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7
doc/html/_sources/fix_eos_cv.txt
View File

@ -45,8 +45,11 @@ Restrictions
""""""""""""
The fix *eos/cv* is only available if LAMMPS is built with the
USER-DPD package.
This command is part of the USER-DPD package. It is only enabled if
LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
This command also requires use of the :doc:`atom_style dpd <atom_style>`
command.
Related commands
""""""""""""""""

11
doc/html/_sources/fix_eos_table.txt
View File

@ -109,13 +109,16 @@ Restrictions
""""""""""""
The fix *eos/table* is only available if LAMMPS is built with the
USER-DPD package.
This command is part of the USER-DPD package. It is only enabled if
LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
This command also requires use of the :doc:`atom_style dpd <atom_style>`
command.
The equation of state must be a monotonically increasing function.
An exit error will occur if the internal temperature or internal
energies are not within the table cutoffs.
An error will occur if the internal temperature or internal energies
are not within the table cutoffs.
Related commands
""""""""""""""""

11
doc/html/_sources/fix_eos_table_rx.txt
View File

@ -140,13 +140,16 @@ Restrictions
""""""""""""
The fix *eos/table/rx* is only available if LAMMPS is built with the
USER-DPD package.
This command is part of the USER-DPD package. It is only enabled if
LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
This command also requires use of the :doc:`atom_style dpd <atom_style>`
command.
The equation of state must be a monotonically increasing function.
An exit error will occur if the internal temperature or internal
energies are not within the table cutoffs.
An error will occur if the internal temperature or internal energies
are not within the table cutoffs.
Related commands
""""""""""""""""

107
doc/html/_sources/fix_rx.txt
View File

@ -42,19 +42,20 @@ the reaction rate equation is defined to be of the form
.. image:: Eqs/fix_rx_reactionRate.jpg
:align: center
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.
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.
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.
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.
----------
@ -64,28 +65,30 @@ 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.
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:
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:
.. image:: Eqs/fix_rx.jpg
:align: center
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.
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.
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:
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:
.. image:: Eqs/fix_rx_localTemp.jpg
:align: center
@ -101,7 +104,8 @@ The self-particle interaction is included in the above equation.
----------
The format of a tabulated file is as follows (without the parenthesized comments):
The format of a tabulated file is as follows (without the
parenthesized comments):
.. parsed-literal::
@ -118,21 +122,23 @@ 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*\ .
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 :doc:`fix eos/table/rx <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 :doc:`set <set>`
command using the "d_" prefix or by reading directly the concentrations from a
data file. For the latter case, the :doc:`read_data <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.
Note that the species tags that are defined in the reaction equations
are used by the :doc:`fix eos/table/rx <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 :doc:`set <set>` command using the "d_" prefix or by
reading directly the concentrations from a data file. For the latter
case, the :doc:`read_data <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.
fix foo all rx reaction.file ...
read_data data.dpd fix foo_SPECIES NULL Species
@ -145,11 +151,14 @@ Restrictions
""""""""""""
The fix *rx* is only available if LAMMPS is built with the USER-DPD package.
This command is part of the USER-DPD package. It is only enabled if
LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
The fix *rx* must be used with the :doc:`atom_style dpd <atom_style>` command.
This command also requires use of the :doc:`atom_style dpd <atom_style>`
command.
The fix *rx* can only be used with a constant energy or constant enthalpy DPD simulation.
This command can only be used with a constant energy or constant
enthalpy DPD simulation.
Related commands
""""""""""""""""
@ -161,10 +170,6 @@ Related commands
**Default:** none
----------
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Section_commands.html#comm

7
doc/html/_sources/fix_shardlow.txt
View File

@ -56,9 +56,8 @@ Restrictions
""""""""""""
This fix is only available if LAMMPS is built with the USER-DPD
package. See the :ref:`Making LAMMPS <start_3>` section
for more info.
This command is part of the USER-DPD package. It is only enabled if
LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
This fix is currently limited to orthogonal simulation cell
geometries.
@ -68,7 +67,7 @@ integration, e.g. :doc:`fix nve <fix_nve>` or :doc:`fix nph <fix_nh>`.
The Shardlow splitting algorithm requires the sizes of the sub-domain
lengths to be larger than twice the cutoff+skin. Generally, the
domain decomposition is dependant on the number of processors
domain decomposition is dependent on the number of processors
requested.
Related commands

