From 8fa54096d38f2ae3c18fa301ab6c20f11231a9f7 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 31 May 2016 14:48:46 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15069 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/src/Section_commands.txt | 2 - doc/src/change_box.txt | 12 +- doc/src/compute.txt | 13 +- doc/src/compute_property_atom.txt | 4 +- doc/src/compute_temp_deform.txt | 2 +- doc/src/fix.txt | 10 +- doc/src/fix_ave_atom.txt | 4 +- doc/src/fix_ave_chunk.txt | 4 +- doc/src/fix_ave_correlate.txt | 10 +- doc/src/fix_ave_histo.txt | 2 +- doc/src/fix_ave_spatial.txt | 418 --------------------------- doc/src/fix_ave_spatial_sphere.txt | 324 --------------------- doc/src/fix_ave_time.txt | 4 +- doc/src/fix_deform.txt | 2 +- doc/src/fix_thermal_conductivity.txt | 11 +- doc/src/fix_viscosity.txt | 6 +- doc/src/prd.txt | 6 +- doc/src/tad.txt | 6 +- doc/src/variable.txt | 2 +- 19 files changed, 47 insertions(+), 795 deletions(-) delete mode 100644 doc/src/fix_ave_spatial.txt delete mode 100644 doc/src/fix_ave_spatial_sphere.txt diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index a67f39c8e8..e02fd934cc 100644 --- a/doc/src/Section_commands.txt +++ b/doc/src/Section_commands.txt @@ -495,7 +495,6 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "ave/correlate"_fix_ave_correlate.html, "ave/histo"_fix_ave_histo.html, "ave/histo/weight"_fix_ave_histo.html, -"ave/spatial"_fix_ave_spatial.html, "ave/time"_fix_ave_time.html, "balance"_fix_balance.html, "bond/break"_fix_bond_break.html, @@ -613,7 +612,6 @@ package"_Section_start.html#start_3. "addtorque"_fix_addtorque.html, "atc"_fix_atc.html, "ave/correlate/long"_fix_ave_correlate_long.html, -"ave/spatial/sphere"_fix_ave_spatial_sphere.html, "colvars"_fix_colvars.html, "drude"_fix_drude.html, "drude/transform/direct"_fix_drude_transform.html, diff --git a/doc/src/change_box.txt b/doc/src/change_box.txt index 7fc6198232..15111fec08 100644 --- a/doc/src/change_box.txt +++ b/doc/src/change_box.txt @@ -315,12 +315,12 @@ been previously used to define the lattice spacing. If you use the {ortho} or {triclinic} keywords, then at the point in the input script when this command is issued, no "dumps"_dump.html can -be active, nor can a "fix ave/spatial"_fix_ave_spatial.html or "fix -deform"_fix_deform.html be active. This is because these commands -test whether the simulation box is orthogonal when they are first -issued. Note that these commands can be used in your script before a -change_box command is issued, so long as an "undump"_undump.html or -"unfix"_unfix.html command is also used to turn them off. +be active, nor can a "fix deform"_fix_deform.html be active. This is +because these commands test whether the simulation box is orthogonal +when they are first issued. Note that these commands can be used in +your script before a change_box command is issued, so long as an +"undump"_undump.html or "unfix"_unfix.html command is also used to +turn them off. [Related commands:] diff --git a/doc/src/compute.txt b/doc/src/compute.txt index b847985bf7..3da2143411 100644 --- a/doc/src/compute.txt +++ b/doc/src/compute.txt @@ -99,11 +99,10 @@ custom"_thermo_style.html or "fix ave/time"_fix_ave_time.html command. Or the values can be referenced in a "variable equal"_variable.html or "variable atom"_variable.html command. :l -Per-atom values can be output via the "dump custom"_dump.html command -or the "fix ave/spatial"_fix_ave_spatial.html command. Or they can be -time-averaged via the "fix ave/atom"_fix_ave_atom.html command or -reduced by the "compute reduce"_compute_reduce.html command. Or the -per-atom values can be referenced in an "atom-style +Per-atom values can be output via the "dump custom"_dump.html command. +Or they can be time-averaged via the "fix ave/atom"_fix_ave_atom.html +command or reduced by the "compute