forked from lijiext/lammps
114 lines
4.5 KiB
Plaintext
114 lines
4.5 KiB
Plaintext
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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compute ti command :h3
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[Syntax:]
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compute ID group ti keyword args ... :pre
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ID, group-ID are documented in "compute"_compute.html command :ulb,l
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ti = style name of this compute command :l
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one or more attribute/arg pairs may be appended :l
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keyword = pair style (lj/cut, gauss, born, etc) or {tail} or {kspace} :l
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pair style args = v_name1 v_name2
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v_name1 = variable with name1 that is energy scale factor and function of lambda
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v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda
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{tail} args = v_name1 v_name2
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v_name1 = variable with name1 that is energy tail correction scale factor and function of lambda
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v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda
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{kspace} args = v_name1 v_name2
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v_name1 = variable with name1 that is K-Space scale factor and function of lambda
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v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda :pre
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:ule
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[Examples:]
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compute 1 all ti lj/cut v_lj v_dlj coul/long v_c v_dc kspace v_ks v_dks :pre
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[Description:]
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Define a computation that calculates the derivative of the interaction
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potential with respect to {lambda}, the coupling parameter used in a
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thermodynamic integration. This derivative can be used to infer a
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free energy difference resulting from an alchemical simulation, as
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described in "Eike"_#Eike.
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Typically this compute will be used in conjunction with the "fix
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adapt"_fix_adapt.html command which can perform alchemical
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transformations by adusting the strength of an interaction potential
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as a simulation runs, as defined by one or more
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"pair_style"_pair_style.html or "kspace_style"_kspace_style.html
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commands. This scaling is done via a prefactor on the energy, forces,
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virial calculated by the pair or K-Space style. The prefactor is
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often a function of a {lambda} parameter which may be adjusted from 0
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to 1 (or vice versa) over the course of a "run"_run.html. The
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time-dependent adjustment is what the "fix adapt"_fix_adapt.html
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command does.
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Assume that the unscaled energy of a pair_style or kspace_style is
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given by U. Then the scaled energy is
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Us = f(lambda) U :pre
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where f() is some function of lambda. What this compute calculates is
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dUs / d(lambda) = U df(lambda)/dlambda = Us / f(lambda) df(lambda)/dlambda :pre
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which is the derivative of the system's scaled potential energy Us
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with respect to {lambda}.
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To do this calculation, you provide two functions, as "equal-style
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variables"_variable.html. The first is specified as {v_name1}, where
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{name1} is the name of the variable, and is f(lambda) in the notation
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above. The second is specified as {v_name2}, where {name2} is the
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name of the variable, and is df(lambda) / dlambda in the notation
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above. I.e. it is the analytic derivative of f() with respect to
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lambda. Note that the {name1} variable is also typically given as an
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argument to the "fix adapt"_fix_adapt.html command.
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An alchemical simulation may use several pair potentials together,
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invoked via the "pair_style hybrid or hybrid/overlay"_pair_hybrid.html
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command. The total dUs/dlambda for the overall system is calculated
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as the sum of each contributing term as listed by the keywords in the
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compute ti command. Individual pair potentials can be listed, which
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will be sub-styles in the hybrid case. You can also include a K-space
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term via the {kspace} keyword. You can also include a pairwise
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long-range tail correction to the energy via the {tail} keyword.
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For each term you can specify a different (or the same) scale factor
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by the two variables that you list. Again, these will typically
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correspond toe the scale factors applied to these various potentials
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and the K-Space contribution via the "fix_adapt"_fix_adapt.html
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command.
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More details about the exact functional forms for the computation of
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du/dl can be found in the paper by "Eike"_#Eike.
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[Output info:]
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This compute calculates a global scalar, namely dUs/dlambda. This
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value can be used by any command that uses a global scalar value from
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a compute as input. See "this section"_Section_howto.html#4_15 for an
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overview of LAMMPS output options.
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The scalar value calculated by this compute is "extensive".
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The scalar value will be in energy "units"_units.html.
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[Restrictions:] none
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[Related commands:]
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"fix adapt"_fix_adapt.html
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[Default:] none
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:link(Eike)
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[(Eike)] Eike and Maginn, Journal of Chemical Physics, 124, 164503 (2006).
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