mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15069 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
d7c5025530
commit
8fa54096d3
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@ -495,7 +495,6 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
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"ave/correlate"_fix_ave_correlate.html,
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"ave/histo"_fix_ave_histo.html,
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"ave/histo/weight"_fix_ave_histo.html,
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"ave/spatial"_fix_ave_spatial.html,
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"ave/time"_fix_ave_time.html,
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"balance"_fix_balance.html,
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"bond/break"_fix_bond_break.html,
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@ -613,7 +612,6 @@ package"_Section_start.html#start_3.
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"addtorque"_fix_addtorque.html,
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"atc"_fix_atc.html,
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"ave/correlate/long"_fix_ave_correlate_long.html,
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"ave/spatial/sphere"_fix_ave_spatial_sphere.html,
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"colvars"_fix_colvars.html,
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"drude"_fix_drude.html,
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"drude/transform/direct"_fix_drude_transform.html,
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@ -315,12 +315,12 @@ been previously used to define the lattice spacing.
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If you use the {ortho} or {triclinic} keywords, then at the point in
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the input script when this command is issued, no "dumps"_dump.html can
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be active, nor can a "fix ave/spatial"_fix_ave_spatial.html or "fix
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deform"_fix_deform.html be active. This is because these commands
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test whether the simulation box is orthogonal when they are first
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issued. Note that these commands can be used in your script before a
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change_box command is issued, so long as an "undump"_undump.html or
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"unfix"_unfix.html command is also used to turn them off.
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be active, nor can a "fix deform"_fix_deform.html be active. This is
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because these commands test whether the simulation box is orthogonal
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when they are first issued. Note that these commands can be used in
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your script before a change_box command is issued, so long as an
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"undump"_undump.html or "unfix"_unfix.html command is also used to
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turn them off.
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[Related commands:]
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@ -99,11 +99,10 @@ custom"_thermo_style.html or "fix ave/time"_fix_ave_time.html command.
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Or the values can be referenced in a "variable equal"_variable.html or
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"variable atom"_variable.html command. :l
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Per-atom values can be output via the "dump custom"_dump.html command
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or the "fix ave/spatial"_fix_ave_spatial.html command. Or they can be
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time-averaged via the "fix ave/atom"_fix_ave_atom.html command or
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reduced by the "compute reduce"_compute_reduce.html command. Or the
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per-atom values can be referenced in an "atom-style
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Per-atom values can be output via the "dump custom"_dump.html command.
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Or they can be time-averaged via the "fix ave/atom"_fix_ave_atom.html
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command or reduced by the "compute reduce"_compute_reduce.html
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command. Or the per-atom values can be referenced in an "atom-style
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variable"_variable.html. :l
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Local values can be reduced by the "compute
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@ -255,7 +254,7 @@ section of "this page"_Section_commands.html#cmd_5.
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[Related commands:]
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"uncompute"_uncompute.html, "compute_modify"_compute_modify.html, "fix
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ave/atom"_fix_ave_atom.html, "fix ave/spatial"_fix_ave_spatial.html,
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"fix ave/time"_fix_ave_time.html, "fix ave/histo"_fix_ave_histo.html
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ave/atom"_fix_ave_atom.html, "fix ave/time"_fix_ave_time.html, "fix
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ave/histo"_fix_ave_histo.html
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[Default:] none
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@ -91,7 +91,7 @@ in the group. This is useful so that the values can be used by other
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"output commands"_Section_howto.html#howto_15 that take computes as
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inputs. See for example, the "compute reduce"_compute_reduce.html,
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"fix ave/atom"_fix_ave_atom.html, "fix ave/histo"_fix_ave_histo.html,
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"fix ave/spatial"_fix_ave_spatial.html, and "atom-style
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"fix ave/chunk"_fix_ave_chunk.html, and "atom-style
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variable"_variable.html commands.
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The list of possible attributes is the same as that used by the "dump
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@ -157,7 +157,7 @@ units for q, etc.
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[Related commands:]
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"dump custom"_dump.html, "compute reduce"_compute_reduce.html, "fix
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ave/atom"_fix_ave_atom.html, "fix ave/spatial"_fix_ave_spatial.html,
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ave/atom"_fix_ave_atom.html, "fix ave/chunk"_fix_ave_chunk.html,
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"fix property/atom"_fix_property_atom.html
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[Default:] none
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@ -88,7 +88,7 @@ matches the box deformation. If not, then the compute will subtract
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off an incorrect stream velocity, yielding a bogus thermal
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temperature. You should NOT assume that your atoms are streaming at
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the same rate the box is deforming. Rather, you should monitor their
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velocity profile, e.g. via the "fix ave/spatial"_fix_ave_spatial.html
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velocity profile, e.g. via the "fix ave/chunk"_fix_ave_chunk.html
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command. And you can compare the results of this compute to "compute
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temp/profile"_compute_temp_profile.html, which actually calculates the
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stream profile before subtracting it. If the two computes do not give
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@ -122,11 +122,10 @@ custom"_thermo_style.html or "fix ave/time"_fix_ave_time.html command.
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Or the values can be referenced in a "variable equal"_variable.html or
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"variable atom"_variable.html command. :ulb,l
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Per-atom values can be output via the "dump custom"_dump.html command
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or the "fix ave/spatial"_fix_ave_spatial.html command. Or they can be
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time-averaged via the "fix ave/atom"_fix_ave_atom.html command or
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reduced by the "compute reduce"_compute_reduce.html command. Or the
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per-atom values can be referenced in an "atom-style
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Per-atom values can be output via the "dump custom"_dump.html command.
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Or they can be time-averaged via the "fix ave/atom"_fix_ave_atom.html
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command or reduced by the "compute reduce"_compute_reduce.html
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command. Or the per-atom values can be referenced in an "atom-style
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variable"_variable.html. :l
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Local values can be reduced by the "compute
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@ -171,7 +170,6 @@ of "this page"_Section_commands.html#cmd_5.
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"ave/chunk"_fix_ave_chunk.html - compute per-chunk time-averaged quantities
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"ave/correlate"_fix_ave_correlate.html - compute/output time correlations
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"ave/histo"_fix_ave_histo.html - compute/output time-averaged histograms
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"ave/spatial"_fix_ave_spatial.html - compute/output time-averaged per-atom quantities by layer
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"ave/time"_fix_ave_time.html - compute/output global time-averaged quantities
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"balance"_fix_balance.html - perform dynamic load-balancing
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"bond/break"_fix_bond_break.html - break bonds on the fly
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@ -38,7 +38,7 @@ Use one or more per-atom vectors as inputs every few timesteps, and
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average them atom by atom over longer timescales. The resulting
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per-atom averages can be used by other "output
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commands"_Section_howto.html#howto_15 such as the "fix
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ave/spatial"_fix_ave_spatial.html or "dump custom"_dump.html commands.
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ave/chunk"_fix_ave_chunk.html or "dump custom"_dump.html commands.
