Loading doc/src/Commands_all.rst +2 −1 Original line number Diff line number Diff line Loading @@ -101,7 +101,8 @@ An alphabetic list of all general LAMMPS commands. * :doc:`region <region>` * :doc:`replicate <replicate>` * :doc:`rerun <rerun>` * :doc:`reset_ids <reset_ids>` * :doc:`reset_atom_ids <reset_atom_ids>` * :doc:`reset_mol_ids <reset_mol_ids>` * :doc:`reset_timestep <reset_timestep>` * :doc:`restart <restart>` * :doc:`run <run>` Loading doc/src/commands_list.rst +2 −1 Original line number Diff line number Diff line Loading @@ -88,7 +88,8 @@ Commands region replicate rerun reset_ids reset_atom_ids reset_mol_ids reset_timestep restart run Loading doc/src/compute_cluster_atom.rst +43 −25 Original line number Diff line number Diff line Loading @@ -15,12 +15,18 @@ Syntax .. parsed-literal:: compute ID group-ID cluster/atom cutoff compute ID group-ID fragment/atom compute ID group-ID fragment/atom keyword value ... compute ID group-ID aggregate/atom cutoff * ID, group-ID are documented in :doc:`compute <compute>` command * *cluster/atom* or *fragment/atom* or *aggregate/atom* = style name of this compute command * cutoff = distance within which to label atoms as part of same cluster (distance units) * zero or more keyword/value pairs may be appended to *fragment/atom* * keyword = *single* .. parsed-literal:: *single* value = *yes* or *no* to treat single atoms (no bonds) as fragments Examples """""""" Loading @@ -29,27 +35,36 @@ Examples compute 1 all cluster/atom 3.5 compute 1 all fragment/atom compute 1 all fragment/atom single no compute 1 all aggregate/atom 3.5 Description """"""""""" Define a computation that assigns each atom a cluster, fragment, or aggregate ID. Define a computation that assigns each atom a cluster, fragment, or aggregate ID. Only atoms in the compute group are clustered and assigned cluster IDs. Atoms not in the compute group are assigned an ID = 0. 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. A fragment is similarly defined as a set of atoms, each of which has an explicit bond (i.e. defined via a :doc:`data file <read_data>`, the :doc:`create_bonds <create_bonds>` command, or through fixes like :doc:`fix bond/create <fix_bond_create>`, :doc:`fix bond/swap <fix_bond_swap>`, or :doc:`fix bond/break <fix_bond_break>`). 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. A fragment is similarly defined as a set of atoms, each of which has a bond to another atom in the fragment. Bonds can be defined initially via the :doc:`data file <read_data>` or :doc:`create_bonds <create_bonds>` commands, or dynamically by fixes which create or break bonds like :doc:`fix bond/react <fix_bond_react>`, :doc:`fix bond/create <fix_bond_create>`, :doc:`fix bond/swap <fix_bond_swap>`, or :doc:`fix bond/break <fix_bond_break>`. 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. For the *fragment/atom* style, the *single* keyword determines whether single atoms (not bonded to another atom) are treated as one-atom fragments or not, based on the *yes* or *no* setting. If the setting is *no* (the default), their fragment IDs are set to 0. An aggregate is defined by combining the rules for clusters and fragments, i.e. a set of atoms, where each of it is within the cutoff Loading @@ -57,19 +72,11 @@ distance from one or more atoms within a fragment that is part of the same cluster. This measure can be used to track molecular assemblies like micelles. Only atoms in the compute group are clustered and assigned cluster IDs. Atoms not in the compute group are assigned a cluster ID = 0. For fragments, only bonds where **both** atoms of the bond are included in the compute group are assigned to fragments, so that only fragments 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 computes *cluster/atom* and *aggregate/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* or *aggregate/atom* style. For computes *cluster/atom* and *aggregate/atom* a neighbor list needed to compute cluster IDs is constructed each time the compute is invoked. Thus it can be inefficient to compute/dump this quantity too frequently or to have multiple *cluster/atom* or *aggregate/atom* style computes. .. note:: Loading @@ -89,6 +96,14 @@ multiple compute/dump commands, each of a *cluster/atom* or :doc:`special_bonds <special_bonds>` command that includes all pairs in the neighbor list. .. note:: For the compute fragment/atom style, each fragment is identified using the current bond topology. This will not account for bonds broken by the :doc:`bond_style quartic <bond_quartic>` command because it does not perform a