From d1428accee11f473320ad2953dda7013bf9f621f Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 7 Jun 2016 15:49:45 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15129 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/html/_sources/fix_eos_cv.txt | 7 +- doc/html/_sources/fix_eos_table.txt | 11 +- doc/html/_sources/fix_eos_table_rx.txt | 11 +- doc/html/_sources/fix_rx.txt | 107 ++++++++-------- doc/html/_sources/fix_shardlow.txt | 7 +- doc/html/_sources/pair_dpd_fdt.txt | 4 +- doc/html/_sources/pair_exp6_rx.txt | 66 +++++----- doc/html/_sources/pair_multi_lucy.txt | 86 +++++++------ doc/html/_sources/pair_multi_lucy_rx.txt | 154 ++++++++++++----------- doc/html/_sources/pair_table_rx.txt | 43 ++++--- doc/html/fix_eos_cv.html | 6 +- doc/html/fix_eos_table.html | 10 +- doc/html/fix_eos_table_rx.html | 10 +- doc/html/fix_rx.html | 104 ++++++++------- doc/html/fix_shardlow.html | 7 +- doc/html/pair_dpd_fdt.html | 4 +- doc/html/pair_exp6_rx.html | 58 +++++---- doc/html/pair_multi_lucy.html | 85 +++++++------ doc/html/pair_multi_lucy_rx.html | 151 +++++++++++----------- doc/html/pair_table_rx.html | 40 +++--- doc/html/searchindex.js | 2 +- 21 files changed, 526 insertions(+), 447 deletions(-) diff --git a/doc/html/_sources/fix_eos_cv.txt b/doc/html/_sources/fix_eos_cv.txt index 70e1d21e94..d1b1fc559d 100644 --- a/doc/html/_sources/fix_eos_cv.txt +++ b/doc/html/_sources/fix_eos_cv.txt @@ -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 ` section for more info. + +This command also requires use of the :doc:`atom_style dpd ` +command. Related commands """""""""""""""" diff --git a/doc/html/_sources/fix_eos_table.txt b/doc/html/_sources/fix_eos_table.txt index 854409302c..c6fc225105 100644 --- a/doc/html/_sources/fix_eos_table.txt +++ b/doc/html/_sources/fix_eos_table.txt @@ -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 ` section for more info. + +This command also requires use of the :doc:`atom_style dpd ` +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 """""""""""""""" diff --git a/doc/html/_sources/fix_eos_table_rx.txt b/doc/html/_sources/fix_eos_table_rx.txt index 0e6f6854c7..9a46afd956 100644 --- a/doc/html/_sources/fix_eos_table_rx.txt +++ b/doc/html/_sources/fix_eos_table_rx.txt @@ -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 ` section for more info. + +This command also requires use of the :doc:`atom_style dpd ` +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 """""""""""""""" diff --git a/doc/html/_sources/fix_rx.txt b/doc/html/_sources/fix_rx.txt index 8ad193cd02..a15c187e7c 100644 --- a/doc/html/_sources/fix_rx.txt +++ b/doc/html/_sources/fix_rx.txt @@ -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 ` 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 ` -command using the "d_" prefix or by reading directly the concentrations from a -data file. For the latter case, the :doc:`read_data ` command with the -fix keyword should be specified, where the fix-ID will be the "fix rx`ID with a `_ suffix, e.g. +Note that the species tags that are defined in the reaction equations +are used by the :doc:`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 ` command using the "d_" prefix or by +reading directly the concentrations from a data file. For the latter +case, the :doc:`read_data ` command with the fix keyword +should be specified, where the fix-ID will be the "fix rx`ID with a `_ 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 ` section for more info. -The fix *rx* must be used with the :doc:`atom_style dpd ` command. +This command also requires use of the :doc:`atom_style dpd ` +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 diff --git a/doc/html/_sources/fix_shardlow.txt b/doc/html/_sources/fix_shardlow.txt index c52e32630e..623c7621a2 100644 --- a/doc/html/_sources/fix_shardlow.txt +++ b/doc/html/_sources/fix_shardlow.txt @@ -56,9 +56,8 @@ Restrictions """""""""""" -This fix is only available if LAMMPS is built with the USER-DPD -package. See the :ref:`Making LAMMPS ` 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 ` section for more info. This fix is currently limited to orthogonal simulation cell geometries. @@ -68,7 +67,7 @@ integration, e.g. :doc:`fix nve ` or :doc:`fix nph `. 