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The group specified with the command means only atoms within the group
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have their averages computed. Results are set to 0.0 for atoms not in
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@ -147,7 +147,7 @@ minimization"_minimize.html.
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[Related commands:]
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"compute"_compute.html, "fix ave/histo"_fix_ave_histo.html, "fix
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ave/spatial"_fix_ave_spatial.html, "fix ave/time"_fix_ave_time.html,
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ave/chunk"_fix_ave_chunk.html, "fix ave/time"_fix_ave_time.html,
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"variable"_variable.html,
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[Default:] none
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@ -67,8 +67,8 @@ fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running :pre
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[NOTE:]
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If you are trying to replace an older fix ave/spatial command with the
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newer, more flexible fix ave/chunk and "compute
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If you are trying to replace a deprectated fix ave/spatial command
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with the newer, more flexible fix ave/chunk and "compute
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chunk/atom"_compute_chunk_atom.html commands, you simply need to split
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the fix ave/spatial arguments across the two new commands. For
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example, this command:
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@ -83,10 +83,10 @@ Each listed value can be the result of a "compute"_compute.html or
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must produce a global quantity, not a per-atom or local quantity. If
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you wish to spatial- or time-average or histogram per-atom quantities
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from a compute, fix, or variable, then see the "fix
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ave/spatial"_fix_ave_spatial.html, "fix ave/atom"_fix_ave_atom.html,
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or "fix ave/histo"_fix_ave_histo.html commands. If you wish to
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convert a per-atom quantity into a single global value, see the
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"compute reduce"_compute_reduce.html command.
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ave/chunk"_fix_ave_chunk.html, "fix ave/atom"_fix_ave_atom.html, or
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"fix ave/histo"_fix_ave_histo.html commands. If you wish to convert a
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per-atom quantity into a single global value, see the "compute
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reduce"_compute_reduce.html command.
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"Computes"_compute.html that produce global quantities are those which
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do not have the word {atom} in their style name. Only a few
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@ -332,7 +332,7 @@ minimization"_minimize.html.
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"fix ave/correlate/long"_fix_ave_correlate_long.html,
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"compute"_compute.html, "fix ave/time"_fix_ave_time.html, "fix
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ave/atom"_fix_ave_atom.html, "fix ave/spatial"_fix_ave_spatial.html,
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ave/atom"_fix_ave_atom.html, "fix ave/chunk"_fix_ave_chunk.html,
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"fix ave/histo"_fix_ave_histo.html, "variable"_variable.html
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[Default:] none
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@ -331,7 +331,7 @@ minimization"_minimize.html.
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[Related commands:]
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"compute"_compute.html, "fix ave/atom"_fix_ave_atom.html, "fix
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ave/spatial"_fix_ave_spatial.html, "fix ave/time"_fix_ave_time.html,
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ave/chunk"_fix_ave_chunk.html, "fix ave/time"_fix_ave_time.html,
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"variable"_variable.html, "fix ave/correlate"_fix_ave_correlate.html,
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[Default:] none
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@ -1,418 +0,0 @@
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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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fix ave/spatial command :h3
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[Syntax:]
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fix ID group-ID ave/spatial Nevery Nrepeat Nfreq dim origin delta ... value1 value2 ... keyword args ... :pre
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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ave/spatial = style name of this fix command :l
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Nevery = use input values every this many timesteps :l
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Nrepeat = # of times to use input values for calculating averages :l
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Nfreq = calculate averages every this many timesteps :l
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dim, origin, delta can be repeated 1, 2, or 3 times for 1d, 2d, or 3d bins :l
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dim = {x} or {y} or {z}
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origin = {lower} or {center} or {upper} or coordinate value (distance units)
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delta = thickness of spatial bins in dim (distance units) :pre
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one or more input values can be listed :l
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value = vx, vy, vz, fx, fy, fz, density/mass, density/number, c_ID, c_ID\[I\], f_ID, f_ID\[I\], v_name :l
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vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
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density/number, density/mass = number or mass density
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c_ID = per-atom vector calculated by a compute with ID
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c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID
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f_ID = per-atom vector calculated by a fix with ID
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f_ID\[I\] = Ith column of per-atom array calculated by a fix with ID
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v_name = per-atom vector calculated by an atom-style variable with name :pre
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zero or more keyword/arg pairs may be appended :l
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keyword = {region} or {bound} or {discard} or {norm} or {ave} or {units} or {file} or {overwrite} or {title1} or {title2} or {title3} :l
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{region} arg = region-ID
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{bound} args = x/y/z lo hi
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x/y/z = {x} or {y} or {z} to bound bins in this dimension
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lo = {lower} or coordinate value (distance units)
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hi = {upper} or coordinate value (distance units)
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{discard} arg = {mixed} or {no} or {yes}
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mixed = discard atoms outside bins only if bin bounds are explicitly set
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no = always keep out-of-bounds atoms
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yes = always discard out-of-bounds atoms
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{norm} arg = {all} or {sample}
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region-ID = ID of region atoms must be in to contribute to spatial averaging
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{ave} args = {one} or {running} or {window M}
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one = output new average value every Nfreq steps
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running = output cumulative average of all previous Nfreq steps
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window M = output average of M most recent Nfreq steps
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{units} arg = {box} or {lattice} or {reduced}
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{file} arg = filename
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filename = file to write results to
|
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{overwrite} arg = none = overwrite output file with only latest output
|
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{title1} arg = string
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string = text to print as 1st line of output file
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{title2} arg = string
|
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string = text to print as 2nd line of output file
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{title3} arg = string
|
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string = text to print as 3rd line of output file :pre
|
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:ule
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|
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[Examples:]
|
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|
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fix 1 all ave/spatial 10000 1 10000 z lower 0.02 c_myCentro units reduced &
|
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title1 "My output values"
|
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fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vx vz norm sample file vel.profile
|
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fix 1 flow ave/spatial 100 5 1000 z lower 1.0 y 0.0 2.5 density/mass ave running
|
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fix 1 flow ave/spatial 100 5 1000 z lower 1.0 y 0.0 2.5 density/mass bound y 5.0 20.0 discard yes ave running :pre
|
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|
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[NOTE:]
|
||||
|
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The fix ave/spatial command has been replaced by the more flexible
|
||||
"fix ave/chunk"_fix_ave_chunk.html and "compute
|
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chunk/atom"_compute_chunk_atom.html commands. The fix ave/spatial
|
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command will be removed from LAMMPS sometime in the summer of 2015.
|
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|
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Any fix ave/spatial command can be replaced by the two new commands.
