Merge branch 'qtb_example' of github.com:stanmoore1/lammps into pair-potential-file-unit-convert
This commit is contained in:
Axel Kohlmeyer
@ -35,7 +35,7 @@ Syntax
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v_name = variable with name that calculates value of aparam
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* zero or more keyword/value pairs may be appended
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* keyword = *scale* or *reset*
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* keyword = *scale* or *reset* or *mass*
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.. parsed-literal::
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@ -45,6 +45,9 @@ Syntax
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*reset* value = *no* or *yes*
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*no* = values will remain altered at the end of a run
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*yes* = reset altered values to their original values at the end of a run
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*mass* value = *no* or *yes*
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*no* = mass is not altered by changes in diameter
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*yes* = mass is altered by changes in diameter
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Examples
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""""""""
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@ -53,7 +56,7 @@ Examples
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fix 1 all adapt 1 pair soft a 1 1 v_prefactor
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fix 1 all adapt 1 pair soft a 2* 3 v_prefactor
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fix 1 all adapt 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
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fix 1 all adapt 1 pair lj/cut epsilon * * v_scale1 pair coul/cut scale 3 3 v_scale2 scale yes reset yes
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fix 1 all adapt 10 atom diameter v_size
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variable ramp_up equal "ramp(0.01,0.5)"
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@ -86,12 +89,13 @@ the end of a simulation. Even if *reset* is specified as *yes*\ , a
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restart file written during a simulation will contain the modified
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settings.
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If the *scale* keyword is set to *no*\ , then the value of the altered
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parameter will be whatever the variable generates. If the *scale*
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keyword is set to *yes*\ , then the value of the altered parameter will
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be the initial value of that parameter multiplied by whatever the
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variable generates. I.e. the variable is now a "scale factor" applied
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in (presumably) a time-varying fashion to the parameter.
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If the *scale* keyword is set to *no*\ , which is the default, then
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the value of the altered parameter will be whatever the variable
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generates. If the *scale* keyword is set to *yes*\ , then the value
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of the altered parameter will be the initial value of that parameter
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multiplied by whatever the variable generates. I.e. the variable is
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now a "scale factor" applied in (presumably) a time-varying fashion to
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the parameter.
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Note that whether scale is *no* or *yes*\ , internally, the parameters
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themselves are actually altered by this fix. Make sure you use the
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@ -107,16 +111,17 @@ style supports it. Note that the :doc:`pair_style <pair_style>` and
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to specify these parameters initially; the fix adapt command simply
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overrides the parameters.
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The *pstyle* argument is the name of the pair style. If :doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is used, *pstyle* should be
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a sub-style name. If there are multiple sub-styles using the same
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pair style, then *pstyle* should be specified as "style:N" where N is
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which instance of the pair style you wish to adapt, e.g. the first,
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second, etc. For example, *pstyle* could be specified as "soft" or
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"lubricate" or "lj/cut:1" or "lj/cut:2". The *pparam* argument is the
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name of the parameter to change. This is the current list of pair
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styles and parameters that can be varied by this fix. See the doc
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pages for individual pair styles and their energy formulas for the
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meaning of these parameters:
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The *pstyle* argument is the name of the pair style. If
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:doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is used,
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*pstyle* should be a sub-style name. If there are multiple
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sub-styles using the same pair style, then *pstyle* should be specified
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as "style:N" where N is which instance of the pair style you wish to
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adapt, e.g. the first, second, etc. For example, *pstyle* could be
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specified as "soft" or "lubricate" or "lj/cut:1" or "lj/cut:2". The
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*pparam* argument is the name of the parameter to change. This is the
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current list of pair styles and parameters that can be varied by this
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fix. See the doc pages for individual pair styles and their energy
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formulas for the meaning of these parameters:
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+---------------------------------------------------------------------+--------------------------------------------------+-------------+
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| :doc:`born <pair_born>` | a,b,c | type pairs |
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@ -234,31 +239,32 @@ the coefficients for the symmetric J,I interaction to the same values.