full update of the bond topology data structures within LAMMPS. **Output info:** This compute calculates a per-atom vector, which can be accessed by Loading @@ -107,4 +122,7 @@ Related commands :doc:`compute coord/atom <compute_coord_atom>` **Default:** none **Default:** The default for fragment/atom is single no. doc/src/delete_atoms.rst +2 −2 Original line number Diff line number Diff line Loading @@ -89,7 +89,7 @@ number of atoms in the system. Note that this is not done for molecular systems (see the :doc:`atom_style <atom_style>` command), regardless of the *compress* setting, since it would foul up the bond connectivity that has already been assigned. However, the :doc:`reset_ids <reset_ids>` command can be used after this command to :doc:`reset_atom_ids <reset_atom_ids>` command can be used after this command to accomplish the same thing. Note that the re-assignment of IDs is not really a compression, where Loading Loading @@ -157,7 +157,7 @@ using molecule template files via the :doc:`molecule <molecule>` and Related commands """""""""""""""" :doc:`create_atoms <create_atoms>`, :doc:`reset_ids <reset_ids>` :doc:`create_atoms <create_atoms>`, :doc:`reset_atom_ids <reset_atom_ids>` Default """"""" Loading doc/src/reset_ids.rst→doc/src/reset_atom_ids.rst +7 −7 Original line number Diff line number Diff line .. index:: reset_ids .. index:: reset_atom_ids reset_ids command ================= reset_atom_ids command ====================== Syntax """""" .. code-block:: LAMMPS reset_ids keyword values ... reset_atom_ids keyword values ... * zero or more keyword/value pairs may be appended * keyword = *sort* Loading @@ -22,8 +22,8 @@ Examples .. code-block:: LAMMPS reset_ids reset_ids sort yes reset_atom_ids reset_atom_ids sort yes Description """"""""""" Loading Loading @@ -77,7 +77,7 @@ processor have consecutive IDs, as the :doc:`create_atoms that are owned by other processors. The :doc:`comm_modify cutoff <comm_modify>` command can be used to correct this issue. Or you can define a pair style before using this command. If you do the former, you should unset the comm_modify cutoff after using reset_ids so that subsequent communication is not inefficient. reset_atom_ids so that subsequent communication is not inefficient. Restrictions """""""""""" Loading Loading
doc/src/Commands_all.rst +2 −1 Original line number Diff line number Diff line Loading @@ -101,7 +101,8 @@ An alphabetic list of all general LAMMPS commands. * :doc:`region <region>` * :doc:`replicate <replicate>` * :doc:`rerun <rerun>` * :doc:`reset_ids <reset_ids>` * :doc:`reset_atom_ids <reset_atom_ids>` * :doc:`reset_mol_ids <reset_mol_ids>` * :doc:`reset_timestep <reset_timestep>` * :doc:`restart <restart>` * :doc:`run <run>` Loading
doc/src/commands_list.rst +2 −1 Original line number Diff line number Diff line Loading @@ -88,7 +88,8 @@ Commands region replicate rerun reset_ids reset_atom_ids reset_mol_ids reset_timestep restart run Loading
doc/src/compute_cluster_atom.rst +43 −25 Original line number Diff line number Diff line Loading @@ -15,12 +15,18 @@ Syntax .. parsed-literal:: compute ID group-ID cluster/atom cutoff compute ID group-ID fragment/atom compute ID group-ID fragment/atom keyword value ... compute ID group-ID aggregate/atom cutoff * ID, group-ID are documented in :doc:`compute <compute>` command * *cluster/atom* or *fragment/atom* or *aggregate/atom* = style name of this compute command * cutoff = distance within which to label atoms as part of same cluster (distance units) * zero or more keyword/value pairs may be appended to *fragment/atom* * keyword = *single* .. parsed-literal:: *single* value = *yes* or *no* to treat single atoms (no bonds) as fragments Examples """""""" Loading @@ -29,27 +35,36 @@ Examples compute 1 all cluster/atom 3.5 compute 1 all fragment/atom compute 1 all fragment/atom single no compute 1 all aggregate/atom 3.5 Description """"""""""" Define a computation that assigns each atom a cluster, fragment, or aggregate ID. Define a computation that assigns each atom a cluster, fragment, or aggregate ID. Only atoms in the compute group are clustered and assigned cluster IDs. Atoms not in the compute group are assigned an ID = 0. 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. A fragment is similarly defined as a set of atoms, each of which has an explicit bond (i.e. defined via a :doc:`data file <read_data>`, the :doc:`create_bonds <create_bonds>` command, or through fixes like :doc:`fix bond/create <fix_bond_create>`, :doc:`fix bond/swap <fix_bond_swap>`, or :doc:`fix bond/break <fix_bond_break>`). 