|
||||
You simply need to split the fix ave/spatial arguments across the two
|
||||
new commands. For example, this command:
|
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|
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fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vx vz norm sample file vel.profile :pre
|
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|
||||
could be replaced by:
|
||||
|
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compute cc1 flow chunk/atom bin/1d y 0.0 1.0
|
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fix 1 flow ave/chunk 100 10 1000 cc1 vx vz norm sample file vel.profile :pre
|
||||
|
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[Description:]
|
||||
|
||||
Use one or more per-atom vectors as inputs every few timesteps, bin
|
||||
their values spatially into 1d, 2d, or 3d bins based on current atom
|
||||
coordinates, and average the bin values over longer timescales. The
|
||||
resulting bin averages can be used by other "output
|
||||
commands"_Section_howto.html#howto_15 such as "thermo_style
|
||||
custom"_thermo_style.html, and can also be written to a file.
|
||||
|
||||
The group specified with the command means only atoms within the group
|
||||
contribute to bin averages. If the {region} keyword is used, the atom
|
||||
must be in both the specified group and the specified geometric
|
||||
"region"_region.html in order to contribute to bin averages.
|
||||
|
||||
Each listed value can be an atom attribute (position, velocity, force
|
||||
component), a mass or number density, or the result of a
|
||||
"compute"_compute.html or "fix"_fix.html or the evaluation of an
|
||||
atom-style "variable"_variable.html. In the latter cases, the
|
||||
compute, fix, or variable must produce a per-atom quantity, not a
|
||||
global quantity. If you wish to time-average global quantities from a
|
||||
compute, fix, or variable, then see the "fix
|
||||
ave/time"_fix_ave_time.html command.
|
||||
|
||||
"Computes"_compute.html that produce per-atom quantities are those
|
||||
which have the word {atom} in their style name. See the doc pages for
|
||||
individual "fixes"_fix.html to determine which ones produce per-atom
|
||||
quantities. "Variables"_variable.html of style {atom} are the only
|
||||
ones that can be used with this fix since all other styles of variable
|
||||
produce global quantities.
|
||||
|
||||
The per-atom values of each input vector are binned and averaged
|
||||
independently of the per-atom values in other input vectors.
|
||||
|
||||
The size and dimensionality of the bins (1d = layers or slabs, 2d =
|
||||
pencils, 3d = boxes) are determined by the {dim}, {origin}, and
|
||||
{delta} settings and how many times they are specified (1, 2, or 3).
|
||||
See details below.
|
||||
|
||||
NOTE: This fix works by creating an array of size Nbins by Nvalues on
|
||||
each processor. Nbins is the total number of bins; Nvalues is the
|
||||
number of input values specified. Each processor loops over its
|
||||
atoms, tallying its values to the appropriate bin. Then the entire
|
||||
array is summed across all processors. This means that using a large
|
||||
number of bins (easy to do for 2d or 3d bins) will incur an overhead
|
||||
in memory and computational cost (summing across processors), so be
|
||||
careful to use reasonable numbers of bins.
|
||||
|
||||
:line
|
||||
|
||||
The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify on what
|
||||
timesteps the input values will be used to bin them and contribute to
|
||||
the average. The final averaged quantities are generated on timesteps
|
||||
that are a multiples of {Nfreq}. The average is over {Nrepeat}
|
||||
quantities, computed in the preceding portion of the simulation every
|
||||
{Nevery} timesteps. {Nfreq} must be a multiple of {Nevery} and
|
||||
{Nevery} must be non-zero even if {Nrepeat} is 1. Also, the timesteps
|
||||
contributing to the average value cannot overlap,
|
||||
i.e. Nrepeat*Nevery can not exceed Nfreq.
|
||||
|
||||
For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
|
||||
timesteps 90,92,94,96,98,100 will be used to compute the final average
|
||||
on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on
|
||||
timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time
|
||||
averaging is done; values are simply generated on timesteps
|
||||
100,200,etc.
|
||||
|
||||
:line
|
||||
|
||||
Each per-atom property is also averaged over atoms in each bin. The
|
||||
way the averaging is one across the {Nrepeat} timesteps to produce
|
||||
output on the {Nfreq} timesteps, and across multiple {Nfreq} outputs,
|
||||
is determined by the {norm} and {av} keyword settings, as discussed
|
||||
below.
|
||||
|
||||
Bins can be 1d layers or slabs, 2d pencils, or 3d boxes. This depends
|
||||
on how many times (1, 2, or 3) the {dim}, {origin}, and {delta}
|
||||
settings are specified in the fix ave/spatial command. For 2d or 3d
|
||||
bins, there is no restriction on specifying dim = x before dim = y, or
|
||||
dim = y before dim = z. Bins in a particular {dim} have a bin size in
|
||||
that dimension given by {delta}. Every Nfreq steps, when averaging is
|
||||
being performed and the per-atom property is calculated for the first
|
||||
time, the number of bins and the bin sizes and boundaries are
|
||||
computed. Thus if the simulation box changes size during a
|
||||
simulation, the number of bins and their boundaries may also change.
|
||||
In each dimension, bins are defined relative to a specified {origin},
|
||||
which may be the lower/upper edge of the simulation box in that
|
||||
dimension, or its center point, or a specified coordinate value.
|
||||
Starting at the origin, sufficient bins are created in both directions
|
||||
to completely span the bin extent in that dimension. By default the
|
||||
bin extent is the entire simulation box.
|
||||
|
||||
The {bound} keyword can be used one or more times to limit the extent
|
||||
of bin coverage in specified dimensions, i.e. to only bin a portion of
|
||||
the box. If the {lo} setting is {lower} or the {hi} setting is
|
||||
{upper}, the bin extent in that direction extends to the box boundary.
|
||||
If a numeric value is used for {lo} and/or {hi}, then the bin extent
|
||||
in the {lo} or {hi} direction extends only to that value, which is
|
||||
assumed to be inside (or at least near) the simulation box boundaries,
|
||||
though LAMMPS does not check for this.
|
||||
|
||||
On each sampling timestep, each atom is mapped to the bin it currently
|
||||
belongs to, based on its current position. Note that the group-ID and
|
||||
region keyword can exclude specific atoms from this operation, as
|
||||
discussed above. Note that between reneighboring timesteps, atoms can
|
||||
move outside the current simulation box. If the box is periodic (in
|
||||
that dimension) the atom is remapping into the periodic box for
|
||||
purposes of binning. If the box in not periodic, the atom may have
|
||||
moved outside the bounds of any bin.
|
||||
|
||||
The {discard} keyword determines what is done with any atom which is
|
||||
outside the bounds of any bin. If {discard} is set to {yes}, the atom
|
||||
will be ignored and not contribute to any bin averages. If {discard}
|
||||
is set to {no}, the atom will be counted as if it were in the first or
|
||||
last bin in that dimension. If (discard} is set to {mixed}, which is
|
||||
the default, it will only be counted in the first or last bin if bins
|
||||
extend to the box boundary in that dimension. This is the case if the
|
||||
{bound} keyword settings are {lower} and {upper}, which is the
|
||||
default. If the {bound} keyword settings are numeric values, then the
|
||||
atom will be ignored if it is outside the bounds of any bin. Note
|
||||
that in this case, it is possible that the first or last bin extends
|
||||
beyond the numeric {bounds} settings, depending on the specified
|
||||
{origin}. If this is the case, the atom is only ignored if it is
|
||||
outside the first or last bin, not if it is simply outside the numeric
|
||||
{bounds} setting.
