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< title > fix adapt/fep command — LAMMPS documentation< / title >
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< li > fix adapt/fep command< / li >
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< div class = "section" id = "fix-adapt-fep-command" >
< span id = "index-0" > < / span > < h1 > fix adapt/fep command< a class = "headerlink" href = "#fix-adapt-fep-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< div class = "section" id = "syntax" >
< h2 > Syntax< a class = "headerlink" href = "#syntax" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > fix ID group-ID adapt/fep N attribute args ... keyword value ...
< / pre > < / div >
< / div >
< ul class = "simple" >
< li > ID, group-ID are documented in < a class = "reference internal" href = "fix.html" > < em > fix< / em > < / a > command< / li >
< li > adapt/fep = style name of this fix command< / li >
< li > N = adapt simulation settings every this many timesteps< / li >
< li > one or more attribute/arg pairs may be appended< / li >
< li > attribute = < em > pair< / em > or < em > kspace< / em > or < em > atom< / em > < / li >
< / ul >
< pre class = "literal-block" >
< em > pair< / em > args = pstyle pparam I J v_name
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pstyle = pair style name, e.g. lj/cut
pparam = parameter to adapt over time
I,J = type pair(s) to set parameter for
v_name = variable with name that calculates value of pparam
< em > kspace< / em > arg = v_name
v_name = variable with name that calculates scale factor on K-space terms
< em > atom< / em > args = aparam v_name
aparam = parameter to adapt over time
I = type(s) to set parameter for
v_name = variable with name that calculates value of aparam
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< / pre >
< ul class = "simple" >
< li > zero or more keyword/value pairs may be appended< / li >
< li > keyword = < em > scale< / em > or < em > reset< / em > or < em > after< / em > < / li >
< / ul >
< pre class = "literal-block" >
< em > scale< / em > value = < em > no< / em > or < em > yes< / em >
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< em > no< / em > = the variable value is the new setting
< em > yes< / em > = the variable value multiplies the original setting
< em > reset< / em > value = < em > no< / em > or < em > yes< / em >
< em > no< / em > = values will remain altered at the end of a run
< em > yes< / em > = reset altered values to their original values at the end
of a run
< em > after< / em > value = < em > no< / em > or < em > yes< / em >
< em > no< / em > = parameters are adapted at timestep N
< em > yes< / em > = parameters are adapted one timestep after N
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< / pre >
< / div >
< div class = "section" id = "examples" >
< h2 > Examples< a class = "headerlink" href = "#examples" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > fix 1 all adapt/fep 1 pair soft a 1 1 v_prefactor
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fix 1 all adapt/fep 1 pair soft a 2* 3 v_prefactor
fix 1 all adapt/fep 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/fep 10 atom diameter 1 v_size
< / pre > < / div >
< / div >
< / div >
< div class = "section" id = "description" >
< h2 > Description< a class = "headerlink" href = "#description" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > Change or adapt one or more specific simulation attributes or settings
over time as a simulation runs.< / p >
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< p > This is an enhanced version of the < a class = "reference internal" href = "fix_adapt.html" > < em > fix adapt< / em > < / a > command
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with two differences,< / p >
< ul class = "simple" >
< li > It is possible to modify the charges of chosen atom types only,
instead of scaling all the charges in the system.< / li >
< li > There is a new option < em > after< / em > for better compatibility with “ fix
ave/time” .< / li >
< / ul >
< p > This version is suited for free energy calculations using
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< a class = "reference internal" href = "compute_ti.html" > < em > compute ti< / em > < / a > or < a class = "reference internal" href = "compute_fep.html" > < em > compute fep< / em > < / a > .< / p >
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< p > If < em > N< / em > is specified as 0, the specified attributes are only changed
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once, before the simulation begins. This is all that is needed if the
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associated variables are not time-dependent. If < em > N< / em > > 0, then changes
are made every < em > N< / em > steps during the simulation, presumably with a
variable that is time-dependent.< / p >
< p > Depending on the value of the < em > reset< / em > keyword, attributes changed by
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this fix will or will not be reset back to their original values at
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the end of a simulation. Even if < em > reset< / em > is specified as < em > yes< / em > , a
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restart file written during a simulation will contain the modified
