- As input to the fix ave/time command, which can +write the values to a file and optionally time average them.
- As input to the fix ave/histo command to histogram values across chunks. E.g. a histogram of cluster sizes or @@ -2266,7 +2276,7 @@ largest cluster or fastest diffusing molecule.
Example calculations with chunks
-Here are chunk commands that can be used to calculate various +
Here are eaxmples using chunk commands to calculate various properties:
(1) Mimic the deprecated fix ave/spatial command, to average atom diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt index 13274c2fe5..4db7f4da7d 100644 --- a/doc/Section_howto.txt +++ b/doc/Section_howto.txt @@ -2142,37 +2142,47 @@ and thus extract D. 6.23 Using chunks to calculate system properties :link(howto_23),h4 -In LAMMPS, chunks are collections of atoms defined by a "compute -chunk/atom"_compute_chunk_atom.html command, which assigns each atom -to a chunk (or to no chunk at all). The per-atom chunk assignments -can be used as input to two other kinds of commands, to calculate -various properties of a system: +In LAMMS, "chunks" are collections of atoms, as defined by the +"compute chunk/atom"_compute_chunk_atom.html command, which assigns +each atom to a chunk ID (or to no chunk at all). The number of chunks +and the assignment of chunk IDs to atoms can be static or change over +time. Examples of "chunks" are molecules or spatial bins or atoms +with similar values (e.g. coordination number or potential energy). + +The per-atom chunk IDs can be used as input to two other kinds of +commands, to calculate various properties of a system: "fix ave/chunk"_fix_ave_chunk.html -a variety of "compute */chunk"_compute.html commands :ul +any of the "compute */chunk"_compute.html commands :ul Here, each of the 3 kinds of chunk-related commands is briefly -overviewed, and some examples given of how to compute -different properties with chunk commands. +overviewed. Then some examples are given of how to compute different +properties with chunk commands. "Compute chunk/atom"_compute_chunk_atom.html command :h5 -This compute assigns atoms to chunks of various styles. Only atoms in -the specified group and optional specified region are assigned to a -chunk. Here is a list of possible chunk definitions: +This compute can assign atoms to chunks of various styles. Only atoms +in the specified group and optional specified region are assigned to a +chunk. Here are some possible chunk definitions: atoms in same molecule | chunk ID = molecule ID | -atoms with same atom type -| chunk ID = atom type | +atoms of same atom type | chunk ID = atom type | all atoms with same atom property (charge, radius, etc) | chunk ID = output of compute property/atom | -atoms in same cluster | chunk ID = output of compute cluster/atom command | +atoms in same cluster | chunk ID = output of "compute cluster/atom"_compute_cluster_atom.html command | atoms in same spatial bin | chunk ID = bin ID | -atoms in same rigid body | chunk ID = ID of an atom in the body | -all atoms with same local defect structure | chunk ID = output of compute centro/atom or coord/atom command :tb(s=|,c=2) +atoms in same rigid body | chunk ID = molecule ID used to define rigid bodies | +atoms with similar potential energy | chunk ID = output of "compute pe/atom"_compute_pe_atom.html | +atoms with same local defect structure | chunk ID = output of "compute centro/atom"_compute_centro_atom.html or "compute coord/atom"_compute_coord_atom.html command :tb(s=|,c=2) + +Note that chunk IDs are integer values, so for atom properties or +computes that produce a floating point value, they will be truncated +to an integer. You could also use the compute in a variable that +scales the floating point value to spread it across multiple intergers. Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins = pencils, 3d bins = boxes, spherical bins, cylindrical bins. -This compute also calculates the number of chunks {Nchunk} which is +This compute also calculates the number of chunks {Nchunk}, which is used by other commands to tally per-chunk data. {Nchunk} can be a static value or change over time (e.g. the number of clusters). The chunk ID for an individual atom can also be static (e.g. a molecule @@ -2182,7 +2192,7 @@ Note that this compute allows the per-atom output of other "computes"_compute.html, "fixes"_fix.html, and "variables"_variable.html to be used to define chunk IDs for each atom. This means you can write your own compute or fix to output a -per-atom quantity to use as chunk ID; See +per-atom quantity to use as chunk ID. See "Section_modify"_Section_modify.html of the documentation for how to do this. You can also define a "per-atom variable"_variable.html in the input script that uses a formula to generate a chunk ID for each @@ -2191,55 +2201,55 @@ atom. "Fix ave/chunk"_fix_ave_chunk_atom.html command :h5 This fix takes the ID of a "compute -chunk/atom"_compute_chunk_atom.html command as input. For each chunk +chunk/atom"_compute_chunk_atom.html command as input. For each chunk, it then sums one or more specified per-atom values over the atoms in each chunk. The per-atom values can be any atom property, such as -force, charge, potential energy, kinetic energy, stress. Additional -keywords are allowed for per-chunk properties like density and -temperature. More generally any per-atom value generated by other -"computes"_compute.html, "fixes"_fix.html, and "per-atom +velocity, force, charge, potential energy, kinetic energy, stress, +etc. Additional keywords are defined for per-chunk properties like +density and temperature. More generally any per-atom value generated +by other "computes"_compute.html, "fixes"_fix.html, and "per-atom variables"_variable.html, can be summed over atoms in each chunk. Similar to other averaging fixes, this fix allows the summed per-chunk values to be time-averaged in various ways, and output to a file. The fix produces a global array as output with one row of values per -chunk. Global arrays or columns thereof can be used as input for -other commands, as described in the following section. +chunk. Compute */chunk commands :h5 -Currently the following computes operate on chunks: +Currently the following computes operate on chunks of atoms to produce +per-chunk values. "compute com/chunk"_compute_com_chunk.html "compute gyration/chunk"_compute_gyration_chunk.html "compute inertia/chunk"_compute_inertia_chunk.html "compute msd/chunk"_compute_msd_chunk.html "compute property/chunk"_compute_property_chunk.html +"compute temp/chunk"_compute_temp_chunk.html +"compute torque/chunk"_compute_vcm_chunk.html "compute vcm/chunk"_compute_vcm_chunk.html :ul They each take the ID of a "compute chunk/atom"_compute_chunk_atom.html command as input. As their names indicate, they calculate the center-of-mass, radius of gyration, -moments of inertia, mean-squared displacement, and velocity of -center-of-mass for each chunk of atoms. The "compute -property/chunk"_compute_property_chunk.html command can be tally the +moments of inertia, mean-squared displacement, temperature, torque, +and velocity of center-of-mass for each chunk of atoms. The "compute +property/chunk"_compute_property_chunk.html command can tally the count of atoms in each chunk and extract other per-chunk properties. The reason these various calculations are not part of the "fix ave/chunk command"_fix_ave_chunk.html, is that each requires a more complicated operation than simply summing and averaging over per-atom -values in each chunk. Most of them require calculation of a center of -mass, which requires summing mass*position over the atoms and dividing -by summed mass. +values in each chunk. For example, many of them require calculation +of a center of mass, which requires summing mass*position over the +atoms and then dividing by summed mass. All of these computes produce a global vector or global array as -output, wih one or more values per chunk. Global vectors or arrays -can be used as input for other commands, e.g. +output, wih one or more values per chunk. They can be used +in various ways: -As input to the "fix ave/time"_fix_ave_time.html command, so the -per-chunk values output to a file it creates. The "fix -ave/time"_fix_ave_time.html command can also average the values for -each chunk over time if desired. :ulb,l +As input to the "fix ave/time"_fix_ave_time.html command, which can +write the values to a file and optionally time average them. :ulb,l As input to the "fix ave/histo"_fix_ave_histo.html command to histogram values across chunks. E.g. a histogram of cluster sizes or @@ -2251,7 +2261,7 @@ largest cluster or fastest diffusing molecule. :l,ule Example calculations with chunks :h5 -Here are chunk commands that can be used to calculate various +Here are eaxmples using chunk commands to calculate various properties: (1) Mimic the deprecated fix ave/spatial command, to average atom diff --git a/doc/compute.html b/doc/compute.html index 4b8bd2d51b..c6a3030e53 100644 --- a/doc/compute.html +++ b/doc/compute.html @@ -180,14 +180,13 @@ are given in the compute section of this page.
- angle/local - theta and energy of each angle -
- atom/molecule - sum per-atom properties for each molecule
- body/local - attributes of body sub-particles
- bond/local - distance and energy of each bond
- centro/atom - centro-symmetry parameter for each atom
- cluster/atom - cluster ID for each atom
- cna/atom - common neighbor analysis (CNA) for each atom
- com - center-of-mass of group of atoms -
- com/molecule - center-of-mass for each molecule +
- com/chunk - center-of-mass for each chunk
- contact/atom - contact count for each spherical particle
- coord/atom - coordination number for each atom
- damage/atom - Peridynamic damage for each atom @@ -201,15 +200,15 @@ page.
- event/displace - detect event on atom displacement
- group/group - energy/force between two groups of atoms
- gyration - radius of gyration of group of atoms -
- gyration/molecule - radius of gyration for each molecule +
- gyration/chunk - radius of gyration for each chunk
- heat/flux - heat flux through a group of atoms
- improper/local - angle of each improper -
- inertia/molecule - inertia tensor for each molecule +
- inertia/chunk - inertia tensor for each chunk
- ke - translational kinetic energy
- ke/atom - kinetic energy for each atom
- ke/rigid - translational kinetic energy of rigid bodies
- msd - mean-squared displacement of group of atoms -
- msd/molecule - mean-squared displacement for each molecule +
- msd/chunk - mean-squared displacement for each chunk
- msd/nongauss - MSD and non-Gaussian parameter of group of atoms
- pair - values computed by a pair style
- pair/local - distance/energy/force of each pairwise interaction @@ -219,7 +218,7 @@ page.
- pressure - total pressure and pressure tensor
- property/atom - convert atom attributes to per-atom vectors/arrays
- property/local - convert local attributes to localvectors/arrays -
- property/molecule - convert molecule attributes to localvectors/arrays +
- property/chunk - extract various per-chunk attributes
- rdf - radial distribution function g(r) histogram of group of atoms
- reduce - combine per-atom quantities into a single global value
- reduce/region - same as compute reduce, within a region @@ -230,6 +229,7 @@ page.
- stress/atom - stress tensor for each atom
- temp - temperature of group of atoms
- temp/asphere - temperature of aspherical particles +
- temp/chunk - temperature of each chunk
- temp/com - temperature after subtracting center-of-mass velocity
- temp/deform - temperature excluding box deformation velocity
- temp/partial - temperature excluding one or more dimensions of velocity @@ -238,7 +238,9 @@ page.
- temp/region - temperature of a region of atoms
- temp/sphere - temperature of spherical particles
- ti - thermodyanmic integration free energy values +
- torque/chunk - torque applied on each chunk
- vacf - velocity-autocorrelation function of group of atoms +
- vcm/chunk - velocity of center-of-mass for each chunk
- voronoi/atom - Voronoi volume and neighbors for each atom
There are also additional compute styles submitted by users which are diff --git a/doc/compute.txt b/doc/compute.txt index c69317808c..0872ded4ae 100644 --- a/doc/compute.txt +++ b/doc/compute.txt @@ -175,14 +175,13 @@ are given in the compute section of "this page"_Section_commands.html#cmd_5. "angle/local"_compute_bond_local.html - theta and energy of each angle -"atom/molecule"_compute_atom_molecule.html - sum per-atom properties for each molecule "body/local"_compute_body_local.html - attributes of body sub-particles "bond/local"_compute_bond_local.html - distance and energy of each bond "centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom "cluster/atom"_compute_cluster_atom.html - cluster ID for each atom "cna/atom"_compute_cna_atom.html - common neighbor analysis (CNA) for each atom "com"_compute_com.html - center-of-mass of group of atoms -"com/molecule"_compute_com_molecule.html - center-of-mass for each molecule +"com/chunk"_compute_com_chunk.html - center-of-mass for each chunk "contact/atom"_compute_contact_atom.html - contact count for each spherical particle "coord/atom"_compute_coord_atom.html - coordination number for each atom "damage/atom"_compute_damage_atom.html - Peridynamic damage for each atom @@ -196,15 +195,15 @@ page"_Section_commands.html#cmd_5. "event/displace"_compute_event_displace.html - detect event on atom displacement "group/group"_compute_group_group.html - energy/force between two groups of atoms "gyration"_compute_gyration.html - radius of gyration of group of atoms -"gyration/molecule"_compute_gyration_molecule.html - radius of gyration for each molecule +"gyration/chunk"_compute_gyration_chunk.html - radius of gyration for each chunk "heat/flux"_compute_heat_flux.html - heat flux through a group of atoms "improper/local"_compute_improper_local.html - angle of each improper -"inertia/molecule"_compute_inertia_molecule.html - inertia tensor for each molecule +"inertia/chunk"_compute_inertia_chunk.html - inertia tensor for each chunk "ke"_compute_ke.html - translational kinetic energy "ke/atom"_compute_ke_atom.html - kinetic energy for each atom "ke/rigid"_compute_ke_rigid.html - translational kinetic energy of rigid bodies "msd"_compute_msd.html - mean-squared displacement of group of atoms -"msd/molecule"_compute_msd_molecule.html - mean-squared displacement for each molecule +"msd/chunk"_compute_msd_chunk.html - mean-squared displacement for each chunk "msd/nongauss"_compute_msd_nongauss.html - MSD and non-Gaussian parameter of group of atoms "pair"_compute_pair.html - values computed by a pair style "pair/local"_compute_pair_local.html - distance/energy/force of each pairwise interaction @@ -214,7 +213,7 @@ page"_Section_commands.html#cmd_5. "pressure"_compute_pressure.html - total pressure and pressure tensor "property/atom"_compute_property_atom.html - convert atom attributes to per-atom vectors/arrays "property/local"_compute_property_local.html - convert local attributes to localvectors/arrays -"property/molecule"_compute_property_molecule.html - convert molecule attributes to localvectors/arrays +"property/chunk"_compute_property_chunk.html - extract various per-chunk attributes "rdf"_compute_rdf.html - radial distribution function g(r) histogram of group of atoms "reduce"_compute_reduce.html - combine per-atom quantities into a single global value "reduce/region"_compute_reduce.html - same as compute reduce, within a region @@ -225,6 +224,7 @@ page"_Section_commands.html#cmd_5. "stress/atom"_compute_stress_atom.html - stress tensor for each atom "temp"_compute_temp.html - temperature of group of atoms "temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles +"temp/chunk"_compute_temp_chunk.html - temperature of each chunk "temp/com"_compute_temp_com.html - temperature after subtracting center-of-mass velocity "temp/deform"_compute_temp_deform.html - temperature excluding box deformation velocity "temp/partial"_compute_temp_partial.html - temperature excluding one or more dimensions of velocity @@ -233,7 +233,9 @@ page"_Section_commands.html#cmd_5. "temp/region"_compute_temp_region.html - temperature of a region of atoms "temp/sphere"_compute_temp_sphere.html - temperature of spherical particles "ti"_compute_ti.html - thermodyanmic integration free energy values +"torque/chunk"_compute_torque_chunk.html - torque applied on each chunk "vacf"_compute_vacf.html - velocity-autocorrelation function of group of atoms +"vcm/chunk"_compute_vcm_chunk.html - velocity of center-of-mass for each chunk "voronoi/atom"_compute_voronoi_atom.html - Voronoi volume and neighbors for each atom :ul There are also additional compute styles submitted by users which are diff --git a/doc/compute_atom_molecule.html b/doc/compute_atom_molecule.html deleted file mode 100644 index 419c065285..0000000000 --- a/doc/compute_atom_molecule.html +++ /dev/null @@ -1,128 +0,0 @@ - -
- -
compute atom/molecule command -
-Syntax: -
-compute ID group-ID atom/molecule input1 input2 ... --
- ID, group-ID are documented in compute command - -
- atom/molecule = style name of this compute command - -
- one or more inputs can be listed - -
- input = c_ID, c_ID[N], f_ID, f_ID[N], v_name
-
-
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 -
- -
Examples: -
-compute 1 all atom/molecule c_ke c_pe -compute 1 top atom/molecule v_myFormula c_stress[3] --
Description: -
-Define a calculation that sums per-atom values on a per-molecule -basis, one per listed input. The inputs can computes, -fixes, or variables that generate per-atom -quantities. Note that attributes stored by atoms, such as mass or -force, can also be summed on a per-molecule basis, by accessing these -quantities via the compute property/atom -command. -
-Each listed input is operated on independently. Only atoms within the -specified group contribute to the per-molecule sum. Note that compute -or fix inputs define their own group which may affect the quantities -they return. For example, if a compute is used as an input which -generates a per-atom vector, it will generate values of 0.0 for atoms -that are not in the group specified for that compute. -
-The ordering of per-molecule quantities produced by this compute is -consistent with the ordering produced by other compute commands that -generate per-molecule datums. Conceptually, the molecule IDs will be -in ascending order for any molecule with one or more of its atoms in -the specified group. -
-If an input begins with "c_", a compute ID must follow which has been -previously defined in the input script and which generates per-atom -quantities. See the individual compute doc page for -details. If no bracketed integer is appended, the vector calculated -by the compute is used. If a bracketed integer is appended, the Ith -column of the array calculated by the compute is used. Users can also -write code for their own compute styles and add them to -LAMMPS. -
-If an input begins with "f_", a fix ID must follow which has been -previously defined in the input script and which generates per-atom -quantities. See the individual fix doc page for details. -Note that some fixes only produce their values on certain timesteps, -which must be compatible with when compute atom/molecule references -the values, else an error results. If no bracketed integer is -appended, the vector calculated by the fix is used. If a bracketed -integer is appended, the Ith column of the array calculated by the fix -is used. Users can also write code for their own fix style and add -them to LAMMPS. -
-If an input begins with "v_", a variable name must follow which has -been previously defined in the input script. It must be an -atom-style variable. Atom-style variables 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 sum -on a per-molecule basis. -
-Here is an example of using this command to sum up the components of -total force on each molecule and print them to a file every 1000 -timesteps. The printed values could also be time-averaged by the fix -ave/time command if desired, by changing "1000 1 1000" to "10 100 -1000" (for example): -
-compute 1 all property/atom fx fy fz -compute 2 all atom/molecule c_1[1] c_1[2] c_1[3] -fix 1 all ave/time 1000 1 1000 c_2 mode vector file tmp.molecule.force --
- -
Output info: -
-This compute calculates a global vector or global array depending on -the number of input values. The length of the vector or number of -rows in the array is the number of molecules. If a single input is -specified, a global vector is produced. If two or more inputs are -specified, a global array is produced where the number of columns = -the number of inputs. The vector or array can be accessed by any -command that uses global values from a compute as input. See this -section for an overview of LAMMPS output -options. -
-All the vector or array values calculated by this compute are -"extensive". -
-The vector or array values will be in whatever units the -input quantities are in. -
-Restrictions: none -
-Related commands: -
- -Default: none -