|
||||
|
||||
For orthogonal simulation boxes, the bins are also layers, pencils, or
|
||||
boxes aligned with the xyz coordinate axes. For triclinic
|
||||
(non-orthogonal) simulation boxes, the bins are so that they are
|
||||
parallel to the tilted faces of the simulation box. See "this
|
||||
section"_Section_howto.html#howto_12 of the manual for a discussion of
|
||||
the geometry of triclinic boxes in LAMMPS. As described there, a
|
||||
tilted simulation box has edge vectors a,b,c. In that nomenclature,
|
||||
bins in the x dimension have faces with normals in the "b" cross "c"
|
||||
direction. Bins in y have faces normal to the "a" cross "c"
|
||||
direction. And bins in z have faces normal to the "a" cross "b"
|
||||
direction. Note that in order to define the size and position of
|
||||
these bins in an unambiguous fashion, the {units} option must be set
|
||||
to {reduced} when using a triclinic simulation box, as noted below.
|
||||
|
||||
:line
|
||||
|
||||
The atom attribute values (vx,vy,vz,fx,fy,fz) are self-explanatory.
|
||||
Note that other atom attributes (including atom postitions x,y,z) can
|
||||
be used as inputs to this fix by using the "compute
|
||||
property/atom"_compute_property_atom.html command and then specifying
|
||||
an input value from that compute.
|
||||
|
||||
The {density/number} value means the number density is computed in
|
||||
each bin, i.e. a weighting of 1 for each atom. The {density/mass}
|
||||
value means the mass density is computed in each bind, i.e. each atom
|
||||
is weighted by its mass. The resulting density is normalized by the
|
||||
volume of the bin so that units of number/volume or density are
|
||||
output. See the "units"_units.html command doc page for the
|
||||
definition of density for each choice of units, e.g. gram/cm^3.
|
||||
|
||||
If a value begins with "c_", a compute ID must follow which has been
|
||||
previously defined in the input script. If no bracketed integer is
|
||||
appended, the per-atom vector calculated by the compute is used. If a
|
||||
bracketed integer is appended, the Ith column of the per-atom array
|
||||
calculated by the compute is used. Users can also write code for
|
||||
their own compute styles and "add them to LAMMPS"_Section_modify.html.
|
||||
|
||||
If a value begins with "f_", a fix ID must follow which has been
|
||||
previously defined in the input script. If no bracketed integer is
|
||||
appended, the per-atom vector calculated by the fix is used. If a
|
||||
bracketed integer is appended, the Ith column of the per-atom array
|
||||
calculated by the fix is used. Note that some fixes only produce
|
||||
their values on certain timesteps, which must be compatible with
|
||||
{Nevery}, else an error results. Users can also write code for their
|
||||
own fix styles and "add them to LAMMPS"_Section_modify.html.
|
||||
|
||||
If a value begins with "v_", a variable name must follow which has
|
||||
been previously defined in the input script. Variables of style
|
||||
{atom} can reference thermodynamic keywords and various per-atom
|
||||
attributes, or invoke other computes, fixes, or variables when they
|
||||
are evaluated, so this is a very general means of generating per-atom
|
||||
quantities to spatially average.
|
||||
|
||||
:line
|
||||
|
||||
Additional optional keywords also affect the operation of this fix.
|
||||
The {region}, {bound}, and {discard} keywords were discussed above.
|
||||
|
||||
The {norm} keyword affects how averaging is done for the output
|
||||
produced every {Nfreq} timesteps. For an {all} setting, a bin
|
||||
quantity is summed over all atoms in all {Nrepeat} samples, as is the
|
||||
count of atoms in the bin. The printed value for the bin is
|
||||
Total-quantity / Total-count. In other words it is an average over
|
||||
the entire {Nfreq} timescale.
|
||||
|
||||
For a {sample} setting, the bin quantity is summed over atoms for only
|
||||
a single sample, as is the count, and a "average sample value" is
|
||||
computed, i.e. Sample-quantity / Sample-count. The printed value for
|
||||
the bin is the average of the {Nrepeat} "average sample values", In
|
||||
other words it is an average of an average.
|
||||
|
||||
The {ave} keyword determines how the bin values produced every {Nfreq}
|
||||
steps are averaged with bin values produced on previous steps that
|
||||
were multiples of {Nfreq}, before they are accessed by another output
|
||||
command or written to a file.
|
||||
|
||||
If the {ave} setting is {one}, then the bin values produced on
|
||||
timesteps that are multiples of {Nfreq} are independent of each other;
|
||||
they are output as-is without further averaging.
|
||||
|
||||
If the {ave} setting is {running}, then the bin values produced on
|
||||
timesteps that are multiples of {Nfreq} are summed and averaged in a
|
||||
cumulative sense before being output. Each output bin value is thus
|
||||
the average of the bin value produced on that timestep with all
|
||||
preceding values for the same bin. This running average begins when
|
||||
the fix is defined; it can only be restarted by deleting the fix via
|
||||
the "unfix"_unfix.html command, or re-defining the fix by
|
||||
re-specifying it.
|
||||
|
||||
If the {ave} setting is {window}, then the bin values produced on
|
||||
timesteps that are multiples of {Nfreq} are summed and averaged within
|
||||
a moving "window" of time, so that the last M values for the same bin
|
||||
are used to produce the output. E.g. if M = 3 and Nfreq = 1000, then
|
||||
the output on step 10000 will be the average of the individual bin
|
||||
values on steps 8000,9000,10000. Outputs on early steps will average
|
||||
over less than M values if they are not available.
|
||||
|
||||
The {units} keyword determines the meaning of the distance units used
|
||||
for the bin size {delta} and for {origin} and {bounds} values if they
|
||||
are coordinate value. For orthogonal simulation boxes, any of the 3
|
||||
options may be used. For non-orthogonal (triclinic) simulation boxes,
|
||||
only the {reduced} option may be used.
|
||||
|
||||
A {box} value selects standard distance units as defined by the
|
||||
"units"_units.html command, e.g. Angstroms for units = real or metal.
|
||||
A {lattice} value means the distance units are in lattice spacings.
|
||||
The "lattice"_lattice.html command must have been previously used to
|
||||
define the lattice spacing. A {reduced} value means normalized
|
||||
unitless values between 0 and 1, which represent the lower and upper
|
||||
faces of the simulation box respectively. Thus an {origin} value of
|
||||
0.5 means the center of the box in any dimension. A {delta} value of
|
||||
0.1 means 10 bins span the box in that dimension.
|
||||
|
||||
Consider a non-orthogonal box, with bins that are 1d layers or slabs
|
||||
in the x dimension. No matter how the box is tilted, an {origin} of
|
||||
0.0 means start layers at the lower "b" cross "c" plane of the
|
||||
simulation box and an {origin} of 1.0 means to start layers at the
|
||||
upper "b" cross "c" face of the box. A {delta} value of 0.1 means
|
||||
there will be 10 layers from 0.0 to 1.0, regardless of the current
|
||||
size or shape of the simulation box.