4
doc/html/_sources/pair_dpd_fdt.txt
View File

@ -124,8 +124,8 @@ Restrictions
""""""""""""
Pair styles *dpd/fdt* and *dpd/fdt/energy* are only available if
LAMMPS is built with the USER-DPD package.
These commands are part of the USER-DPD package. They are only
enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
Pair styles *dpd/fdt* and *dpd/fdt/energy* require use of the
:doc:`communicate vel yes <communicate>` option so that velocites are

66
doc/html/_sources/pair_exp6_rx.txt
View File

@ -25,12 +25,13 @@ Examples
Description
"""""""""""
Style *exp6/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 :doc:`fix rx <fix_rx>` command.
The species of one CG particle can interact with a species in a neighboring CG
particle through a site-site interaction potential model. The *exp6/rx* style
computes an exponential-6 potential given by
Style *exp6/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 :doc:`fix rx <fix_rx>` command. The species of
one CG particle can interact with a species in a neighboring CG
particle through a site-site interaction potential model. The
*exp6/rx* style computes an exponential-6 potential given by
.. image:: Eqs/pair_exp6_rx.jpg
:align: center
@ -38,22 +39,23 @@ computes an exponential-6 potential given by
where the *epsilon* parameter determines the depth of the potential
minimum located at *Rm*\ , and *alpha* determines the softness of the repulsion.
The coefficients must be defined for each species in a given particle type
via the :doc:`pair_coeff <pair_coeff>` command as in the examples above, where
the first argument is the filename that includes the exponential-6 parameters
for each species. The file includes the species tag followed by the *alpha*\ ,
*epsilon* and *Rm* parameters. The format of the file is described below.
The coefficients must be defined for each species in a given particle
type via the :doc:`pair_coeff <pair_coeff>` command as in the examples
above, where the first argument is the filename that includes the
exponential-6 parameters for each species. The file includes the
species tag followed by the *alpha*\ , *epsilon* and *Rm*
parameters. The format of the file is described below.
The second and third arguments specify 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 :doc:`fix rx <fix_rx>` 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).
The second and third arguments specify 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 :doc:`fix rx <fix_rx>` 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).
The fourth and fifth arguments specify the *Rm* and *epsilon* scaling exponents.
@ -63,7 +65,8 @@ The final argument specifies the interaction cutoff.
----------
The format of a tabulated file is as follows (without the parenthesized comments):
The format of a tabulated file is as follows (without the
parenthesized comments):
.. parsed-literal::
@ -80,14 +83,14 @@ 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 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:
.. image:: Eqs/pair_exp6_rx_oneFluid.jpg
@ -121,7 +124,8 @@ Restrictions
""""""""""""
None
This command is part of the USER-DPD package. It is only enabled if
LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
Related commands
""""""""""""""""

86
doc/html/_sources/pair_multi_lucy.txt
View File

@ -24,15 +24,16 @@ Examples
Description
"""""""""""
Style *multi/lucy* computes a density-dependent force following from the many-body
form described in :ref:`(Moore) <Moore>` and :ref:`(Warren) <Warren>` as
Style *multi/lucy* computes a density-dependent force following from
the many-body form described in :ref:`(Moore) <Moore>` and
:ref:`(Warren) <Warren>` as
.. image:: Eqs/pair_multi_lucy.jpg
:align: center
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:
.. image:: Eqs/pair_multi_lucy2.jpg
:align: center
@ -42,24 +43,29 @@ The density-dependent energy for a given particle is given by:
.. image:: Eqs/pair_multi_lucy_energy.jpg
:align: center
See the supporting information of :ref:`(Brennan) <Brennan>` or the publication by :ref:`(Moore) <Moore>`
for more details on the functional form.
See the supporting information of :ref:`(Brennan) <Brennan>` or the
publication by :ref:`(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 :doc:`pair_coeff <pair_coeff>` command as in the examples
@ -69,13 +75,14 @@ above.
* keyword
* cutoff (distance units)
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.
----------
@ -109,19 +116,19 @@ 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 :doc:`pair_style multi/lucy <pair_multi_lucy>` command. Let
Ntable = *N* in the pair_style command, and Nfile = "N" in the
specified in the :doc:`pair_style multi/lucy <pair_multi_lucy>` 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
@ -186,7 +193,10 @@ This pair style can only be used via the *pair* keyword of the
Restrictions
""""""""""""
none
This command is part of the USER-DPD package. It is only enabled if
LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
Related commands
""""""""""""""""