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 diff --git a/doc/html/_sources/pair_dpd_fdt.txt b/doc/html/_sources/pair_dpd_fdt.txt index 602da2752b..1c35614fa6 100644 --- a/doc/html/_sources/pair_dpd_fdt.txt +++ b/doc/html/_sources/pair_dpd_fdt.txt @@ -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 ` section for more info. Pair styles *dpd/fdt* and *dpd/fdt/energy* require use of the :doc:`communicate vel yes ` option so that velocites are diff --git a/doc/html/_sources/pair_exp6_rx.txt b/doc/html/_sources/pair_exp6_rx.txt index 0a5576911c..99aec901b7 100644 --- a/doc/html/_sources/pair_exp6_rx.txt +++ b/doc/html/_sources/pair_exp6_rx.txt @@ -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 ` 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 ` 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 ` 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 ` 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 ` 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 ` 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 ` section for more info. Related commands """""""""""""""" diff --git a/doc/html/_sources/pair_multi_lucy.txt b/doc/html/_sources/pair_multi_lucy.txt index 00db4c15df..c4132d4f1c 100644 --- a/doc/html/_sources/pair_multi_lucy.txt +++ b/doc/html/_sources/pair_multi_lucy.txt @@ -24,15 +24,16 @@ Examples Description """"""""""" -Style *multi/lucy* computes a density-dependent force following from the many-body -form described in :ref:`(Moore) ` and :ref:`(Warren) ` as +Style *multi/lucy* computes a density-dependent force following from +the many-body form described in :ref:`(Moore) ` and +:ref:`(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) ` or the publication by :ref:`(Moore) ` -for more details on the functional form. +See the supporting information of :ref:`(Brennan) ` or the +publication by :ref:`(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 ` 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 ` command. Let -Ntable = *N* in the pair_style command, and Nfile = "N" in the +specified in the :doc:`pair_style 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 ` section for more info. Related commands """""""""""""""" diff --git a/doc/html/_sources/pair_multi_lucy_rx.txt b/doc/html/_sources/pair_multi_lucy_rx.txt index b134a14b4d..23f67d0bc5 100644 --- a/doc/html/_sources/pair_multi_lucy_rx.txt +++ b/doc/html/_sources/pair_multi_lucy_rx.txt @@ -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 ` 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) ` and :ref:`(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 ` 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) ` and +:ref:`(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) ` or the publication by :ref:`(Moore) ` -for more details on the functional form. +See the supporting information of :ref:`(Brennan) ` or the +publication by :ref:`(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 ` 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 ` 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 ` 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 ` 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 ` +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 ` section for more info. Related commands """""""""""""""" diff --git a/doc/html/_sources/pair_table_rx.txt b/doc/html/_sources/pair_table_rx.txt index e1af9b0ea4..1c5a57b038 100644 --- a/doc/html/_sources/pair_table_rx.txt +++ b/doc/html/_sources/pair_table_rx.txt @@ -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 ` 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 ` 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 ` 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 ` +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. ` 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 ` 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 ` 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 ` section for more info. Related commands """""""""""""""" diff --git a/doc/html/fix_eos_cv.html b/doc/html/fix_eos_cv.html index 6248d4586f..ccc917df54 100644 --- a/doc/html/fix_eos_cv.html +++ b/doc/html/fix_eos_cv.html @@ -158,8 +158,10 @@ possible.

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 Making LAMMPS section for more info.

+

This command also requires use of the atom_style dpd +command.