These are compute styles contributed by users, which can be used if diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index c364e4cf02..a7618b2b1c 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -485,6 +485,7 @@ each style or click on the style itself for a full description: "pressure"_compute_pressure.html, "property/atom"_compute_property_atom.html, "property/local"_compute_property_local.html, +"property/molecule"_compute_property_molecule.html, "rdf"_compute_rdf.html, "reduce"_compute_reduce.html, "reduce/region"_compute_reduce.html, diff --git a/doc/compute.html b/doc/compute.html index d78ed5a88d..4680194fa2 100644 --- a/doc/compute.html +++ b/doc/compute.html @@ -193,6 +193,7 @@ available in LAMMPS:
Syntax: +
+compute ID group-ID property/molecule input1 input2 ... ++
possible attributes = mol ++
mol = molecule ID ++ +
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. 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. +
+If multiple input attributes are specified then they must all generate +the same amount of information, so that the resulting local array has +the same number of rows for each column. This means that only bond +attributes can be specified together, or angle attributes, etc. Bond +and angle attributes can not be mixed in the same compute +property/local command. +
+The local data is generated by looping over all the atoms owned on a +processor and extracting bond, angle, etc info. For bonds, info about +an individual bond will only be included if both atoms in the bond are +in the specified compute group. Likewise for angles, dihedrals, etc. +
+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 compute +bond/local command can be combined with bond +atom indices from this command and output by the dump +local command in a consistent way. +
+The batom1 and batom2 attributes refer the atom IDs of the 2 atoms +in each bond. The btype attribute refers to the +type of the bond, from 1 to Nbtypes = # of bond types. The number of +bond types is defined in the data file read by the +read_data command. The attributes that start with +"a", "d", "i", refer to similar values for angles, +dihedrals, and impropers. +
+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. +
+Restrictions: none +
+Related commands: none +
+Default: none +
+ diff --git a/doc/compute_property_molecule.txt b/doc/compute_property_molecule.txt new file mode 100644 index 0000000000..794ddf593a --- /dev/null +++ b/doc/compute_property_molecule.txt @@ -0,0 +1,80 @@ +"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 :pre + mol = molecule ID :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#4_15. 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. + +If multiple input attributes are specified then they must all generate +the same amount of information, so that the resulting local array has +the same number of rows for each column. This means that only bond +attributes can be specified together, or angle attributes, etc. Bond +and angle attributes can not be mixed in the same compute +property/local command. + +The local data is generated by looping over all the atoms owned on a +processor and extracting bond, angle, etc info. For bonds, info about +an individual bond will only be included if both atoms in the bond are +in the specified compute group. Likewise for angles, dihedrals, etc. + +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 "compute +bond/local"_compute_bond_local.html command can be combined with bond +atom indices from this command and output by the "dump +local"_dump.html command in a consistent way. + +The {batom1} and {batom2} attributes refer the atom IDs of the 2 atoms +in each "bond"_bond_style.html. The {btype} attribute refers to the +type of the bond, from 1 to Nbtypes = # of bond types. The number of +bond types is defined in the data file read by the +"read_data"_read_data.html command. The attributes that start with +"a", "d", "i", refer to similar values for "angles"_angle_style.html, +"dihedrals"_dihedral_style.html, and "impropers"_improper_style.html. + +[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#4_15 for an overview of LAMMPS output +options. + +[Restrictions:] none + +[Related commands:] none + +[Default:] none