ -186,7 +195,11 @@ This pair style can only be used via the {pair} keyword of the
|
|||
|
||||
:line
|
||||
|
||||
[Restrictions:] none
|
||||
[Restrictions:]
|
||||
|
||||
This command is part of the USER-DPD package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
|
|
|
|||
|
|
@ -26,14 +26,16 @@ pair_coeff * 3 rxn.table ENTRY1 h2o no2 10.0 :pre
|
|||
|
||||
[Description:]
|
||||
|
||||
Style {table/rx} is used in reaction DPD simulations,where the coarse-grained (CG)
|
||||
particles are composed of {m} species whose reaction rate kinetics are determined
|
||||
from a set of {n} reaction rate equations through the "fix rx"_fix_rx.html command.
|
||||
The species of one CG particle can interact with a species in a neighboring CG
|
||||
particle through a site-site interaction potential model. Style {table/rx} creates
|
||||
interpolation tables of length {N} from pair potential and force values listed in a
|
||||
file(s) as a function of distance. The files are read by the
|
||||
"pair_coeff"_pair_coeff.html command.
|
||||
Style {table/rx} is used in reaction DPD simulations,where the
|
||||
coarse-grained (CG) particles are composed of {m} species whose
|
||||
reaction rate kinetics are determined from a set of {n} reaction rate
|
||||
equations through the "fix rx"_fix_rx.html command. The species of
|
||||
one CG particle can interact with a species in a neighboring CG
|
||||
particle through a site-site interaction potential model. Style
|
||||
{table/rx} creates interpolation tables of length {N} from pair
|
||||
potential and force values listed in a file(s) as a function of
|
||||
distance. The files are read by the "pair_coeff"_pair_coeff.html
|
||||
command.
|
||||
|
||||
The interpolation tables are created by fitting cubic splines to the
|
||||
file values and interpolating energy and force values at each of {N}
|
||||
|
|
@ -54,7 +56,7 @@ used to find the appropriate set of coefficients which are used to
|
|||
evaluate a cubic polynomial which computes the energy or force.
|
||||
|
||||
For the {bitmap} style, the N means to create interpolation tables
|
||||
that are 2^N in length. <The pair distance is used to index into the
|
||||
that are 2^N in length. The pair distance is used to index into the
|
||||
table via a fast bit-mapping technique "(Wolff)"_#Wolff and a linear
|
||||
interpolation is performed between adjacent table values.
|
||||
|
||||
|
|
@ -76,15 +78,15 @@ that extend to the largest tabulated distance. If specified, only
|
|||
file values up to the cutoff are used to create the interpolation
|
||||
table. The format of this file is described below.
|
||||
|
||||
The species tags define the site-site interaction potential between two
|
||||
species contained within two different particles.
|
||||
The species tags must either correspond to the species defined in the reaction
|
||||
kinetics files specified with the "fix rx"_fix_rx.html command
|
||||
or they must correspond to the tag "1fluid", signifying interaction
|
||||
with a product species mixture determined through a one-fluid approximation.
|
||||
The interaction potential is weighted by the geometric average of the
|
||||
concentrations of the two species. The coarse-grained potential
|
||||
is stored before and after the reaction kinetics solver is applied, where
|
||||
The species tags define the site-site interaction potential between
|
||||
two species contained within two different particles. The species
|
||||
tags must either correspond to the species defined in the reaction
|
||||
kinetics files specified with the "fix rx"_fix_rx.html command or they
|
||||
must correspond to the tag "1fluid", signifying interaction with a
|
||||
product species mixture determined through a one-fluid approximation.
|
||||
The interaction potential is weighted by the geometric average of the
|
||||
concentrations of the two species. The coarse-grained potential is
|
||||
stored before and after the reaction kinetics solver is applied, where
|
||||
the difference is defined to be the internal chemical energy (uChem).
|
||||
|
||||
:line
|
||||
|
|
@ -217,7 +219,11 @@ This pair style can only be used via the {pair} keyword of the
|
|||
|
||||
:line
|
||||
|
||||
[Restrictions:] none
|
||||
[Restrictions:]
|
||||
|
||||
This command is part of the USER-DPD package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue