Loading doc/src/Section_commands.txt +1 −0 Original line number Diff line number Diff line Loading @@ -775,6 +775,7 @@ KOKKOS, o = USER-OMP, t = OPT. "erotate/sphere"_compute_erotate_sphere.html, "erotate/sphere/atom"_compute_erotate_sphere_atom.html, "event/displace"_compute_event_displace.html, "fragment/atom"_compute_cluster_atom.html, "global/atom"_compute_global_atom.html, "group/group"_compute_group_group.html, "gyration"_compute_gyration.html, Loading doc/src/compute_cluster_atom.txt +26 −14 Original line number Diff line number Diff line Loading @@ -7,37 +7,49 @@ :line compute cluster/atom command :h3 compute fragment/atom command :h3 [Syntax:] compute ID group-ID cluster/atom cutoff :pre compute ID group-ID cluster/atom cutoff compute ID group-ID fragment/atom :pre ID, group-ID are documented in "compute"_compute.html command cluster/atom = style name of this compute command cutoff = distance within which to label atoms as part of same cluster (distance units) :ul {cluster/atom} or {fragment/atom} = style name of this compute command cutoff = distance within which to label atoms as part of same cluster (distance units, cluster/atom only) :ul [Examples:] compute 1 all cluster/atom 1.0 :pre compute 1 all cluster/atom 3.5 compute 1 all fragment/atom :pre [Description:] Define a computation that assigns each atom a cluster ID. Define a computation that assigns each atom a cluster ID or fragment ID. A cluster is defined as a set of atoms, each of which is within the cutoff distance from one or more other atoms in the cluster. If an atom has no neighbors within the cutoff distance, then it is a 1-atom cluster. The ID of every atom in the cluster will be the smallest atom ID of any atom in the cluster. cluster. A fragment is similarly define as a set of atoms, each of which has an explicit bond (i.e. defined via a "data file"_read_data.html, the "create_bonds"_create_bonds.html command, or through fixes like "fix bond/create"_fix_bond_create.html, "fix bond/swap"_fix_bond_swap.html, or "fix bond/break"_fix_bond_break.html). The cluster ID or fragment ID of every atom in the cluster will be set to the smallest atom ID of any atom in the cluster or fragment, respectively. Only atoms in the compute group are clustered and assigned cluster IDs. Atoms not in the compute group are assigned a cluster ID = 0. The neighbor list needed to compute this quantity is constructed each time the calculation is performed (i.e. each time a snapshot of atoms is dumped). Thus it can be inefficient to compute/dump this quantity too frequently or to have multiple compute/dump commands, each of a {cluster/atom} style. For fragments, only bonds where [both] atoms of the bond are included in the compute group are assigned to fragments, so that only fragmets are detected where [all] atoms are in the compute group. Thus atoms may be included in the compute group, yes still have a fragment ID of 0. For compute {cluster/atom} the neighbor list needed to compute this quantity is constructed each time the calculation is performed (i.e. each time a snapshot of atoms is dumped). Thus it can be inefficient to compute/dump this quantity too frequently or to have multiple compute/dump commands, each of a {cluster/atom} style. NOTE: If you have a bonded system, then the settings of "special_bonds"_special_bonds.html command can remove pairwise Loading Loading
doc/src/Section_commands.txt +1 −0 Original line number Diff line number Diff line Loading @@ -775,6 +775,7 @@ KOKKOS, o = USER-OMP, t = OPT. "erotate/sphere"_compute_erotate_sphere.html, "erotate/sphere/atom"_compute_erotate_sphere_atom.html, "event/displace"_compute_event_displace.html, "fragment/atom"_compute_cluster_atom.html, "global/atom"_compute_global_atom.html, "group/group"_compute_group_group.html, "gyration"_compute_gyration.html, Loading
doc/src/compute_cluster_atom.txt +26 −14 Original line number Diff line number Diff line Loading @@ -7,37 +7,49 @@ :line compute cluster/atom command :h3 compute fragment/atom command :h3 [Syntax:] compute ID group-ID cluster/atom cutoff :pre compute ID group-ID cluster/atom cutoff compute ID group-ID fragment/atom :pre ID, group-ID are documented in "compute"_compute.html command cluster/atom = style name of this compute command cutoff = distance within which to label atoms as part of same cluster (distance units) :ul {cluster/atom} or {fragment/atom} = style name of this compute command cutoff = distance within which to label atoms as part of same cluster (distance units, cluster/atom only) :ul [Examples:] compute 1 all cluster/atom 1.0 :pre compute 1 all cluster/atom 3.5 compute 1 all fragment/atom :pre [Description:] Define a computation that assigns each atom a cluster ID. Define a computation that assigns each atom a cluster ID or fragment ID. A cluster is defined as a set of atoms, each of which is within the cutoff distance from one or more other atoms in the cluster. If an atom has no neighbors within the cutoff distance, then it is a 1-atom cluster. The ID of every atom in the cluster will be the smallest atom ID of any atom in the cluster. cluster. A fragment is similarly define as a set of atoms, each of which has an explicit bond (i.e. defined via a "data file"_read_data.html, the "create_bonds"_create_bonds.html command, or through fixes like "fix bond/create"_fix_bond_create.html, "fix bond/swap"_fix_bond_swap.html, or "fix bond/break"_fix_bond_break.html). The cluster ID or fragment ID of every atom in the cluster will be set to the smallest atom ID of any atom in the cluster or fragment, respectively. Only atoms in the compute group are clustered and assigned cluster IDs. Atoms not in the compute group are assigned a cluster ID = 0. The neighbor list needed to compute this quantity is constructed each time the calculation is performed (i.e. each time a snapshot of atoms is dumped). Thus it can be inefficient to compute/dump this quantity too frequently or to have multiple compute/dump commands, each of a {cluster/atom} style. For fragments, only bonds where [both] atoms of the bond are included in the compute group are assigned to fragments, so that only fragmets are detected where [all] atoms are in the compute group. Thus atoms may be included in the compute group, yes still have a fragment ID of 0. For compute {cluster/atom} the neighbor list needed to compute this quantity is constructed each time the calculation is performed (i.e. each time a snapshot of atoms is dumped). Thus it can be inefficient to compute/dump this quantity too frequently or to have multiple compute/dump commands, each of a {cluster/atom} style. NOTE: If you have a bonded system, then the settings of "special_bonds"_special_bonds.html command can remove pairwise Loading