reduce"_compute_reduce.html +command. Or the per-atom values can be referenced in an "atom-style variable"_variable.html. :l Local values can be reduced by the "compute @@ -255,7 +254,7 @@ section of "this page"_Section_commands.html#cmd_5. [Related commands:] "uncompute"_uncompute.html, "compute_modify"_compute_modify.html, "fix -ave/atom"_fix_ave_atom.html, "fix ave/spatial"_fix_ave_spatial.html, -"fix ave/time"_fix_ave_time.html, "fix ave/histo"_fix_ave_histo.html +ave/atom"_fix_ave_atom.html, "fix ave/time"_fix_ave_time.html, "fix +ave/histo"_fix_ave_histo.html [Default:] none diff --git a/doc/src/compute_property_atom.txt b/doc/src/compute_property_atom.txt index 9b7483fd8d..6fe4c79b37 100644 --- a/doc/src/compute_property_atom.txt +++ b/doc/src/compute_property_atom.txt @@ -91,7 +91,7 @@ in the group. This is useful so that the values can be used by other "output commands"_Section_howto.html#howto_15 that take computes as inputs. See for example, the "compute reduce"_compute_reduce.html, "fix ave/atom"_fix_ave_atom.html, "fix ave/histo"_fix_ave_histo.html, -"fix ave/spatial"_fix_ave_spatial.html, and "atom-style +"fix ave/chunk"_fix_ave_chunk.html, and "atom-style variable"_variable.html commands. The list of possible attributes is the same as that used by the "dump @@ -157,7 +157,7 @@ units for q, etc. [Related commands:] "dump custom"_dump.html, "compute reduce"_compute_reduce.html, "fix -ave/atom"_fix_ave_atom.html, "fix ave/spatial"_fix_ave_spatial.html, +ave/atom"_fix_ave_atom.html, "fix ave/chunk"_fix_ave_chunk.html, "fix property/atom"_fix_property_atom.html [Default:] none diff --git a/doc/src/compute_temp_deform.txt b/doc/src/compute_temp_deform.txt index ed7da650e0..168b0b3880 100644 --- a/doc/src/compute_temp_deform.txt +++ b/doc/src/compute_temp_deform.txt @@ -88,7 +88,7 @@ matches the box deformation. If not, then the compute will subtract off an incorrect stream velocity, yielding a bogus thermal temperature. You should NOT assume that your atoms are streaming at the same rate the box is deforming. Rather, you should monitor their -velocity profile, e.g. via the "fix ave/spatial"_fix_ave_spatial.html +velocity profile, e.g. via the "fix ave/chunk"_fix_ave_chunk.html command. And you can compare the results of this compute to "compute temp/profile"_compute_temp_profile.html, which actually calculates the stream profile before subtracting it. If the two computes do not give diff --git a/doc/src/fix.txt b/doc/src/fix.txt index 0f65677b58..577d2b1f2e 100644 --- a/doc/src/fix.txt +++ b/doc/src/fix.txt @@ -122,11 +122,10 @@ custom"_thermo_style.html or "fix ave/time"_fix_ave_time.html command. Or the values can be referenced in a "variable equal"_variable.html or "variable atom"_variable.html command. :ulb,l -Per-atom values can be output via the "dump custom"_dump.html command -or the "fix ave/spatial"_fix_ave_spatial.html command. Or they can be -time-averaged via the "fix ave/atom"_fix_ave_atom.html command or -reduced by the "compute reduce"_compute_reduce.html command. Or the -per-atom values can be referenced in an "atom-style +Per-atom values can be output via the "dump custom"_dump.html command. +Or they can be time-averaged via the "fix ave/atom"_fix_ave_atom.html +command or reduced by the "compute reduce"_compute_reduce.html +command. Or the per-atom values can be referenced in an "atom-style variable"_variable.html. :l Local values can be reduced by the "compute @@ -171,7 +170,6 @@ of "this page"_Section_commands.html#cmd_5. "ave/chunk"_fix_ave_chunk.html - compute per-chunk time-averaged quantities "ave/correlate"_fix_ave_correlate.html - compute/output time correlations "ave/histo"_fix_ave_histo.html - compute/output time-averaged histograms -"ave/spatial"_fix_ave_spatial.html - compute/output time-averaged per-atom quantities by layer "ave/time"_fix_ave_time.html - compute/output global time-averaged quantities "balance"_fix_balance.html - perform dynamic load-balancing "bond/break"_fix_bond_break.html - break bonds on the fly diff --git a/doc/src/fix_ave_atom.txt b/doc/src/fix_ave_atom.txt index af38f3a1e0..1d5053d37b 100644 --- a/doc/src/fix_ave_atom.txt +++ b/doc/src/fix_ave_atom.txt @@ -38,7 +38,7 @@ Use one or more per-atom vectors as inputs every few timesteps, and average them atom by atom over longer timescales. The resulting per-atom averages can be used by other "output commands"_Section_howto.html#howto_15 such as the "fix -ave/spatial"_fix_ave_spatial.html or "dump custom"_dump.html commands. +ave/chunk"_fix_ave_chunk.html or "dump custom"_dump.html commands. The group specified with the command means only atoms within the group have their averages computed. Results are set to 0.0 for atoms not in @@ -147,7 +147,7 @@ minimization"_minimize.html. [Related commands:] "compute"_compute.html, "fix ave/histo"_fix_ave_histo.html, "fix -ave/spatial"_fix_ave_spatial.html, "fix ave/time"_fix_ave_time.html, +ave/chunk"_fix_ave_chunk.html, "fix ave/time"_fix_ave_time.html, "variable"_variable.html, [Default:] none diff --git a/doc/src/fix_ave_chunk.txt b/doc/src/fix_ave_chunk.txt index fd31369d2a..0ebbafd6ca 100644 --- a/doc/src/fix_ave_chunk.txt +++ b/doc/src/fix_ave_chunk.txt @@ -67,8 +67,8 @@ fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running :pre [NOTE:] -If you are trying to replace an older fix ave/spatial command with the -newer, more flexible fix ave/chunk and "compute +If you are trying to replace a deprectated fix ave/spatial command +with the newer, more flexible fix ave/chunk and "compute chunk/atom"_compute_chunk_atom.html commands, you simply need to split the fix ave/spatial arguments across the two new commands. For example, this command: diff --git a/doc/src/fix_ave_correlate.txt b/doc/src/fix_ave_correlate.txt index 2394185b5d..ae785b4fc5 100644 --- a/doc/src/fix_ave_correlate.txt +++ b/doc/src/fix_ave_correlate.txt @@ -83,10 +83,10 @@ 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, -or "fix ave/histo"_fix_ave_histo.html commands. If you wish to -convert a per-atom quantity into a single global value, see the -"compute reduce"_compute_reduce.html command. +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 convert a +per-atom quantity into a single global value, see the "compute +reduce"_compute_reduce.html command. "Computes"_compute.html that produce global quantities are those which do not have the word {atom} in their style name. Only a few @@ -332,7 +332,7 @@ minimization"_minimize.html. "fix ave/correlate/long"_fix_ave_correlate_long.html, "compute"_compute.html, "fix ave/time"_fix_ave_time.html, "fix -ave/atom"_fix_ave_atom.html, "fix ave/spatial"_fix_ave_spatial.html, +ave/atom"_fix_ave_atom.html, "fix ave/chunk"_fix_ave_chunk.html, "fix ave/histo"_fix_ave_histo.html, "variable"_variable.html [Default:] none diff --git a/doc/src/fix_ave_histo.txt b/doc/src/fix_ave_histo.txt index 58b234d363..3d287d4fe4 100644 --- a/doc/src/fix_ave_histo.txt +++ b/doc/src/fix_ave_histo.txt @@ -331,7 +331,7 @@ minimization"_minimize.html. [Related commands:] "compute"_compute.html, "fix ave/atom"_fix_ave_atom.html, "fix -ave/spatial"_fix_ave_spatial.html, "fix ave/time"_fix_ave_time.html, +ave/chunk"_fix_ave_chunk.html, "fix ave/time"_fix_ave_time.html, "variable"_variable.html, "fix ave/correlate"_fix_ave_correlate.html, [Default:] none diff --git a/doc/src/fix_ave_spatial.txt b/doc/src/fix_ave_spatial.txt deleted file mode 100644 index 12b452cd56..0000000000 --- a/doc/src/fix_ave_spatial.txt +++ /dev/null @@ -1,418 +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 command :h3 - -[Syntax:] - -fix ID group-ID ave/spatial Nevery Nrepeat Nfreq dim origin delta ... 