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A wild-card asterisk can be used in place of or in conjunction with
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the I,J arguments to set the coefficients for multiple pairs of atom
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types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the
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number of atom types, then an asterisk with no numeric values means
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all types from 1 to N. A leading asterisk means all types from 1 to n
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(inclusive). A trailing asterisk means all types from n to N
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types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N =
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the number of atom types, then an asterisk with no numeric values
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means all types from 1 to N. A leading asterisk means all types from
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1 to n (inclusive). A trailing asterisk means all types from n to N
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(inclusive). A middle asterisk means all types from m to n
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(inclusive). Note that only type pairs with I <= J are considered; if
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asterisks imply type pairs where J < I, they are ignored.
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IMPROTANT NOTE: If :doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is being used, then the *pstyle* will
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be a sub-style name. You must specify I,J arguments that correspond
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to type pair values defined (via the :doc:`pair_coeff <pair_coeff>`
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command) for that sub-style.
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IMPROTANT NOTE: If :doc:`pair_style hybrid or hybrid/overlay
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<pair_hybrid>` is being used, then the *pstyle* will be a sub-style
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name. You must specify I,J arguments that correspond to type pair
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values defined (via the :doc:`pair_coeff <pair_coeff>` command) for
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that sub-style.
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The *v_name* argument for keyword *pair* is the name of an
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:doc:`equal-style variable <variable>` which will be evaluated each time
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this fix is invoked to set the parameter to a new value. It should be
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specified as v_name, where name is the variable name. Equal-style
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variables can specify formulas with various mathematical functions,
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and include :doc:`thermo_style <thermo_style>` command keywords for the
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simulation box parameters and timestep and elapsed time. Thus it is
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easy to specify parameters that change as a function of time or span
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consecutive runs in a continuous fashion. For the latter, see the
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*start* and *stop* keywords of the :doc:`run <run>` command and the
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*elaplong* keyword of :doc:`thermo_style custom <thermo_style>` for
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details.
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:doc:`equal-style variable <variable>` which will be evaluated each
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time this fix is invoked to set the parameter to a new value. It
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should be specified as v_name, where name is the variable name.
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Equal-style variables can specify formulas with various mathematical
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functions, and include :doc:`thermo_style <thermo_style>` command
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keywords for the simulation box parameters and timestep and elapsed
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time. Thus it is easy to specify parameters that change as a function
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of time or span consecutive runs in a continuous fashion. For the
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latter, see the *start* and *stop* keywords of the :doc:`run <run>`
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command and the *elaplong* keyword of :doc:`thermo_style custom
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<thermo_style>` for details.
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For example, these commands would change the prefactor coefficient of
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the :doc:`pair_style soft <pair_soft>` potential from 10.0 to 30.0 in a
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@ -319,23 +325,28 @@ The *atom* keyword enables various atom properties to be changed. The
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current list of atom parameters that can be varied by this fix:
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* charge = charge on particle
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* diameter, or, diameter/disc = diameter of particle
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* diameter or diameter/disc = diameter of particle
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The *v_name* argument of the *atom* keyword is the name of an
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:doc:`equal-style variable <variable>` which will be evaluated each time
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this fix is invoked to set, or scale the parameter to a new value.
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It should be specified as v_name, where name is the variable name. See the
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discussion above describing the formulas associated with equal-style
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variables. The new value is assigned to the corresponding attribute
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for all atoms in the fix group.
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:doc:`equal-style variable <variable>` which will be evaluated each
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time this fix is invoked to set, or scale the parameter to a new
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value. It should be specified as v_name, where name is the variable
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name. See the discussion above describing the formulas associated
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with equal-style variables. The new value is assigned to the
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corresponding attribute for all atoms in the fix group.
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If the atom parameter is *diameter* and per-atom density and per-atom
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mass are defined for particles (e.g. :doc:`atom_style granular <atom_style>`), then the mass of each particle is also
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changed when the diameter changes. The mass is set from the particle volume
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for 3d systems (density is assumed to stay constant). For 2d, the default is
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for LAMMPS to model particles with a radius attribute as spheres.