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settings.< / p >
< p > If the < em > scale< / em > keyword is set to < em > no< / em > , then the value the parameter is
set to will be whatever the variable generates. If the < em > scale< / em >
keyword is set to < em > yes< / em > , 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. Internally,
the parameters themselves are actually altered; make sure you use the
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< em > reset yes< / em > option if you want the parameters to be restored to their
initial values after the run.< / p >
< p > If the < em > after< / em > keyword is set to < em > yes< / em > , then the parameters are
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changed one timestep after the multiple of N. In this manner, if a fix
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such as “ fix ave/time” is used to calculate averages at every N
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timesteps, all the contributions to the average will be obtained with
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the same values of the parameters.< / p >
< hr class = "docutils" / >
< p > The < em > pair< / em > keyword enables various parameters of potentials defined by
the < a class = "reference internal" href = "pair_style.html" > < em > pair_style< / em > < / a > command to be changed, if the pair
style supports it. Note that the < a class = "reference internal" href = "pair_style.html" > < em > pair_style< / em > < / a > and
< a class = "reference internal" href = "pair_coeff.html" > < em > pair_coeff< / em > < / a > commands must be used in the usual manner
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to specify these parameters initially; the fix adapt command simply
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overrides the parameters.< / p >
< p > The < em > pstyle< / em > argument is the name of the pair style. If < a class = "reference internal" href = "pair_hybrid.html" > < em > pair_style hybrid or hybrid/overlay< / em > < / a > is used, < em > pstyle< / em > should be
a sub-style name. For example, < em > pstyle< / em > could be specified as “ soft”
or “ lubricate” . The < em > pparam< / em > argument is the name of the parameter to
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change. This is the current list of pair styles and parameters that
can be varied by this fix. See the doc pages for individual pair
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styles and their energy formulas for the meaning of these parameters:< / p >
< table border = "1" class = "docutils" >
< colgroup >
< col width = "51%" / >
< col width = "31%" / >
< col width = "18%" / >
< / colgroup >
< tbody valign = "top" >
< tr class = "row-odd" > < td > < a class = "reference internal" href = "pair_born.html" > < em > born< / em > < / a > < / td >
< td > a,b,c< / td >
< td > type pairs< / td >
< / tr >
< tr class = "row-even" > < td > < a class = "reference internal" href = "pair_buck.html" > < em > buck< / em > < / a > < / td >
< td > a,c< / td >
< td > type pairs< / td >
< / tr >
< tr class = "row-odd" > < td > < a class = "reference internal" href = "pair_coul.html" > < em > coul/cut< / em > < / a > < / td >
< td > scale< / td >
< td > type pairs< / td >
< / tr >
< tr class = "row-even" > < td > < a class = "reference internal" href = "pair_coul.html" > < em > coul/debye< / em > < / a > < / td >
< td > scale< / td >
< td > type pairs< / td >
< / tr >
< tr class = "row-odd" > < td > < a class = "reference internal" href = "pair_coul.html" > < em > coul/long< / em > < / a > < / td >
< td > scale< / td >
< td > type pairs< / td >
< / tr >
< tr class = "row-even" > < td > < a class = "reference internal" href = "pair_lj.html" > < em > lj/cut< / em > < / a > < / td >
< td > epsilon,sigma< / td >
< td > type pairs< / td >
< / tr >
< tr class = "row-odd" > < td > < a class = "reference internal" href = "pair_lj_expand.html" > < em > lj/expand< / em > < / a > < / td >
< td > epsilon,sigma,delta< / td >
< td > type pairs< / td >
< / tr >
< tr class = "row-even" > < td > < a class = "reference internal" href = "pair_lubricate.html" > < em > lubricate< / em > < / a > < / td >
< td > mu< / td >
< td > global< / td >
< / tr >
< tr class = "row-odd" > < td > < a class = "reference internal" href = "pair_gauss.html" > < em > gauss< / em > < / a > < / td >
< td > a< / td >
< td > type pairs< / td >
< / tr >
< tr class = "row-even" > < td > < a class = "reference internal" href = "pair_soft.html" > < em > soft< / em > < / a > < / td >
< td > a< / td >
< td > type pairs< / td >
< / tr >
< / tbody >
< / table >
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< div class = "admonition note" >
< p class = "first admonition-title" > Note< / p >
< p class = "last" > It is easy to add new potentials and their parameters to this
list. All it typically takes is adding an extract() method to the
pair_*.cpp file associated with the potential.< / p >
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< / div >
< p > Some parameters are global settings for the pair style, e.g. the
viscosity setting “ mu” for < a class = "reference internal" href = "pair_lubricate.html" > < em > pair_style lubricate< / em > < / a > .