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 -dim, origin, delta can be repeated 1, 2, or 3 times for 1d, 2d, or 3d bins :l - dim = {x} or {y} or {z} - origin = {lower} or {center} or {upper} or coordinate value (distance units) - delta = thickness of spatial bins in dim (distance units) :pre -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 {bound} or {discard} or {norm} or {ave} or {units} or {file} or {overwrite} or {title1} or {title2} or {title3} :l - {region} arg = region-ID - {bound} args = x/y/z lo hi - x/y/z = {x} or {y} or {z} to bound bins in this dimension - lo = {lower} or coordinate value (distance units) - hi = {upper} or coordinate value (distance units) - {discard} arg = {mixed} or {no} or {yes} - mixed = discard atoms outside bins only if bin bounds are explicitly set - no = always keep out-of-bounds atoms - yes = always discard out-of-bounds atoms - {norm} arg = {all} or {sample} - region-ID = ID of region atoms must be in to contribute to spatial averaging - {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 - {units} arg = {box} or {lattice} or {reduced} - {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 10000 1 10000 z lower 0.02 c_myCentro units reduced & - title1 "My output values" -fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vx vz norm sample file vel.profile -fix 1 flow ave/spatial 100 5 1000 z lower 1.0 y 0.0 2.5 density/mass ave running -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 - -[NOTE:] - - The fix ave/spatial command has been replaced by the more flexible -"fix ave/chunk"_fix_ave_chunk.html and "compute -chunk/atom"_compute_chunk_atom.html commands. The fix ave/spatial -command will be removed from LAMMPS sometime in the summer of 2015. - -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: - -fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vx vz norm sample file vel.profile :pre - -could be replaced by: - -compute cc1 flow chunk/atom bin/1d y 0.0 1.0 -fix 1 flow ave/chunk 100 10 1000 cc1 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 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. diff --git a/doc/src/fix_ave_spatial_sphere.txt b/doc/src/fix_ave_spatial_sphere.txt deleted file mode 100644 index 8223e7fd5b..0000000000 --- a/doc/src/fix_ave_spatial_sphere.txt +++ /dev/null @@ -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. diff --git a/doc/src/fix_ave_time.txt b/doc/src/fix_ave_time.txt index 386bbcf6a0..7eca1abe6d 100644 --- a/doc/src/fix_ave_time.txt +++ b/doc/src/fix_ave_time.txt @@ -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:] diff --git a/doc/src/fix_deform.txt b/doc/src/fix_deform.txt index 1d786cc322..e2cbe14868 100644 --- a/doc/src/fix_deform.txt +++ b/doc/src/fix_deform.txt @@ -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 diff --git a/doc/src/fix_thermal_conductivity.txt b/doc/src/fix_thermal_conductivity.txt index 307bb9982a..05984b7e3f 100644 --- a/doc/src/fix_thermal_conductivity.txt +++ b/doc/src/fix_thermal_conductivity.txt @@ -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:] diff --git a/doc/src/fix_viscosity.txt b/doc/src/fix_viscosity.txt index 4b9c8174b0..87cc9618e4 100644 --- a/doc/src/fix_viscosity.txt +++ b/doc/src/fix_viscosity.txt @@ -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:] diff --git a/doc/src/prd.txt b/doc/src/prd.txt index b4f5184e1d..484e36004c 100644 --- a/doc/src/prd.txt +++ b/doc/src/prd.txt @@ -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:] diff --git a/doc/src/tad.txt b/doc/src/tad.txt index 6a291d181d..8e93b93c3b 100644 --- a/doc/src/tad.txt +++ b/doc/src/tad.txt @@ -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:] diff --git a/doc/src/variable.txt b/doc/src/variable.txt index 408e4beda9..c84dc8df99 100644 --- a/doc/src/variable.txt +++ b/doc/src/variable.txt @@ -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