- diff --git a/doc/compute_atom_molecule.txt b/doc/compute_atom_molecule.txt deleted file mode 100644 index 88e8c9eb6d..0000000000 --- a/doc/compute_atom_molecule.txt +++ /dev/null @@ -1,118 +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 - -compute atom/molecule command :h3 - -[Syntax:] - -compute ID group-ID atom/molecule input1 input2 ... :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -atom/molecule = style name of this compute command :l -one or more inputs can be listed :l -input = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l - 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 -:ule - -[Examples:] - -compute 1 all atom/molecule c_ke c_pe -compute 1 top atom/molecule v_myFormula c_stress\[3\] :pre - -[Description:] - -Define a calculation that sums per-atom values on a per-molecule -basis, one per listed input. The inputs can "computes"_compute.html, -"fixes"_fix.html, or "variables"_variable.html that generate per-atom -quantities. Note that attributes stored by atoms, such as mass or -force, can also be summed on a per-molecule basis, by accessing these -quantities via the "compute property/atom"_compute_property_atom.html -command. - -Each listed input is operated on independently. Only atoms within the -specified group contribute to the per-molecule sum. Note that compute -or fix inputs define their own group which may affect the quantities -they return. For example, if a compute is used as an input which -generates a per-atom vector, it will generate values of 0.0 for atoms -that are not in the group specified for that compute. - -The ordering of per-molecule quantities produced by this compute is -consistent with the ordering produced by other compute commands that -generate per-molecule datums. Conceptually, the molecule IDs will be -in ascending order for any molecule with one or more of its atoms in -the specified group. - -If an input begins with "c_", a compute ID must follow which has been -previously defined in the input script and which generates per-atom -quantities. See the individual "compute"_compute.html doc page for -details. If no bracketed integer is appended, the vector calculated -by the compute is used. If a bracketed integer is appended, the Ith -column of the 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 an input begins with "f_", a fix ID must follow which has been -previously defined in the input script and which generates per-atom -quantities. See the individual "fix"_fix.html doc page for details. -Note that some fixes only produce their values on certain timesteps, -which must be compatible with when compute atom/molecule references -the values, else an error results. If no bracketed integer is -appended, the vector calculated by the fix is used. If a bracketed -integer is appended, the Ith column of the array calculated by the fix -is used. Users can also write code for their own fix style and "add -them to LAMMPS"_Section_modify.html. - -If an input begins with "v_", a variable name must follow which has -been previously defined in the input script. It must be an -"atom-style variable"_variable.html. Atom-style variables 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 sum -on a per-molecule basis. - -Here is an example of using this command to sum up the components of -total force on each molecule and print them to a file every 1000 -timesteps. The printed values could also be time-averaged by the fix -ave/time command if desired, by changing "1000 1 1000" to "10 100 -1000" (for example): - -compute 1 all property/atom fx fy fz -compute 2 all atom/molecule c_1\[1\] c_1\[2\] c_1\[3\] -fix 1 all ave/time 1000 1 1000 c_2 mode vector file tmp.molecule.force :pre - -:line - -[Output info:] - -This compute calculates a global vector or global array depending on -the number of input values. The length of the vector or number of -rows in the array is the number of molecules. If a single input is -specified, a global vector is produced. If two or more inputs are -specified, a global array is produced where the number of columns = -the number of inputs. The vector or array can be accessed by any -command that uses global values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. - -All the vector or array values calculated by this compute are -"extensive". - -The vector or array values will be in whatever "units"_units.html the -input quantities are in. - -[Restrictions:] none - -[Related commands:] - -"compute"_compute.html, "fix"_fix.html, "variable"_variable.html - -[Default:] none diff --git a/doc/compute_chunk_atom.html b/doc/compute_chunk_atom.html new file mode 100644 index 0000000000..24d4598c62 --- /dev/null +++ b/doc/compute_chunk_atom.html @@ -0,0 +1,568 @@ + ++ +
compute chunk/atom command +
+Syntax: +
+compute ID group-ID chunk/atom style args keyword values ... ++
- ID, group-ID are documented in compute command + +
- chunk/atom = style name of this compute command
+
+
style = bin/1d or bin/2d or bin/3d or type or molecule or compute/fix/variable + bin/1d args = dim origin delta + 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) + bin/2d args = dim origin delta dim origin delta + 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) + bin/3d args = dim origin delta dim origin delta dim origin delta + 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) + type args = none + molecule args = none + compute/fix/variable = c_ID, c_ID[I], f_ID, f_ID[I], v_name with no args + 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 +
+ - zero or more keyword/values pairs may be appended + +
- keyword = region or nchunk or static or compress or bound or discard or units
+
+
region value = region-ID + region-ID = ID of region atoms must be in to be part of a chunk + nchunk value = once or every + once = only compute the number of chunks once + every = re-compute the number of chunks whenever invoked + limit values = 0 or Nc max or Nc exact + 0 = no limit on the number of chunks + Nc max = limit number of chunks to be <= Nc + Nc exact = set number of chunks to exactly Nc + ids value = once or nfreq or every + once = assign chunk IDs to atoms only once, they persist thereafter + nfreq = assign chunk IDs to atoms only once every Nfreq steps (if invoked by fix ave/chunk which sets Nfreq) + every = assign chunk IDs to atoms whenever invoked + compress value = yes or no + yes = compress chunk IDs to eliminate IDs with no atoms + no = do not compress chunk IDs even if some IDs have no atoms + discard value = yes or no or mixed + yes = discard atoms with out-of-range chunk IDs by assigning a chunk ID = 0 + no = keep atoms with out-of-range chunk IDs by assigning a valid chunk ID + mixed = keep or discard such atoms according to spatial binning rule + bound values = x/y/z lo hi + x/y/z = x or y or z to bound sptial bins in this dimension + lo = lower or coordinate value (distance units) + hi = upper or coordinate value (distance units) + units value = box or lattice or reduced +
+ +
Examples: +
+compute 1 all chunk/atom type +compute 1 all chunk/atom bin/1d z lower 0.02 units reduced +compute 1 all chunk/atom bin/2d z lower 1.0 y 0.0 2.5 +compute 1 all chunk/atom molecule region sphere nchunk once ids once compress yes ++
Description: +
+Define a computation that calculates an integer chunk ID from 1 to +Nchunk for each atom in the group. Values of chunk IDs are determined +by the style of chunk, which can be based on atom type or molecule +ID or spatial binning or a per-atom property or value calculated by +another compute, fix, or atom-style +variable. Per-atom chunk IDs can be used by other +computes with "chunk" in their style name, such as compute +com/chunk or compute +msd/chunk. Or they can be used by the fix +ave/chunk command to sum and time average a +variety of per-atom properties over the atoms in each chunk. Or they +can simply be accessed by any command that uses per-atom values from a +compute as input, as discussed in Section_howto +15. +
+See Section_howto 23 for an overview of +how this compute can be used with a variety of other commands to +tabulate properties of a simulation. The howto section gives several +examples of input script commands that can be used to calculate +interesting properties. +
+Conceptually it is important to realize that this compute does two +simple things. First, it sets the value of Nchunk = the number of +chunks, which can be a constant value or change over time. Second, it +assigns each atom to a chunk via a chunk ID. Chunk IDs range from 1 +to Nchunk inclusive; some chunks may have no atoms assigned to them. +Atoms that do not belong to any chunk are assigned a value of 0. Note +that the two operations are not always performed together. For +example, spatial bins can be setup once (which sets Nchunk), and +atoms assigned to those bins many times thereafter (setting their +chunk IDs). +
+All other commands in LAMMPS that use chunk IDs assume there are +Nchunk number of chunks, and that every atom is assigned to one of +those chunks, or not assigned to any chunk. +
+There are many options for specifying for how and when Nchunk is +calculated, and how and when chunk IDs are assigned to atoms. The +details depend on the chunk style and its args, as well as +optional keyword settings. They can also depend on whether a fix +ave/chunk command is using this compute, since +that command requires Nchunk to remain static across windows of +timesteps it specifies, while it accumulates per-chunk averages. +
+The details are described below. +
++ +
+ +
The different chunk styles operate as follows. For each style, how it +calculates Nchunk and assigns chunk IDs to atoms is explained. Note +that using the optional keywords can change both of those actions, as +described further below where the keywords are discussed. +
++ +
The binning styles perform a spatial binning of atoms, and assign an +atom the chunk ID corresponding to the bin number it is in. Nchunk +is set to the number of bins, which can change if the simulation box +size changes. +
+The bin/1d, bin/2d, and bin/3d styles define bins as 1d layers +(slabs), 2d pencils, or 3d boxes. The dim, origin, and delta +settings are specified 1, 2, or 3 times. For 2d or 3d bins, there is +no restriction on specifying dim = x before dim = y or z, or dim = y +before dim = z. Bins in a particular dim have a bin size in that +dimension given by delta. 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 simulation box +or the bounds specified by the optional bounds keyword. +
+For orthogonal simulation boxes, the bins are layers, pencils, or +boxes aligned with the xyz coordinate axes. For triclinic +(non-orthogonal) simulation boxes, the bin faces are parallel to the +tilted faces of the simulation box. See this +section 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. +
+The meaning of origin and delta for triclinic boxes is as follows. +Consider a triclinic 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 in reduced units +means there will be 10 layers from 0.0 to 1.0, regardless of the +current size or shape of the simulation box. +
+The created bins (and hence the chunk IDs) are numbered consecutively +from 1 to the number of bins = Nchunk. For 2d and 3d bins, the +numbering varies most rapidly in the first dimension (which could be +x, y, or z), next rapidly in the 2nd dimension, and most slowly in the +3rd dimension. +
+Each time this compute is invoked, each atom is mapped to a bin based +on its current position. 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 all bins. If an atom is not inside +any bin, the discard keyword is used to determine how a chunk ID is +assigned to the atom. +
++ +
The type style uses the atom type as the chunk ID. Nchunk is set +to the number of atom types defined for the simulation, e.g. via the +create_box or read_data commands. +
++ +
The molecule style uses the molecule ID of each atom as its chunk +ID. Nchunk is set to the largest chunk ID. Note that this excludes +molecule IDs for atoms which are not in the specified group or +optional region. +
+There is no requirement that all atoms in a particular molecule are +assigned the same chunk ID (zero or non-zero), though you probably +want that to be the case, if you wish to compute a per-molecule +property. LAMMPS will issue a warning if that is not the case, but +only the first time that Nchunk is calculated. +
+Note that atoms with a molecule ID = 0, which may be non-molecular +solvent atoms, have an out-of-range chunk ID. These atoms are +discarded (not assigned to any chunk) or assigned to Nchunk, +depending on the value of the discard keyword. +
++ +
The compute/fix/variable styles set the chunk ID of each atom based +on a quantity calculated and stored by a compute, fix, or variable. +In each case, it must be a per-atom quantity. In each case the +referenced floating point values are converted to an integer chunk ID +as follows. The floating point value is truncated (rounded down) to +an integer value. If the integer value is <= 0, then a chunk ID of 0 +is assigned to the atom. If the integer value is > 0, it becomes the +chunk ID to the atom. Nchunk is set to the largest chunk ID. Note +that this excludes atoms which are not in the specified group or +optional region. +
+If the style 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. +
+If the style 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 the +timestep on which this compute accesses the fix, else an error +results. Users can also write code for their own fix styles and add +them to LAMMPS. +
+If a value begins with "v_", a variable name for an atom or +atomfile style variable 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 +treat as a chunk ID. +
++ +
+ +
Normally, Nchunk = the number of chunks, is re-calculated every time +this fix is invoked, though the value may or may not change. As +explained below, the nchunk keyword can be set to once which means +Nchunk will never change. +
+If a fix ave/chunk command uses this compute, it +can also turn off the re-calculation of Nchunk for one or more +windows of timesteps. The extent of the windows, during which Nchunk +is held constant, are determined by the Nevery, Nrepeat, Nfreq +values and the ave keyword setting that are used by the fix +ave/chunk command. +
+Specifically, if ave = one, then for each span of Nfreq +timesteps, Nchunk is held constant between the first timestep when +averaging is done (within the Nfreq-length window), and the last +timestep when averaging is done (multiple of Nfreq). If ave = +running or window, then Nchunk is held constant forever, +starting on the first timestep when the fix +ave/chunk command invokes this compute. +
+Note that multiple fix ave/chunk commands can use +the same compute chunk/atom compute. However, the time windows they +induce for holding Nchunk constant must be identical, else an error +will be generated. +
++ +
+ +
The various optional keywords operate as follows. Note that some of +them function differently or are ignored by different chunk styles. +Some of them also have different default values, depending on +the chunk style, as listed below. +
+The region keyword applies to all chunk styles. If used, an atom +must be in both the specified group and the specified geometric +region to be assigned to a chunk. +
++ +
The nchunk keyword applies to all chunk styles. It specifies how +often Nchunk is recalculated, which in turn can affect the chunk IDs +assigned to individual atoms. +
+If nchunk is set to once, then Nchunk is only calculated once, +the first time this compute is invoked. If nchunk is set to +every, then Nchunk is re-calculated every time the compute is +invoked. Note that, as described above, the use of this compute +by the fix ave/chunk command can override +the every setting. +
+The default values for nchunk are listed below and depend on the +chunk style and other system and keyword settings. They attempt to +represent typical use cases for the various chunk styles. The +nchunk value can always be set explicitly if desired. +
++ +
The limit keyword can be used to limit the calculated value of +Nchunk = the number of chunks. The limit is applied each time +Nchunk is calculated, which also limits the chunk IDs assigned to +any atom. The limit keyword is used by all chunk styles except the +binning styles, which ignore it. This is because the number of bins +can be tailored using the bound keyword (described below) which +effectively limits the size of Nchunk. +
+If limit is set to Nc = 0, then no limit is imposed on Nchunk, +though the compress keyword can still be used to reduce Nchunk, as +described below. +
+If Nc > 0, then the effect of the limit keyword depends on whether +the compress keyword is also used with a setting of yes, and +whether the compress keyword is specified before the limit keyword +or after. +
+In all cases, Nchunk is first calculated in the usual way for each +chunk style, as described above. +
+First, here is what occurs if compress yes is not set. If limit +is set to Nc max, then Nchunk is reset to the smaller of Nchunk +and Nc. If limit is set to Nc exact, then Nchunk is reset to +Nc, whether the original Nchunk was larger or smaller than Nc. +If Nchunk shrank due to the limit setting, then atom chunk IDs > +Nchunk will be reset to 0 or Nchunk, depending on the setting of +the discard keyword. If Nchunk grew, there will simply be some +chunks with no atoms assigned to them. +
+If compress yes is set, and the compress keyword comes before the +limit keyword, the compression operation is performed first, as +described below, which resets Nchunk. The limit keyword is then +applied to the new Nchunk value, exactly as described in the +preceeding paragraph. Note that in this case, all atoms will end up +with chunk IDs <= Nc, but their original values (e.g. molecule ID or +compute/fix/variable value) may have been > Nc, because of the +compression operation. +
+If compress yes is set, and the compress keyword comes after the +limit keyword, then the limit value of Nc is applied first to +the uncompressed value of Nchunk, but only if Nc < Nchunk +(whether Nc max or Nc exact is used). This effectively means all +atoms with chunk IDs > Nc have their chunk IDs reset to 0 or Nc, +depending on the setting of the discard keyword. The compression +operation is then performed, which may shrink Nchunk further. If +the new Nchunk < Nc and limit = Nc exact is specified, then +Nchunk is reset to Nc, which results in extra chunks with no atoms +assigned to them. Note that in this case, all atoms will end up with +chunk IDs <= Nc, and their original values (e.g. molecule ID or +compute/fix/variable value) will also have been <= Nc. +
++ +
The ids keyword applies to all chunk styles. If the setting is +once then the chunk IDs assigned to atoms the first time this +compute is invoked will be permanent, and never be re-computed. +
+If the setting is nfreq and if a fix ave/chunk +command is using this compute, then in each of the Nchunk = constant +time windows (discussed above), the chunk ID's assigned to atoms on +the first step of the time window will persist until the end of the +time window. +
+If the setting is every, which is the default, then chunk IDs are +re-calculated on any timestep this compute is invoked. +
+IMPORTANT NOTE: If you want the persistent chunk-IDs calculated by +this compute to be continuous when running from a restart +file, then you should use the same ID for this +compute, as in the original run. This is so that the fix this compute +creates to store per-atom quantities will also have the same ID, and +thus be initialized correctly with chunk IDs from the restart file. +
++ +
The compress keyword applies to all chunk styles and affects how +Nchunk is calculated, which in turn affects the chunk IDs assigned +to each atom. It is useful for converting a "sparse" set of chunk IDs +(with many IDs that have no atoms assigned to them), into a "dense" +set of IDs, where every chunk has one or more atoms assigned to it. +
+Two possible use cases are as follows. If a large simulation box is +mostly empty space, then the binning style may produce many bins +with no atoms. If compress is set to yes, only bins with atoms +will be contribute to Nchunk. Likewise, the molecule or +compute/fix/variable styles may produce large Nchunk values. For +example, the compute cluster/atom command +assigns every atom an atom ID for one of the atoms it is clustered +with. For a million-atom system with 5 clusters, there would only be +5 unique chunk IDs, but the largest chunk ID might be 1 million, +resulting in Nchunk = 1 million. If compress is set to yes, +Nchunk will be reset to 5. +
+If compress is set to no, which is the default, no compression is +done. If it is set to yes, all chunk IDs with no atoms are removed +from the list of chunk IDs, and the list is sorted. The remaining +chunk IDs are renumbered from 1 to Nchunk where Nchunk is the new +length of the list. The chunk IDs assigned to each atom reflect +the new renumbering from 1 to Nchunk. +
+The original chunk IDs (before renumbering) can be accessed by the +compute property/chunk command and its +id keyword, or by the fix ave/chunk command +which outputs the original IDs as one of the columns in its global +output array. For example, using the "compute cluster/atom" command +discussed above, the original 5 unique chunk IDs might be atom IDs +(27,4982,58374,857838,1000000). After compresion, these will be +renumbered to (1,2,3,4,5). The original values (27,...,1000000) can +be output to a file by the fix ave/chunk command, +or by using the fix ave/time command in +conjunction with the compute +property/chunk command. +
+IMPORTANT NOTE: The compression operation requires global +communication across all processors to share their chunk ID values. +It can require large memory on every processor to store them, even +after they are compressed, if there are are a large number of unique +chunk IDs with atoms assigned to them. It uses a STL map to find +unique chunk IDs and store them in sorted order. Each time an atom is +assigned a compressed chunk ID, it must access the STL map. All of +this means that compression can be expensive, both in memory and CPU +time. The use of the limit keyword in conjunction with the +compress keyword can affect these costs, depending on which keyword +is used first. So use this option with care. +
++ +
The discard keyword applies to all chunk styles. It affects what +chunk IDs are assigned to atoms that do not match one of the valid +chunk IDs from 1 to Nchunk. Note that it does not apply to atoms +that are not in the specified group or optionally specified region. +Those atoms are always assigned a chunk ID = 0. +
+If the calculated chunk ID for an atom is not within the range 1 to +Nchunk then it is a "discard" atom. Note that Nchunk may have +been shrunk by the limit keyword. Or the compress keyword may +have eliminated chunk IDs that were valid before the compression took +place, and are now not in the compressed list. Also note that for the +molecule chunk style, if new molecules are added to the system, +their chunk IDs may exceed a previously calculated Nchunk. +Likewise, evaluation of a compute/fix/variable on a later timestep may +return chunk IDs that are invalid for the previously calculated +Nchunk. +
+All the chunk styles except the binning styles, must use discard +set to either yes or no. If discard is set to yes, which is +the default, then every "discard" atom has its chunk ID set to 0. If +discard is set to no, every "discard" atom has its chunk ID set to +Nchunk. I.e. it becomes part of the last chunk. +