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Other parameters apply to atom type pairs within the pair style,
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e.g. the prefactor “ a” for < a class = "reference internal" href = "pair_soft.html" > < em > pair_style soft< / em > < / a > .< / p >
< p > Note that for many of the potentials, the parameter that can be varied
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is effectively a prefactor on the entire energy expression for the
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potential, e.g. the lj/cut epsilon. The parameters listed as “ scale”
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are exactly that, since the energy expression for the
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< a class = "reference internal" href = "pair_coul.html" > < em > coul/cut< / em > < / a > potential (for example) has no labeled
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prefactor in its formula. To apply an effective prefactor to some
potentials, multiple parameters need to be altered. For example, the
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< a class = "reference internal" href = "pair_buck.html" > < em > Buckingham potential< / em > < / a > needs both the A and C terms
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altered together. To scale the Buckingham potential, you should thus
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list the pair style twice, once for A and once for C.< / p >
< p > If a type pair parameter is specified, the < em > I< / em > and < em > J< / em > settings should
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be specified to indicate which type pairs to apply it to. If a global
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parameter is specified, the < em > I< / em > and < em > J< / em > settings still need to be
specified, but are ignored.< / p >
< p > Similar to the < a class = "reference internal" href = "pair_coeff.html" > < em > pair_coeff command< / em > < / a > , I and J can be
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specified in one of two ways. Explicit numeric values can be used for
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each, as in the 1st example above. I < = J is required. LAMMPS sets
the coefficients for the symmetric J,I interaction to the same values.< / p >
< p > 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 “ < em > n” or “ n< / em > ” or “ m*n” . If N = the
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number of atom types, then an asterisk with no numeric values means
all types from 1 to N. A leading asterisk means all types from 1 to n
(inclusive). A trailing asterisk means all types from n to N
(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
asterisks imply type pairs where J < I, they are ignored.< / p >
< p > IMPROTANT NOTE: If < a class = "reference internal" href = "pair_hybrid.html" > < em > pair_style hybrid or hybrid/overlay< / em > < / a > is being used, then the < em > pstyle< / em > 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 < a class = "reference internal" href = "pair_coeff.html" > < em > pair_coeff< / em > < / a >
command) for that sub-style.< / p >
< p > The < em > v_name< / em > argument for keyword < em > pair< / em > is the name of an
< a class = "reference internal" href = "variable.html" > < em > equal-style variable< / em > < / a > 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
specified as v_name, where name is the variable name. Equal-style
variables can specify formulas with various mathematical functions,
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and include < a class = "reference internal" href = "thermo_style.html" > < em > thermo_style< / em > < / a > command keywords for the
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simulation box parameters and timestep and elapsed time. Thus it is
easy to specify parameters that change as a function of time or span
consecutive runs in a continuous fashion. For the latter, see the
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< em > start< / em > and < em > stop< / em > keywords of the < a class = "reference internal" href = "run.html" > < em > run< / em > < / a > command and the
< em > elaplong< / em > keyword of < a class = "reference internal" href = "thermo_style.html" > < em > thermo_style custom< / em > < / a > for
details.< / p >
< p > For example, these commands would change the prefactor coefficient of
the < a class = "reference internal" href = "pair_soft.html" > < em > pair_style soft< / em > < / a > potential from 10.0 to 30.0 in a
linear fashion over the course of a simulation:< / p >
< div class = "highlight-python" > < div class = "highlight" > < pre > variable prefactor equal ramp(10,30)
fix 1 all adapt 1 pair soft a * * v_prefactor
< / pre > < / div >
< / div >
< hr class = "docutils" / >
< p > The < em > kspace< / em > keyword used the specified variable as a scale factor on
