Loading doc/src/fix_bond_react.rst +17 −7 Original line number Diff line number Diff line Loading @@ -14,19 +14,22 @@ Syntax react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ... ... * ID, group-ID are documented in :doc:`fix <fix>` command. Group-ID is ignored. * ID, group-ID are documented in :doc:`fix <fix>` command. * bond/react = style name of this fix command * the common keyword/values may be appended directly after 'bond/react' * this applies to all reaction specifications (below) * common_keyword = *stabilization* * common_keyword = *stabilization* or *reset_mol_ids* .. parsed-literal:: *stabilization* values = *no* or *yes* *group-ID* *xmax* *no* = no reaction site stabilization *no* = no reaction site stabilization (default) *yes* = perform reaction site stabilization *group-ID* = user-assigned prefix for the dynamic group of atoms not currently involved in a reaction *xmax* = xmax value that is used by an internally-created :doc:`nve/limit <fix_nve_limit>` integrator *reset_mol_ids* values = *yes* or *no* *yes* = update molecule IDs based on new global topology (default) *no* = do not update molecule IDs * react = mandatory argument indicating new reaction specification * react-ID = user-assigned name for the reaction Loading @@ -50,9 +53,9 @@ Syntax *stabilize_steps* value = timesteps timesteps = number of timesteps to apply the internally-created :doc:`nve/limit <fix_nve_limit>` fix to reacting atoms *update_edges* value = *none* or *charges* or *custom* none = do not update topology near the edges of reaction templates charges = update atomic charges of all atoms in reaction templates custom = force the update of user-specified atomic charges *none* = do not update topology near the edges of reaction templates *charges* = update atomic charges of all atoms in reaction templates *custom* = force the update of user-specified atomic charges Examples """""""" Loading Loading @@ -154,6 +157,13 @@ due to the internal dynamic grouping performed by fix bond/react. If the group-ID is an existing static group, react-group-IDs should also be specified as this static group, or a subset. The *reset_mol_ids* keyword invokes the :doc:`reset_mol_ids <reset_mol_ids>` command after a reaction occurs, to ensure that molecule IDs are consistent with the new bond topology. The group-ID used for :doc:`reset_mol_ids <reset_mol_ids>` is the group-ID for this fix. Resetting molecule IDs is necessarily a global operation, and so can be slow for very large systems. The following comments pertain to each *react* argument (in other words, can be customized for each reaction, or reaction step): Loading Loading @@ -553,7 +563,7 @@ Default """"""" The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60, update_edges = none reset_mol_ids = yes, update_edges = none ---------- Loading Loading
doc/src/fix_bond_react.rst +17 −7 Original line number Diff line number Diff line Loading @@ -14,19 +14,22 @@ Syntax react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ... ... * ID, group-ID are documented in :doc:`fix <fix>` command. Group-ID is ignored. * ID, group-ID are documented in :doc:`fix <fix>` command. * bond/react = style name of this fix command * the common keyword/values may be appended directly after 'bond/react' * this applies to all reaction specifications (below) * common_keyword = *stabilization* * common_keyword = *stabilization* or *reset_mol_ids* .. parsed-literal:: *stabilization* values = *no* or *yes* *group-ID* *xmax* *no* = no reaction site stabilization *no* = no reaction site stabilization (default) *yes* = perform reaction site stabilization *group-ID* = user-assigned prefix for the dynamic group of atoms not currently involved in a reaction *xmax* = xmax value that is used by an internally-created :doc:`nve/limit <fix_nve_limit>` integrator *reset_mol_ids* values = *yes* or *no* *yes* = update molecule IDs based on new global topology (default) *no* = do not update molecule IDs * react = mandatory argument indicating new reaction specification * react-ID = user-assigned name for the reaction Loading @@ -50,9 +53,9 @@ Syntax *stabilize_steps* value = timesteps timesteps = number of timesteps to apply the internally-created :doc:`nve/limit <fix_nve_limit>` fix to reacting atoms *update_edges* value = *none* or *charges* or *custom* none = do not update topology near the edges of reaction templates charges = update atomic charges of all atoms in reaction templates custom = force the update of user-specified atomic charges *none* = do not update topology near the edges of reaction templates *charges* = update atomic charges of all atoms in reaction templates *custom* = force the update of user-specified atomic charges Examples """""""" Loading Loading @@ -154,6 +157,13 @@ due to the internal dynamic grouping performed by fix bond/react. If the group-ID is an existing static group, react-group-IDs should also be specified as this static group, or a subset. The *reset_mol_ids* keyword invokes the :doc:`reset_mol_ids <reset_mol_ids>` command after a reaction occurs, to ensure that molecule IDs are consistent with the new bond topology. The group-ID used for :doc:`reset_mol_ids <reset_mol_ids>` is the group-ID for this fix. Resetting molecule IDs is necessarily a global operation, and so can be slow for very large systems. The following comments pertain to each *react* argument (in other words, can be customized for each reaction, or reaction step): Loading Loading @@ -553,7 +563,7 @@ Default """"""" The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60, update_edges = none reset_mol_ids = yes, update_edges = none ---------- Loading