+The binning styles use the discard keyword to decide whether to +discard atoms outside the spatial domain covered by bins, or to assign +them to the bin they are nearest to. Details are as follows. +
+If discard is set to yes, an out-of-domain atom will have its +chunk ID set to 0. If discard is set to no, the atom will have +its chunk ID set to the first or last bin in that dimension. If +(discard is set to mixed, which is the default, it will only have +its chunk ID set to the first or last bin if bins extend to the +simulation 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 have its chunk ID set to 0 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 chunk ID of the atom +is only set to 0 if it is outside the first or last bin, not if it is +simply outside the numeric bounds setting. +
++ +
The bound keyword only applies to the binning styles; otherwise it +is ignored. It can be used one or more times to limit the extent of +bin coverage in a specified dimension, 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. Note that using the bound +keyword typically reduces the total number of bins and thus the number +of chunks Nchunk. +
+The units keyword only applies to the binning styles; otherwise it +is ignored. It determines the meaning of the distance units used for +the bin sizes delta and for origin and bounds values if they are +coordinate values. 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 command, e.g. Angstroms for units = real or metal. +A lattice value means the distance units are in lattice spacings. +The lattice 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. +
++ +
+ +
Output info: +
+This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +Section_howto 15 for an overview of +LAMMPS output options. +
+The per-atom vector values are unitless chunk IDs, ranging from 1 to +Nchunk (inclusive) for atoms assigned to chunks, and 0 for atoms not +belonging to a chunk. +
+Restrictions: +
+Even if the nchunk keyword is set to once, the chunk IDs assigned +to each atom are not stored in a restart files. This means you cannot +expect those assignments to persist in a restarted simulation. +Instead you must re-specify this command and assign atoms to chunks when +the restarted simulation begins. +
+Related commands: +
+ +Default: +
+The option defaults are as follows: +
+- region = none +
- nchunk = every if compress is yes, overriding other defaults listed here +
- nchunk = once for type style +
- nchunk = once for mol style if region is none +
- nchunk = every for mol style if region is set +
- nchunk = once for binning style if the simulation box size is static or units = reduced +
- nchunk = every for binning style if the simulation box size is dynamic and units is lattice or box +
- nchunk = every for compute/fix/variable style +
- limit = 0 +
- ids = every +
- compress = no +
- discard = yes for all styles except binning +
- discard = mixed for binning styles +
- bound = lower and upper in all dimensions +
- units = lattice +
+ +
compute com/chunk command +
+Syntax: +
+compute ID group-ID com/chunk chunkID ++
- ID, group-ID are documented in compute command +
- com/chunk = style name of this compute command +
- chunkID = ID of compute chunk/atom command +
Examples: +
+compute 1 fluid com/chunk molchunk ++
Description: +
+Define a computation that calculates the center-of-mass for multiple +chunks of atoms. +
+In LAMMPS, chunks are collections of atoms defined by a compute +chunk/atom command, which assigns each atom +to a single chunk (or no chunk). The ID for this command is specified +as chunkID. For example, a single chunk could be the atoms in a +molecule or atoms in a spatial bin. See the compute +chunk/atom doc page and "Section_howto +23 for details of how chunks can be +defined and examples of how they can be used to measure properties of +a system. +
+This compute calculates the x,y,z coordinates of the center-of-mass +for each chunk, which includes all effects due to atoms passing thru +periodic boundaries. +
+Note that only atoms in the specified group contribute to the +calculation. The compute chunk/atom command +defines its own group; atoms will have a chunk ID = 0 if they are not +in that group, signifying they are not assigned to a chunk, and will +thus also not contribute to this calculation. You can specify the +"all" group for this command if you simply want to include atoms with +non-zero chunk IDs. +
+IMPORTANT NOTE: The coordinates of an atom contribute to the chunk's +center-of-mass in "unwrapped" form, by using the image flags +associated with each atom. See the dump custom command +for a discussion of "unwrapped" coordinates. See the Atoms section of +the read_data command for a discussion of image flags +and how they are set for each atom. You can reset the image flags +(e.g. to 0) before invoking this compute by using the set +image command. +
+The simplest way to output the results of the compute com/chunk +calculation to a file is to use the fix ave/time +command, for example: +
+compute cc1 chunk/atom molecule +compute myChunk all com/chunk cc1 +fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector ++
Output info: +
+This compute calculates a global array where the number of rows = the +number of chunks Nchunk as calculated by the specified compute +chunk/atom command. The number of columns = +3 for the x,y,z center-of-mass coordinates of each chunk. These +values can be accessed by any command that uses global array values +from a compute as input. See Section_howto +15 for an overview of LAMMPS output +options. +
+The array values are "intensive". The array values will be in +distance units. +
+Restrictions: none +
+Related commands: +
+ +Default: none +
+ diff --git a/doc/compute_com_chunk.txt b/doc/compute_com_chunk.txt new file mode 100644 index 0000000000..1e9191996c --- /dev/null +++ b/doc/compute_com_chunk.txt @@ -0,0 +1,87 @@ +"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 + +compute com/chunk command :h3 + +[Syntax:] + +compute ID group-ID com/chunk chunkID :pre + +ID, group-ID are documented in "compute"_compute.html command +com/chunk = style name of this compute command +chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :ul + +[Examples:] + +compute 1 fluid com/chunk molchunk :pre + +[Description:] + +Define a computation that calculates the center-of-mass for multiple +chunks of atoms. + +In LAMMPS, chunks are collections of atoms defined by a "compute +chunk/atom"_compute_chunk_atom.html command, which assigns each atom +to a single chunk (or no chunk). The ID for this command is specified +as chunkID. For example, a single chunk could be the atoms in a +molecule or atoms in a spatial bin. See the "compute +chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto +23"_Section_howto.html#howto_23 for details of how chunks can be +defined and examples of how they can be used to measure properties of +a system. + +This compute calculates the x,y,z coordinates of the center-of-mass +for each chunk, which includes all effects due to atoms passing thru +periodic boundaries. + +Note that only atoms in the specified group contribute to the +calculation. The "compute chunk/atom"_compute_chunk_atom.html command +defines its own group; atoms will have a chunk ID = 0 if they are not +in that group, signifying they are not assigned to a chunk, and will +thus also not contribute to this calculation. You can specify the +"all" group for this command if you simply want to include atoms with +non-zero chunk IDs. + +IMPORTANT NOTE: The coordinates of an atom contribute to the chunk's +center-of-mass in "unwrapped" form, by using the image flags +associated with each atom. See the "dump custom"_dump.html command +for a discussion of "unwrapped" coordinates. See the Atoms section of +the "read_data"_read_data.html command for a discussion of image flags +and how they are set for each atom. You can reset the image flags +(e.g. to 0) before invoking this compute by using the "set +image"_set.html command. + +The simplest way to output the results of the compute com/chunk +calculation to a file is to use the "fix ave/time"_fix_ave_time.html +command, for example: + +compute cc1 chunk/atom molecule +compute myChunk all com/chunk cc1 +fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector :pre + +[Output info:] + +This compute calculates a global array where the number of rows = the +number of chunks {Nchunk} as calculated by the specified "compute +chunk/atom"_compute_chunk_atom.html command. The number of columns = +3 for the x,y,z center-of-mass coordinates of each chunk. These +values can be accessed by any command that uses global array values +from a compute as input. See "Section_howto +15"_Section_howto.html#howto_15 for an overview of LAMMPS output +options. + +The array values are "intensive". The array values will be in +distance "units"_units.html. + +[Restrictions:] none + +[Related commands:] + +"compute com"_compute_com.html + +[Default:] none diff --git a/doc/compute_com_molecule.html b/doc/compute_com_molecule.html deleted file mode 100644 index b82fa1ed76..0000000000 --- a/doc/compute_com_molecule.html +++ /dev/null @@ -1,73 +0,0 @@ - -- -
compute com/molecule command -
-Syntax: -
-compute ID group-ID com/molecule --
- ID, group-ID are documented in compute command -
- com/molecule = style name of this compute command -
Examples: -
-compute 1 fluid com/molecule --
Description: -
-Define a computation that calculates the center-of-mass of individual -molecules. The calculation includes all effects due to atoms passing -thru periodic boundaries. -
-The x,y,z coordinates of the center-of-mass for a particular molecule -are only computed if one or more of its atoms are in the specified -group. Normally all atoms in the molecule should be in the group, -however this is not required. LAMMPS will warn you if this is not the -case. Only atoms in the group contribute to the center-of-mass -calculation for the molecule. -
-The ordering of per-molecule quantities produced by this compute is -consistent with the ordering produced by other compute commands that -generate per-molecule datums. Conceptually, the molecule IDs will be -in ascending order for any molecule with one or more of its atoms in -the specified group. -
-IMPORTANT NOTE: The coordinates of an atom contribute to the -molecule's center-of-mass in "unwrapped" form, by using the image -flags associated with each atom. See the dump custom -command for a discussion of "unwrapped" coordinates. See the Atoms -section of the read_data command for a discussion of -image flags and how they are set for each atom. You can reset the -image flags (e.g. to 0) before invoking this compute by using the set -image command. -
-Output info: -
-This compute calculates a global array where the number of rows = -Nmolecules and the number of columns = 3 for the x,y,z center-of-mass -coordinates of each molecule. These values can be accessed by any -command that uses global array values from a compute as input. See -Section_howto 15 for an overview of -LAMMPS output options. -
-The array values are "intensive". The array values will be in -distance units. -
-Restrictions: none -
-Related commands: -
- -Default: none -
- diff --git a/doc/compute_com_molecule.txt b/doc/compute_com_molecule.txt deleted file mode 100644 index 1086f09f1b..0000000000 --- a/doc/compute_com_molecule.txt +++ /dev/null @@ -1,68 +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 - -compute com/molecule command :h3 - -[Syntax:] - -compute ID group-ID com/molecule :pre - -ID, group-ID are documented in "compute"_compute.html command -com/molecule = style name of this compute command :ul - -[Examples:] - -compute 1 fluid com/molecule :pre - -[Description:] - -Define a computation that calculates the center-of-mass of individual -molecules. The calculation includes all effects due to atoms passing -thru periodic boundaries. - -The x,y,z coordinates of the center-of-mass for a particular molecule -are only computed if one or more of its atoms are in the specified -group. Normally all atoms in the molecule should be in the group, -however this is not required. LAMMPS will warn you if this is not the -case. Only atoms in the group contribute to the center-of-mass -calculation for the molecule. - -The ordering of per-molecule quantities produced by this compute is -consistent with the ordering produced by other compute commands that -generate per-molecule datums. Conceptually, the molecule IDs will be -in ascending order for any molecule with one or more of its atoms in -the specified group. - -IMPORTANT NOTE: The coordinates of an atom contribute to the -molecule's center-of-mass in "unwrapped" form, by using the image -flags associated with each atom. See the "dump custom"_dump.html -command for a discussion of "unwrapped" coordinates. See the Atoms -section of the "read_data"_read_data.html command for a discussion of -image flags and how they are set for each atom. You can reset the -image flags (e.g. to 0) before invoking this compute by using the "set -image"_set.html command. - -[Output info:] - -This compute calculates a global array where the number of rows = -Nmolecules and the number of columns = 3 for the x,y,z center-of-mass -coordinates of each molecule. These values can be accessed by any -command that uses global array values from a compute as input. See -"Section_howto 15"_Section_howto.html#howto_15 for an overview of -LAMMPS output options. - -The array values are "intensive". The array values will be in -distance "units"_units.html. - -[Restrictions:] none - -[Related commands:] - -"compute com"_compute_com.html - -[Default:] none diff --git a/doc/compute_gyration_chunk.html b/doc/compute_gyration_chunk.html new file mode 100644 index 0000000000..cf65951ffb --- /dev/null +++ b/doc/compute_gyration_chunk.html @@ -0,0 +1,122 @@ + ++ +
compute gyration/chunk command +
+Syntax: +
+compute ID group-ID gyration/chunk chunkID keyword value ... ++
- ID, group-ID are documented in compute command + +
- gyration/chunk = style name of this compute command + +
- chunkID = ID of compute chunk/atom command + +
- zero or more keyword/value pairs may be appended + +
- keyword = tensor
+
+
tensor value = none +
+ +
Examples: +
+compute 1 molecule gyration/chunk molchunk +compute 2 molecule gyration/chunk molchunk tensor ++
Description: +
+Define a computation that calculates the radius of gyration Rg for +multiple chunks of atoms. +
+In LAMMPS, chunks are collections of atoms defined by a compute +chunk/atom command, which assigns each atom +to a single chunk (or no chunk). The ID for this command is specified +as chunkID. For example, a single chunk could be the atoms in a +molecule or atoms in a spatial bin. See the compute +chunk/atom doc page and "Section_howto +23 for details of how chunks can be +defined and examples of how they can be used to measure properties of +a system. +
+This compute calculates the radius of gyration Rg for each chunk, +which includes all effects due to atoms passing thru periodic +boundaries. +
+Rg is a measure of the size of a chunk, and is computed by this +formula +
+
+where M is the total mass of the chunk, Rcm is the center-of-mass +position of the chunk, and the sum is over all atoms in the +chunk. +
+Note that only atoms in the specified group contribute to the +calculation. The compute chunk/atom command +defines its own group; atoms will have a chunk ID = 0 if they are not +in that group, signifying they are not assigned to a chunk, and will +thus also not contribute to this calculation. You can specify the +"all" group for this command if you simply want to include atoms with +non-zero chunk IDs. +
+If the tensor keyword is specified, then the scalar Rg value is not +calculated, but an Rg tensor is instead calculated for each chunk. +The formula for the components of the tensor is the same as the above +formula, except that (Ri - Rcm)^2 is replaced by (Rix - Rcmx) * (Riy - +Rcmy) for the xy component, etc. The 6 components of the tensor are +ordered xx, yy, zz, xy, xz, yz. +
+IMPORTANT NOTE: The coordinates of an atom contribute to Rg in +"unwrapped" form, by using the image flags associated with each atom. +See the dump custom command for a discussion of +"unwrapped" coordinates. See the Atoms section of the +read_data command for a discussion of image flags and +how they are set for each atom. You can reset the image flags +(e.g. to 0) before invoking this compute by using the set +image command. +
+The simplest way to output the results of the compute gyration/chunk +calculation to a file is to use the fix ave/time +command, for example: +
+compute cc1 chunk/atom molecule +compute myChunk all gyration/chunk cc1 +fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector ++
Output info: +
+This compute calculates a global vector if the tensor keyword is not +specified and a global array if it is. The length of the vector or +number of rows in the array = the number of chunks Nchunk as +calculated by the specified compute +chunk/atom command. If the tensor keyword +is specified, the global array has 6 columns. The vector or array can +be accessed by any command that uses global values from a compute as +input. See this section for an overview +of LAMMPS output options. +
+All the vector or array values calculated by this compute are +"intensive". The vector or array values will be in distance +units, since they are the square root of values +represented by the formula above. +
+Restrictions: none +
+Related commands: none +
+ +Default: none +
+ diff --git a/doc/compute_gyration_chunk.txt b/doc/compute_gyration_chunk.txt new file mode 100644 index 0000000000..f6b3ff8979 --- /dev/null +++ b/doc/compute_gyration_chunk.txt @@ -0,0 +1,111 @@ +"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 + +compute gyration/chunk command :h3 + +[Syntax:] + +compute ID group-ID gyration/chunk chunkID keyword value ... :pre + +ID, group-ID are documented in "compute"_compute.html command :ulb,l +gyration/chunk = style name of this compute command :l +chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :l +zero or more keyword/value pairs may be appended :l +keyword = {tensor} :l + {tensor} value = none :pre +:ule + +[Examples:] + +compute 1 molecule gyration/chunk molchunk +compute 2 molecule gyration/chunk molchunk tensor :pre + +[Description:] + +Define a computation that calculates the radius of gyration Rg for +multiple chunks of atoms. + +In LAMMPS, chunks are collections of atoms defined by a "compute +chunk/atom"_compute_chunk_atom.html command, which assigns each atom +to a single chunk (or no chunk). The ID for this command is specified +as chunkID. For example, a single chunk could be the atoms in a +molecule or atoms in a spatial bin. See the "compute +chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto +23"_Section_howto.html#howto_23 for details of how chunks can be +defined and examples of how they can be used to measure properties of +a system. + +This compute calculates the radius of gyration Rg for each chunk, +which includes all effects due to atoms passing thru periodic +boundaries. + +Rg is a measure of the size of a chunk, and is computed by this +formula + +:c,image(Eqs/compute_gyration.jpg) + +where M is the total mass of the chunk, Rcm is the center-of-mass +position of the chunk, and the sum is over all atoms in the +chunk. + +Note that only atoms in the specified group contribute to the +calculation. The "compute chunk/atom"_compute_chunk_atom.html command +defines its own group; atoms will have a chunk ID = 0 if they are not +in that group, signifying they are not assigned to a chunk, and will +thus also not contribute to this calculation. You can specify the +"all" group for this command if you simply want to include atoms with +non-zero chunk IDs. + +If the {tensor} keyword is specified, then the scalar Rg value is not +calculated, but an Rg tensor is instead calculated for each chunk. +The formula for the components of the tensor is the same as the above +formula, except that (Ri - Rcm)^2 is replaced by (Rix - Rcmx) * (Riy - +Rcmy) for the xy component, etc. The 6 components of the tensor are +ordered xx, yy, zz, xy, xz, yz. + +IMPORTANT NOTE: The coordinates of an atom contribute to Rg in +"unwrapped" form, by using the image flags associated with each atom. +See the "dump custom"_dump.html command for a discussion of +"unwrapped" coordinates. See the Atoms section of the +"read_data"_read_data.html command for a discussion of image flags and +how they are set for each atom. You can reset the image flags +(e.g. to 0) before invoking this compute by using the "set +image"_set.html command. + +The simplest way to output the results of the compute gyration/chunk +calculation to a file is to use the "fix ave/time"_fix_ave_time.html +command, for example: + +compute cc1 chunk/atom molecule +compute myChunk all gyration/chunk cc1 +fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector :pre + +[Output info:] + +This compute calculates a global vector if the {tensor} keyword is not +specified and a global array if it is. The length of the vector or +number of rows in the array = the number of chunks {Nchunk} as +calculated by the specified "compute +chunk/atom"_compute_chunk_atom.html command. If the {tensor} keyword +is specified, the global array has 6 columns. The vector or array can +be accessed by any command that uses global values from a compute as +input. See "this section"_Section_howto.html#howto_15 for an overview +of LAMMPS output options. + +All the vector or array values calculated by this compute are +"intensive". The vector or array values will be in distance +"units"_units.html, since they are the square root of values +represented by the formula above. + +[Restrictions:] none + +[Related commands:] none + +"compute gyration"_compute_gyration.html + +[Default:] none diff --git a/doc/compute_gyration_molecule.html b/doc/compute_gyration_molecule.html deleted file mode 100644 index 3004e34fe3..0000000000 --- a/doc/compute_gyration_molecule.html +++ /dev/null @@ -1,104 +0,0 @@ - -- -
compute gyration/molecule command -
-Syntax: -
-compute ID group-ID gyration/molecule keyword value ... --
- ID, group-ID are documented in compute command - -
- gyration/molecule = style name of this compute command - -
- zero or more keyword/value pairs may be appended - -
- keyword = tensor