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the energy, forces, virial calculated by whatever K-Space solver is
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defined by the < a class = "reference internal" href = "kspace_style.html" > < em > kspace_style< / em > < / a > command. If the
variable has a value of 1.0, then the solver is unaltered.< / p >
< p > The < em > kspace< / em > keyword works this way whether the < em > scale< / em > keyword
is set to < em > no< / em > or < em > yes< / em > .< / p >
< hr class = "docutils" / >
< p > The < em > atom< / em > keyword enables various atom properties to be changed. The
< em > aparam< / em > argument is the name of the parameter to change. This is the
current list of atom parameters that can be varied by this fix:< / p >
< ul class = "simple" >
< li > charge = charge on particle< / li >
< li > diameter = diameter of particle< / li >
< / ul >
< p > The < em > I< / em > argument indicates which atom types are affected. A wild-card
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asterisk can be used in place of or in conjunction with the I argument
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to set the coefficients for multiple atom types.< / p >
< p > The < em > v_name< / em > argument of the < em > atom< / em > keyword is the name of an
< a class = "reference internal" href = "variable.html" > < em > equal-style variable< / em > < / a > 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
specified as v_name, where name is the variable name. See the
discussion above describing the formulas associated with equal-style
variables. The new value is assigned to the corresponding attribute
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for all atoms in the fix group.< / p >
< p > If the atom parameter is < em > diameter< / em > and per-atom density and per-atom
mass are defined for particles (e.g. < a class = "reference internal" href = "atom_style.html" > < em > atom_style granular< / em > < / a > ), then the mass of each particle is also
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changed when the diameter changes (density is assumed to stay
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constant).< / p >
< p > For example, these commands would shrink the diameter of all granular
particles in the “ center” group from 1.0 to 0.1 in a linear fashion
over the course of a 1000-step simulation:< / p >
< div class = "highlight-python" > < div class = "highlight" > < pre > variable size equal ramp(1.0,0.1)
fix 1 center adapt 10 atom diameter * v_size
< / pre > < / div >
< / div >
< p > For < a class = "reference internal" href = "run_style.html" > < em > rRESPA time integration< / em > < / a > , this fix changes
parameters on the outermost rRESPA level.< / p >
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< hr class = "docutils" / >
< div class = "section" id = "restart-fix-modify-output-run-start-stop-minimize-info" >
< h2 > Restart, fix_modify, output, run start/stop, minimize info< a class = "headerlink" href = "#restart-fix-modify-output-run-start-stop-minimize-info" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > No information about this fix is written to < a class = "reference internal" href = "restart.html" > < em > binary restart files< / em > < / a > . None of the < a class = "reference internal" href = "fix_modify.html" > < em > fix_modify< / em > < / a > 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 < a class = "reference internal" href = "Section_howto.html#howto-15" > < span > output commands< / span > < / a > . No parameter of this fix can
be used with the < em > start/stop< / em > keywords of the < a class = "reference internal" href = "run.html" > < em > run< / em > < / a > command.
This fix is not invoked during < a class = "reference internal" href = "minimize.html" > < em > energy minimization< / em > < / a > .< / p >
< / div >
< div class = "section" id = "restrictions" >
< h2 > Restrictions< a class = "headerlink" href = "#restrictions" title = "Permalink to this headline" > ¶< / a > < / h2 >
< blockquote >
< div > none< / div > < / blockquote >
< / div >
< div class = "section" id = "related-commands" >
< h2 > Related commands< a class = "headerlink" href = "#related-commands" title = "Permalink to this headline" > ¶< / a > < / h2 >
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< p > < a class = "reference internal" href = "compute_fep.html" > < em > compute fep< / em > < / a > , < a class = "reference internal" href = "fix_adapt.html" > < em > fix adapt< / em > < / a > , < a class = "reference internal" href = "compute_ti.html" > < em > compute ti< / em > < / a > < / p >
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< / div >
< div class = "section" id = "default" >
< h2 > Default< a class = "headerlink" href = "#default" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > The option defaults are scale = no, reset = no, after = no.< / p >
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© Copyright 2013 Sandia Corporation.
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