diff --git a/doc/src/Howto_output.rst b/doc/src/Howto_output.rst index d17b865bbd..fe9a8f5f79 100644 --- a/doc/src/Howto_output.rst +++ b/doc/src/Howto_output.rst @@ -22,14 +22,17 @@ commands you specify. As discussed below, LAMMPS gives you a variety of ways to determine what quantities are computed and printed when the thermodynamics, dump, or fix commands listed above perform output. Throughout this -discussion, note that users can also :doc:`add their own computes and fixes to LAMMPS ` which can then generate values that can then be -output with these commands. +discussion, note that users can also :doc:`add their own computes and +fixes to LAMMPS ` which can then generate values that can then +be output with these commands. -The following sub-sections discuss different LAMMPS command related +The following sub-sections discuss different LAMMPS commands related to output and the kind of data they operate on and produce: -* :ref:`Global/per-atom/local data ` +* :ref:`Global/per-atom/local/per-grid data ` * :ref:`Scalar/vector/array data ` +* :ref:`Per-grid data ` +* :ref:`Disambiguation ` * :ref:`Thermodynamic output ` * :ref:`Dump file output ` * :ref:`Fixes that write output files ` @@ -42,27 +45,32 @@ to output and the kind of data they operate on and produce: .. _global: -Global/per-atom/local data --------------------------- +Global/per-atom/local/per-grid data +----------------------------------- -Various output-related commands work with three different styles of -data: global, per-atom, or local. A global datum is one or more -system-wide values, e.g. the temperature of the system. A per-atom -datum is one or more values per atom, e.g. the kinetic energy of each -atom. Local datums are calculated by each processor based on the -atoms it owns, but there may be zero or more per atom, e.g. a list of -bond distances. +Various output-related commands work with four different styles of +data: global, per-atom, local, and per-grid. A global datum is one or +more system-wide values, e.g. the temperature of the system. A +per-atom datum is one or more values per atom, e.g. the kinetic energy +of each atom. Local datums are calculated by each processor based on +the atoms it owns, but there may be zero or more per atom, e.g. a list +of bond distances. + +A per-grid datum is one or more values per grid point, for a grid +which overlays the simulation domain. Each processor owns the grid +points which fall within its sub-domain. Thus the grid points and the +data they store are distributed across processors. .. _scalar: Scalar/vector/array data ------------------------ -Global, per-atom, and local datums can each come in three kinds: a -single scalar value, a vector of values, or a 2d array of values. The -doc page for a "compute" or "fix" or "variable" that generates data -will specify both the style and kind of data it produces, e.g. a -per-atom vector. +Global, per-atom, and local datums can come in three kinds: a single +scalar value, a vector of values, or a 2d array of values. The doc +page for a "compute" or "fix" or "variable" that generates data will +specify both the style and kind of data it produces, e.g. a per-atom +vector. When a quantity is accessed, as in many of the output commands discussed below, it can be referenced via the following bracket @@ -83,6 +91,39 @@ the dimension twice (array -> scalar). Thus a command that uses scalar values as input can typically also process elements of a vector or array. +.. _grid: + +Per-grid data +------------------------ + +Per-grid data can come in two kinds: a vector of values (one per grid +point), or a 2d array of values (multiple values per grid point). The +doc page for a "compute" or "fix" that generates data will specify +both the style and kind of data it produces, e.g. a per-grid vector or +array. + +Only computes and fixes produce and output per-grid data. Per-grid +variables have not (yet) been implemented. A compute or fix may +define one or more grids, e.g. of differing sizes. Each grid can +store one or more data fields. + +Another command accesses grid data in the following syntax: + +* c_ID:gname:dname +* c_ID:gname:dname[I] +* f_ID:gname:dname +* f_ID:gname:dname[I] + +The prefix "c_" or "f_" refers to the ID of the compute or fix. Gname +is the name of the grid, which is assinged by the compute or fix. +Dname is the name of the data field, which is also assinged by the +compute or fix. If the data field is a per-grid vector (one value per +grid point), then no brackets are used to access the values. If the +data field is a per-grid array (multiple values per grid point), then +brackets are used to specify the column I of the array. I ranges from +1 to Ncol inclusive, where Ncol is the number of columns in the array +and is defined by the compute or fix. + .. _disambiguation: Disambiguation @@ -90,15 +131,15 @@ Disambiguation Some computes and fixes produce data in multiple styles, e.g. a global scalar and a per-atom vector. Usually the context in which the input -script references the data determines which style is meant. Example: if -a compute provides both a global scalar and a per-atom vector, the +script references the data determines which style is meant. Example: +if a compute provides both a global scalar and a per-atom vector, the former will be accessed by using ``c_ID`` in an equal-style variable, while the latter will be accessed by using ``c_ID`` in an