154
doc/html/_sources/pair_multi_lucy_rx.txt
View File

@ -25,20 +25,22 @@ Examples
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 :doc:`fix rx <fix_rx>` 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
:ref:`(Moore) <Moore>` and :ref:`(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 :doc:`fix rx <fix_rx>` 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 :ref:`(Moore) <Moore>` and
:ref:`(Warren) <Warren>` as
.. image:: Eqs/pair_multi_lucy.jpg
:align: center
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:
.. image:: Eqs/pair_multi_lucy2.jpg
:align: center
@ -48,24 +50,29 @@ The density-dependent energy for a given particle is given by:
.. image:: Eqs/pair_multi_lucy_energy.jpg
:align: center
See the supporting information of :ref:`(Brennan) <Brennan>` or the publication by :ref:`(Moore) <Moore>`
for more details on the functional form.
See the supporting information of :ref:`(Brennan) <Brennan>` or the
publication by :ref:`(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 :doc:`pair_coeff <pair_coeff>` command as in the examples
@ -77,23 +84,24 @@ above.
* species2
* cutoff (distance units)
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 :doc:`fix rx <fix_rx>` 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 :doc:`fix rx <fix_rx>` 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).
@ -128,34 +136,34 @@ 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 :doc:`pair_style multi/lucy/rx <pair_multi_lucy_rx>` 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 :doc:`pair_style multi/lucy/rx <pair_multi_lucy_rx>`
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::
@ -163,14 +171,15 @@ computed; for "RSQ", squared distances uniformly spaced between
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
@ -205,7 +214,10 @@ This pair style can only be used via the *pair* keyword of the
Restrictions
""""""""""""
none
This command is part of the USER-DPD package. It is only enabled if
LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
Related commands
""""""""""""""""

43
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@ -28,14 +28,16 @@ Examples
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 :doc:`fix rx <fix_rx>` 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
:doc:`pair_coeff <pair_coeff>` 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 :doc:`fix rx <fix_rx>` 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 :doc:`pair_coeff <pair_coeff>`
command.
The interpolation tables are created by fitting cubic splines to the
file values and interpolating energy and force values at each of *N*
@ -56,7 +58,7 @@ 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 :ref:`(Wolff) <Wolff>` and a linear
interpolation is performed between adjacent table values.
@ -78,15 +80,15 @@ 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 :doc:`fix rx <fix_rx>` 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 :doc:`fix rx <fix_rx>` 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).
@ -227,7 +229,10 @@ This pair style can only be used via the *pair* keyword of the
Restrictions
""""""""""""
none
This command is part of the USER-DPD package. It is only enabled if
LAMMPS was built with that package. See the :ref:`Making LAMMPS <start_3>` section for more info.
Related commands
""""""""""""""""

6
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@ -158,8 +158,10 @@ possible.</p>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>The fix <em>eos/cv</em> is only available if LAMMPS is built with the
USER-DPD package.</p>
<p>This command is part of the USER-DPD package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>This command also requires use of the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style dpd</span></a>
command.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>

10
doc/html/fix_eos_table.html
View File

@ -210,11 +210,13 @@ one that matches the specified keyword.</p>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>The fix <em>eos/table</em> is only available if LAMMPS is built with the
USER-DPD package.</p>
<p>This command is part of the USER-DPD package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>This command also requires use of the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style dpd</span></a>
command.</p>
<p>The equation of state must be a monotonically increasing function.</p>
<p>An exit error will occur if the internal temperature or internal
energies are not within the table cutoffs.</p>
<p>An error will occur if the internal temperature or internal energies
are not within the table cutoffs.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>

10
doc/html/fix_eos_table_rx.html
View File

@ -231,11 +231,13 @@ the reactions with the <a class="reference internal" href="fix_rx.html"><span cl
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>The fix <em>eos/table/rx</em> is only available if LAMMPS is built with the
USER-DPD package.</p>
<p>This command is part of the USER-DPD package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>This command also requires use of the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style dpd</span></a>
command.</p>
<p>The equation of state must be a monotonically increasing function.</p>
<p>An exit error will occur if the internal temperature or internal
energies are not within the table cutoffs.</p>
<p>An error will occur if the internal temperature or internal energies
are not within the table cutoffs.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>