|
||||
|
||||
The {file} keyword allows a filename to be specified. Every {Nfreq}
|
||||
timesteps, a section of bin info will be written to a text file in the
|
||||
following format. A line with the timestep and number of bin is
|
||||
written. Then one line per bin is written, containing the bin ID
|
||||
(1-N), the coordinate of the center of the bin, the number of atoms
|
||||
in the bin, and one or more calculated values. The number of values
|
||||
in each line corresponds to the number of values specified in the fix
|
||||
ave/spatial command. The number of atoms and the value(s) are average
|
||||
quantities. If the value of the {units} keyword is {box} or
|
||||
{lattice}, the "coord" is printed in box units. If the value of the
|
||||
{units} keyword is {reduced}, the "coord" is printed in reduced units
|
||||
(0-1).
|
||||
|
||||
The {overwrite} keyword will continuously overwrite the output file
|
||||
with the latest output, so that it only contains one timestep worth of
|
||||
output. This option can only be used with the {ave running} setting.
|
||||
|
||||
The {title1} and {title2} and {title3} keywords allow specification of
|
||||
the strings that will be printed as the first 3 lines of the output
|
||||
file, assuming the {file} keyword was used. LAMMPS uses default
|
||||
values for each of these, so they do not need to be specified.
|
||||
|
||||
By default, these header lines are as follows:
|
||||
|
||||
# Spatial-averaged data for fix ID and group name
|
||||
# Timestep Number-of-bins
|
||||
# Bin Coord1 Coord2 Coord3 Count value1 value2 ... :pre
|
||||
|
||||
In the first line, ID and name are replaced with the fix-ID and group
|
||||
name. The second line describes the two values that are printed at
|
||||
the first of each section of output. In the third line the values are
|
||||
replaced with the appropriate fields from the fix ave/spatial command.
|
||||
The Coord2 and Coord3 entries in the third line only appear for 2d and
|
||||
3d bins respectively. For 1d bins, the word Coord1 is replaced by
|
||||
just Coord.
|
||||
|
||||
:line
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
files"_restart.html. None of the "fix_modify"_fix_modify.html options
|
||||
are relevant to this fix.
|
||||
|
||||
This fix computes a global array of values which can be accessed by
|
||||
various "output commands"_Section_howto.html#howto_15. The values can
|
||||
only be accessed on timesteps that are multiples of {Nfreq} since that
|
||||
is when averaging is performed. The global array has # of rows =
|
||||
Nbins and # of columns = Ndim+1+Nvalues, where Ndim = 1,2,3 for
|
||||
1d,2d,3d bins. The first 1 or 2 or 3 columns have the bin coordinates
|
||||
(center of the bin) in the appropriate dimensions, the next column has
|
||||
the count of atoms in that bin, and the remaining columns are the
|
||||
Nvalue quantities. When the array is accessed with an I that exceeds
|
||||
the current number of bins, than a 0.0 is returned by the fix instead
|
||||
of an error, since the number of bins can vary as a simulation runs,
|
||||
depending on the simulation box size. 2d or 3d bins are ordered so
|
||||
that the last dimension(s) vary fastest. The array values calculated
|
||||
by this fix are "intensive", since they are already normalized by the
|
||||
count of atoms in each bin.
|
||||
|
||||
No parameter of this fix can be used with the {start/stop} keywords of
|
||||
the "run"_run.html command. This fix is not invoked during "energy
|
||||
minimization"_minimize.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
When the {ave} keyword is set to {running} or {window} then the number
|
||||
of bins must remain the same during the simulation, so that the
|
||||
appropriate averaging can be done. This will be the case if the
|
||||
simulation box size doesn't change or if the {units} keyword is set to
|
||||
{reduced}.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"compute"_compute.html, "fix ave/atom"_fix_ave_atom.html, "fix
|
||||
ave/histo"_fix_ave_histo.html, "fix ave/time"_fix_ave_time.html,
|
||||
"variable"_variable.html, "fix ave/correlate"_fix_ave_correlate.html,
|
||||
"fix ave/spatial/sphere"_fix_ave_spatial_sphere.html
|
||||
|
||||
[Default:]
|
||||
|
||||
The option defaults are bound = lower and upper in all dimensions,
|
||||
discard = mixed, norm = all, ave = one, units = lattice, no file
|
||||
output, and title 1,2,3 = strings as described above.
|
||||
|
|
@ -1,324 +0,0 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
fix ave/spatial/sphere command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID ave/spatial/sphere Nevery Nrepeat Nfreq origin_x origin_y origin_z r_min r_max nbins value1 value2 ... keyword args ... :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
ave/spatial = style name of this fix command :l
|
||||
Nevery = use input values every this many timesteps :l
|
||||
Nrepeat = # of times to use input values for calculating averages :l
|
||||
Nfreq = calculate averages every this many timesteps :l
|
||||
origin_x, origin_y, origin_z = center of the sphere. can be the result of variables or computes (see below) :l
|
||||
r_min = radial distance at which binning begins :l
|
||||
r_max = radial distance at which binning ends :l
|
||||
nbins = number of spherical shells to create between r_min and r_max :l
|
||||
one or more input values can be listed :l
|
||||
value = vx, vy, vz, fx, fy, fz, density/mass, density/number, c_ID, c_ID\[I\], f_ID, f_ID\[I\], v_name :l
|
||||
vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
|
||||
density/number, density/mass = number or mass density
|
||||
c_ID = per-atom vector calculated by a compute with ID
|
||||
c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID
|
||||
f_ID = per-atom vector calculated by a fix with ID
|
||||
f_ID\[I\] = Ith column of per-atom array calculated by a fix with ID
|
||||
v_name = per-atom vector calculated by an atom-style variable with name :pre
|
||||
|
||||
zero or more keyword/arg pairs may be appended :l
|
||||
keyword = {region} or {norm} or {units} or {ave} or {file} or {overwrite} or {title1} or {title2} or {title3} :l
|
||||
{region} arg = region-ID
|
||||
region-ID = ID of region atoms must be in to contribute to spatial averaging
|
||||
{norm} arg = {all} or {sample}
|
||||
{units} arg = {box} or {lattice} or {reduced}
|
||||
{ave} args = {one} or {running} or {window M}
|
||||
one = output new average value every Nfreq steps
|
||||
running = output cumulative average of all previous Nfreq steps
|
||||
window M = output average of M most recent Nfreq steps
|
||||
{file} arg = filename
|
||||
filename = file to write results to
|
||||
{overwrite} arg = none = overwrite output file with only latest output
|
||||
{title1} arg = string
|
||||
string = text to print as 1st line of output file
|
||||
{title2} arg = string
|
||||
string = text to print as 2nd line of output file
|
||||
{title3} arg = string
|
||||
string = text to print as 3rd line of output file :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 1 all ave/spatial/sphere 10000 1 10000 0.5 0.5 0.5 0.1 0.5 5 density/number vx vy vz units reduced title1 "My output values"
|
||||
fix 1 flow ave/spatial/sphere 100 10 1000 20.0 20.0 20.0 0.0 20.0 20 vx vz norm sample file vel.profile :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Use one or more per-atom vectors as inputs every few timesteps, bin
|
||||
their values spatially into spherical shells based on current atom
|
||||
coordinates, and average the bin values over longer timescales. The
|
||||
resulting bin averages can be used by other "output
|
||||
commands"_Section_howto.html#howto_15 such as "thermo_style
|
||||
custom"_thermo_style.html, and can also be written to a file.