atom-style -variable. Note that atom-style variable formulas can also access global -scalars, but in this case it is not possible to do directly because of -the ambiguity. Instead, an equal-style variable can be defined which -accesses the global scalar, and that variable used in the atom-style -variable formula in place of ``c_ID``. +variable. Note that atom-style variable formulas can also access +global scalars, but in this case it is not possible to do this +directly because of the ambiguity. Instead, an equal-style variable +can be defined which accesses the global scalar, and that variable can +be used in the atom-style variable formula in place of ``c_ID``. .. _thermo: @@ -141,9 +182,10 @@ There is also a :doc:`dump custom ` format where the user specifies what values are output with each atom. Pre-defined atom attributes can be specified (id, x, fx, etc). Three additional kinds of keywords can also be specified (c_ID, f_ID, v_name), where a -:doc:`compute ` or :doc:`fix ` or :doc:`variable ` -provides the values to be output. In each case, the compute, fix, or -variable must generate per-atom values for input to the :doc:`dump custom ` command. +:doc:`compute ` or :doc:`fix ` or :doc:`variable +` provides the values to be output. In each case, the +compute, fix, or variable must generate per-atom values for input to +the :doc:`dump custom ` command. There is also a :doc:`dump local ` format where the user specifies what local values to output. A pre-defined index keyword can be @@ -154,18 +196,23 @@ provides the values to be output. In each case, the compute or fix must generate local values for input to the :doc:`dump local ` command. +There is also a :doc:`dump grid ` format where the user +specifies what per-grid values to output (c_ID:gname:fname or +f_ID:gname:fname) from computes of fixes that generate per-grid data. + .. _fixoutput: Fixes that write output files ----------------------------- Several fixes take various quantities as input and can write output -files: :doc:`fix ave/time `, :doc:`fix ave/chunk `, :doc:`fix ave/histo `, -:doc:`fix ave/correlate `, and :doc:`fix print `. +files: :doc:`fix ave/time `, :doc:`fix ave/chunk +`, :doc:`fix ave/histo `, :doc:`fix +ave/correlate `, and :doc:`fix print `. -The :doc:`fix ave/time ` command enables direct output to -a file and/or time-averaging of global scalars or vectors. The user -specifies one or more quantities as input. These can be global +The :doc:`fix ave/time ` command enables direct output +to a file and/or time-averaging of global scalars or vectors. The +user specifies one or more quantities as input. These can be global :doc:`compute ` values, global :doc:`fix ` values, or :doc:`variables ` of any style except the atom style which produces per-atom values. Since a variable can refer to keywords used @@ -184,8 +231,14 @@ atoms, e.g. individual molecules. The per-atom quantities can be atom density (mass or number) or atom attributes such as position, velocity, force. They can also be per-atom quantities calculated by a :doc:`compute `, by a :doc:`fix `, or by an atom-style -:doc:`variable `. The chunk-averaged output of this fix can -also be used as input to other output commands. +:doc:`variable `. The chunk-averaged output of this fix is +global and can also be used as input to other output commands. + +Note that the :doc:`fix ave/grid ` command can also +average the same per-atom quantities within spatial bins, but it does +this for a distributed grid whose grid points are owned by different +processors. It outputs per-grid data, not global data, so is more +efficient for large numbers of averaging bins. The :doc:`fix ave/histo ` command enables direct output to a file of histogrammed quantities, which can be global or per-atom @@ -202,38 +255,53 @@ written to the screen and log file or to a separate file, periodically during a running simulation. The line can contain one or more :doc:`variable ` values for any style variable except the vector or atom styles). As explained above, variables themselves can -contain references to global values generated by :doc:`thermodynamic keywords `, :doc:`computes `, -:doc:`fixes `, or other :doc:`variables `, or to per-atom -values for a specific atom. Thus the :doc:`fix print ` -command is a means to output a wide variety of quantities separate -from normal thermodynamic or dump file output. +contain references to global values generated by :doc:`thermodynamic +keywords `, :doc:`computes `, :doc:`fixes +`, or other :doc:`variables `, or to per-atom values +for a specific atom. Thus the :doc:`fix print ` command is +a means to output a wide variety of quantities separate from normal +thermodynamic or dump file output. .. _computeoutput: Computes that process output quantities --------------------------------------- -The :doc:`compute reduce ` and :doc:`compute reduce/region ` commands take one or more per-atom -or local vector quantities as inputs and "reduce" them (sum, min, max, +The :doc:`compute reduce ` and :doc:`compute +reduce/region ` commands take one or more per-atom or +local vector quantities as inputs and "reduce" them (sum, min, max, ave) to scalar quantities. These are produced as output values which can be used as input to other output commands. -The :doc:`compute slice ` command take one or more global -vector or array quantities as inputs and extracts a subset of their -values to create a new vector or