104
doc/html/fix_rx.html
View File

@ -156,46 +156,50 @@ defined within the file associated with this command.</p>
<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="_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
differential equations (ODEs) that describe the change in concentration of a
given species as a function of time are then constructed based on the <em>n</em>
reaction rate equations.</p>
<p>The ODE systems are solved over the full DPD timestep <em>dt</em> using a 4th order
Runge-Kutta <em>rk4</em> method with a fixed step-size <em>h</em>, specified by the
<em>lammps_rk4</em> 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
<em>dt/num_steps</em>. Smaller step-sizes tend to yield more accurate results but there
is not control on the error.</p>
<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 differential equations (ODEs) that describe the change
in concentration of a given species as a function of time are then
constructed based on the <em>n</em> reaction rate equations.</p>
<p>The ODE systems are solved over the full DPD timestep <em>dt</em> using a 4th
order Runge-Kutta <em>rk4</em> method with a fixed step-size <em>h</em>, specified
by the <em>lammps_rk4</em> 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 <em>dt/num_steps</em>. Smaller
step-sizes tend to yield more accurate results but there is not
control on the error.</p>
<hr class="docutils" />
<p>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.</p>
<p>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&#8217;s stoichiometric
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>
<p>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&#8217;s stoichiometric 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="_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
by specifying the exponent as zero.</p>
<p>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 <em>none</em>.
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>
<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 by specifying the exponent as zero.</p>
<p>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 <em>none</em>. 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="_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="_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>
<p>The format of a tabulated file is as follows (without the
parenthesized comments):</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Rxn equations and parameters (one or more comment or blank lines)</span>
</pre></div>
</div>
@ -208,29 +212,34 @@ The local-average particle internal temperature is defined as:</p>
<p>A section begins with a non-blank line whose 1st character is not a
&#8220;#&#8221;; blank lines or lines starting with &#8220;#&#8221; can be used as comments
between sections.</p>
<p>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 <em>A</em>, the temperature exponent <em>n</em>, and the activation energy <em>Ea</em>.</p>
<p>Note that the species tags that are defined in the reaction equations are
used by the <a class="reference internal" href="fix_eos_table_rx.html"><span class="doc">fix eos/table/rx</span></a> command to define the
thermodynamic properties of each species. Furthermore, the number of species
molecules (i.e., concentration) can be specified either with the <a class="reference internal" href="set.html"><span class="doc">set</span></a>
command using the &#8220;<a href="#id1"><span class="problematic" id="id2">d_</span></a>&#8221; prefix or by reading directly the concentrations from a
data file. For the latter case, the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command with the
fix keyword should be specified, where the fix-ID will be the &#8220;fix rx`ID with a &lt;SPECIES&#8221;&gt;`_ suffix, e.g.</p>
<p>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 <em>A</em>, the
temperature exponent <em>n</em>, and the activation energy <em>Ea</em>.</p>
<p>Note that the species tags that are defined in the reaction equations
are used by the <a class="reference internal" href="fix_eos_table_rx.html"><span class="doc">fix eos/table/rx</span></a> command to
define the thermodynamic properties of each species. Furthermore, the
number of species molecules (i.e., concentration) can be specified
either with the <a class="reference internal" href="set.html"><span class="doc">set</span></a> command using the &#8220;<a href="#id1"><span class="problematic" id="id2">d_</span></a>&#8221; prefix or by
reading directly the concentrations from a data file. For the latter
case, the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command with the fix keyword
should be specified, where the fix-ID will be the &#8220;fix rx`ID with a &lt;SPECIES&#8221;&gt;`_ suffix, e.g.</p>
<p>fix foo all rx reaction.file ...
read_data data.dpd fix foo_SPECIES NULL Species</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>The fix <em>rx</em> is only available if LAMMPS is built with the USER-DPD package.</p>
<p>The fix <em>rx</em> must be used with the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style dpd</span></a> command.</p>
<p>The fix <em>rx</em> can only be used with a constant energy or constant enthalpy DPD simulation.</p>
<p>This command is part of the USER-DPD package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>This command also requires use of the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style dpd</span></a>
command.</p>
<p>This command can only be used with a constant energy or constant
enthalpy DPD simulation.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>
@ -238,7 +247,6 @@ read_data data.dpd fix foo_SPECIES NULL Species</p>
<a class="reference internal" href="fix_shardlow.html"><span class="doc">fix shardlow</span></a>,
<span class="xref doc">pair dpd/fdt/energy</span></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
</div>
</div>