|
||||
|
||||
The group specified with the command means only atoms within the group
|
||||
contribute to bin averages. If the {region} keyword is used, the atom
|
||||
must be in both the group and the specified geometric
|
||||
"region"_region.html in order to contribute to bin averages.
|
||||
|
||||
Each listed value can be an atom attribute (position, velocity, force
|
||||
component), a mass or number density, or the result of a
|
||||
"compute"_compute.html or "fix"_fix.html or the evaluation of an
|
||||
atom-style "variable"_variable.html. In the latter cases, the
|
||||
compute, fix, or variable must produce a per-atom quantity, not a
|
||||
global quantity. If you wish to time-average global quantities from a
|
||||
compute, fix, or variable, then see the "fix
|
||||
ave/time"_fix_ave_time.html command.
|
||||
|
||||
"Computes"_compute.html that produce per-atom quantities are those
|
||||
which have the word {atom} in their style name. See the doc pages for
|
||||
individual "fixes"_fix.html to determine which ones produce per-atom
|
||||
quantities. "Variables"_variable.html of style {atom} are the only
|
||||
ones that can be used with this fix since all other styles of variable
|
||||
produce global quantities.
|
||||
|
||||
The per-atom values of each input vector are binned and averaged
|
||||
independently of the per-atom values in other input vectors.
|
||||
|
||||
{Nbins} specifies the number of spherical shells which will be created
|
||||
between r_min and r_max centered at (origin_x, origin_y, origin_z).
|
||||
|
||||
NOTE: This fix works by creating an array of size Nbins by Nvalues on
|
||||
each processor. Nbins is the total number of bins; Nvalues is the
|
||||
number of input values specified. Each processor loops over its
|
||||
atoms, tallying its values to the appropriate bin. Then the entire
|
||||
array is summed across all processors. This means that using a large
|
||||
number of bins will incur an overhead in memory and computational cost
|
||||
(summing across processors), so be careful to use reasonable numbers
|
||||
of bins.
|
||||
|
||||
:line
|
||||
|
||||
The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify on what
|
||||
timesteps the input values will be used to bin them and contribute to
|
||||
the average. The final averaged quantities are generated on timesteps
|
||||
that are a multiples of {Nfreq}. The average is over {Nrepeat}
|
||||
quantities, computed in the preceding portion of the simulation every
|
||||
{Nevery} timesteps. {Nfreq} must be a multiple of {Nevery} and
|
||||
{Nevery} must be non-zero even if {Nrepeat} is 1.
|
||||
Also, the timesteps
|
||||
contributing to the average value cannot overlap,
|
||||
i.e. Nrepeat*Nevery can not exceed Nfreq.
|
||||
|
||||
For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
|
||||
timesteps 90,92,94,96,98,100 will be used to compute the final average
|
||||
on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on
|
||||
timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time
|
||||
averaging is done; values are simply generated on timesteps
|
||||
100,200,etc.
|
||||
|
||||
:line
|
||||
|
||||
The {origin_x}, {origin_y}, and {origin_z} parameters may be specified
|
||||
by either a compute or a variable. This allows, for example, the
|
||||
center of the spherical bins to be attached to the center of mass of a
|
||||
group of atoms. If a variable origin is used and periodic boundary
|
||||
conditions are in effect, then the origin will be wrapped across
|
||||
periodic boundaries whenever it changes so that it is always inside
|
||||
the simulation box.
|
||||
|
||||
:line
|
||||
|
||||
The atom attribute values (vx,vy,vz,fx,fy,fz) are self-explanatory.
|
||||
Note that other atom attributes (including atom postitions x,y,z) can
|
||||
be used as inputs to this fix by using the "compute
|
||||
property/atom"_compute_property_atom.html command and then specifying
|
||||
an input value from that compute.
|
||||
|
||||
The {density/number} value means the number density is computed in
|
||||
each bin, i.e. a weighting of 1 for each atom. The {density/mass}
|
||||
value means the mass density is computed in each bin, i.e. each atom
|
||||
is weighted by its mass. The resulting density is normalized by the
|
||||
volume of the bin so that units of number/volume or density are
|
||||
output. See the "units"_units.html command doc page for the
|
||||
definition of density for each choice of units, e.g. gram/cm^3.
|
||||
The bin volume will always be calculated in box units, independent
|
||||
of the use of the {units} keyword in this command.
|
||||
|
||||
If a value begins with "c_", a compute ID must follow which has been
|
||||
previously defined in the input script. If no bracketed integer is
|
||||
appended, the per-atom vector calculated by the compute is used. If a
|
||||
bracketed integer is appended, the Ith column of the per-atom array
|
||||
calculated by the compute is used. Users can also write code for
|
||||
their own compute styles and "add them to LAMMPS"_Section_modify.html.
|
||||
|
||||
If a value begins with "f_", a fix ID must follow which has been
|
||||
previously defined in the input script. If no bracketed integer is
|
||||
appended, the per-atom vector calculated by the fix is used. If a
|
||||
bracketed integer is appended, the Ith column of the per-atom array
|
||||
calculated by the fix is used. Note that some fixes only produce
|
||||
their values on certain timesteps, which must be compatible with
|
||||
{Nevery}, else an error results. Users can also write code for their
|
||||
own fix styles and "add them to LAMMPS"_Section_modify.html.
|
||||
|
||||
If a value begins with "v_", a variable name must follow which has
|
||||
been previously defined in the input script. Variables of style
|
||||
{atom} can reference thermodynamic keywords and various per-atom
|
||||
attributes, or invoke other computes, fixes, or variables when they
|
||||
are evaluated, so this is a very general means of generating per-atom
|
||||
quantities to spatially average.
|
||||
|
||||
:line
|
||||
|
||||
Additional optional keywords also affect the operation of this fix.
|
||||
The {region} keyword was discussed above.
|
||||
|
||||
The {norm} keyword affects how averaging is done for the output
|
||||
produced every {Nfreq} timesteps. For an {all} setting, a bin
|
||||
quantity is summed over all atoms in all {Nrepeat} samples, as is the
|
||||
count of atoms in the bin. The printed value for the bin is
|
||||
Total-quantity / Total-count. In other words it is an average over
|
||||
the entire {Nfreq} timescale.