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. A fragment is similarly defined as a set of atoms, each of which has a bond to another atom in the fragment. Bonds can be defined initially via the :doc:`data file <read_data>` or :doc:`create_bonds <create_bonds>` commands, or dynamically by fixes which create or break bonds like :doc:`fix bond/react <fix_bond_react>`, :doc:`fix bond/create <fix_bond_create>`, :doc:`fix bond/swap <fix_bond_swap>`, or :doc:`fix bond/break <fix_bond_break>`. 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. For the *fragment/atom* style, the *single* keyword determines whether single atoms (not bonded to another atom) are treated as one-atom fragments or not, based on the *yes* or *no* setting. If the setting is *no* (the default), their fragment IDs are set to 0. An aggregate is defined by combining the rules for clusters and fragments, i.e. a set of atoms, where each of it is within the cutoff Loading @@ -57,19 +72,11 @@ distance from one or more atoms within a fragment that is part of the same cluster. This measure can be used to track molecular assemblies like micelles. Only atoms in the compute group are clustered and assigned cluster IDs. Atoms not in the compute group are assigned a cluster ID = 0. For fragments, only bonds where **both** atoms of the bond are included in the compute group are assigned to fragments, so that only fragments 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 computes *cluster/atom* and *aggregate/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* or *aggregate/atom* style. For computes *cluster/atom* and *aggregate/atom* a neighbor list needed to compute cluster IDs is constructed each time the compute is invoked. Thus it can be inefficient to compute/dump this quantity too frequently or to have multiple *cluster/atom* or *aggregate/atom* style computes. .. note:: Loading @@ -89,6 +96,14 @@ multiple compute/dump commands, each of a *cluster/atom* or :doc:`special_bonds <special_bonds>` command that includes all pairs in the neighbor list. .. note:: For the compute fragment/atom style, each fragment is identified using the current bond topology. This will not account for bonds broken by the :doc:`bond_style quartic <bond_quartic>` command because it does not perform a full update of the bond topology data structures within LAMMPS. **Output info:** This compute calculates a per-atom vector, which can be accessed by Loading @@ -107,4 +122,7 @@ Related commands :doc:`compute coord/atom <compute_coord_atom>` **Default:** none **Default:** The default for fragment/atom is single no.
doc/src/delete_atoms.rst +2 −2 Original line number Diff line number Diff line Loading @@ -89,7 +89,7 @@ number of atoms in the system. Note that this is not done for molecular systems (see the :doc:`atom_style <atom_style>` command), regardless of the *compress* setting, since it would foul up the bond connectivity that has already been assigned. However, the :doc:`reset_ids <reset_ids>` command can be used after this command to :doc:`reset_atom_ids <reset_atom_ids>` command can be used after this command to accomplish the same thing. Note that the re-assignment of IDs is not really a compression, where Loading Loading @@ -157,7 +157,7 @@ using molecule template files via the :doc:`molecule <molecule>` and Related commands """""""""""""""" :doc:`create_atoms <create_atoms>`, :doc:`reset_ids <reset_ids>` :doc:`create_atoms <create_atoms>`, :doc:`reset_atom_ids <reset_atom_ids>` Default """"""" Loading
doc/src/reset_ids.rst→doc/src/reset_atom_ids.rst +7 −7 Original line number Diff line number Diff line .. index:: reset_ids .. index:: reset_atom_ids reset_ids command ================= reset_atom_ids command ====================== Syntax """""" .. code-block:: LAMMPS reset_ids keyword values ... reset_atom_ids keyword values ... * zero or more keyword/value pairs may be appended * keyword = *sort* Loading @@ -22,8 +22,8 @@ Examples .. code-block:: LAMMPS reset_ids reset_ids sort yes reset_atom_ids reset_atom_ids sort yes Description """"""""""" Loading Loading @@ -77,7 +77,7 @@ processor have consecutive IDs, as the :doc:`create_atoms that are owned by other processors. The :doc:`comm_modify cutoff <comm_modify>` command can be used to correct this issue. Or you can define a pair style before using this command. If you do the former, you should unset the comm_modify cutoff after using reset_ids so that subsequent communication is not inefficient. reset_atom_ids so that subsequent communication is not inefficient. Restrictions """""""""""" Loading