array. These are produced as output -values which can be used as input to other output commands. +The :doc:`compute slice ` command take one or more +global vector or array quantities as inputs and extracts a subset of +their values to create a new vector or array. These are produced as +output values which can be used as input to other output commands. -The :doc:`compute property/atom ` command takes a -list of one or more pre-defined atom attributes (id, x, fx, etc) and +The :doc:`compute property/atom ` command takes +a list of one or more pre-defined atom attributes (id, x, fx, etc) and stores the values in a per-atom vector or array. These are produced as output values which can be used as input to other output commands. -The list of atom attributes is the same as for the :doc:`dump custom ` command. +The list of atom attributes is the same as for the :doc:`dump custom +` command. -The :doc:`compute property/local ` command takes -a list of one or more pre-defined local attributes (bond info, angle -info, etc) and stores the values in a local vector or array. These -are produced as output values which can be used as input to other -output commands. +The :doc:`compute property/local ` command +takes a list of one or more pre-defined local attributes (bond info, +angle info, etc) and stores the values in a local vector or array. +These are produced as output values which can be used as input to +other output commands. + +The :doc:`compute property/grid ` command takes +a list of one or more pre-defined per-grid attributes (id, grid point +coords, etc) and stores the values in a per-grid vector or array. +These are produced as output values which can be used as input to the +:doc:`dump grid ` command. + +The :doc:`compute property/chunk ` command +takes a list of one or more pre-defined chunk attributes (id, count, +coords for spatial bins) and stores the values in a global vector or +array. These are produced as output values which can be used as input +to other output commands. .. _fixprocoutput: @@ -247,18 +315,42 @@ a time. The :doc:`fix ave/atom ` command performs time-averaging of per-atom vectors. The per-atom quantities can be atom attributes such as position, velocity, force. They can also be per-atom -quantities calculated by a :doc:`compute `, by a -:doc:`fix `, or by an atom-style :doc:`variable `. The +quantities calculated by a :doc:`compute `, by a :doc:`fix +`, or by an atom-style :doc:`variable `. The time-averaged per-atom output of this fix can be used as input to other output commands. -The :doc:`fix store/state ` command can archive one or -more per-atom attributes at a particular time, so that the old values -can be used in a future calculation or output. The list of atom -attributes is the same as for the :doc:`dump custom ` command, -including per-atom quantities calculated by a :doc:`compute `, -by a :doc:`fix `, or by an atom-style :doc:`variable `. -The output of this fix can be used as input to other output commands. +The :doc:`fix store/state ` command can archive one +or more per-atom attributes at a particular time, so that the old +values can be used in a future calculation or output. The list of +atom attributes is the same as for the :doc:`dump custom ` +command, including per-atom quantities calculated by a :doc:`compute +`, by a :doc:`fix `, or by an atom-style :doc:`variable +`. The output of this fix can be used as input to other +output commands. + +The :doc:`fix ave/grid ` command performs time-averaging +of either per-atom or per-grid data. + +For per-atom data it performs averaging for the atoms within each grid +cell, similar to the :doc:`fix ave/chunk ` command when +its chunks are defined as regular 2d or 3d bins. The per-atom +quantities can be atom density (mass or number) or atom attributes +such as position, velocity, force. They can also be per-atom +quantities calculated by a :doc:`compute `, by a :doc:`fix +`, or by an atom-style :doc:`variable `. + +The chief difference between the :doc:`fix ave/grid ` +and :doc:`fix ave/chunk ` commands when used in this +context is that the former uses a distributed grid, while the latter +uses a global grid. Distributed means that each processor owns the +subset of grid points within its subdomain. Global means that each +processor owns a copy of the entire grid. Distributed is thus more +efficient for large grids. + +For per-grid data, the :doc:`fix ave/grid ` command +takes inputs for grid data produced by other computes or fixes and +averages the values for each grid point over time. .. _compute: @@ -266,24 +358,25 @@ Computes that generate values to output --------------------------------------- Every :doc:`compute ` in LAMMPS produces either global or -per-atom or local values. The values can be scalars or vectors or -arrays of data. These values can be output using the other commands -described in this section. The page for each compute command +per-atom or local or per-grid values. The values can be scalars or +vectors or arrays of data. These values can be output using the other +commands described in this section. The page for each compute command describes what it produces. Computes that produce per-atom or local -values have the word "atom" or "local" in their style name. Computes -without the word "atom" or "local" produce global values. +or per-grid values have the word "atom" or "local" or "grid as the +last word in their style