-
-
tensor value = none -
- -
Examples: -
-compute 1 molecule gyration/molecule -compute 2 molecule gyration/molecule tensor --
Description: -
-Define a computation that calculates the radius of gyration Rg of -individual molecules. The calculation includes all effects due to -atoms passing thru periodic boundaries. -
-Rg is a measure of the size of a molecule, and is computed as the -square root of the Rg^2 value in this formula -
-
-where M is the total mass of the molecule, Rcm is the center-of-mass -position of the molecule, and the sum is over all atoms in the -molecule and in the group. -
-If the tensor keyword is specified, then the scalar Rg value is not -calculated, but a 6-element Rg^2 tensor is instead calculated for each -molecule. The formula for the components of the tensor is the same as -the above formula, except that (Ri - Rcm)^2 is replaced by (Rix - -Rcmx) * (Riy - Rcmy) for the xy component, etc. The 6 components of -the tensor are ordered xx, yy, zz, xy, xz, yz. Note -that unlike the scalar Rg, each of the 6 values of the tensor is -effectively a "squared" value, since the cross-terms may be negative -and taking a sqrt() would be invalid. -
-Rg for a particular molecule is only computed if one or more of its -atoms are in the specified group. Normally all atoms in the molecule -should be in the group, however this is not required. LAMMPS will -warn you if this is not the case. Only atoms in the group contribute -to the Rg calculation for the molecule. -
-The ordering of per-molecule quantities produced by this compute is -consistent with the ordering produced by other compute commands that -generate per-molecule datums. Conceptually, the molecule IDs will be -in ascending order for any molecule with one or more of its atoms in -the specified group. -
-IMPORTANT NOTE: The coordinates of an atom contribute to Rg in -"unwrapped" form, by using the image flags associated with each atom. -See the dump custom command for a discussion of -"unwrapped" coordinates. See the Atoms section of the -read_data command for a discussion of image flags and -how they are set for each atom. You can reset the image flags -(e.g. to 0) before invoking this compute by using the set -image command. -
-Output info: -
-This compute calculates a global vector if the tensor keyword is not -specified and a global array if it is. The length of the vector or -number of rows in the array is the number of molecules. If the -tensor keyword is specified, the global array has 6 columns. The -vector or array can be accessed by any command that uses global values -from a compute as input. See this -section for an overview of LAMMPS output -options. -
-All the vector or array values calculated by this compute are -"intensive". The vector and aray values will be in distance and -distance^2 units respectively. -
-Restrictions: none -
-Related commands: none -
- -Default: none -
- diff --git a/doc/compute_gyration_molecule.txt b/doc/compute_gyration_molecule.txt deleted file mode 100644 index 4d113d40c8..0000000000 --- a/doc/compute_gyration_molecule.txt +++ /dev/null @@ -1,94 +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 - -compute gyration/molecule command :h3 - -[Syntax:] - -compute ID group-ID gyration/molecule keyword value ... :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -gyration/molecule = style name of this compute command :l -zero or more keyword/value pairs may be appended :l -keyword = {tensor} :l - {tensor} value = none :pre -:ule - -[Examples:] - -compute 1 molecule gyration/molecule -compute 2 molecule gyration/molecule tensor :pre - -[Description:] - -Define a computation that calculates the radius of gyration Rg of -individual molecules. The calculation includes all effects due to -atoms passing thru periodic boundaries. - -Rg is a measure of the size of a molecule, and is computed as the -square root of the Rg^2 value in this formula - -:c,image(Eqs/compute_gyration.jpg) - -where M is the total mass of the molecule, Rcm is the center-of-mass -position of the molecule, and the sum is over all atoms in the -molecule and in the group. - -If the {tensor} keyword is specified, then the scalar Rg value is not -calculated, but a 6-element Rg^2 tensor is instead calculated for each -molecule. The formula for the components of the tensor is the same as -the above formula, except that (Ri - Rcm)^2 is replaced by (Rix - -Rcmx) * (Riy - Rcmy) for the xy component, etc. The 6 components of -the tensor are ordered xx, yy, zz, xy, xz, yz. Note -that unlike the scalar Rg, each of the 6 values of the tensor is -effectively a "squared" value, since the cross-terms may be negative -and taking a sqrt() would be invalid. - -Rg for a particular molecule is only computed if one or more of its -atoms are in the specified group. Normally all atoms in the molecule -should be in the group, however this is not required. LAMMPS will -warn you if this is not the case. Only atoms in the group contribute -to the Rg calculation for the molecule. - -The ordering of per-molecule quantities produced by this compute is -consistent with the ordering produced by other compute commands that -generate per-molecule datums. Conceptually, the molecule IDs will be -in ascending order for any molecule with one or more of its atoms in -the specified group. - -IMPORTANT NOTE: The coordinates of an atom contribute to Rg in -"unwrapped" form, by using the image flags associated with each atom. -See the "dump custom"_dump.html command for a discussion of -"unwrapped" coordinates. See the Atoms section of the -"read_data"_read_data.html command for a discussion of image flags and -how they are set for each atom. You can reset the image flags -(e.g. to 0) before invoking this compute by using the "set -image"_set.html command. - -[Output info:] - -This compute calculates a global vector if the {tensor} keyword is not -specified and a global array if it is. The length of the vector or -number of rows in the array is the number of molecules. If the -{tensor} keyword is specified, the global array has 6 columns. The -vector or array can be accessed by any command that uses global values -from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. - -All the vector or array values calculated by this compute are -"intensive". The vector and aray values will be in distance and -distance^2 "units"_units.html respectively. - -[Restrictions:] none - -[Related commands:] none - -"compute gyration"_compute_gyration.html - -[Default:] none diff --git a/doc/compute_inertia_chunk.html b/doc/compute_inertia_chunk.html new file mode 100644 index 0000000000..5803968105 --- /dev/null +++ b/doc/compute_inertia_chunk.html @@ -0,0 +1,93 @@ + ++ +
compute inertia/chunk command +
+Syntax: +
+compute ID group-ID inertia/chunk chunkID ++
- ID, group-ID are documented in compute command +
- inertia/molecule = style name of this compute command +
- chunkID = ID of compute chunk/atom command +
Examples: +
+compute 1 fluid inertia/chunk molchunk ++
Description: +
+Define a computation that calculates the inertia tensor for multiple +chunks of atoms. +
+In LAMMPS, chunks are collections of atoms defined by a compute +chunk/atom command, which assigns each atom +to a single chunk (or no chunk). The ID for this command is specified +as chunkID. For example, a single chunk could be the atoms in a +molecule or atoms in a spatial bin. See the compute +chunk/atom doc page and "Section_howto +23 for details of how chunks can be +defined and examples of how they can be used to measure properties of +a system. +
+This compute calculates the 6 components of the symmetric intertia +tensor for each chunk, ordered Ixx,Iyy,Izz,Ixy,Iyz,Ixz. The +calculation includes all effects due to atoms passing thru periodic +boundaries. +
+Note that only atoms in the specified group contribute to the +calculation. The compute chunk/atom command +defines its own group; atoms will have a chunk ID = 0 if they are not +in that group, signifying they are not assigned to a chunk, and will +thus also not contribute to this calculation. You can specify the +"all" group for this command if you simply want to include atoms with +non-zero chunk IDs. +
+IMPORTANT NOTE: The coordinates of an atom contribute to the chunk's +inertia tensor in "unwrapped" form, by using the image flags +associated with each atom. See the dump custom command +for a discussion of "unwrapped" coordinates. See the Atoms section of +the read_data command for a discussion of image flags +and how they are set for each atom. You can reset the image flags +(e.g. to 0) before invoking this compute by using the set +image command. +
+The simplest way to output the results of the compute inertia/chunk +calculation to a file is to use the fix ave/time +command, for example: +
+compute cc1 chunk/atom molecule +compute myChunk all inertia/chunk cc1 +fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector ++
Output info: +
+This compute calculates a global array where the number of rows = the +number of chunks Nchunk as calculated by the specified compute +chunk/atom command. The number of columns = +6 for the 6 components of the inertia tensor for each chunk, ordered +as listed above. These values can be accessed by any command that +uses global array values from a compute as input. See Section_howto +15 for an overview of LAMMPS output +options. +
+The array values are "intensive". The array values will be in +mass*distance^2 units. +
+Restrictions: none +
+Related commands: +
+ +Default: none +
+ diff --git a/doc/compute_inertia_chunk.txt b/doc/compute_inertia_chunk.txt new file mode 100644 index 0000000000..f268ff3d75 --- /dev/null +++ b/doc/compute_inertia_chunk.txt @@ -0,0 +1,88 @@ +"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 + +compute inertia/chunk command :h3 + +[Syntax:] + +compute ID group-ID inertia/chunk chunkID :pre + +ID, group-ID are documented in "compute"_compute.html command +inertia/molecule = style name of this compute command +chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :ul + +[Examples:] + +compute 1 fluid inertia/chunk molchunk :pre + +[Description:] + +Define a computation that calculates the inertia tensor for multiple +chunks of atoms. + +In LAMMPS, chunks are collections of atoms defined by a "compute +chunk/atom"_compute_chunk_atom.html command, which assigns each atom +to a single chunk (or no chunk). The ID for this command is specified +as chunkID. For example, a single chunk could be the atoms in a +molecule or atoms in a spatial bin. See the "compute +chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto +23"_Section_howto.html#howto_23 for details of how chunks can be +defined and examples of how they can be used to measure properties of +a system. + +This compute calculates the 6 components of the symmetric intertia +tensor for each chunk, ordered Ixx,Iyy,Izz,Ixy,Iyz,Ixz. The +calculation includes all effects due to atoms passing thru periodic +boundaries. + +Note that only atoms in the specified group contribute to the +calculation. The "compute chunk/atom"_compute_chunk_atom.html command +defines its own group; atoms will have a chunk ID = 0 if they are not +in that group, signifying they are not assigned to a chunk, and will +thus also not contribute to this calculation. You can specify the +"all" group for this command if you simply want to include atoms with +non-zero chunk IDs. + +IMPORTANT NOTE: The coordinates of an atom contribute to the chunk's +inertia tensor in "unwrapped" form, by using the image flags +associated with each atom. See the "dump custom"_dump.html command +for a discussion of "unwrapped" coordinates. See the Atoms section of +the "read_data"_read_data.html command for a discussion of image flags +and how they are set for each atom. You can reset the image flags +(e.g. to 0) before invoking this compute by using the "set +image"_set.html command. + +The simplest way to output the results of the compute inertia/chunk +calculation to a file is to use the "fix ave/time"_fix_ave_time.html +command, for example: + +compute cc1 chunk/atom molecule +compute myChunk all inertia/chunk cc1 +fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector :pre + +[Output info:] + +This compute calculates a global array where the number of rows = the +number of chunks {Nchunk} as calculated by the specified "compute +chunk/atom"_compute_chunk_atom.html command. The number of columns = +6 for the 6 components of the inertia tensor for each chunk, ordered +as listed above. These values can be accessed by any command that +uses global array values from a compute as input. See "Section_howto +15"_Section_howto.html#howto_15 for an overview of LAMMPS output +options. + +The array values are "intensive". The array values will be in +mass*distance^2 "units"_units.html. + +[Restrictions:] none + +[Related commands:] + +"variable inertia() function"_variable.html + +[Default:] none diff --git a/doc/compute_inertia_molecule.html b/doc/compute_inertia_molecule.html deleted file mode 100644 index 86f3e5dfb6..0000000000 --- a/doc/compute_inertia_molecule.html +++ /dev/null @@ -1,75 +0,0 @@ - -- -
compute inertia/molecule command -
-Syntax: -
-compute ID group-ID inertia/molecule --
- ID, group-ID are documented in compute command -
- inertia/molecule = style name of this compute command -
Examples: -
-compute 1 fluid inertia/molecule --
Description: -
-Define a computation that calculates the inertia tensor of individual -molecules. The calculation includes all effects due to atoms passing -thru periodic boundaries. -
-The symmetric intertia tensor has 6 components, ordered -Ixx,Iyy,Izz,Ixy,Iyz,Ixz. The tensor for a particular molecule is only -computed if one or more of its atoms is in the specified group. -Normally all atoms in the molecule should be in the group, however -this is not required. LAMMPS will warn you if this is not the case. -Only atoms in the group contribute to the inertia tensor and -associated center-of-mass calculation for the molecule. -
-The ordering of per-molecule quantities produced by this compute is -consistent with the ordering produced by other compute commands that -generate per-molecule datums. Conceptually, the molecule IDs will be -in ascending order for any molecule with one or more of its atoms in -the specified group. -
-IMPORTANT NOTE: The coordinates of an atom contribute to the -molecule's inertia tensor in "unwrapped" form, by using the image -flags associated with each atom. See the dump custom -command for a discussion of "unwrapped" coordinates. See the Atoms -section of the read_data command for a discussion of -image flags and how they are set for each atom. You can reset the -image flags (e.g. to 0) before invoking this compute by using the set -image command. -
-Output info: -
-This compute calculates a global array where the number of rows = -Nmolecules and the number of columns = 6 for the 6 components of the -inertia tensor of each molecule, ordered as listed above. These -values can be accessed by any command that uses global array values -from a compute as input. See Section_howto -15 for an overview of LAMMPS output -options. -
-The array values are "intensive". The array values will be in -distance units. -
-Restrictions: none -
-Related commands: -
- -Default: none -
- diff --git a/doc/compute_inertia_molecule.txt b/doc/compute_inertia_molecule.txt deleted file mode 100644 index d5ae0c1305..0000000000 --- a/doc/compute_inertia_molecule.txt +++ /dev/null @@ -1,70 +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 - -compute inertia/molecule command :h3 - -[Syntax:] - -compute ID group-ID inertia/molecule :pre - -ID, group-ID are documented in "compute"_compute.html command -inertia/molecule = style name of this compute command :ul - -[Examples:] - -compute 1 fluid inertia/molecule :pre - -[Description:] - -Define a computation that calculates the inertia tensor of individual -molecules. The calculation includes all effects due to atoms passing -thru periodic boundaries. - -The symmetric intertia tensor has 6 components, ordered -Ixx,Iyy,Izz,Ixy,Iyz,Ixz. The tensor for a particular molecule is only -computed if one or more of its atoms is in the specified group. -Normally all atoms in the molecule should be in the group, however -this is not required. LAMMPS will warn you if this is not the case. -Only atoms in the group contribute to the inertia tensor and -associated center-of-mass calculation for the molecule. - -The ordering of per-molecule quantities produced by this compute is -consistent with the ordering produced by other compute commands that -generate per-molecule datums. Conceptually, the molecule IDs will be -in ascending order for any molecule with one or more of its atoms in -the specified group. - -IMPORTANT NOTE: The coordinates of an atom contribute to the -molecule's inertia tensor in "unwrapped" form, by using the image -flags associated with each atom. See the "dump custom"_dump.html -command for a discussion of "unwrapped" coordinates. See the Atoms -section of the "read_data"_read_data.html command for a discussion of -image flags and how they are set for each atom. You can reset the -image flags (e.g. to 0) before invoking this compute by using the "set -image"_set.html command. - -[Output info:] - -This compute calculates a global array where the number of rows = -Nmolecules and the number of columns = 6 for the 6 components of the -inertia tensor of each molecule, ordered as listed above. These -values can be accessed by any command that uses global array values -from a compute as input. See "Section_howto -15"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. - -The array values are "intensive". The array values will be in -distance "units"_units.html. - -[Restrictions:] none - -[Related commands:] - -"variable inertia() function"_variable.html - -[Default:] none diff --git a/doc/compute_msd_chunk.html b/doc/compute_msd_chunk.html new file mode 100644 index 0000000000..7338a41626 --- /dev/null +++ b/doc/compute_msd_chunk.html @@ -0,0 +1,125 @@ + ++ +
compute msd/chunk command +
+Syntax: +
+compute ID group-ID msd/chunk chunkID ++
- ID, group-ID are documented in compute command +
- msd/molecule = style name of this compute command +
- chunkID = ID of compute chunk/atom command +
Examples: +
+compute 1 all msd/chunk molchunk ++
Description: +
+Define a computation that calculates the mean-squared displacement +(MSD) for multiple chunks of atoms. +
+In LAMMPS, chunks are collections of atoms defined by a compute +chunk/atom command, which assigns each atom +to a single chunk (or no chunk). The ID for this command is specified +as chunkID. For example, a single chunk could be the atoms in a +molecule or atoms in a spatial bin. See the compute +chunk/atom doc page and "Section_howto +23 for details of how chunks can be +defined and examples of how they can be used to measure properties of +a system. +
+Four quantites are calculated by this compute for each chunk. The +first 3 quantities are the squared dx,dy,dz displacements of the +center-of-mass. The 4th component is the total squared displacement, +i.e. (dx*dx + dy*dy + dz*dz) of the center-of-mass. These +calculations include all effects due to atoms passing thru periodic +boundaries. +
+Note that only atoms in the specified group contribute to the +calculation. The compute chunk/atom command +defines its own group; atoms will have a chunk ID = 0 if they are not +in that group, signifying they are not assigned to a chunk, and will +thus also not contribute to this calculation. You can specify the +"all" group for this command if you simply want to include atoms with +non-zero chunk IDs. +
+The slope of the mean-squared displacement (MSD) versus time is +proportional to the diffusion coefficient of the diffusing chunks. +
+The displacement of the center-of-mass of the chunk is from its +original center-of-mass position, calculated on the timestep this +compute command was first invoked. +
+IMPORTANT NOTE: The number of chunks Nchunk calculated by the +compute chunk/atom command must remain +constant each time this compute is invoked, so that the displacement +for each chunk from its original position can be computed +consistently. If Nchunk does not remain constant, an error will be +generated. If needed, you can enforce a constant Nchunk by using +the nchunk once or ids once options when specifying the compute +chunk/atom command. +
+IMPORTANT NOTE: This compute stores the original position (of the +center-of-mass) of each chunk. When a displacement is calculated on a +later timestep, it is assumed that the same atoms are assigned to the +same chunk ID. However LAMMPS has no simple way to insure this is the +case, though you can use the ids once option when specifying the +compute chunk/atom command. Note that if +this is not the case, the MSD calculation does not have a sensible +meaning. +
+IMPORTANT NOTE: The initial coordinates of the atoms in each chunk are +stored in "unwrapped" form, by using the image flags associated with +each atom. See the dump custom command for a discussion +of "unwrapped" coordinates. See the Atoms section of the +read_data command for a discussion of image flags and +how they are set for each atom. You can reset the image flags +(e.g. to 0) before invoking this compute by using the set +image command. +
+IMPORTANT NOTE: Unlike the compute msd command, +this compute does not store the initial center-of-mass coorindates of +its molecules in a restart file. Thus you cannot continue the MSD per +chunk calculation of this compute when running from a restart +file. +
+The simplest way to output the results of the compute com/msd +calculation to a file is to use the fix ave/time +command, for example: +
+compute cc1 chunk/atom molecule +compute myChunk all com/msd cc1 +fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector ++
Output info: +
+This compute calculates a global array where the number of rows = the +number of chunks Nchunk as calculated by the specified compute +chunk/atom command. The number of columns = +4 for dx,dy,dz and the total displacement. These values can be +accessed by any command that uses global array values from a compute +as input. See this section for an +overview of LAMMPS output options. +
+The array values are "intensive". The array values will be in +distance^2 units. +
+Restrictions: none +