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However, if the atom parameter is *diameter/disc*, then the mass is
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set from the particle area (the density is assumed to be in mass/distance^2 units).
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mass are defined for particles (e.g. :doc:`atom_style granular
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<atom_style>`), then the mass of each particle is, by default, also
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changed when the diameter changes. The mass is set from the particle
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volume for 3d systems (density is assumed to stay constant). For 2d,
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the default is for LAMMPS to model particles with a radius attribute
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as spheres. However, if the atom parameter is *diameter/disc*, then the
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mass is set from the particle area (the density is assumed to be in
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mass/distance^2 units). The mass of the particle may also be kept constant
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if the *mass* keyword is set to *no*. This can be useful to account for
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diameter changes that do not involve mass changes, e.g., thermal expansion.
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For example, these commands would shrink the diameter of all granular
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particles in the "center" group from 1.0 to 0.1 in a linear fashion
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@ -348,13 +359,63 @@ over the course of a 1000-step simulation:
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----------
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This fix can be used in long simulations which are restarted one or
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more times to continuously adapt simulation parameters, but it must be
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done carefully. There are two issues to consider. The first is how
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to adapt the parameters in a continuous manner from one simulation to
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the next. The second is how, if desired, to reset the parameters to
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their original values at the end of the last restarted run.
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Note that all the parameters changed by this fix are written into a
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restart file in their current changed state. A new restarted
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simulation does not know their original time=0 values, unless the
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input script explicitly resets the parameters (after the restart file
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is read), to their original values.
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Also note, that the time-dependent variable(s) used in the restart
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script should typically be written as a function of time elapsed since
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the original simulation began.
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With this in mind, if the *scale* keyword is set to *no* (the default)
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in a restarted simulation, original parameters are not needed. The
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adapted parameters should seamlessly continue their variation relative
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to the preceding simulation.
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If the *scale* keyword is set to *yes*, then the input script should
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typically reset the parameters being adapted to their original values,
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so that the scaling formula specified by the variable will operate
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correctly. An exception is if the *atom* keyword is being used with
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*scale yes*. In this case, information is added to the restart file
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so that per-atom properties in the new run will automatically be
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scaled relative to their original values. This will only work if the
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fix adapt command specified in the restart script has the same ID as
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the one used in the original script.
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In a restarted run, if the *reset* keyword is set to *yes*, and the
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run ends in this script (as opposed to just writing more restart
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files, parameters will be restored to the values they were at the
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beginning of the run command in the restart script. Which as
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explained above, may or may not be the original values of the
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parameters. Again, an exception is if the *atom* keyword is being
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used with *reset yes* (in all the runs). In that case, the original
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per-atom parameters are stored in the restart file, and will be
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restored when the restarted run finally completes.
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----------
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**Restart, fix_modify, output, run start/stop, minimize info:**
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No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
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are relevant to this fix. No global or per-atom quantities are stored
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by this fix for access by various :doc:`output commands <Howto_output>`.
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No parameter of this fix can be used with the *start/stop* keywords of
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the :doc:`run <run>` command. This fix is not invoked during :doc:`energy minimization <minimize>`.
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If the *atom* keyword is used and the *scale* or *reset* keyword is
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set to *yes*, then this fix writes information to a restart file so
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that in a restarted run scaling can continue in a seamless manner
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and/or the per-atom values can be restored, as explained above.
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None of the :doc:`fix_modify <fix_modify>` options are relevant to
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this fix. No global or per-atom quantities are stored by this fix for
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access by various :doc:`output commands <Howto_output>`. No parameter
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of this fix can be used with the *start/stop* keywords of the
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:doc:`run <run>` command. This fix is not invoked during :doc:`energy
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minimization <minimize>`.
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For :doc:`rRESPA time integration <run_style>`, this fix changes
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parameters on the outermost rRESPA level.
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@ -371,4 +432,4 @@ Related commands
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Default
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"""""""
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The option defaults are scale = no, reset = no.
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The option defaults are scale = no, reset = no, mass = yes.
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