Merge pull request #306 from timattox/USER-DPD_updates

[Syntax:]

fix ID group-ID eos/table/rx style file1 N keyword file2 :pre

fix ID group-ID eos/table/rx style file1 N keyword ... :pre

ID, group-ID are documented in "fix"_fix.html command

eos/table/rx = style name of this fix command

file1 = filename containing the tabulated equation of state

N = use N values in {linear} tables

keyword = name of table keyword correponding to table file

file2 = filename containing the heats of formation of each species :ul

file2 = filename containing the heats of formation of each species (optional)

deltaHf = heat of formation for a single species in energy units (optional)

energyCorr = energy correction in energy units (optional)

tempCorrCoeff = temperature correction coefficient (optional) :ul

[Examples:]

fix 1 all eos/table/rx linear eos.table 10000 KEYWORD thermo.table :pre

fix 1 all eos/table/rx linear eos.table 10000 KEYWORD thermo.table

fix 1 all eos/table/rx linear eos.table 10000 KEYWORD 1.5

fix 1 all eos/table/rx linear eos.table 10000 KEYWORD 1.5 0.025 0.0 :pre

[Description:]

species {j} in particle {i}, {u_j} is the internal energy of species j,

{DeltaH_f,j} is the heat of formation of species {j}, N is the number of

molecules represented by the coarse-grained particle, kb is the

Boltzmann constant, and T is the temperature of the system.

Boltzmann constant, and T is the temperature of the system.  Additionally,

it is possible to modify the concentration-dependent particle internal 

energy relation by adding an energy correction, temperature-dependent 

correction, and/or a molecule-dependent correction.  An energy correction can

be specified as a constant (in energy units).  A temperature correction can be 

specified by multiplying a temperature correction coefficient by the 

internal temperature.  A molecular correction can be specified by 

by multiplying a molecule correction coefficient by the average number of 

product gas particles in the coarse-grain particle. 

Fix {eos/table/rx} creates interpolation tables of length {N} from {m}

internal energy values of each species {u_j} listed in a file as a

The second filename specifies a file containing heat of formation

{DeltaH_f,j} for each species.

In cases where the coarse-grain particle represents a single molecular

species (i.e., no reactions occur and fix {rx} is not present in the input file), 

fix {eos/table/rx} can be applied in a similar manner to fix {eos/table} 

within a non-reactive DPD simulation.  In this case, the heat of formation 

filename is replaced with the heat of formation value for the single species.

Additionally, the energy correction and temperature correction coefficients may 

also be specified as fix arguments.  

:line

The format of a tabulated file is as follows (without the

used as the species name must correspond with the tags used to define

the reactions with the "fix rx"_fix_rx.html command.

Alternatively, corrections to the EOS can be included by specifying

three additional columns that correspond to the energy correction, 

the temperature correction coefficient and molecule correction 

coefficient.  In this case, the format of the file is as follows:

# HEAT OF FORMATION TABLE     (one or more comment or blank lines) :pre

                              (blank)

h2      0.00 1.23 0.025  0.0  (species name, heat of formation, energy correction, temperature correction coefficient, molecule correction coefficient)

no2     0.34 0.00 0.000 -1.76

n2      0.00 0.00 0.000 -1.76

...

no      0.93 0.00 0.000 -1.76 :pre

:line

[Restrictions:]

[Syntax:]

pair_style exp6/rx cutoff :pre

pair_style exp6/rx cutoff ... :pre

cutoff = global cutoff for DPD interactions (distance units) :ul

cutoff = global cutoff for DPD interactions (distance units)

weighting = fractional or molecular (optional) :ul

[Examples:]

pair_style exp6/rx 10.0

pair_coeff * * exp6.params h2o h2o 1.0 1.0 10.0

pair_coeff * * exp6.params h2o 1fluid 1.0 1.0 10.0

pair_coeff * * exp6.params 1fluid 1fluid 1.0 1.0 10.0 :pre

pair_style exp6/rx 10.0 fractional

pair_style exp6/rx 10.0 molecular

pair_coeff * * exp6.params h2o h2o exponent 1.0 1.0 10.0

pair_coeff * * exp6.params h2o 1fluid exponent 1.0 1.0 10.0

pair_coeff * * exp6.params 1fluid 1fluid exponent 1.0 1.0 10.0

pair_coeff * * exp6.params 1fluid 1fluid none 10.0

pair_coeff * * exp6.params 1fluid 1fluid polynomial filename 10.0 :pre

[Description:]

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

weighted by the geometric average of either the mole fraction concentrations 

or the number of molecules associated with the interacting coarse-grained 

particles (see the {fractional} or {molecular} weighting pair style options). 