|
||||
|
||||
For a {sample} setting, the bin quantity is summed over atoms for only
|
||||
a single sample, as is the count, and a "average sample value" is
|
||||
computed, i.e. Sample-quantity / Sample-count. The printed value for
|
||||
the bin is the average of the {Nrepeat} "average sample values", In
|
||||
other words it is an average of an average.
|
||||
|
||||
The {ave} keyword determines how the bin values produced every {Nfreq}
|
||||
steps are averaged with bin values produced on previous steps that
|
||||
were multiples of {Nfreq}, before they are accessed by another output
|
||||
command or written to a file.
|
||||
|
||||
If the {ave} setting is {one}, then the bin values produced on
|
||||
timesteps that are multiples of {Nfreq} are independent of each other;
|
||||
they are output as-is without further averaging.
|
||||
|
||||
If the {ave} setting is {running}, then the bin values produced on
|
||||
timesteps that are multiples of {Nfreq} are summed and averaged in a
|
||||
cumulative sense before being output. Each output bin value is thus
|
||||
the average of the bin value produced on that timestep with all
|
||||
preceding values for the same bin. This running average begins when
|
||||
the fix is defined; it can only be restarted by deleting the fix via
|
||||
the "unfix"_unfix.html command, or re-defining the fix by
|
||||
re-specifying it.
|
||||
|
||||
If the {ave} setting is {window}, then the bin values produced on
|
||||
timesteps that are multiples of {Nfreq} are summed and averaged within
|
||||
a moving "window" of time, so that the last M values for the same bin
|
||||
are used to produce the output. E.g. if M = 3 and Nfreq = 1000, then
|
||||
the output on step 10000 will be the average of the individual bin
|
||||
values on steps 8000,9000,10000. Outputs on early steps will average
|
||||
over less than M values if they are not available.
|
||||
|
||||
The {units} keyword determines the meaning of the distance units used
|
||||
for the sphere origin and the two radial lengths. For orthogonal
|
||||
simulation boxes, any of the 3 options may be used. For
|
||||
non-orthogonal (triclinic) simulation boxes, only the {reduced} option
|
||||
may be used.
|
||||
|
||||
A {box} value selects standard distance units as defined by the
|
||||
"units"_units.html command, e.g. Angstroms for units = real or metal.
|
||||
A {lattice} value means the distance units are in lattice spacings.
|
||||
The "lattice"_lattice.html command must have been previously used to
|
||||
define the lattice spacing.
|
||||
|
||||
NOTE: The {lattice} style may only be used if the lattice spacing is
|
||||
the same in each direction.
|
||||
|
||||
A {reduced} value means normalized unitless values between 0 and 1,
|
||||
which represent the lower and upper faces of the simulation box
|
||||
respectively. Thus an {origin} value of 0.5 means the center of the
|
||||
box in any dimension.
|
||||
|
||||
The {file} keyword allows a filename to be specified. Every {Nfreq}
|
||||
timesteps, a section of bin info will be written to a text file in the
|
||||
following format. A line with the timestep and number of bin is
|
||||
written. Then one line per bin is written, containing the bin ID
|
||||
(1-N), the coordinate of the center of the bin, the number of atoms in
|
||||
the bin, and one or more calculated values. The number of values in
|
||||
each line corresponds to the number of values specified in the fix
|
||||
ave/spatial command. The number of atoms and the value(s) are average
|
||||
quantities. If the value of the {units} keyword is {box} or
|
||||
{lattice}, the "coord" is printed in box units. If the value of the
|
||||
{units} keyword is {reduced}, the "coord" is printed in reduced units
|
||||
(0-1).
|
||||
|
||||
The {overwrite} keyword will continuously overwrite the output file
|
||||
with the latest output, so that it only contains one timestep worth of
|
||||
output. This option can only be used with the {ave running} setting.
|
||||
|
||||
The {title1} and {title2} and {title3} keywords allow specification of
|
||||
the strings that will be printed as the first 3 lines of the output
|
||||
file, assuming the {file} keyword was used. LAMMPS uses default
|
||||
values for each of these, so they do not need to be specified.
|
||||
|
||||
By default, these header lines are as follows:
|
||||
|
||||
# Spatial-averaged data for fix ID and group name
|
||||
# Timestep Number-of-bins
|
||||
# Bin r Count value1 value2 ... :pre
|
||||
|
||||
In the first line, ID and name are replaced with the fix-ID and group
|
||||
name. The second line describes the two values that are printed at
|
||||
the first of each section of output. In the third line the values are
|
||||
replaced with the appropriate fields from the fix ave/spatial command.
|
||||
The Coord2 and Coord3 entries in the third line only appear for 2d and
|
||||
3d bins respectively. For 1d bins, the word Coord1 is replaced by
|
||||
just Coord.
|
||||
|
||||
:line
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
files"_restart.html. None of the "fix_modify"_fix_modify.html options
|
||||
are relevant to this fix.
|
||||
|
||||
This fix computes a global array of values which can be accessed by
|
||||
various "output commands"_Section_howto.html#howto_15. The values can
|
||||
only be accessed on timesteps that are multiples of {Nfreq} since that
|
||||
is when averaging is performed. The global array has # of rows =
|
||||
Nbins and # of columns = 2+Nvalues. The first column contains the
|
||||
radius at the center of the shell. For units {reduced}, this is in
|
||||
reduced units, while for units {box} and {lattice} this is in box
|
||||
units. The next column has the count of atoms in that bin, and the
|
||||
remaining columns are the Nvalue quantities. When the array is
|
||||
accessed with an I that exceeds the current number of bins, than a 0.0
|
||||
is returned by the fix instead of an error. The array values
|
||||
calculated by this fix are "intensive", since they are already
|
||||
normalized by the count of atoms in each bin.
|
||||
|
||||
No parameter of this fix can be used with the {start/stop} keywords of
|
||||
the "run"_run.html command. This fix is not invoked during "energy
|
||||
minimization"_minimize.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
When the {ave} keyword is set to {running} or {window} then the number
|
||||
of bins must remain the same during the simulation, so that the
|
||||
appropriate averaging can be done. This will be the case if the
|
||||
simulation box size doesn't change or if the {units} keyword is set to
|
||||
{reduced}.
|
||||
|
||||
This style is part of the USER-MISC package. It is only enabled if
|
||||
LAMMPS is build with that package. See the "Making of
|
||||
LAMMPS"_Section_start.html#3 section for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"compute"_compute.html, "fix ave/atom"_fix_ave_atom.html, "fix
|
||||
ave/histo"_fix_ave_histo.html, "fix ave/time"_fix_ave_time.html,
|
||||
"variable"_variable.html, "fix ave/correlate"_fix_ave_correlate.html,
|
||||
"fix ave/spatial"_fix_ave_spatial.html,
|
||||
|
||||
[Default:]
|
||||
|
||||
The option defaults are norm = all, ave = one, units = lattice, no
|
||||
file output, and title 1,2,3 = strings as described above.