7
doc/html/fix_shardlow.html
View File

@ -170,16 +170,15 @@ examples/USER/dpd directory.</p>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>This fix is only available if LAMMPS is built with the USER-DPD
package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section
for more info.</p>
<p>This command is part of the USER-DPD package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>This fix is currently limited to orthogonal simulation cell
geometries.</p>
<p>This fix must be used with an additional fix that specifies time
integration, e.g. <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a>.</p>
<p>The Shardlow splitting algorithm requires the sizes of the sub-domain
lengths to be larger than twice the cutoff+skin. Generally, the
domain decomposition is dependant on the number of processors
domain decomposition is dependent on the number of processors
requested.</p>
</div>
<div class="section" id="related-commands">

4
doc/html/pair_dpd_fdt.html
View File

@ -227,8 +227,8 @@ specified.</p>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>Pair styles <em>dpd/fdt</em> and <em>dpd/fdt/energy</em> are only available if
LAMMPS is built with the USER-DPD package.</p>
<p>These commands are part of the USER-DPD package. They are only
enabled if LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
<p>Pair styles <em>dpd/fdt</em> and <em>dpd/fdt/energy</em> require use of the
<span class="xref doc">communicate vel yes</span> option so that velocites are
stored by ghost atoms.</p>

58
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@ -146,34 +146,37 @@
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Style <em>exp6/rx</em> is used in reaction DPD simulations, where the coarse-grained (CG)
particles are composed of <em>m</em> species whose reaction rate kinetics are determined
from a set of <em>n</em> reaction rate equations through the <a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a> command.
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>
<p>Style <em>exp6/rx</em> is used in reaction DPD simulations, where the
coarse-grained (CG) particles are composed of <em>m</em> species whose
reaction rate kinetics are determined from a set of <em>n</em> reaction rate
equations through the <a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a> command. 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="_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
via the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command as in the examples above, where
the first argument is the filename that includes the exponential-6 parameters
for each species. The file includes the species tag followed by the <em>alpha</em>,
<em>epsilon</em> and <em>Rm</em> parameters. The format of the file is described below.</p>
<p>The coefficients must be defined for each species in a given particle
type via the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command as in the examples
above, where the first argument is the filename that includes the
exponential-6 parameters for each species. The file includes the
species tag followed by the <em>alpha</em>, <em>epsilon</em> and <em>Rm</em>
parameters. The format of the file is described below.</p>
<p>The second and third arguments specify 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 <a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a> command
or they must correspond to the tag &#8220;1fluid&#8221;, 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).</p>
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 <a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a> command or they must correspond to the tag &#8220;1fluid&#8221;,
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).</p>
<p>The fourth and fifth arguments specify the <em>Rm</em> and <em>epsilon</em> scaling exponents.</p>
<p>The final argument specifies the interaction cutoff.</p>
<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>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># exponential-6 parameters for various species (one or more comment or blank lines)</span>
</pre></div>
</div>
@ -187,12 +190,12 @@ difference is defined to be the internal chemical energy (uChem).</p>
&#8220;#&#8221;; blank lines or lines starting with &#8220;#&#8221; can be used as comments
between sections.</p>
<p>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 <em>alpha</em>
corresponding parameters. The first argument is the species tag, the
second argument is the exp6 tag, the 3rd argument is the <em>alpha</em>
parameter (energy units), the 4th argument is the <em>epsilon</em> parameter
(energy-distance^6 units), and the 5th argument is the <em>Rm</em>
parameter (distance units). If a species tag of &#8220;1fluid&#8221; is listed as a
pair coefficient, a one-fluid approximation is specified where a
(energy-distance^6 units), and the 5th argument is the <em>Rm</em> parameter
(distance units). If a species tag of &#8220;1fluid&#8221; 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:</p>
<img alt="_images/pair_exp6_rx_oneFluid.jpg" class="align-center" src="_images/pair_exp6_rx_oneFluid.jpg" />
@ -212,7 +215,8 @@ pair interaction.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>None</p>
<p>This command is part of the USER-DPD package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>