+Related commands: +
+ +Default: none +
+ diff --git a/doc/compute_msd_chunk.txt b/doc/compute_msd_chunk.txt new file mode 100644 index 0000000000..19cc2bddc6 --- /dev/null +++ b/doc/compute_msd_chunk.txt @@ -0,0 +1,120 @@ +"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 + +compute msd/chunk command :h3 + +[Syntax:] + +compute ID group-ID msd/chunk chunkID :pre + +ID, group-ID are documented in "compute"_compute.html command +msd/molecule = style name of this compute command +chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :ul + +[Examples:] + +compute 1 all msd/chunk molchunk :pre + +[Description:] + +Define a computation that calculates the mean-squared displacement +(MSD) for multiple chunks of atoms. + +In LAMMPS, chunks are collections of atoms defined by a "compute +chunk/atom"_compute_chunk_atom.html command, which assigns each atom +to a single chunk (or no chunk). The ID for this command is specified +as chunkID. For example, a single chunk could be the atoms in a +molecule or atoms in a spatial bin. See the "compute +chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto +23"_Section_howto.html#howto_23 for details of how chunks can be +defined and examples of how they can be used to measure properties of +a system. + +Four quantites are calculated by this compute for each chunk. The +first 3 quantities are the squared dx,dy,dz displacements of the +center-of-mass. The 4th component is the total squared displacement, +i.e. (dx*dx + dy*dy + dz*dz) of the center-of-mass. These +calculations include all effects due to atoms passing thru periodic +boundaries. + +Note that only atoms in the specified group contribute to the +calculation. The "compute chunk/atom"_compute_chunk_atom.html command +defines its own group; atoms will have a chunk ID = 0 if they are not +in that group, signifying they are not assigned to a chunk, and will +thus also not contribute to this calculation. You can specify the +"all" group for this command if you simply want to include atoms with +non-zero chunk IDs. + +The slope of the mean-squared displacement (MSD) versus time is +proportional to the diffusion coefficient of the diffusing chunks. + +The displacement of the center-of-mass of the chunk is from its +original center-of-mass position, calculated on the timestep this +compute command was first invoked. + +IMPORTANT NOTE: The number of chunks {Nchunk} calculated by the +"compute chunk/atom"_compute_chunk_atom.html command must remain +constant each time this compute is invoked, so that the displacement +for each chunk from its original position can be computed +consistently. If {Nchunk} does not remain constant, an error will be +generated. If needed, you can enforce a constant {Nchunk} by using +the {nchunk once} or {ids once} options when specifying the "compute +chunk/atom"_compute_chunk_atom.html command. + +IMPORTANT NOTE: This compute stores the original position (of the +center-of-mass) of each chunk. When a displacement is calculated on a +later timestep, it is assumed that the same atoms are assigned to the +same chunk ID. However LAMMPS has no simple way to insure this is the +case, though you can use the {ids once} option when specifying the +"compute chunk/atom"_compute_chunk_atom.html command. Note that if +this is not the case, the MSD calculation does not have a sensible +meaning. + +IMPORTANT NOTE: The initial coordinates of the atoms in each chunk are +stored in "unwrapped" form, by using the image flags associated with +each atom. See the "dump custom"_dump.html command for a discussion +of "unwrapped" coordinates. See the Atoms section of the +"read_data"_read_data.html command for a discussion of image flags and +how they are set for each atom. You can reset the image flags +(e.g. to 0) before invoking this compute by using the "set +image"_set.html command. + +IMPORTANT NOTE: Unlike the "compute msd"_compute_msd.html command, +this compute does not store the initial center-of-mass coorindates of +its molecules in a restart file. Thus you cannot continue the MSD per +chunk calculation of this compute when running from a "restart +file"_read_restart.html. + +The simplest way to output the results of the compute com/msd +calculation to a file is to use the "fix ave/time"_fix_ave_time.html +command, for example: + +compute cc1 chunk/atom molecule +compute myChunk all com/msd cc1 +fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector :pre + +[Output info:] + +This compute calculates a global array where the number of rows = the +number of chunks {Nchunk} as calculated by the specified "compute +chunk/atom"_compute_chunk_atom.html command. The number of columns = +4 for dx,dy,dz and the total displacement. These values can be +accessed by any command that uses global array values from a compute +as input. See "this section"_Section_howto.html#howto_15 for an +overview of LAMMPS output options. + +The array values are "intensive". The array values will be in +distance^2 "units"_units.html. + +[Restrictions:] none + +[Related commands:] + +"compute msd"_compute_msd.html + +[Default:] none diff --git a/doc/compute_msd_molecule.html b/doc/compute_msd_molecule.html deleted file mode 100644 index d1f2b2c507..0000000000 --- a/doc/compute_msd_molecule.html +++ /dev/null @@ -1,91 +0,0 @@ - -- -
compute msd/molecule command -
-Syntax: -
-compute ID group-ID msd/molecule --
- ID, group-ID are documented in compute command -
- msd/molecule = style name of this compute command -
Examples: -
-compute 1 all msd/molecule --
Description: -
-Define a computation that calculates the mean-squared displacement -(MSD) of individual molecules. The calculation includes all effects -due to atoms passing thru periodic boundaries. -
-Four quantites are calculated by this compute for each molecule. The -first 3 quantities are the squared dx,dy,dz displacements of the -center-of-mass. The 4th component is the total squared displacement, -i.e. (dx*dx + dy*dy + dz*dz) of the center-of-mass. -
-The slope of the mean-squared displacement (MSD) versus time is -proportional to the diffusion coefficient of the diffusing molecules. -
-The displacement of the center-of-mass of the molecule is from its -original center-of-mass position at the time the compute command was -issued. -
-The MSD for a particular molecule is only computed if one or more of -its atoms are in the specified group. Normally all atoms in the -molecule should be in the group, however this is not required. LAMMPS -will warn you if this is not the case. Only atoms in the group -contribute to the center-of-mass calculation for the molecule, which -is used to caculate its initial and current position. -
-The ordering of per-molecule quantities produced by this compute is -consistent with the ordering produced by other compute commands that -generate per-molecule datums. Conceptually, the molecule IDs will be -in ascending order for any molecule with one or more of its atoms in -the specified group. -
-IMPORTANT NOTE: The initial coordinates of each molecule are stored in -"unwrapped" form, by using the image flags associated with each atom. -See the dump custom command for a discussion of -"unwrapped" coordinates. See the Atoms section of the -read_data command for a discussion of image flags and -how they are set for each atom. You can reset the image flags -(e.g. to 0) before invoking this compute by using the set -image command. -
-IMPORTANT NOTE: Unlike the compute msd command, -this compute does not store the initial center-of-mass coorindates of -its molecules in a restart file. Thus you cannot continue the MSD per -molecule calculation of this compute when running from a restart -file. -
-Output info: -
-This compute calculates a global array where the number of rows = -Nmolecules and the number of columns = 4 for dx,dy,dz and the total -displacement. These values can be accessed by any command that uses -global array values from a compute as input. See this -section for an overview of LAMMPS output -options. -
-The array values are "intensive". The array values will be in -distance^2 units. -
-Restrictions: none -
-Related commands: -
- -Default: none -
- diff --git a/doc/compute_msd_molecule.txt b/doc/compute_msd_molecule.txt deleted file mode 100644 index f3a224270d..0000000000 --- a/doc/compute_msd_molecule.txt +++ /dev/null @@ -1,86 +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 - -compute msd/molecule command :h3 - -[Syntax:] - -compute ID group-ID msd/molecule :pre - -ID, group-ID are documented in "compute"_compute.html command -msd/molecule = style name of this compute command :ul - -[Examples:] - -compute 1 all msd/molecule :pre - -[Description:] - -Define a computation that calculates the mean-squared displacement -(MSD) of individual molecules. The calculation includes all effects -due to atoms passing thru periodic boundaries. - -Four quantites are calculated by this compute for each molecule. The -first 3 quantities are the squared dx,dy,dz displacements of the -center-of-mass. The 4th component is the total squared displacement, -i.e. (dx*dx + dy*dy + dz*dz) of the center-of-mass. - -The slope of the mean-squared displacement (MSD) versus time is -proportional to the diffusion coefficient of the diffusing molecules. - -The displacement of the center-of-mass of the molecule is from its -original center-of-mass position at the time the compute command was -issued. - -The MSD for a particular molecule is only computed if one or more of -its atoms are in the specified group. Normally all atoms in the -molecule should be in the group, however this is not required. LAMMPS -will warn you if this is not the case. Only atoms in the group -contribute to the center-of-mass calculation for the molecule, which -is used to caculate its initial and current position. - -The ordering of per-molecule quantities produced by this compute is -consistent with the ordering produced by other compute commands that -generate per-molecule datums. Conceptually, the molecule IDs will be -in ascending order for any molecule with one or more of its atoms in -the specified group. - -IMPORTANT NOTE: The initial coordinates of each molecule are stored in -"unwrapped" form, by using the image flags associated with each atom. -See the "dump custom"_dump.html command for a discussion of -"unwrapped" coordinates. See the Atoms section of the -"read_data"_read_data.html command for a discussion of image flags and -how they are set for each atom. You can reset the image flags -(e.g. to 0) before invoking this compute by using the "set -image"_set.html command. - -IMPORTANT NOTE: Unlike the "compute msd"_compute_msd.html command, -this compute does not store the initial center-of-mass coorindates of -its molecules in a restart file. Thus you cannot continue the MSD per -molecule calculation of this compute when running from a "restart -file"_read_restart.html. - -[Output info:] - -This compute calculates a global array where the number of rows = -Nmolecules and the number of columns = 4 for dx,dy,dz and the total -displacement. These values can be accessed by any command that uses -global array values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. - -The array values are "intensive". The array values will be in -distance^2 "units"_units.html. - -[Restrictions:] none - -[Related commands:] - -"compute msd"_compute_msd.html - -[Default:] none diff --git a/doc/compute_property_chunk.html b/doc/compute_property_chunk.html new file mode 100644 index 0000000000..aac4407a87 --- /dev/null +++ b/doc/compute_property_chunk.html @@ -0,0 +1,127 @@ + ++ +
compute property/chunk command +
+Syntax: +
+compute ID group-ID property/chunk chunkID input1 input2 ... ++
- ID, group-ID are documented in compute command + +
- property/chunk = style name of this compute command + +
- input = one or more attributes
+
+
attributes = count, id, coord1, coord2, coord3 + count = # of atoms in chunk + id = original chunk IDs before compression by compute chunk/atom + coord123 = coordinates for spatial bins calculated by compute chunk/atom +
+ +
Examples: +
+compute 1 all property/chunk count +compute 1 all property/chunk ID coord1 ++
Description: +
+Define a computation that stores the specified attributes of chunks of +atoms. +
+In LAMMPS, chunks are collections of atoms defined by a compute +chunk/atom command, which assigns each atom +to a single chunk (or no chunk). The ID for this command is specified +as chunkID. For example, a single chunk could be the atoms in a +molecule or atoms in a spatial bin. See the compute +chunk/atom doc page and "Section_howto +23 for details of how chunks can be +defined and examples of how they can be used to measure properties of +a system. +
+This compute calculates and stores the specified attributes of chunks +as global data so they can be accessed by other output +commands and used in conjunction with +other commands that generate per-chunk data, such as compute +com/chunk or compute +msd/chunk. +
+Note that only atoms in the specified group contribute to the +calculation of the count attribute. The compute +chunk/atom command defines its own group; +atoms will have a chunk ID = 0 if they are not in that group, +signifying they are not assigned to a chunk, and will thus also not +contribute to this calculation. You can specify the "all" group for +this command if you simply want to include atoms with non-zero chunk +IDs. +
+The count attribute is the number of atoms in the chunk. +
+The id attribute stores the original chunk ID for each chunk. It +can only be used if the compress keyword was set to yes for the +compute chunk/atom command referenced by +chunkID. This means that the original chunk IDs (e.g. molecule IDs) +will have been compressed to remove chunk IDs with no atoms assigned +to them. Thus a compresed chunk ID of 3 may correspond to an original +chunk ID (molecule ID in this case) of 415. The id attribute will +then be 415 for the 3rd chunk. +
+The coordN attributes can only be used if a binning style was used +in the compute chunk/atom command referenced +by chunkID. For bin/1d, bin/2d, and bin/3d styles the attribute +is the center point of the bin in the corresponding dimension. Style +bin/1d only defines a coord1 attribute. Style bin/2d adds a +coord2 attribute. Style bin/3d adds a coord3 attribute. +
+Note that if the value of the units keyword used in the compute +chunk/atom command is box or lattice, the +coordN attributes will be in distance units. If the +value of the units keyword is reduced, the coordN attributes +will be in unitless reduced units (0-1). +
+The simplest way to output the results of the compute property/chunk +calculation to a file is to use the fix ave/time +command, for example: +
+compute cc1 chunk/atom molecule +compute myChunk1 all property/chunk cc1 +compute myChunk2 all com/chunk cc1 +fix 1 all ave/time 100 1 100 c_myChunk1 c_myChunk2 file tmp.out mode vector ++
Output info: +
+This compute calculates a global vector or global array depending on +the number of input values. The length of the vector or number of +rows in the array is the number of chunks. +
+This compute calculates a global vector or global array where the +number of rows = the number of chunks Nchunk as calculated by the +specified compute chunk/atom command. If a +single input is specified, a global vector is produced. If two or +more inputs are specified, a global array is produced where the number +of columns = the number of inputs. The vector or array can be +accessed by any command that uses global values from a compute as +input. See this section for an overview +of LAMMPS output options. +
+The vector or array values are "intensive". The values will be +unitless or in the units discussed above. +
+Restrictions: none +
+Related commands: +
+ +Default: none +
+ diff --git a/doc/compute_property_chunk.txt b/doc/compute_property_chunk.txt new file mode 100644 index 0000000000..8ec160e9df --- /dev/null +++ b/doc/compute_property_chunk.txt @@ -0,0 +1,118 @@ +"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 + +compute property/chunk command :h3 + +[Syntax:] + +compute ID group-ID property/chunk chunkID input1 input2 ... :pre + +ID, group-ID are documented in "compute"_compute.html command :ulb,l +property/chunk = style name of this compute command :l +input = one or more attributes :l + attributes = count, id, coord1, coord2, coord3 + count = # of atoms in chunk + id = original chunk IDs before compression by "compute chunk/atom"_compute_chunk_atom.html + coord123 = coordinates for spatial bins calculated by "compute chunk/atom"_compute_chunk_atom.html :pre +:ule + +[Examples:] + +compute 1 all property/chunk count +compute 1 all property/chunk ID coord1 :pre + +[Description:] + +Define a computation that stores the specified attributes of chunks of +atoms. + +In LAMMPS, chunks are collections of atoms defined by a "compute +chunk/atom"_compute_chunk_atom.html command, which assigns each atom +to a single chunk (or no chunk). The ID for this command is specified +as chunkID. For example, a single chunk could be the atoms in a +molecule or atoms in a spatial bin. See the "compute +chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto +23"_Section_howto.html#howto_23 for details of how chunks can be +defined and examples of how they can be used to measure properties of +a system. + +This compute calculates and stores the specified attributes of chunks +as global data so they can be accessed by other "output +commands"_Section_howto.html#howto_15 and used in conjunction with +other commands that generate per-chunk data, such as "compute +com/chunk"_compute_com_chunk.html or "compute +msd/chunk"_compute_msd_chunk.html. + +Note that only atoms in the specified group contribute to the +calculation of the {count} attribute. The "compute +chunk/atom"_compute_chunk_atom.html command defines its own group; +atoms will have a chunk ID = 0 if they are not in that group, +signifying they are not assigned to a chunk, and will thus also not +contribute to this calculation. You can specify the "all" group for +this command if you simply want to include atoms with non-zero chunk +IDs. + +The {count} attribute is the number of atoms in the chunk. + +The {id} attribute stores the original chunk ID for each chunk. It +can only be used if the {compress} keyword was set to {yes} for the +"compute chunk/atom"_compute_chunk_atom.html command referenced by +chunkID. This means that the original chunk IDs (e.g. molecule IDs) +will have been compressed to remove chunk IDs with no atoms assigned +to them. Thus a compresed chunk ID of 3 may correspond to an original +chunk ID (molecule ID in this case) of 415. The {id} attribute will +then be 415 for the 3rd chunk. + +The {coordN} attributes can only be used if a {binning} style was used +in the "compute chunk/atom"_compute_chunk_atom.html command referenced +by chunkID. For {bin/1d}, {bin/2d}, and {bin/3d} styles the attribute +is the center point of the bin in the corresponding dimension. Style +{bin/1d} only defines a {coord1} attribute. Style {bin/2d} adds a +{coord2} attribute. Style {bin/3d} adds a {coord3} attribute. + +Note that if the value of the {units} keyword used in the "compute +chunk/atom command"_compute_chunk_atom.html is {box} or {lattice}, the +{coordN} attributes will be in distance "units"_units.html. If the +value of the {units} keyword is {reduced}, the {coordN} attributes +will be in unitless reduced units (0-1). + +The simplest way to output the results of the compute property/chunk +calculation to a file is to use the "fix ave/time"_fix_ave_time.html +command, for example: + +compute cc1 chunk/atom molecule +compute myChunk1 all property/chunk cc1 +compute myChunk2 all com/chunk cc1 +fix 1 all ave/time 100 1 100 c_myChunk1 c_myChunk2 file tmp.out mode vector :pre + +[Output info:] + +This compute calculates a global vector or global array depending on +the number of input values. The length of the vector or number of +rows in the array is the number of chunks. + +This compute calculates a global vector or global array where the +number of rows = the number of chunks {Nchunk} as calculated by the +specified "compute chunk/atom"_compute_chunk_atom.html command. If a +single input is specified, a global vector is produced. If two or +more inputs are specified, a global array is produced where the number +of columns = the number of inputs. The vector or array can be +accessed by any command that uses global values from a compute as +input. See "this section"_Section_howto.html#howto_15 for an overview +of LAMMPS output options. + +The vector or array values are "intensive". The values will be +unitless or in the units discussed above. + +[Restrictions:] none + +[Related commands:] + +"fix ave/chunk"_fix_ave_chunk.html + +[Default:] none diff --git a/doc/compute_property_molecule.html b/doc/compute_property_molecule.html deleted file mode 100644 index c0b4453fe1..0000000000 --- a/doc/compute_property_molecule.html +++ /dev/null @@ -1,77 +0,0 @@ - -- -
compute property/molecule command -
-Syntax: -
-compute ID group-ID property/molecule input1 input2 ... --
- ID, group-ID are documented in compute command - -
- property/molecule = style name of this compute command - -
- input = one or more attributes
-
-
possible attributes = mol cout - mol = molecule ID - count = # of atoms in molecule -
- -
Examples: -
-compute 1 all property/molecule mol --
Description: -
-Define a computation that stores the specified attributes as global -data so it can be accessed by other output -commands and used in conjunction with -other commands that generate per-molecule data, such as compute -com/molecule and compute -msd/molecule. -
-The ordering of per-molecule quantities produced by this compute is -consistent with the ordering produced by other compute commands that -generate per-molecule datums. Conceptually, the molecule IDs will be -in ascending order for any molecule with one or more of its atoms in -the specified group. -
-The mol attribute is the molecule ID. This attribute can be used to -produce molecule IDs as labels for per-molecule datums generated by -other computes or fixes when they are output to a file, e.g. by the -fix ave/time command. -
-The count attribute is the number of atoms in the molecule. -
-Output info: -
