diff --git a/doc/fix_deposit.html b/doc/fix_deposit.html index 6b07e16612..42648291c0 100644 --- a/doc/fix_deposit.html +++ b/doc/fix_deposit.html @@ -29,14 +29,10 @@
region value = region-ID region-ID = ID of region to use as insertion volume - mol value = template-ID - template-ID = ID of molecule template specified in a separate molecule command - rigid value = fix-ID - fix-ID = ID of fix rigid/small command id value = max or next max = atom ID for new atom(s) is max ID of all current atoms plus one next = atom ID for new atom(s) increments by one for every deposition @@ -59,6 +55,12 @@ vzlo,vzhi = range of z velocities for inserted atom/molecule (velocity units) target values = tx ty tz tx,ty,tz = location of target point (distance units) + mol value = template-ID + template-ID = ID of molecule template specified in a separate molecule command + rigid value = fix-ID + fix-ID = ID of fix rigid/small command + shake value = fix-ID + fix-ID = ID of fix shake command units value = lattice or box lattice = the geometry is defined in lattice units box = the geometry is defined in simulation box units @@ -130,6 +132,11 @@ treated as rigid bodies, use the rigid keyword, specifying as its value the ID of a separate fix rigid/small command which also appears in your input script. +If you wish to insert molecules via the mol keyword, that will have +their bonds or angles constrained via SHAKE, use the shake keyword, +specifying as its value the ID of a separate fix +shake command which also appears in your input script. +
Each timestep a particle is inserted, the coordinates for its atoms are chosen as follows. For insertion of individual atoms, the "position" referred to in the following description is the coordinate diff --git a/doc/fix_deposit.txt b/doc/fix_deposit.txt index 36f07972aa..45d9085163 100644 --- a/doc/fix_deposit.txt +++ b/doc/fix_deposit.txt @@ -19,13 +19,9 @@ type = atom type to assign to inserted atoms (offset for moleclue insertion) :l M = insert a single atom or molecule every M steps :l seed = random # seed (positive integer) :l one or more keyword/value pairs may be appended to args :l -keyword = {region} or {mol} or {id} or {global} or {local} or {near} or {attempt} or {rate} or {vx} or {vy} or {vz} or {units} :l +keyword = {region} or {id} or {global} or {local} or {near} or {attempt} or {rate} or {vx} or {vy} or {vz} or {mol} or {rigid} or {shake} or {units} :l {region} value = region-ID region-ID = ID of region to use as insertion volume - {mol} value = template-ID - template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command - {rigid} value = fix-ID - fix-ID = ID of "fix rigid/small"_fix_rigid.html command {id} value = {max} or {next} max = atom ID for new atom(s) is max ID of all current atoms plus one next = atom ID for new atom(s) increments by one for every deposition @@ -48,6 +44,12 @@ keyword = {region} or {mol} or {id} or {global} or {local} or {near} or {attempt vzlo,vzhi = range of z velocities for inserted atom/molecule (velocity units) {target} values = tx ty tz tx,ty,tz = location of target point (distance units) + {mol} value = template-ID + template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command + {rigid} value = fix-ID + fix-ID = ID of "fix rigid/small"_fix_rigid.html command + {shake} value = fix-ID + fix-ID = ID of "fix shake"_fix_shake.html command {units} value = {lattice} or {box} lattice = the geometry is defined in lattice units box = the geometry is defined in simulation box units :pre @@ -118,6 +120,11 @@ treated as rigid bodies, use the {rigid} keyword, specifying as its value the ID of a separate "fix rigid/small"_fix_rigid_small.html command which also appears in your input script. +If you wish to insert molecules via the {mol} keyword, that will have +their bonds or angles constrained via SHAKE, use the {shake} keyword, +specifying as its value the ID of a separate "fix +shake"_fix_shake.html command which also appears in your input script. + Each timestep a particle is inserted, the coordinates for its atoms are chosen as follows. For insertion of individual atoms, the "position" referred to in the following description is the coordinate