85
doc/html/pair_multi_lucy.html
View File

@ -145,29 +145,35 @@
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Style <em>multi/lucy</em> computes a density-dependent force following from the many-body
form described in <a class="reference internal" href="pair_multi_lucy_rx.html#moore"><span class="std std-ref">(Moore)</span></a> and <a class="reference internal" href="pair_multi_lucy_rx.html#warren"><span class="std std-ref">(Warren)</span></a> as</p>
<p>Style <em>multi/lucy</em> computes a density-dependent force following from
the many-body form described in <a class="reference internal" href="pair_multi_lucy_rx.html#moore"><span class="std std-ref">(Moore)</span></a> and
<a class="reference internal" href="pair_multi_lucy_rx.html#warren"><span class="std std-ref">(Warren)</span></a> as</p>
<img alt="_images/pair_multi_lucy.jpg" class="align-center" src="_images/pair_multi_lucy.jpg" />
<p>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:</p>
<p>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:</p>
<img alt="_images/pair_multi_lucy2.jpg" class="align-center" src="_images/pair_multi_lucy2.jpg" />
<p>The density-dependent energy for a given particle is given by:</p>
<img alt="_images/pair_multi_lucy_energy.jpg" class="align-center" src="_images/pair_multi_lucy_energy.jpg" />
<p>See the supporting information of <a class="reference internal" href="pair_multi_lucy_rx.html#brennan"><span class="std std-ref">(Brennan)</span></a> or the publication by <a class="reference internal" href="pair_multi_lucy_rx.html#moore"><span class="std std-ref">(Moore)</span></a>
for more details on the functional form.</p>
<p>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.</p>
<p>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 <em>N</em> 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 <em>R</em>. The interpolation is done in
one of 2 styles: <em>lookup</em> and <em>linear</em>.</p>
<p>For the <em>lookup</em> style, the density is used to find the nearest table entry, which is the
density-dependent energy and force.</p>
<p>For the <em>linear</em> 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.</p>
<p>See the supporting information of <a class="reference internal" href="pair_multi_lucy_rx.html#brennan"><span class="std std-ref">(Brennan)</span></a> or the
publication by <a class="reference internal" href="pair_multi_lucy_rx.html#moore"><span class="std std-ref">(Moore)</span></a> for more details on the functional
form.</p>
<p>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.</p>
<p>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 <em>N</em> 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 <em>R</em>. The interpolation is done in one of 2 styles: <em>lookup</em>
and <em>linear</em>.</p>
<p>For the <em>lookup</em> style, the density is used to find the nearest table
entry, which is the density-dependent energy and force.</p>
<p>For the <em>linear</em> 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.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command as in the examples
above.</p>
@ -176,13 +182,14 @@ above.</p>
<li>keyword</li>
<li>cutoff (distance units)</li>
</ul>
<p>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.</p>
<p>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.</p>
<hr class="docutils" />
<p>The format of a tabulated file is a series of one or more sections,
defined as follows (without the parenthesized comments):</p>
@ -208,19 +215,19 @@ for the table. Each parameter is a keyword followed by one or more
numeric values.</p>
<p>The parameter &#8220;N&#8221; is required and its value is the number of table
entries that follow. Note that this may be different than the <em>N</em>
specified in the <a class="reference internal" href="#"><span class="doc">pair_style multi/lucy</span></a> command. Let
Ntable = <em>N</em> in the pair_style command, and Nfile = &#8220;N&#8221; in the
specified in the <a class="reference internal" href="#"><span class="doc">pair_style multi/lucy</span></a> command.
Let Ntable = <em>N</em> in the pair_style command, and Nfile = &#8220;N&#8221; 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 &#8220;RSQ&#8221; parameter. This is because the
internal table abscissa is always RSQ (separation distance squared),
for efficient lookup.</p>
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 &#8220;RSQ&#8221; parameter. This is because the internal
table abscissa is always RSQ (separation distance squared), for
efficient lookup.</p>
<p>All other parameters are optional. If &#8220;R&#8221; or &#8220;RSQ&#8221; 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
@ -270,8 +277,8 @@ commands do need to be specified in the restart input script.</p>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<blockquote>
<div>none</div></blockquote>
<p>This command is part of the USER-DPD package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>