-This compute calculates a global vector or global array depending on -the number of input values. The length of the vector or number of -rows in the array is the number of molecules. If a single input is -specified, a global vector is produced. If two or more inputs are -specified, a global array is produced where the number of columns = -the number of inputs. The vector or array can be accessed by any -command that uses global values from a compute as input. See this -section for an overview of LAMMPS output -options. -
-The vector or array values will be integers that correspond to the -specified attribute. -
-Restrictions: none -
-Related commands: none -
-Default: none -
- diff --git a/doc/compute_property_molecule.txt b/doc/compute_property_molecule.txt deleted file mode 100644 index 7768879500..0000000000 --- a/doc/compute_property_molecule.txt +++ /dev/null @@ -1,68 +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 - -compute property/molecule command :h3 - -[Syntax:] - -compute ID group-ID property/molecule input1 input2 ... :pre - -ID, group-ID are documented in "compute"_compute.html command :ulb,l -property/molecule = style name of this compute command :l -input = one or more attributes :l - possible attributes = mol cout - mol = molecule ID - count = # of atoms in molecule :pre -:ule - -[Examples:] - -compute 1 all property/molecule mol :pre - -[Description:] - -Define a computation that stores the specified attributes as global -data so it can be accessed by other "output -commands"_Section_howto.html#howto_15 and used in conjunction with -other commands that generate per-molecule data, such as "compute -com/molecule"_compute_com_molecule.html and "compute -msd/molecule"_compute_msd_molecule.html. - -The ordering of per-molecule quantities produced by this compute is -consistent with the ordering produced by other compute commands that -generate per-molecule datums. Conceptually, the molecule IDs will be -in ascending order for any molecule with one or more of its atoms in -the specified group. - -The {mol} attribute is the molecule ID. This attribute can be used to -produce molecule IDs as labels for per-molecule datums generated by -other computes or fixes when they are output to a file, e.g. by the -"fix ave/time"_fix_ave_time.html command. - -The {count} attribute is the number of atoms in the molecule. - -[Output info:] - -This compute calculates a global vector or global array depending on -the number of input values. The length of the vector or number of -rows in the array is the number of molecules. If a single input is -specified, a global vector is produced. If two or more inputs are -specified, a global array is produced where the number of columns = -the number of inputs. The vector or array can be accessed by any -command that uses global values from a compute as input. See "this -section"_Section_howto.html#howto_15 for an overview of LAMMPS output -options. - -The vector or array values will be integers that correspond to the -specified attribute. - -[Restrictions:] none - -[Related commands:] none - -[Default:] none diff --git a/doc/compute_temp_chunk.html b/doc/compute_temp_chunk.html new file mode 100644 index 0000000000..26f227e880 --- /dev/null +++ b/doc/compute_temp_chunk.html @@ -0,0 +1,185 @@ + ++ +
compute temp/chunk command +
+Syntax: +
+compute ID group-ID temp/chunk chunkID keyword value ... ++
- ID, group-ID are documented in compute command + +
- temp/chunk = style name of this compute command + +
- chunkID = ID of compute chunk/atom command + +
- zero or more keyword/value pairs may be appended + +
- keyword = com or biasor adof or cdof
+
+
com value = yes or no + yes = subtract center-of-mass velocity from each chunk before calculating temperature + no = do not subtract center-of-mass velocity + bias value = bias-ID + bias-ID = ID of a temperature compute that removes a velocity bias + adof value = dof_per_atom + dof_per_atom = define this many degrees-of-freedom per atom + cdof value = dof_per_chunk + dof_per_chunk = define this many degrees-of-freedom per chunk +
+ +
Examples: +
+compute 1 fluid temp/chunk molchunk ++
compute 1 fluid temp/chunk molchunk bias tpartial adof 2.0 ++
Description: +
+Define a computation that calculates the temperature of multiple +chunks of atoms. Note that unlike other computes with style names +temp/* which calculate the temperature of an entire group of atoms, +this compute cannot be used by any command that uses such a +temperature compute, e.g. thermo_modify, fix +temp/rescale, fix npt, etc. That +is because this compute calculates multiple temperatures, one per +chunk. +
+In LAMMPS, chunks are collections of atoms defined by a compute +chunk/atom command, which assigns each atom +to a single chunk (or no chunk). The ID for this command is specified +as chunkID. For example, a single chunk could be the atoms in a +molecule or atoms in a spatial bin. See the compute +chunk/atom doc page and "Section_howto +23 for details of how chunks can be +defined and examples of how they can be used to measure properties of +a system. +
+This compute calculates the temperature for each chunk by the formula +KE = DOF/2 k T, where KE = total kinetic energy of the chunk of atoms +(sum of 1/2 m v^2), DOF = the total number of degrees of freedom for +all atoms in the chunk, k = Boltzmann constant, and T = temperature. +
+The DOF is calculated as N*adof + cdof, where N = number of atoms in +the chunk, adof = degrees of freedom per atom, and cdof = degrees of +freedom per chunk. By default adof = 2 or 3 = dimensionality of +system, as set via the dimension command, and cdof = +0.0. This gives the usual formula for temperature. +
+Note that currently this temperature only includes translational +degrees of freedom for each atom. No rotational degrees of freedom +are included for finite-size particles. Also no degrees of freedom +are subtracted for any velocity bias or constraints that are applied, +such as compute temp/partial, or fix +shake or fix rigid. This is because +those degrees of freedom (e.g. a constrained bond) could apply to sets +of atoms that are both included and excluded from a specific chunk, +and hence the concept is somewhat ill-defined. In some cases, you can +use the adof and cdof keywords to adjust the calculated degress of +freedom appropriately, as explained below. +
+Also note that a bias can be subtracted from atom velocities before +they are used in the above formula for KE, by using the bias +keyword. This allows, for example, a thermal temperature to be +computed after removal of a flow velocity profile. +
+Note that this compute and the fix ave/chunk temp +command can calculate different things. This compute calculates the +temperature for each chunk for a single snapshot. Fix ave/chunk can +do that but can time average those values over many snapshots, or it +can compute a temperature as if the atoms in the chunk on different +timesteps were collected together as one set of atoms to calculate +their temperature. This compute allows the center-of-mass velocity of +each chunk to be subtracted before calculating the temperature; fix +ave/chunk does not. +
+Note that only atoms in the specified group contribute to the +calculation. The compute chunk/atom command +defines its own group; atoms will have a chunk ID = 0 if they are not +in that group, signifying they are not assigned to a chunk, and will +thus also not contribute to this calculation. You can specify the +"all" group for this command if you simply want to include atoms with +non-zero chunk IDs. +
+The simplest way to output the results of the compute temp/chunk +calculation to a file is to use the fix ave/time +command, for example: +
+compute cc1 chunk/atom molecule +compute myChunk all temp/chunk cc1 +fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector ++
+ +
The keyword/value option pairs are used in the following ways. +
+The com keyword can be used with a value of yes to subtract the +velocity of the center-of-mass for each chunk from the velocity of the +atoms in that chunk, before calculating the temperature. This can be +useful if the atoms are streaming or otherwise moving collectively, +and you wish to calculate only the thermal temperature. +
+For the bias keyword, bias-ID refers to the ID of a temperature +compute that removes a "bias" velocity from each atom. This also +allows compute temp/chunk to compute the thermal temperature of each +chunk after the translational kinetic energy components have been +altered in a prescribed way, e.g. to remove a velocity profile. Note +that the temperature compute will apply its bias globally to the +entire system, not on a per-chunk basis. +
+The adof and cdof keywords define the values used in the degree of +freedom (DOF) formula used for each chunk, as described above. They +can be used to calculate a more appropriate temperature for some kinds +of chunks. Here are 3 examples. +
+If spatially binned chunks contain some number of water molecules and +fix shake is used to make each molecule rigid, then +you could calculate a temperature with 6 degrees of freedom (DOF) (3 +translational, 3 rotational) per molecule by setting adof to 2.0. +If compute temp/partial is used with the +bias keyword to only allow the x component of velocity to contribute +to the temperature, then adof = 1.0 would be appropriate. If each +chunk consists of a large molecule, with some number of its bonds +constrained by fix shake or the entire molecule by +fix rigid/small, then cdof could be set to the +remaining degrees of freedom for the entire molecule (entire chunk in +this case). +
++ +
Output info: +
+This compute calculates a global vector where the number of rows = the +number of chunks Nchunk as calculated by the specified compute +chunk/atom command. These values can be +accessed by any command that uses global vector values from a compute +as input. See Section_howto 15 for an +overview of LAMMPS output options. +
+The vector values are "intensive". The vector values will be in +temperature units. +
+Restrictions: +
+The com and bias keywords cannot be used together. +
+Related commands: +
+compute temp, fix ave/chunk +temp +
+Default: +
+The option defaults are com no, no bias, adof = dimensionality of the +system (2 or 3), and cdof = 0.0. +
+ diff --git a/doc/compute_temp_chunk.txt b/doc/compute_temp_chunk.txt new file mode 100644 index 0000000000..83ed0e41d5 --- /dev/null +++ b/doc/compute_temp_chunk.txt @@ -0,0 +1,173 @@ +"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 + +compute temp/chunk command :h3 + +[Syntax:] + +compute ID group-ID temp/chunk chunkID keyword value ... :pre + +ID, group-ID are documented in "compute"_compute.html command :ulb,l +temp/chunk = style name of this compute command :l +chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :l +zero or more keyword/value pairs may be appended :l +keyword = {com} or {bias}or {adof} or {cdof} :l + {com} value = {yes} or {no} + yes = subtract center-of-mass velocity from each chunk before calculating temperature + no = do not subtract center-of-mass velocity + {bias} value = bias-ID + bias-ID = ID of a temperature compute that removes a velocity bias + {adof} value = dof_per_atom + dof_per_atom = define this many degrees-of-freedom per atom + {cdof} value = dof_per_chunk + dof_per_chunk = define this many degrees-of-freedom per chunk :pre +:ule + +[Examples:] + +compute 1 fluid temp/chunk molchunk :pre +compute 1 fluid temp/chunk molchunk bias tpartial adof 2.0 :pre + +[Description:] + +Define a computation that calculates the temperature of multiple +chunks of atoms. Note that unlike other computes with style names +temp/* which calculate the temperature of an entire group of atoms, +this compute cannot be used by any command that uses such a +temperature compute, e.g. "thermo_modify"_thermo_modify.html, "fix +temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_nh.html, etc. That +is because this compute calculates multiple temperatures, one per +chunk. + +In LAMMPS, chunks are collections of atoms defined by a "compute +chunk/atom"_compute_chunk_atom.html command, which assigns each atom +to a single chunk (or no chunk). The ID for this command is specified +as chunkID. For example, a single chunk could be the atoms in a +molecule or atoms in a spatial bin. See the "compute +chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto +23"_Section_howto.html#howto_23 for details of how chunks can be +defined and examples of how they can be used to measure properties of +a system. + +This compute calculates the temperature for each chunk by the formula +KE = DOF/2 k T, where KE = total kinetic energy of the chunk of atoms +(sum of 1/2 m v^2), DOF = the total number of degrees of freedom for +all atoms in the chunk, k = Boltzmann constant, and T = temperature. + +The DOF is calculated as N*adof + cdof, where N = number of atoms in +the chunk, adof = degrees of freedom per atom, and cdof = degrees of +freedom per chunk. By default adof = 2 or 3 = dimensionality of +system, as set via the "dimension"_dimension.html command, and cdof = +0.0. This gives the usual formula for temperature. + +Note that currently this temperature only includes translational +degrees of freedom for each atom. No rotational degrees of freedom +are included for finite-size particles. Also no degrees of freedom +are subtracted for any velocity bias or constraints that are applied, +such as "compute temp/partial"_compute_temp_partial.html, or "fix +shake"_fix_shake.html or "fix rigid"_fix_rigid.html. This is because +those degrees of freedom (e.g. a constrained bond) could apply to sets +of atoms that are both included and excluded from a specific chunk, +and hence the concept is somewhat ill-defined. In some cases, you can +use the {adof} and {cdof} keywords to adjust the calculated degress of +freedom appropriately, as explained below. + +Also note that a bias can be subtracted from atom velocities before +they are used in the above formula for KE, by using the {bias} +keyword. This allows, for example, a thermal temperature to be +computed after removal of a flow velocity profile. + +Note that this compute and the "fix ave/chunk temp"_fix_ave_chunk.html +command can calculate different things. This compute calculates the +temperature for each chunk for a single snapshot. Fix ave/chunk can +do that but can time average those values over many snapshots, or it +can compute a temperature as if the atoms in the chunk on different +timesteps were collected together as one set of atoms to calculate +their temperature. This compute allows the center-of-mass velocity of +each chunk to be subtracted before calculating the temperature; fix +ave/chunk does not. + +Note that only atoms in the specified group contribute to the +calculation. The "compute chunk/atom"_compute_chunk_atom.html command +defines its own group; atoms will have a chunk ID = 0 if they are not +in that group, signifying they are not assigned to a chunk, and will +thus also not contribute to this calculation. You can specify the +"all" group for this command if you simply want to include atoms with +non-zero chunk IDs. + +The simplest way to output the results of the compute temp/chunk +calculation to a file is to use the "fix ave/time"_fix_ave_time.html +command, for example: + +compute cc1 chunk/atom molecule +compute myChunk all temp/chunk cc1 +fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector :pre + +:line + +The keyword/value option pairs are used in the following ways. + +The {com} keyword can be used with a value of {yes} to subtract the +velocity of the center-of-mass for each chunk from the velocity of the +atoms in that chunk, before calculating the temperature. This can be +useful if the atoms are streaming or otherwise moving collectively, +and you wish to calculate only the thermal temperature. + +For the {bias} keyword, {bias-ID} refers to the ID of a temperature +compute that removes a "bias" velocity from each atom. This also +allows compute temp/chunk to compute the thermal temperature of each +chunk after the translational kinetic energy components have been +altered in a prescribed way, e.g. to remove a velocity profile. Note +that the temperature compute will apply its bias globally to the +entire system, not on a per-chunk basis. + +The {adof} and {cdof} keywords define the values used in the degree of +freedom (DOF) formula used for each chunk, as described above. They +can be used to calculate a more appropriate temperature for some kinds +of chunks. Here are 3 examples. + +If spatially binned chunks contain some number of water molecules and +"fix shake"_fix_shake.html is used to make each molecule rigid, then +you could calculate a temperature with 6 degrees of freedom (DOF) (3 +translational, 3 rotational) per molecule by setting {adof} to 2.0. +If "compute temp/partial"_compute_temp_partial.html is used with the +{bias} keyword to only allow the x component of velocity to contribute +to the temperature, then {adof} = 1.0 would be appropriate. If each +chunk consists of a large molecule, with some number of its bonds +constrained by "fix shake"_fix_shake.html or the entire molecule by +"fix rigid/small"_fix_rigid.html, then {cdof} could be set to the +remaining degrees of freedom for the entire molecule (entire chunk in +this case). + +:line + +[Output info:] + +This compute calculates a global vector where the number of rows = the +number of chunks {Nchunk} as calculated by the specified "compute +chunk/atom"_compute_chunk_atom.html command. These values can be +accessed by any command that uses global vector values from a compute +as input. See "Section_howto 15"_Section_howto.html#howto_15 for an +overview of LAMMPS output options. + +The vector values are "intensive". The vector values will be in +temperature "units"_units.html. + +[Restrictions:] + +The {com} and {bias} keywords cannot be used together. + +[Related commands:] + +"compute temp"_compute_temp.html, "fix ave/chunk +temp"_fix_ave_chunk.html + +[Default:] + +The option defaults are com no, no bias, adof = dimensionality of the +system (2 or 3), and cdof = 0.0. diff --git a/doc/compute_torque_chunk.html b/doc/compute_torque_chunk.html new file mode 100644 index 0000000000..133d4ac03a --- /dev/null +++ b/doc/compute_torque_chunk.html @@ -0,0 +1,92 @@ + ++ +
compute torque/chunk command +
+Syntax: +
+compute ID group-ID torque/chunk chunkID ++
- ID, group-ID are documented in compute command +
- torque/molecule = style name of this compute command +
- chunkID = ID of compute chunk/atom command +
Examples: +
+compute 1 fluid torque/chunk molchunk ++
Description: +
+Define a computation that calculates the torque on multiple chunks of +atoms. +
+In LAMMPS, chunks are collections of atoms defined by a compute +chunk/atom command, which assigns each atom +to a single chunk (or no chunk). The ID for this command is specified +as chunkID. For example, a single chunk could be the atoms in a +molecule or atoms in a spatial bin. See the compute +chunk/atom doc page and "Section_howto +23 for details of how chunks can be +defined and examples of how they can be used to measure properties of +a system. +
+This compute calculates the 3 components of the torque vector for eqch +chunk, due to the forces on the individual atoms in the chunk around +the center-of-mass of the chunk. The calculation includes all effects +due to atoms passing thru periodic boundaries. +
+Note that only atoms in the specified group contribute to the +calculation. The compute chunk/atom command +defines its own group; atoms will have a chunk ID = 0 if they are not +in that group, signifying they are not assigned to a chunk, and will +thus also not contribute to this calculation. You can specify the +"all" group for this command if you simply want to include atoms with +non-zero chunk IDs. +
+IMPORTANT NOTE: The coordinates of an atom contribute to the chunk's +torque in "unwrapped" form, by using the image flags associated with +each atom. See the dump custom command for a discussion +of "unwrapped" coordinates. See the Atoms section of the +read_data command for a discussion of image flags and +how they are set for each atom. You can reset the image flags +(e.g. to 0) before invoking this compute by using the set +image command. +
+The simplest way to output the results of the compute torque/chunk +calculation to a file is to use the fix ave/time +command, for example: +
+compute cc1 chunk/atom molecule +compute myChunk all torque/chunk cc1 +fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector ++
Output info: +
+This compute calculates a global array where the number of rows = the +number of chunks Nchunk as calculated by the specified compute +chunk/atom command. The number of columns = +3 for the 3 xyz components of the torque for each chunk. These values +can be accessed by any command that uses global array values from a +compute as input. See Section_howto 15 +for an overview of LAMMPS output options. +
+The array values are "intensive". The array values will be in +force-distance units. +
+Restrictions: none +
+Related commands: +
+ +Default: none +