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.

The fourth argument specifies the type of scaling that will be used 

to scale the EXP-6 paramters as reactions occur.  Currently, there

are three scaling options:  {exponent}, {polynomial} and {none}.

The final argument specifies the interaction cutoff.

Exponent scaling requires two additional arguments for scaling 

the {Rm} and {epsilon} parameters, respectively.  The scaling factor

is computed by phi^exponent, where phi is the number of molecules  

represented by the coarse-grain particle and exponent is specified 

as a pair coefficient argument for {Rm} and {epsilon}, respectively.

The {Rm} and {epsilon} parameters are multiplied by the scaling 

factor to give the scaled interaction paramters for the CG particle.

Polynomial scaling requires a filename to be specified as a pair 

coeff argument.  The file contains the coefficients to a fifth order

polynomial for the {alpha}, {epsilon} and {Rm} parameters that depend 

upon phi (the number of molecules represented by the CG particle). 

The format of a polynomial file is provided below.

The {none} option to the scaling does not have any additional pair coeff

arguments.  This is equivalent to specifying the {exponent} option with 

{Rm} and {epsilon} exponents of 0.0 and 0.0, respectively.

The final argument specifies the interaction cutoff (optional).

:line

...

co2  exp6  13.00 0.03 3.20 :pre

The format of the polynomial scaling file as follows (without the

parenthesized comments):

# POLYNOMIAL FILE          (one or more comment or blank lines) :pre

#  General Functional Form:

#  A*phi^5 + B*phi^4 + C*phi^3 + D*phi^2 + E*phi + F 

#

#  Parameter  A        B         C        D         E        F

                           (blank)

alpha        0.0000   0.00000   0.00008  0.04955  -0.73804  13.63201

epsilon      0.0000   0.00478  -0.06283  0.24486  -0.33737   2.60097

rm           0.0001  -0.00118  -0.00253  0.05812  -0.00509   1.50106 :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.

"pair_coeff"_pair_coeff.html

[Default:] none

[Default:] fractional weighting

pair_style multi/lucy/rx style N keyword ... :pre

style = {lookup} or {linear} = method of interpolation

N = use N values in {lookup}, {linear} tables :ul

N = use N values in {lookup}, {linear} tables

weighting = fractional or molecular (optional) :ul

[Examples:]

pair_style multi/lucy/rx linear 1000

pair_style multi/lucy/rx linear 1000 fractional

pair_style multi/lucy/rx linear 1000 molecular

pair_coeff * * multibody.table ENTRY1 h2o h2o 7.0

pair_coeff * * multibody.table ENTRY1 h2o 1fluid 7.0 :pre

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

The interaction potential is weighted by the geometric average of 

either the mole fraction concentrations or the number of molecules 

associated with the interacting coarse-grained particles (see the 

{fractional} or {molecular} weighting pair style options). 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).

"pair_coeff"_pair_coeff.html

[Default:] none

[Default:] fractional weighting

:line

[Syntax:]

pair_style table style N :pre

pair_style table style N ... :pre

style = {lookup} or {linear} or {spline} or {bitmap} = method of interpolation

N = use N values in {lookup}, {linear}, {spline} tables

N = use 2^N values in {bitmap} tables

weighting = fractional or molecular (optional) :ul

[Examples:]

pair_style table/rx linear 1000

pair_style table/rx bitmap 12

pair_style table/rx linear 1000 fractional

pair_style table/rx linear 1000 molecular

pair_coeff * * rxn.table ENTRY1 h2o h2o 10.0

pair_coeff * * rxn.table ENTRY1 1fluid 1fluid 10.0

pair_coeff * 3 rxn.table ENTRY1 h2o no2 10.0 :pre

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

The interaction potential is weighted by the geometric average of 

either the mole fraction concentrations or the number of molecules 

associated with the interacting coarse-grained particles (see the 

{fractional} or {molecular} weighting pair style options). 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).

"pair_coeff"_pair_coeff.html

[Default:] none

[Default:] fractional weighting

:line