151
doc/html/pair_multi_lucy_rx.html
View File

@ -146,34 +146,41 @@
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Style <em>multi/lucy/rx</em> is used in reaction DPD simulations, where the coarse-grained
(CG) particles are composed of <em>m</em> species whose reaction rate kinetics are determined
from a set of <em>n</em> reaction rate equations through the <a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a> 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 <em>multi/lucy/rx</em> computes the
site-site density-dependent force following from the many-body form described in
<a class="reference internal" href="#moore"><span class="std std-ref">(Moore)</span></a> and <a class="reference internal" href="#warren"><span class="std std-ref">(Warren)</span></a> as</p>
<p>Style <em>multi/lucy/rx</em> is used in reaction DPD simulations, where the
coarse-grained (CG) particles are composed of <em>m</em> species whose
reaction rate kinetics are determined from a set of <em>n</em> reaction rate
equations through the <a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a> 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
<em>multi/lucy/rx</em> computes the site-site density-dependent force
following from the many-body form described in <a class="reference internal" href="#moore"><span class="std std-ref">(Moore)</span></a> and
<a class="reference internal" href="#warren"><span class="std std-ref">(Warren)</span></a> as</p>
<img alt="_images/pair_multi_lucy.jpg" class="align-center" src="_images/pair_multi_lucy.jpg" />
<p>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:</p>
<p>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:</p>
<img alt="_images/pair_multi_lucy2.jpg" class="align-center" src="_images/pair_multi_lucy2.jpg" />
<p>The density-dependent energy for a given particle is given by:</p>
<img alt="_images/pair_multi_lucy_energy.jpg" class="align-center" src="_images/pair_multi_lucy_energy.jpg" />
<p>See the supporting information of <a class="reference internal" href="#brennan"><span class="std std-ref">(Brennan)</span></a> or the publication by <a class="reference internal" href="#moore"><span class="std std-ref">(Moore)</span></a>
for more details on the functional form.</p>
<p>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.</p>
<p>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 <em>N</em> 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 <em>R</em>. The interpolation is done in
one of 2 styles: <em>lookup</em> and <em>linear</em>.</p>
<p>For the <em>lookup</em> style, the density is used to find the nearest table entry, which is the
density-dependent energy and force.</p>
<p>For the <em>linear</em> 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.</p>
<p>See the supporting information of <a class="reference internal" href="#brennan"><span class="std std-ref">(Brennan)</span></a> or the
publication by <a class="reference internal" href="#moore"><span class="std std-ref">(Moore)</span></a> for more details on the functional
form.</p>
<p>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.</p>
<p>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 <em>N</em> 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 <em>R</em>. The interpolation is done in one of 2 styles: <em>lookup</em>
and <em>linear</em>.</p>
<p>For the <em>lookup</em> style, the density is used to find the nearest table
entry, which is the density-dependent energy and force.</p>
<p>For the <em>linear</em> 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.</p>
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command as in the examples
above.</p>
@ -184,22 +191,23 @@ above.</p>
<li>species2</li>
<li>cutoff (distance units)</li>
</ul>
<p>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.</p>
<p>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 <a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a> command
or they must correspond to the tag &#8220;1fluid&#8221;, signifying interaction
with a product species mixture determined through a one-fluid approximation.
<p>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.</p>
<p>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 <a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a> command or they
must correspond to the tag &#8220;1fluid&#8221;, 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
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).</p>
<hr class="docutils" />
<p>The format of a tabulated file is a series of one or more sections,
@ -226,46 +234,47 @@ for the table. Each parameter is a keyword followed by one or more
numeric values.</p>
<p>The parameter &#8220;N&#8221; is required and its value is the number of table
entries that follow. Note that this may be different than the <em>N</em>
specified in the <a class="reference internal" href="#"><span class="doc">pair_style multi/lucy/rx</span></a> command. Let
Ntable = <em>N</em> in the pair_style command, and Nfile = &#8220;N&#8221; 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 &#8220;RSQ&#8221; parameter. This is because the
internal table abscissa is always RSQ (separation distance squared),
for efficient lookup.</p>
<p>All other parameters are optional. If &#8220;R&#8221; or &#8220;RSQ&#8221; 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 <em>density</em> uniformly or however you wish to position table
values in regions of large gradients.</p>
specified in the <a class="reference internal" href="#"><span class="doc">pair_style multi/lucy/rx</span></a>
command. Let Ntable = <em>N</em> in the pair_style command, and Nfile = &#8220;N&#8221;
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 &#8220;RSQ&#8221; parameter. This is
because the internal table abscissa is always RSQ (separation distance
squared), for efficient lookup.</p>
<p>All other parameters are optional. If &#8220;R&#8221; or &#8220;RSQ&#8221; 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
<em>density</em> uniformly or however you wish to position table values in
regions of large gradients.</p>
<p>If used, the parameters &#8220;R&#8221; or &#8220;RSQ&#8221; are followed by 2 values <em>rlo</em>
and <em>rhi</em>. 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 &#8220;R&#8221;, distances uniformly spaced between <em>rlo</em> and <em>rhi</em> are
computed; for &#8220;RSQ&#8221;, squared distances uniformly spaced between
<em>rlo*rlo</em> and <em>rhi*rhi</em> are computed.</p>
and <em>rhi</em>. 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 &#8220;R&#8221;, distances uniformly spaced
between <em>rlo</em> and <em>rhi</em> are computed; for &#8220;RSQ&#8221;, squared distances
uniformly spaced between <em>rlo*rlo</em> and <em>rhi*rhi</em> are computed.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">If you use &#8220;R&#8221; or &#8220;RSQ&#8221;, 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.</p>
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.</p>
</div>
<p>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.</p>
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.</p>
<p>Note that one file can contain many sections, each with a tabulated
potential. LAMMPS reads the file section by section until it finds
one that matches the specified keyword.</p>
@ -288,8 +297,8 @@ commands do need to be specified in the restart input script.</p>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<blockquote>
<div>none</div></blockquote>
<p>This command is part of the USER-DPD package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>