+ diff --git a/doc/compute_torque_chunk.txt b/doc/compute_torque_chunk.txt new file mode 100644 index 0000000000..df62deaf5c --- /dev/null +++ b/doc/compute_torque_chunk.txt @@ -0,0 +1,87 @@ +"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 + +compute torque/chunk command :h3 + +[Syntax:] + +compute ID group-ID torque/chunk chunkID :pre + +ID, group-ID are documented in "compute"_compute.html command +torque/molecule = style name of this compute command +chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :ul + +[Examples:] + +compute 1 fluid torque/chunk molchunk :pre + +[Description:] + +Define a computation that calculates the torque on multiple chunks of +atoms. + +In LAMMPS, chunks are collections of atoms defined by a "compute +chunk/atom"_compute_chunk_atom.html command, which assigns each atom +to a single chunk (or no chunk). The ID for this command is specified +as chunkID. For example, a single chunk could be the atoms in a +molecule or atoms in a spatial bin. See the "compute +chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto +23"_Section_howto.html#howto_23 for details of how chunks can be +defined and examples of how they can be used to measure properties of +a system. + +This compute calculates the 3 components of the torque vector for eqch +chunk, due to the forces on the individual atoms in the chunk around +the center-of-mass of the chunk. The calculation includes all effects +due to atoms passing thru periodic boundaries. + +Note that only atoms in the specified group contribute to the +calculation. The "compute chunk/atom"_compute_chunk_atom.html command +defines its own group; atoms will have a chunk ID = 0 if they are not +in that group, signifying they are not assigned to a chunk, and will +thus also not contribute to this calculation. You can specify the +"all" group for this command if you simply want to include atoms with +non-zero chunk IDs. + +IMPORTANT NOTE: The coordinates of an atom contribute to the chunk's +torque in "unwrapped" form, by using the image flags associated with +each atom. See the "dump custom"_dump.html command for a discussion +of "unwrapped" coordinates. See the Atoms section of the +"read_data"_read_data.html command for a discussion of image flags and +how they are set for each atom. You can reset the image flags +(e.g. to 0) before invoking this compute by using the "set +image"_set.html command. + +The simplest way to output the results of the compute torque/chunk +calculation to a file is to use the "fix ave/time"_fix_ave_time.html +command, for example: + +compute cc1 chunk/atom molecule +compute myChunk all torque/chunk cc1 +fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector :pre + +[Output info:] + +This compute calculates a global array where the number of rows = the +number of chunks {Nchunk} as calculated by the specified "compute +chunk/atom"_compute_chunk_atom.html command. The number of columns = +3 for the 3 xyz components of the torque for each chunk. These values +can be accessed by any command that uses global array values from a +compute as input. See "Section_howto 15"_Section_howto.html#howto_15 +for an overview of LAMMPS output options. + +The array values are "intensive". The array values will be in +force-distance "units"_units.html. + +[Restrictions:] none + +[Related commands:] + +"variable torque() function"_variable.html + +[Default:] none diff --git a/doc/compute_vcm_chunk.html b/doc/compute_vcm_chunk.html new file mode 100644 index 0000000000..ef17b94ddd --- /dev/null +++ b/doc/compute_vcm_chunk.html @@ -0,0 +1,82 @@ + ++ +
compute vcm/chunk command +
+Syntax: +
+compute ID group-ID vcm/chunk chunkID ++
- ID, group-ID are documented in compute command +
- vcm/chunk = style name of this compute command +
- chunkID = ID of compute chunk/atom command +
Examples: +
+compute 1 fluid vcm/chunk molchunk ++
Description: +
+Define a computation that calculates the center-of-mass velocity for +multiple chunks of atoms. +
+In LAMMPS, chunks are collections of atoms defined by a compute +chunk/atom command, which assigns each atom +to a single chunk (or no chunk). The ID for this command is specified +as chunkID. For example, a single chunk could be the atoms in a +molecule or atoms in a spatial bin. See the compute +chunk/atom doc page and "Section_howto +23 for details of how chunks can be +defined and examples of how they can be used to measure properties of +a system. +
+This compute calculates the x,y,z components of the center-of-mass +velocity for each chunk. This is done by summing mass*velocity for +each atom in the chunk and dividing the sum by the total mass of the +chunk. +
+Note that only atoms in the specified group contribute to the +calculation. The compute chunk/atom command +defines its own group; atoms will have a chunk ID = 0 if they are not +in that group, signifying they are not assigned to a chunk, and will +thus also not contribute to this calculation. You can specify the +"all" group for this command if you simply want to include atoms with +non-zero chunk IDs. +
+The simplest way to output the results of the compute vcm/chunk +calculation to a file is to use the fix ave/time +command, for example: +
+compute cc1 chunk/atom molecule +compute myChunk all vcm/chunk cc1 +fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector ++
Output info: +
+This compute calculates a global array where the number of rows = the +number of chunks Nchunk as calculated by the specified compute +chunk/atom command. The number of columns = +3 for the x,y,z center-of-mass velocity coordinates of each chunk. +These values can be accessed by any command that uses global array +values from a compute as input. See Section_howto +15 for an overview of LAMMPS output +options. +
+The array values are "intensive". The array values will be in +velocity units. +
+Restrictions: none +
+Related commands: none +
+Default: none +
+ diff --git a/doc/compute_vcm_chunk.txt b/doc/compute_vcm_chunk.txt new file mode 100644 index 0000000000..5e7bbc0891 --- /dev/null +++ b/doc/compute_vcm_chunk.txt @@ -0,0 +1,77 @@ +"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 + +compute vcm/chunk command :h3 + +[Syntax:] + +compute ID group-ID vcm/chunk chunkID :pre + +ID, group-ID are documented in "compute"_compute.html command +vcm/chunk = style name of this compute command +chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :ul + +[Examples:] + +compute 1 fluid vcm/chunk molchunk :pre + +[Description:] + +Define a computation that calculates the center-of-mass velocity for +multiple chunks of atoms. + +In LAMMPS, chunks are collections of atoms defined by a "compute +chunk/atom"_compute_chunk_atom.html command, which assigns each atom +to a single chunk (or no chunk). The ID for this command is specified +as chunkID. For example, a single chunk could be the atoms in a +molecule or atoms in a spatial bin. See the "compute +chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto +23"_Section_howto.html#howto_23 for details of how chunks can be +defined and examples of how they can be used to measure properties of +a system. + +This compute calculates the x,y,z components of the center-of-mass +velocity for each chunk. This is done by summing mass*velocity for +each atom in the chunk and dividing the sum by the total mass of the +chunk. + +Note that only atoms in the specified group contribute to the +calculation. The "compute chunk/atom"_compute_chunk_atom.html command +defines its own group; atoms will have a chunk ID = 0 if they are not +in that group, signifying they are not assigned to a chunk, and will +thus also not contribute to this calculation. You can specify the +"all" group for this command if you simply want to include atoms with +non-zero chunk IDs. + +The simplest way to output the results of the compute vcm/chunk +calculation to a file is to use the "fix ave/time"_fix_ave_time.html +command, for example: + +compute cc1 chunk/atom molecule +compute myChunk all vcm/chunk cc1 +fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector :pre + +[Output info:] + +This compute calculates a global array where the number of rows = the +number of chunks {Nchunk} as calculated by the specified "compute +chunk/atom"_compute_chunk_atom.html command. The number of columns = +3 for the x,y,z center-of-mass velocity coordinates of each chunk. +These values can be accessed by any command that uses global array +values from a compute as input. See "Section_howto +15"_Section_howto.html#howto_15 for an overview of LAMMPS output +options. + +The array values are "intensive". The array values will be in +velocity "units"_units.html. + +[Restrictions:] none + +[Related commands:] none + +[Default:] none diff --git a/doc/compute_vcm_molecule.html b/doc/compute_vcm_molecule.html deleted file mode 100644 index f64b4075fc..0000000000 --- a/doc/compute_vcm_molecule.html +++ /dev/null @@ -1,65 +0,0 @@ - -- -
compute vcm/molecule command -
-Syntax: -
-compute ID group-ID vcm/molecule --
- ID, group-ID are documented in compute command -
- vcm/molecule = style name of this compute command -
Examples: -
-compute 1 fluid vcm/molecule --
Description: -
-Define a computation that calculates the center-of-mass velocity of -individual molecules. The x,y,z components of the velocity of each -molecule are computed. This is calcualted by summing mass*velocity -for each atom in the molecule and dividing the sum by the total mass -of the molecule. -
-The velocity of a particular molecule is only computed if one or more -of its atoms are in the specified group. Normally all atoms in the -molecule should be in the group, however this is not required. LAMMPS -will warn you if this is not the case. Only atoms in the group -contribute to the velocity calculation for the molecule. -
-The ordering of per-molecule quantities produced by this compute is -consistent with the ordering produced by other compute commands that -generate per-molecule datums. Conceptually, the molecule IDs will be -in ascending order for any molecule with one or more of its atoms in -the specified group. -
-Output info: -
-This compute calculates a global array where the number of rows = -Nmolecules and the number of columns = 3 for the vx,vy,vz components -of the center-of-mass velocity of each molecule. These values can be -accessed by any command that uses global array values from a compute -as input. See Section_howto 15 for an -overview of LAMMPS output options. -
-The array values are "intensive". The array values will be in -distance units. -
-Restrictions: none -
-Related commands: -
- -Default: none -
- diff --git a/doc/compute_vcm_molecule.txt b/doc/compute_vcm_molecule.txt deleted file mode 100644 index d1c9d6b93f..0000000000 --- a/doc/compute_vcm_molecule.txt +++ /dev/null @@ -1,60 +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 - -compute vcm/molecule command :h3 - -[Syntax:] - -compute ID group-ID vcm/molecule :pre - -ID, group-ID are documented in "compute"_compute.html command -vcm/molecule = style name of this compute command :ul - -[Examples:] - -compute 1 fluid vcm/molecule :pre - -[Description:] - -Define a computation that calculates the center-of-mass velocity of -individual molecules. The x,y,z components of the velocity of each -molecule are computed. This is calcualted by summing mass*velocity -for each atom in the molecule and dividing the sum by the total mass -of the molecule. - -The velocity of a particular molecule is only computed if one or more -of its atoms are in the specified group. Normally all atoms in the -molecule should be in the group, however this is not required. LAMMPS -will warn you if this is not the case. Only atoms in the group -contribute to the velocity calculation for the molecule. - -The ordering of per-molecule quantities produced by this compute is -consistent with the ordering produced by other compute commands that -generate per-molecule datums. Conceptually, the molecule IDs will be -in ascending order for any molecule with one or more of its atoms in -the specified group. - -[Output info:] - -This compute calculates a global array where the number of rows = -Nmolecules and the number of columns = 3 for the vx,vy,vz components -of the center-of-mass velocity of each molecule. These values can be -accessed by any command that uses global array values from a compute -as input. See "Section_howto 15"_Section_howto.html#howto_15 for an -overview of LAMMPS output options. - -The array values are "intensive". The array values will be in -distance "units"_units.html. - -[Restrictions:] none - -[Related commands:] - -"compute atom/molecule"_compute_atom_molecule.html - -[Default:] none diff --git a/doc/fix_ave_chunk.html b/doc/fix_ave_chunk.html new file mode 100644 index 0000000000..ee10e43d5c --- /dev/null +++ b/doc/fix_ave_chunk.html @@ -0,0 +1,455 @@ + ++ +
fix ave/chunk command +
+Syntax: +
+fix ID group-ID ave/chunk Nevery Nrepeat Nfreq chunkID value1 value2 ... keyword args ... ++
- ID, group-ID are documented in fix command + +
- ave/chunk = style name of this fix command + +
- Nevery = use input values every this many timesteps + +
- Nrepeat = # of times to use input values for calculating averages + +
- Nfreq = calculate averages every this many timesteps + +
- chunkID = ID of compute chunk/atom command + +
- one or more input values can be listed + +
- value = vx, vy, vz, fx, fy, fz, density/mass, density/number, temp, c_ID, c_ID[I], f_ID, f_ID[I], v_name
+
+
vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component) + density/number, density/mass = number or mass density + temp = temperature + 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 +
+ - zero or more keyword/arg pairs may be appended + +
- keyword = norm or ave or bias or adof or cdof or file or overwrite or title1 or title2 or title3
+
+
norm arg = all or sample or none = how output on Nfreq steps is normalized + all = output is sum of atoms across all Nrepeat samples, divided by atom count + sample = output is sum of Nrepeat sample averages, divided by Nrepeat + none = output is sum of Nrepeat sums, divided by Nrepeat + 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 + bias arg = bias-ID + bias-ID = ID of a temperature compute that removes a velocity bias for temperature calculation + adof value = dof_per_atom + dof_per_atom = define this many degrees-of-freedom per atom for temperature calculation + cdof value = dof_per_chunk + dof_per_chunk = define this many degrees-of-freedom per chunk for temperature calculation + 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 +
+ +
Examples: +
+fix 1 all ave/chunk 10000 1 10000 binchunk c_myCentro ttle1 "My output values" +fix 1 flow ave/chunk 100 10 1000 molchunk vx vz norm sample file vel.profile +fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running +fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running ++
IMPORTANT NOTE: +
+If you are trying to replace an older fix ave/spatial command with the +newer, more flexible fix ave/chunk and compute +chunk/atom 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 ++
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 ++
Description: +
+Use one or more per-atom vectors as inputs every few timesteps, sum +their values for multiple chunks of atoms, and average the values for +each chunk over longer timescales. The resulting chunk averages can +be used by other output commands such as +thermo_style custom, and can also be written to a +file. +
+In LAMMPS, chunks are collections of atoms defined by a compute +chunk/atom command, which assigns each atom +to a single chunk (or no chunk). The ID for this command is specified +as chunkID. For example, a single chunk could be the atoms in a +molecule or atoms in a spatial bin. See the compute +chunk/atom doc page and "Section_howto +23 for details of how chunks can be +defined and examples of how they can be used to measure properties of +a system. +
+Note that only atoms in the specified group contribute to the summing +and averaging calculations. The compute +chunk/atom command defines its own group as +well as an optional region. Atoms will have a chunk ID = 0, meaning +they belong to no chunk, if they are not in that group or region. +Thus you can specify the "all" group for this command if you simply +want to use the chunk definitions provided by chunkID. +
+Each specified per-atom value can be an atom attribute (position, +velocity, force component), a mass or number density, or the result of +a compute or fix or the evaluation of an +atom-style variable. In the latter cases, the +compute, fix, or variable must produce a per-atom quantity, not a +global quantity. Note that the compute +property/atom command provides access to +any attribute defined and stored by atoms. If you wish to +time-average global quantities from a compute, fix, or variable, then +see the fix ave/time command. +
+Computes that produce per-atom quantities are those +which have the word atom in their style name. See the doc pages for +individual fixes to determine which ones produce per-atom +quantities. Variables 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 summed and averaged +independently of the per-atom values in other input vectors. +
+IMPORTANT NOTE: This fix works by creating an array of size Nchunk +by Nvalues on each processor. Nchunk is the number of chunks which +is defined by the compute chunk/atom +command. Nvalues is the number of input values specified. Each +processor loops over its atoms, tallying its values to the appropriate +chunk. Then the entire array is summed across all processors. This +means that using a large number of chunks will incur an overhead in +memory and computational cost (summing across processors), so be +careful to define a reasonable number of chunks. +
++ +
The Nevery, Nrepeat, and Nfreq arguments specify on what +timesteps the input values will be accessed 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. Nfreq > +(Nrepeat-1)*Nevery is required. +
+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. +
+Each input value can also be averaged over the atoms in each chunk. +The way the averaging is done across the Nrepeat timesteps to +produce output on the Nfreq timesteps, and across multiple Nfreq +outputs, is determined by the norm and ave keyword settings, as +discussed below. +
+IMPORTANT NOTE: To perform per-chunk averaging within a Nfreq time +window, the number of chunks Nchunk defined by the compute +chunk/atom command must remain constant. If +the ave keyword is set to running or window then Nchunk must +remain constant for the duration of the simulation. This fix forces +the chunk/atom compute specified by chunkID to hold Nchunk constant +for the appropriate time windows, by not allowing it to re-calcualte +Nchunk, which can also affect how it assigns chunk IDs to atoms. +More details are given on the compute +chunk/atom doc page. +
++ +
The atom attribute values (vx,vy,vz,fx,fy,fz) are self-explanatory. +As noted above, any other atom attributes can be used as input values +to this fix by using the compute +property/atom command and then specifying +an input value from that compute. +
+The density/number value means the number density is computed for +each chunk, i.e. a weighting of 1 for each atom. The density/mass +value means the mass density is computed for each , i.e. each atom is +weighted by its mass. The resulting density is normalized by the +volume of the chunk so that units of number/volume or density are +output. See the units command doc page for the +definition of density for each choice of units, e.g. gram/cm^3. If +the chunks defined by the compute chunk/atom +command are spatial bins, the volume is the bin volume. Otherwise it +is the volume of the entire simulation box. +
+The temp value means the temperature is computed for each chunk, by +the formula KE = DOF/2 k T, where KE = total kinetic energy of the +chunk of atoms (sum of 1/2 m v^2), DOF = the total number of degrees +of freedom for all atoms in the chunk, k = Boltzmann constant, and T = +temperature. +
+The DOF is calculated as N*adof + cdof, where N = number of atoms in +the chunk, adof = degrees of freedom per atom, and cdof = degrees of +freedom per chunk. By default adof = 2 or 3 = dimensionality of +system, as set via the dimension command, and cdof = +0.0. This gives the usual formula for temperature. +
+Note that currently this temperature only includes translational +degrees of freedom for each atom. No rotational degrees of freedom +are included for finite-size particles. Also no degrees of freedom +are subtracted for any velocity bias or constraints that are applied, +such as compute temp/partial, or fix +shake or fix rigid. This is because +those degrees of freedom (e.g. a constrained bond) could apply to sets +of atoms that are both included and excluded from a specific chunk, +and hence the concept is somewhat ill-defined. In some cases, you can +use the adof and cdof keywords to adjust the calculated degress of +freedom appropriately, as explained below. +
+Also note that a bias can be subtracted from atom velocities before +they are used in the above formula for KE, by using the bias +keyword. This allows, for example, a thermal temperature to be +computed after removal of a flow velocity profile. +
+Note that this fix and the compute +temp/chunk command can calculate different +things. The compute calculates the temperature for each chunk for a +single snapshot. This fix can do that but can time average those +values over many snapshots, or it can compute a temperature as if the +atoms in the chunk on different timesteps were collected together as +one set of atoms to calculate their temperature. The compute allows +the center-of-mass velocity of each chunk to be subtracted before +calculating the temperature; this fix does not. +
+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. +
+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. +
+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 average within chunks. +
++ +
Additional optional keywords also affect the operation of this fix +and its outputs. +
+The norm keyword affects how averaging is done for the per-chunk +values that are output every Nfreq timesteps. +
+It the norm setting is all, which is the default, a chunk value is +summed over all atoms in all Nrepeat samples, as is the count of +atoms in the chunk. The averaged output value for the chunk on the +Nfreq timesteps is Total-sum / Total-count. In other words it is an +average over atoms across the entire Nfreq timescale. +
+If the norm setting is sample, the chunk value is summed over atoms +for each sample, as is the count, and an "average sample value" is +computed for each sample, i.e. Sample-sum / Sample-count. The outuput +value for the chunk on the Nfreq timesteps is the average of the +Nrepeat "average sample values", i.e. the sum of Nrepeat "average +sample values" divided by Nrepeat. In other words it is an average +of an average. +
+If the norm setting is none, a similar computation as for the +sample seting is done, except the individual "average sample values" +are "summed sample values". A summed sample value is simply the chunk +value summed over atoms in the sample, without dividing by the number +of atoms in the sample. The outuput value for the chunk on the +Nfreq timesteps is the average of the Nrepeat "summed sample +values", i.e. the sum of Nrepeat "summed sample values" divided by +Nrepeat. +