|
||||
|
|
@ -79,7 +79,7 @@ Each listed value can be the result of a "compute"_compute.html or
|
|||
must produce a global quantity, not a per-atom or local quantity. If
|
||||
you wish to spatial- or time-average or histogram per-atom quantities
|
||||
from a compute, fix, or variable, then see the "fix
|
||||
ave/spatial"_fix_ave_spatial.html, "fix ave/atom"_fix_ave_atom.html,
|
||||
ave/chunk"_fix_ave_chunk.html, "fix ave/atom"_fix_ave_atom.html,
|
||||
or "fix ave/histo"_fix_ave_histo.html commands. If you wish to sum a
|
||||
per-atom quantity into a single global quantity, see the "compute
|
||||
reduce"_compute_reduce.html command.
|
||||
|
|
@ -322,7 +322,7 @@ minimization"_minimize.html.
|
|||
[Related commands:]
|
||||
|
||||
"compute"_compute.html, "fix ave/atom"_fix_ave_atom.html, "fix
|
||||
ave/spatial"_fix_ave_spatial.html, "fix ave/histo"_fix_ave_histo.html,
|
||||
ave/chunk"_fix_ave_chunk.html, "fix ave/histo"_fix_ave_histo.html,
|
||||
"variable"_variable.html, "fix ave/correlate"_fix_ave_correlate.html,
|
||||
|
||||
[Default:]
|
||||
|
|
|
|||
|
|
@ -496,7 +496,7 @@ box. E.g. for a shearing system the box deformation velocity may vary
|
|||
from 0 at the bottom to 10 at the top of the box. But the stream
|
||||
velocity profile of the atoms may vary from -5 at the bottom to +5 at
|
||||
the top. You can monitor these effects using the "fix
|
||||
ave/spatial"_fix_ave_spatial.html, "compute
|
||||
ave/chunk"_fix_ave_chunk.html, "compute
|
||||
temp/deform"_compute_temp_deform.html, and "compute
|
||||
temp/profile"_compute_temp_profile.html commands. One way to induce
|
||||
atoms to stream consistent with the box deformation is to give them an
|
||||
|
|
|
|||
|
|
@ -63,8 +63,8 @@ temperature profile (assuming z = edim) to the file tmp.profile:
|
|||
|
||||
compute ke all ke/atom
|
||||
variable temp atom c_ke/1.5
|
||||
fix 3 all ave/spatial 10 100 1000 z lower 0.05 v_temp &
|
||||
file tmp.profile units reduced :pre
|
||||
compute layers all chunk/atom bin/1d z lower 0.05 units reduced
|
||||
fix 3 all ave/chunk 10 100 1000 layers v_temp file tmp.profile :pre
|
||||
|
||||
Note that by default, Nswap = 1, though this can be changed by the
|
||||
optional {swap} keyword. Setting this parameter appropriately, in
|
||||
|
|
@ -145,10 +145,9 @@ bewteen solvent particles.
|
|||
|
||||
[Related commands:]
|
||||
|
||||
"fix ehex"_fix_ehex.html, "fix heat"_fix_heat.html,
|
||||
"fix ave/spatial"_fix_ave_spatial.html, "fix
|
||||
viscosity"_fix_viscosity.html, "compute
|
||||
heat/flux"_compute_heat_flux.html
|
||||
"fix ehex"_fix_ehex.html, "fix heat"_fix_heat.html, "fix
|
||||
ave/chunk"_fix_ave_chunk.html, "fix viscosity"_fix_viscosity.html,
|
||||
"compute heat/flux"_compute_heat_flux.html
|
||||
|
||||
[Default:]
|
||||
|
||||
|
|
|
|||
|
|
@ -60,8 +60,8 @@ directions. Over time, this induces a shear velocity profile in the
|
|||
system which can be measured using commands such as the following,
|
||||
which writes the profile to the file tmp.profile:
|
||||
|
||||
fix f1 all ave/spatial 100 10 1000 z lower 0.05 vx &
|
||||
file tmp.profile units reduced :pre
|
||||
compute layers all chunk/atom z lower 0.05 units reduced
|
||||
fix f1 all ave/chunk 100 10 1000 layers vx file tmp.profile :pre
|
||||
|
||||
Note that by default, Nswap = 1 and vtarget = INF, though this can be
|
||||
changed by the optional {swap} and {vtarget} keywords. When vtarget =
|
||||
|
|
@ -152,7 +152,7 @@ solvent particles.
|
|||
|
||||
[Related commands:]
|
||||
|
||||
"fix ave/spatial"_fix_ave_spatial.html, "fix
|
||||
"fix ave/chunk"_fix_ave_chunk.html, "fix
|
||||
thermal/conductivity"_fix_thermal_conductivity.html
|
||||
|
||||
[Default:]
|
||||
|
|
|
|||
|
|
@ -295,9 +295,9 @@ for dephasing.
|
|||
|
||||
This command cannot be used when any fixes are defined that keep track
|
||||
of elapsed time to perform time-dependent operations. Examples
|
||||
include the "ave" fixes such as "fix
|
||||
ave/spatial"_fix_ave_spatial.html. Also "fix
|
||||
dt/reset"_fix_dt_reset.html and "fix deposit"_fix_deposit.html.
|
||||
include the "ave" fixes such as "fix ave/chunk"_fix_ave_chunk.html.
|
||||
Also "fix dt/reset"_fix_dt_reset.html and "fix
|
||||
deposit"_fix_deposit.html.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
|
|
|
|||
|
|
@ -284,9 +284,9 @@ restart, but "fix langevin"_fix_langevin.html will not.
|
|||
|
||||
This command cannot be used when any fixes are defined that keep track
|
||||
of elapsed time to perform time-dependent operations. Examples
|
||||
include the "ave" fixes such as "fix
|
||||
ave/spatial"_fix_ave_spatial.html. Also "fix
|
||||
dt/reset"_fix_dt_reset.html and "fix deposit"_fix_deposit.html.
|
||||
include the "ave" fixes such as "fix ave/chunk"_fix_ave_chunk.html.
|
||||
Also "fix dt/reset"_fix_dt_reset.html and "fix
|
||||
deposit"_fix_deposit.html.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
|
|
|
|||
|
|
@ -1096,7 +1096,7 @@ variable formula.
|
|||
|
||||
Referencing a variable with a leading "v_" is an optional or required
|
||||
kind of argument for some commands (e.g. the "fix
|
||||
ave/spatial"_fix_ave_spatial.html or "dump custom"_dump.html or
|
||||
ave/chunk"_fix_ave_chunk.html or "dump custom"_dump.html or
|
||||
"thermo_style"_thermo_style.html commands) if you wish it to evaluate
|
||||
a variable periodically during a run. It can also be used in a
|
||||
variable formula if you wish to reference a second variable. The
|
||||
|
|
|
|||
Loading…
Reference in New Issue