40
doc/html/pair_table_rx.html
View File

@ -147,14 +147,16 @@ N = use 2^N values in <em>bitmap</em> tables</p>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>Style <em>table/rx</em> is used in reaction DPD simulations,where the coarse-grained (CG)
particles are composed of <em>m</em> species whose reaction rate kinetics are determined
from a set of <em>n</em> reaction rate equations through the <a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a> 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 <em>table/rx</em> creates
interpolation tables of length <em>N</em> from pair potential and force values listed in a
file(s) as a function of distance. The files are read by the
<a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a> command.</p>
<p>Style <em>table/rx</em> is used in reaction DPD simulations,where the
coarse-grained (CG) particles are composed of <em>m</em> species whose
reaction rate kinetics are determined from a set of <em>n</em> reaction rate
equations through the <a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a> 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
<em>table/rx</em> creates interpolation tables of length <em>N</em> from pair
potential and force values listed in a file(s) as a function of
distance. The files are read by the <a class="reference internal" href="pair_coeff.html"><span class="doc">pair_coeff</span></a>
command.</p>
<p>The interpolation tables are created by fitting cubic splines to the
file values and interpolating energy and force values at each of <em>N</em>
distances. During a simulation, these tables are used to interpolate
@ -170,7 +172,7 @@ stored at each of the <em>N</em> values in the table. The pair distance is
used to find the appropriate set of coefficients which are used to
evaluate a cubic polynomial which computes the energy or force.</p>
<p>For the <em>bitmap</em> style, the N means to create interpolation tables
that are 2^N in length. &lt;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 <a class="reference internal" href="#wolff"><span class="std std-ref">(Wolff)</span></a> and a linear
interpolation is performed between adjacent table values.</p>
<p>The following coefficients must be defined for each pair of atoms
@ -190,15 +192,15 @@ 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.</p>
<p>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 <a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a> command
or they must correspond to the tag &#8220;1fluid&#8221;, signifying interaction
with a product species mixture determined through a one-fluid approximation.
<p>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 <a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a> command or they
must correspond to the tag &#8220;1fluid&#8221;, 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
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).</p>
<hr class="docutils" />
<p>Here are some guidelines for using the pair_style table/rx command to
@ -312,8 +314,8 @@ commands do need to be specified in the restart input script.</p>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<blockquote>
<div>none</div></blockquote>
<p>This command is part of the USER-DPD package. It is only enabled if
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands</h2>

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