+The ave keyword determines how the per-chunk values produced every +Nfreq steps are averaged with 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, which is the default, then the chunk +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 chunk values produced on +timesteps that are multiples of Nfreq are summed and averaged in a +cumulative sense before being output. Each output chunk value is thus +the average of the chunk value produced on that timestep with all +preceding values for the same chunk. This running average begins when +the fix is defined; it can only be restarted by deleting the fix via +the unfix command, or re-defining the fix by +re-specifying it. +
+If the ave setting is window, then the chunk 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 +chunk 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 +chunk values on steps 8000,9000,10000. Outputs on early steps will +average over less than M values if they are not available. +
+The bias keyword specifies the ID of a temperature compute that +removes a "bias" velocity from each atom, specified as bias-ID. It +is only used when the temp value is calculated, to compute the +thermal temperature of each chunk after the translational kinetic +energy components have been altered in a prescribed way, e.g. to +remove a flow velocity profile. See the doc pages for individual +computes that calculate a temperature to see which ones implement a +bias. +
+The adof and cdof keywords define the values used in the degree of +freedom (DOF) formula described above for for temperature calculation +for each chunk. They are only used when the temp value is +calculated. They can be used to calculate a more appropriate +temperature for some kinds of chunks. Here are 3 examples. +
+If spatially binned chunks contain some number of water molecules and +fix shake is used to make each molecule rigid, then +you could calculate a temperature with 6 degrees of freedom (DOF) (3 +translational, 3 rotational) per molecule by setting adof to 2.0. +If compute temp/partial is used with the +bias keyword to only allow the x component of velocity to contribute +to the temperature, then adof = 1.0 would be appropriate. If each +chunk consists of a large molecule, with some number of its bonds +constrained by fix shake or the entire molecule by +fix rigid/small, then cdof could be set to the +remaining degrees of freedom for the entire molecule (entire chunk in +this case). +
+The file keyword allows a filename to be specified. Every Nfreq +timesteps, a section of chunk info will be written to a text file in +the following format. A line with the timestep and number of chunks +is written. Then one line per chunk is written, containing the chunk +ID (1-Nchunk), an optional original ID value, optional coordinate +values for chunks that represent spatial bins, the number of atoms in +the chunk, and one or more calculated values. More explanation of the +optional values is given below. The number of values in each line +corresponds to the number of values specified in the fix ave/chunk +command. The number of atoms and the value(s) are summed or average +quantities, as explained above. +
+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: +
+# Chunk-averaged data for fix ID and group name +# Timestep Number-of-chunks +# Chunk (OrigID) (Coord1) (Coord2) (Coord3) Ncount value1 value2 ... ++
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 value names, e.g. fx or c_myCompute2. +
+The words in parenthesis only appear with corresponding columns if the +chunk style specified for the compute +chunk/atom command supports them. The OrigID +column is only used if the compress keyword was set to yes for the +compute chunk/atom command. This means that +the original chunk IDs (e.g. molecule IDs) will have been compressed +to remove chunk IDs with no atoms assigned to them. Thus a compresed +chunk ID of 3 may correspond to an original chunk ID or molecule ID of +415. The OrigID column will list 415 for the 3rd chunk. +
+The CoordN columns only appear if a binning style was used in the +compute chunk/atom command. For bin/1d, +bin/2d, and bin/3d styles the column values are the center point +of the bin in the corresponding dimension. Just Coord1 is used for +bin/1d, Coord2 is added for bin/2d, Coord3 is added for bin/3d. +
+Note that if the value of the units keyword used in the compute +chunk/atom command is box or lattice, the +coordinate values will be in distance units. If the +value of the units keyword is reduced, the coordinate values will +be in unitless reduced units (0-1). +
++ +
Restart, fix_modify, output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. +
+This fix computes a global array of values which can be accessed by +various output commands. 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 = +the number of chunks Nchunk as calculated by the specified compute +chunk/atom command. The # of columns = +M+1+Nvalues, where M = 1 to 4, depending on whether the optional +columns for OrigID and CoordN are used, as explained above. +Following the optional columns, the next column contains the count of +atoms in the chunk, and the remaining columns are the Nvalue +quantities. When the array is accessed with a row I that exceeds the +current number of chunks, than a 0.0 is returned by the fix instead of +an error, since the number of chunks can vary as a simulation runs +depending on how that value is computed by the compute chunk/atom +command. +
+The array values calculated by this fix are treated as "intensive", +since they are typically already normalized by the count of atoms in +each chunk. +
+No parameter of this fix can be used with the start/stop keywords of +the run command. This fix is not invoked during energy +minimization. +
+Restrictions: none +
+Related commands: +
+compute, fix ave/atom, fix +ave/histo, fix ave/time, +variable, fix ave/correlate +
+Default: +
+The option defaults are norm = all, ave = one, bias = none, no file output, and +title 1,2,3 = strings as described above. +
+ diff --git a/doc/fix_ave_chunk.txt b/doc/fix_ave_chunk.txt new file mode 100644 index 0000000000..cf57948b36 --- /dev/null +++ b/doc/fix_ave_chunk.txt @@ -0,0 +1,439 @@ +"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/chunk command :h3 + +[Syntax:] + +fix ID group-ID ave/chunk Nevery Nrepeat Nfreq chunkID value1 value2 ... keyword args ... :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +ave/chunk = 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 +chunkID = ID of "compute chunk/atom"_compute_chunk_atom.html command :l +one or more input values can be listed :l +value = vx, vy, vz, fx, fy, fz, density/mass, density/number, temp, 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 + temp = temperature + 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 = {norm} or {ave} or {bias} or {adof} or {cdof} or {file} or {overwrite} or {title1} or {title2} or {title3} :l + {norm} arg = {all} or {sample} or {none} = how output on {Nfreq} steps is normalized + all = output is sum of atoms across all {Nrepeat} samples, divided by atom count + sample = output is sum of {Nrepeat} sample averages, divided by {Nrepeat} + none = output is sum of {Nrepeat} sums, divided by {Nrepeat} + {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 + {bias} arg = bias-ID + bias-ID = ID of a temperature compute that removes a velocity bias for temperature calculation + {adof} value = dof_per_atom + dof_per_atom = define this many degrees-of-freedom per atom for temperature calculation + {cdof} value = dof_per_chunk + dof_per_chunk = define this many degrees-of-freedom per chunk for temperature calculation + {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/chunk 10000 1 10000 binchunk c_myCentro ttle1 "My output values" +fix 1 flow ave/chunk 100 10 1000 molchunk vx vz norm sample file vel.profile +fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running +fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running :pre + +[IMPORTANT NOTE:] + +If you are trying to replace an older 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: + +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, sum +their values for multiple chunks of atoms, and average the values for +each chunk over longer timescales. The resulting chunk 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. + +In LAMMPS, chunks are collections of atoms defined by a "compute +chunk/atom"_compute_chunk_atom.html command, which assigns each atom +to a single chunk (or no chunk). The ID for this command is specified +as chunkID. For example, a single chunk could be the atoms in a +molecule or atoms in a spatial bin. See the "compute +chunk/atom"_compute_chunk_atom.html doc page and ""Section_howto +23"_Section_howto.html#howto_23 for details of how chunks can be +defined and examples of how they can be used to measure properties of +a system. + +Note that only atoms in the specified group contribute to the summing +and averaging calculations. The "compute +chunk/atom"_compute_chunk_atom.html command defines its own group as +well as an optional region. Atoms will have a chunk ID = 0, meaning +they belong to no chunk, if they are not in that group or region. +Thus you can specify the "all" group for this command if you simply +want to use the chunk definitions provided by chunkID. + +Each specified per-atom 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. Note that the "compute +property/atom"_compute_property_atom.html command provides access to +any attribute defined and stored by atoms. 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 summed and averaged +independently of the per-atom values in other input vectors. + +IMPORTANT NOTE: This fix works by creating an array of size {Nchunk} +by Nvalues on each processor. {Nchunk} is the number of chunks which +is defined by the "compute chunk/atom"_doc/compute_chunk_atom.html +command. Nvalues is the number of input values specified. Each +processor loops over its atoms, tallying its values to the appropriate +chunk. Then the entire array is summed across all processors. This +means that using a large number of chunks will incur an overhead in +memory and computational cost (summing across processors), so be +careful to define a reasonable number of chunks. + +:line + +The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify on what +timesteps the input values will be accessed 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. Nfreq > +(Nrepeat-1)*Nevery is required. + +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. + +Each input value can also be averaged over the atoms in each chunk. +The way the averaging is done across the {Nrepeat} timesteps to +produce output on the {Nfreq} timesteps, and across multiple {Nfreq} +outputs, is determined by the {norm} and {ave} keyword settings, as +discussed below. + +IMPORTANT NOTE: To perform per-chunk averaging within a {Nfreq} time +window, the number of chunks {Nchunk} defined by the "compute +chunk/atom"_compute_chunk_atom.html command must remain constant. If +the {ave} keyword is set to {running} or {window} then {Nchunk} must +remain constant for the duration of the simulation. This fix forces +the chunk/atom compute specified by chunkID to hold {Nchunk} constant +for the appropriate time windows, by not allowing it to re-calcualte +{Nchunk}, which can also affect how it assigns chunk IDs to atoms. +More details are given on the "compute +chunk/atom"_compute_chunk_atom.html doc page. + +:line + +The atom attribute values (vx,vy,vz,fx,fy,fz) are self-explanatory. +As noted above, any other atom attributes can be used as input values +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 for +each chunk, i.e. a weighting of 1 for each atom. The {density/mass} +value means the mass density is computed for each , i.e. each atom is +weighted by its mass. The resulting density is normalized by the +volume of the chunk 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 +the chunks defined by the "compute chunk/atom"_compute_chunk_atom.html +command are spatial bins, the volume is the bin volume. Otherwise it +is the volume of the entire simulation box. + +The {temp} value means the temperature is computed for each chunk, by +the formula KE = DOF/2 k T, where KE = total kinetic energy of the +chunk of atoms (sum of 1/2 m v^2), DOF = the total number of degrees +of freedom for all atoms in the chunk, k = Boltzmann constant, and T = +temperature. + +The DOF is calculated as N*adof + cdof, where N = number of atoms in +the chunk, adof = degrees of freedom per atom, and cdof = degrees of +freedom per chunk. By default adof = 2 or 3 = dimensionality of +system, as set via the "dimension"_dimension.html command, and cdof = +0.0. This gives the usual formula for temperature. + +Note that currently this temperature only includes translational +degrees of freedom for each atom. No rotational degrees of freedom +are included for finite-size particles. Also no degrees of freedom +are subtracted for any velocity bias or constraints that are applied, +such as "compute temp/partial"_compute_temp_partial.html, or "fix +shake"_fix_shake.html or "fix rigid"_fix_rigid.html. This is because +those degrees of freedom (e.g. a constrained bond) could apply to sets +of atoms that are both included and excluded from a specific chunk, +and hence the concept is somewhat ill-defined. In some cases, you can +use the {adof} and {cdof} keywords to adjust the calculated degress of +freedom appropriately, as explained below. + +Also note that a bias can be subtracted from atom velocities before +they are used in the above formula for KE, by using the {bias} +keyword. This allows, for example, a thermal temperature to be +computed after removal of a flow velocity profile. + +Note that this fix and the "compute +temp/chunk"_compute_temp_chunk.html command can calculate different +things. The compute calculates the temperature for each chunk for a +single snapshot. This fix can do that but can time average those +values over many snapshots, or it can compute a temperature as if the +atoms in the chunk on different timesteps were collected together as +one set of atoms to calculate their temperature. The compute allows +the center-of-mass velocity of each chunk to be subtracted before +calculating the temperature; this fix does not. + +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 average within chunks. + +:line + +Additional optional keywords also affect the operation of this fix +and its outputs. + +The {norm} keyword affects how averaging is done for the per-chunk +values that are output every {Nfreq} timesteps. + +It the {norm} setting is {all}, which is the default, a chunk value is +summed over all atoms in all {Nrepeat} samples, as is the count of +atoms in the chunk. The averaged output value for the chunk on the +{Nfreq} timesteps is Total-sum / Total-count. In other words it is an +average over atoms across the entire {Nfreq} timescale. + +If the {norm} setting is {sample}, the chunk value is summed over atoms +for each sample, as is the count, and an "average sample value" is +computed for each sample, i.e. Sample-sum / Sample-count. The outuput +value for the chunk on the {Nfreq} timesteps is the average of the +{Nrepeat} "average sample values", i.e. the sum of {Nrepeat} "average +sample values" divided by {Nrepeat}. In other words it is an average +of an average. + +If the {norm} setting is {none}, a similar computation as for the +{sample} seting is done, except the individual "average sample values" +are "summed sample values". A summed sample value is simply the chunk +value summed over atoms in the sample, without dividing by the number +of atoms in the sample. The outuput value for the chunk on the +{Nfreq} timesteps is the average of the {Nrepeat} "summed sample +values", i.e. the sum of {Nrepeat} "summed sample values" divided by +{Nrepeat}. + +The {ave} keyword determines how the per-chunk values produced every +{Nfreq} steps are averaged with 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}, which is the default, then the chunk +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 chunk values produced on +timesteps that are multiples of {Nfreq} are summed and averaged in a +cumulative sense before being output. Each output chunk value is thus +the average of the chunk value produced on that timestep with all +preceding values for the same chunk. 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 chunk 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 +chunk 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 +chunk values on steps 8000,9000,10000. Outputs on early steps will +average over less than M values if they are not available. + +The {bias} keyword specifies the ID of a temperature compute that +removes a "bias" velocity from each atom, specified as {bias-ID}. It +is only used when the {temp} value is calculated, to compute the +thermal temperature of each chunk after the translational kinetic +energy components have been altered in a prescribed way, e.g. to +remove a flow velocity profile. See the doc pages for individual +computes that calculate a temperature to see which ones implement a +bias. + +The {adof} and {cdof} keywords define the values used in the degree of +freedom (DOF) formula described above for for temperature calculation +for each chunk. They are only used when the {temp} value is +calculated. They can be used to calculate a more appropriate +temperature for some kinds of chunks. Here are 3 examples. + +If spatially binned chunks contain some number of water molecules and +"fix shake"_fix_shake.html is used to make each molecule rigid, then +you could calculate a temperature with 6 degrees of freedom (DOF) (3 +translational, 3 rotational) per molecule by setting {adof} to 2.0. +If "compute temp/partial"_compute_temp_partial.html is used with the +{bias} keyword to only allow the x component of velocity to contribute +to the temperature, then {adof} = 1.0 would be appropriate. If each +chunk consists of a large molecule, with some number of its bonds +constrained by "fix shake"_fix_shake.html or the entire molecule by +"fix rigid/small"_fix_rigid.html, then {cdof} could be set to the +remaining degrees of freedom for the entire molecule (entire chunk in +this case). + +The {file} keyword allows a filename to be specified. Every {Nfreq} +timesteps, a section of chunk info will be written to a text file in +the following format. A line with the timestep and number of chunks +is written. Then one line per chunk is written, containing the chunk +ID (1-Nchunk), an optional original ID value, optional coordinate +values for chunks that represent spatial bins, the number of atoms in +the chunk, and one or more calculated values. More explanation of the +optional values is given below. The number of values in each line +corresponds to the number of values specified in the fix ave/chunk +command. The number of atoms and the value(s) are summed or average +quantities, as explained above. + +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: + +# Chunk-averaged data for fix ID and group name +# Timestep Number-of-chunks +# Chunk (OrigID) (Coord1) (Coord2) (Coord3) Ncount 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 value names, e.g. fx or c_myCompute[2]. + +The words in parenthesis only appear with corresponding columns if the +chunk style specified for the "compute +chunk/atom"_compute_chunk_atom.html command supports them. The OrigID +column is only used if the {compress} keyword was set to {yes} for the +"compute chunk/atom"_compute_chunk_atom.html command. This means that +the original chunk IDs (e.g. molecule IDs) will have been compressed +to remove chunk IDs with no atoms assigned to them. Thus a compresed +chunk ID of 3 may correspond to an original chunk ID or molecule ID of +415. The OrigID column will list 415 for the 3rd chunk. + +The CoordN columns only appear if a {binning} style was used in the +"compute chunk/atom"_compute_chunk_atom.html command. For {bin/1d}, +{bin/2d}, and {bin/3d} styles the column values are the center point +of the bin in the corresponding dimension. Just Coord1 is used for +{bin/1d}, Coord2 is added for {bin/2d}, Coord3 is added for {bin/3d}. + +Note that if the value of the {units} keyword used in the "compute +chunk/atom command"_compute_chunk_atom.html is {box} or {lattice}, the +coordinate values will be in distance "units"_units.html. If the +value of the {units} keyword is {reduced}, the coordinate values will +be in unitless reduced units (0-1). + +: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 = +the number of chunks {Nchunk} as calculated by the specified "compute +chunk/atom"_compute_chunk_atom.html command. The # of columns = +M+1+Nvalues, where M = 1 to 4, depending on whether the optional +columns for OrigID and CoordN are used, as explained above. +Following the optional columns, the next column contains the count of +atoms in the chunk, and the remaining columns are the Nvalue +quantities. When the array is accessed with a row I that exceeds the +current number of chunks, than a 0.0 is returned by the fix instead of +an error, since the number of chunks can vary as a simulation runs +depending on how that value is computed by the compute chunk/atom +command. + +The array values calculated by this fix are treated as "intensive", +since they are typically already normalized by the count of atoms in +each chunk. + +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:] none + +[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 + +[Default:] + +The option defaults are norm = all, ave = one, bias = none, no file output, and +title 1,2,3 = strings as described above. diff --git a/doc/fix_ave_spatial.html b/doc/fix_ave_spatial.html index eef4ea7fa1..9d41f243ac 100644 --- a/doc/fix_ave_spatial.html +++ b/doc/fix_ave_spatial.html @@ -83,6 +83,24 @@ 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 +IMPORTANT NOTE: +
+The fix ave/spatial command has been replaced by the more flexible +fix ave/chunk and compute +chunk/atom 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 ++
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 +
Description:
Use one or more per-atom vectors as inputs every few timesteps, bin diff --git a/doc/fix_ave_spatial.txt b/doc/fix_ave_spatial.txt index 9737302122..5c2f28f8da 100644 --- a/doc/fix_ave_spatial.txt +++ b/doc/fix_ave_spatial.txt @@ -68,6 +68,24 @@ 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 +[IMPORTANT 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