name. Computes without the word "atom" or +"local" or "grid" produce global values. .. _fix: Fixes that generate values to output ------------------------------------ -Some :doc:`fixes ` in LAMMPS produces either global or per-atom or -local values which can be accessed by other commands. The values can -be scalars or vectors or arrays of data. These values can be output -using the other commands described in this section. The page for -each fix command tells whether it produces any output quantities and -describes them. +Some :doc:`fixes ` in LAMMPS produces either global or per-atom +or local or per-grid values which can be accessed by other commands. +The values can be scalars or vectors or arrays of data. These values +can be output using the other commands described in this section. The +page for each fix command tells whether it produces any output +quantities and describes them. .. _variable: @@ -300,6 +393,8 @@ computes, fixes, and other variables. The values generated by variables can be used as input to and thus output by the other commands described in this section. +Per-grid variables have not (yet) been implemented. + .. _table: Summary table of output options and data flow between commands @@ -319,44 +414,52 @@ Also note that, as described above, when a command takes a scalar as input, that could be an element of a vector or array. Likewise a vector input could be a column of an array. -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| Command | Input | Output | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`thermo_style custom ` | global scalars | screen, log file | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`dump custom ` | per-atom vectors | dump file | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`dump local ` | local vectors | dump file | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`fix print ` | global scalar from variable | screen, file | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`print ` | global scalar from variable | screen | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`computes ` | N/A | global/per-atom/local scalar/vector/array | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`fixes ` | N/A | global/per-atom/local scalar/vector/array | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`variables ` | global scalars and vectors, per-atom vectors | global scalar and vector, per-atom vector | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`compute reduce ` | per-atom/local vectors | global scalar/vector | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`compute slice ` | global vectors/arrays | global vector/array | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`compute property/atom ` | per-atom vectors | per-atom vector/array | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`compute property/local ` | local vectors | local vector/array | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`fix vector ` | global scalars | global vector | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`fix ave/atom ` | per-atom vectors | per-atom vector/array | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`fix ave/time ` | global scalars/vectors | global scalar/vector/array, file | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`fix ave/chunk ` | per-atom vectors | global array, file | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`fix ave/histo ` | global/per-atom/local scalars and vectors | global array, file | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`fix ave/correlate ` | global scalars | global array, file | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ -| :doc:`fix store/state ` | per-atom vectors | per-atom vector/array | -+--------------------------------------------------------+----------------------------------------------+-------------------------------------------+ ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| Command | Input | Output | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`thermo_style custom ` | global scalars | screen, log file | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`dump custom ` | per-atom vectors | dump file | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`dump local ` | local vectors | dump file | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`dump grid ` | per-grid vectors | dump file | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`fix print ` | global scalar from variable | screen, file | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`print ` | global scalar from variable | screen | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`computes ` | N/A | global/per-atom/local/per-grid scalar/vector/array | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`fixes ` | N/A | global/per-atom/local/per-grid scalar/vector/array | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`variables ` | global scalars and vectors, per-atom vectors | global scalar and vector, per-atom vector | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`compute reduce ` | per-atom/local vectors | global scalar/vector | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`compute slice ` | global vectors/arrays | global vector/array | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`compute property/atom ` | N/A | per-atom vector/array | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`compute property/local ` | N/A | local vector/array | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`compute property/grid ` | N/A | per-grid vector/array | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`compute property/chunk ` | N/A | global vector/array | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`fix vector ` | global scalars | global vector | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`fix ave/atom ` | per-atom vectors | per-atom vector/array | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`fix ave/time ` | global scalars/vectors | global scalar/vector/array, file | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`fix ave/chunk ` | per-atom vectors | global array, file | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`fix ave/grid ` | per-atom vectors or per-grid vectors | per-grid vector/array | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`fix ave/histo ` | global/per-atom/local scalars and vectors | global array, file | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`fix ave/correlate ` | global scalars | global array, file | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ +| :doc:`fix store/state ` | per-atom vectors | per-atom vector/array | ++--------------------------------------------------------+----------------------------------------------+----------------------------------------------------+ diff --git a/doc/src/compute_property_chunk.rst b/doc/src/compute_property_chunk.rst index 48b3641e84..ba4a8368d7 100644 --- a/doc/src/compute_property_chunk.rst +++ b/doc/src/compute_property_chunk.rst @@ -12,7 +12,8 @@ Syntax * ID, group-ID are documented in :doc:`compute ` command * property/chunk = style name of this compute command -* input = one or more attributes +* chunkID = ID of :doc:`compute chunk/atom ` command that defines the chunks +* input1,etc = one or more attributes .. parsed-literal:: @@ -26,8 +27,8 @@ Examples .. code-block:: LAMMPS - compute 1 all property/chunk count - compute 1 all property/chunk ID coord1 + compute 1 all property/chunk bin2d id count + compute 1 all property/chunk myChunks id coord1 Description """"""""""" @@ -35,24 +36,28 @@ Description Define a computation that stores the specified attributes of chunks of atoms. -In LAMMPS, chunks are collections of atoms defined by a :doc:`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 :doc:`compute chunk/atom ` and :doc:`Howto chunk ` -doc pages for details of how chunks can be defined and examples of how -they can be used to measure properties of a system. +In LAMMPS, chunks are collections of atoms defined by a :doc:`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 :doc:`compute chunk/atom +` and :doc:`Howto chunk ` doc pages +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 :doc:`output commands ` and used in conjunction with other -commands that generate per-chunk data, such as :doc:`compute com/chunk ` or :doc:`compute msd/chunk `. +as global data so they can be accessed by other :doc:`output commands +` and used in conjunction with other commands that +generate per-chunk data, such as :doc:`compute com/chunk +` or :doc:`compute msd/chunk `. Note that only atoms in the specified group contribute to the -calculation of the *count* attribute. The :doc:`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. +calculation of the *count* attribute. The :doc:`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. @@ -61,21 +66,23 @@ can only be used if the *compress* keyword was set to *yes* for the :doc:`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 compressed 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 third chunk. +to them. Thus a compressed 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 third chunk. The *coordN* attributes can only be used if a *binning* style was used -in the :doc:`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. +in the :doc:`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 :doc:`compute chunk/atom command ` is *box* or *lattice*, the -*coordN* attributes will be in distance :doc:`units `. If the -value of the *units* keyword is *reduced*, the *coordN* attributes -will be in unitless reduced units (0-1). +Note that if the value of the *units* keyword used in the +:doc:`compute chunk/atom command ` is *box* or +*lattice*, the *coordN* attributes will be in distance :doc:`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 :doc:`fix ave/time ` diff --git a/doc/src/compute_property_grid.rst b/doc/src/compute_property_grid.rst new file mode 100644 index 0000000000..9d037e629c --- /dev/null +++ b/doc/src/compute_property_grid.rst @@ -0,0 +1,110 @@ +.. index:: compute property/grid + +compute property/grid command +============================= + +Syntax +"""""" + +.. parsed-literal:: + + compute ID group-ID property/grid input1 input2 ... + +* ID, group-ID are documented in :doc:`compute ` command +* property/grid = style name of this compute command +* input1,etc = one or more attributes + + .. parsed-literal:: + + attributes = id, ix, iy, iz, x, y, z, xs, ys, zs, xc, yc, zc, xsc, ysc, zsc + id = ID of grid point, x fastest, y next, z slowest + ix,iy,iz = grid indices in each dimension (1 to N inclusive) + x,y,z = coords of lower left corner of grid cell + xs,ys,zs = scaled coords of lower left corner of grid cell (0.0 to 1.0) + xc,yc,zc = coords of center point of grid cell + xsc,ysc,zsc = scaled coords of center point of grid cell (0.0 to 1.0) + +Examples +"""""""" + +.. code-block:: LAMMPS + + compute 1 all property/grid id ix iy iz + compute 1 all property/grid id xc yc zc + +Description +""""""""""" + +Define a computation that stores the specified attributes of a +distributed grid. In LAMMPS, distributed grids are regular 2d or 3d +grids which overlay a 2d or 3d simulation domain. Each processor owns +the grid points within its subdomain. + +See the :doc:`Howto grid ` doc page for details of how +distributed grids can be defined by various commands and examples of +how they can be used to measure properties of a system. + +This compute stores the specified attributes of grids as per-grid data +so they can be accessed by other :doc:`output commands ` +such as :doc:`dump grid `. + +The *id* attribute stores the grid ID for each grid point. For a +global grid of size Nx by Ny by Nz (in 3d simulations) the grid IDs +range from 1 to Nx*Ny*Nz. They are ordered with the X index of the 3d +grid varying fastest, then Y, then Z slowest. For 2d grids (in 2d +simulations), the grid IDs range from 1 to Nx*Ny, with X varying +fastest and Y slowest. + +The *ix*, *iy*, *iz* attributes are the indices of a grid point in +each dimension. They range from 1 to Nx inclusive in the X dimension, +and similar for Y and Z. + +The *x*, *y*, *z* attributes are the coordinates of the lower left +corner point of each grid cell. + +The *xs*, *ys*, *zs* attributes are also coordinates of the lower left +corner point of each grid cell, except in scaled coordinates, where +the lower-left corner of the entire simulation box is (0,0,0) and he +upper right corner is (1,1,1). + + +Only in triclinic. + +For 2d simulations, none of the attributes which refer to +the Z dimension can be used. + + + +Output info +""""""""""" + +This compute calculates a per-grid vector or array depending on the +number of input values. The length of the vector or number of rows +for each processor is the the number of grid points it owns. + +This compute calculates a global vector or global array where the +number of rows = the number of chunks *Nchunk* as calculated by the +specified :doc:`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 the :doc:`Howto output ` page 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 +"""""""""""""""" + +:doc:`fix ave/grid ` + +Default +""""""" + +none diff --git a/doc/src/compute_property_local.rst b/doc/src/compute_property_local.rst index 357f46b70d..b62bb744be 100644 --- a/doc/src/compute_property_local.rst +++ b/doc/src/compute_property_local.rst @@ -57,10 +57,11 @@ Description """"""""""" Define a computation that stores the specified attributes as local -data so it can be accessed by other :doc:`output commands `. If the input attributes refer to bond -information, then the number of datums generated, aggregated across -all processors, equals the number of bonds in the system. Ditto for -pairs, angles, etc. +data so it can be accessed by other :doc:`output commands +`. If the input attributes refer to bond information, +then the number of datums generated, aggregated across all processors, +equals the number of bonds in the system. Ditto for pairs, angles, +etc. If multiple attributes are specified then they must all generate the same amount of information, so that the resulting local array has the @@ -101,17 +102,20 @@ specified compute group. Likewise for angles, dihedrals, etc. For bonds and angles, a bonds/angles that have been broken by setting their bond/angle type to 0 will not be included. Bonds/angles that have been turned off (see the :doc:`fix shake ` or -:doc:`delete_bonds ` commands) by setting their bond/angle -type negative are written into the file. This is consistent with the -:doc:`compute bond/local ` and :doc:`compute angle/local ` commands +:doc:`delete_bonds ` commands) by setting their +bond/angle type negative are written into the file. This is +consistent with the :doc:`compute bond/local ` and +:doc:`compute angle/local ` commands Note that as atoms migrate from processor to processor, there will be no consistent ordering of the entries within the local vector or array from one timestep to the next. The only consistency that is guaranteed is that the ordering on a particular timestep will be the same for local vectors or arrays generated by other compute commands. -For example, output from the :doc:`compute bond/local ` command can be combined with bond -atom indices from this command and output by the :doc:`dump local ` command in a consistent way. +For example, output from the :doc:`compute bond/local +` command can be combined with bond atom indices +from this command and output by the :doc:`dump local ` command +in a consistent way. The *natom1* and *natom2*, or *patom1* and *patom2* attributes refer to the atom IDs of the 2 atoms in each pairwise interaction computed @@ -149,8 +153,8 @@ the array is the number of bonds, angles, etc. If a single input is specified, a local vector is produced. If two or more inputs are specified, a local array is produced where the number of columns = the number of inputs. The vector or array can be accessed by any command -that uses local values from a compute as input. See the :doc:`Howto output ` page for an overview of LAMMPS output -options. +that uses local values from a compute as input. See the :doc:`Howto +output ` page for an overview of LAMMPS output options. The vector or array values will be integers that correspond to the specified attribute.