IMPORTANT NOTE: LAMMPS also maintains a data structure that stores a -list of 1st, 2nd, and 3rd neighbors of each atom (within the bond +
IMPORTANT NOTE: LAMMPS stores and maintains a data structure with a +list of the 1st, 2nd, and 3rd neighbors of each atom (within the bond topology of the system) for use in weighting pairwise interactions for -bonded atoms. Adding a bond adds a single entry to this list. The -"extra special per atom" parameter must typically be set to allow for -it. There are 3 ways to do this. See the read_data -or create_box or "special_bonds extra" commands for +bonded atoms. Note that adding a single bond always adds a new 1st +neighbor but may also induce *many* new 2nd and 3rd neighbors, +depending on the molecular topology of your system. The "extra +special per atom" parameter must typically be set to allow for the new +maximum total size (1st + 2nd + 3rd neighbors) of this per-atom list. +There are 3 ways to do this. See the read_data or +create_box or "special_bonds extra" commands for details.
IMPORTANT NOTE: Even if you do not use the atype, dtype, or diff --git a/doc/fix_bond_create.txt b/doc/fix_bond_create.txt index 637d5ac172..1c56049422 100755 --- a/doc/fix_bond_create.txt +++ b/doc/fix_bond_create.txt @@ -143,13 +143,16 @@ data file with no atoms can be used if you wish to add unbonded atoms via the "create atoms"_create_atoms.html command, e.g. for a percolation simulation. -IMPORTANT NOTE: LAMMPS also maintains a data structure that stores a -list of 1st, 2nd, and 3rd neighbors of each atom (within the bond +IMPORTANT NOTE: LAMMPS stores and maintains a data structure with a +list of the 1st, 2nd, and 3rd neighbors of each atom (within the bond topology of the system) for use in weighting pairwise interactions for -bonded atoms. Adding a bond adds a single entry to this list. The -"extra special per atom" parameter must typically be set to allow for -it. There are 3 ways to do this. See the "read_data"_read_data.html -or "create_box"_create_box.html or "special_bonds extra" commands for +bonded atoms. Note that adding a single bond always adds a new 1st +neighbor but may also induce *many* new 2nd and 3rd neighbors, +depending on the molecular topology of your system. The "extra +special per atom" parameter must typically be set to allow for the new +maximum total size (1st + 2nd + 3rd neighbors) of this per-atom list. +There are 3 ways to do this. See the "read_data"_read_data.html or +"create_box"_create_box.html or "special_bonds extra" commands for details. IMPORTANT NOTE: Even if you do not use the {atype}, {dtype}, or diff --git a/doc/fix_oneway.html b/doc/fix_oneway.html index 02f7a2d358..9b48b802b0 100644 --- a/doc/fix_oneway.html +++ b/doc/fix_oneway.html @@ -13,7 +13,7 @@
Syntax:
-fix ID group-ID N oneway region-ID direction +fix ID group-ID oneway N region-ID direction
Examples:
-fix ions 10 oneway semi -x -fix all 1 oneway left -z -fix all 1 oneway right z +fix ions oneway 10 semi -x +fix all oneway 1 left -z +fix all oneway 1 right zDescription:
diff --git a/doc/fix_oneway.txt b/doc/fix_oneway.txt index 4f0b4ae279..2d85c581eb 100644 --- a/doc/fix_oneway.txt +++ b/doc/fix_oneway.txt @@ -10,7 +10,7 @@ fix oneway command :h3 [Syntax:] -fix ID group-ID N oneway region-ID direction :pre +fix ID group-ID oneway N region-ID direction :pre ID, group-ID are documented in "fix"_fix.html command :ulb,l oneway = style name of this fix command :l @@ -21,9 +21,9 @@ direction = {x} or {-x} or {y} or {-y} or {z} or {-z} = coordinate and direction [Examples:] -fix ions 10 oneway semi -x -fix all 1 oneway left -z -fix all 1 oneway right z :pre +fix ions oneway 10 semi -x +fix all oneway 1 left -z +fix all oneway 1 right z :pre [Description:] diff --git a/doc/special_bonds.html b/doc/special_bonds.html index eea9a06889..252b7b0ae6 100644 --- a/doc/special_bonds.html +++ b/doc/special_bonds.html @@ -171,18 +171,24 @@ interaction between atoms 2 and 5 will be unaffected (full weighting of 1.0). If the dihedral keyword is specified as no which is the default, then the 2,5 interaction will also be weighted by 0.5. -The extra keyword is used when additional bonds will be created +
The extra keyword can be used when additional bonds will be created during a simulation run, e.g. by the fix bond/create command. It can also be used if molecules will be added to the system, e.g. via the fix deposit, or fix pour commands, which will have atoms with more special neighbors than any atom in the -current system has. A list of 1-2,1-3,1-4 neighbors for each atom is -calculated and stored by LAMMPS. If new bonds are created (or -molecules added with atoms with more special neighbors), the list -needs to grow. Using the extra keyword leaves empty space in the -list for N additional bonds to be added. If you do not do this, you -may get an error when bonds (or molecules) are added. +current system has. +
+IMPORTANT NOTE: LAMMPS stores and maintains a data structure with a +list of the 1st, 2nd, and 3rd neighbors of each atom (within the bond +topology of the system). If new bonds are created (or molecules added +containing atoms with more special neighbors), the size of this list +needs to grow. Note that adding a single bond always adds a new 1st +neighbor but may also induce *many* new 2nd and 3rd neighbors, +depending on the molecular topology of your syste. Using the extra +keyword leaves empty space in the list for this N additional 1st, 2nd, +or 3rd neighbors to be added. If you do not do this, you may get an +error when bonds (or molecules) are added.
IMPORTANT NOTE: If you reuse this command in an input script, you should set all the options you need each time. This command cannot be diff --git a/doc/special_bonds.txt b/doc/special_bonds.txt index 39eb1cd551..36918b7b5f 100644 --- a/doc/special_bonds.txt +++ b/doc/special_bonds.txt @@ -165,18 +165,24 @@ interaction between atoms 2 and 5 will be unaffected (full weighting of 1.0). If the {dihedral} keyword is specified as {no} which is the default, then the 2,5 interaction will also be weighted by 0.5. -The {extra} keyword is used when additional bonds will be created +The {extra} keyword can be used when additional bonds will be created during a simulation run, e.g. by the "fix bond/create"_fix_bond_create.html command. It can also be used if molecules will be added to the system, e.g. via the "fix deposit"_fix_deposit.html, or "fix pour"_fix_pour.html commands, which will have atoms with more special neighbors than any atom in the -current system has. A list of 1-2,1-3,1-4 neighbors for each atom is -calculated and stored by LAMMPS. If new bonds are created (or -molecules added with atoms with more special neighbors), the list -needs to grow. Using the {extra} keyword leaves empty space in the -list for N additional bonds to be added. If you do not do this, you -may get an error when bonds (or molecules) are added. +current system has. + +IMPORTANT NOTE: LAMMPS stores and maintains a data structure with a +list of the 1st, 2nd, and 3rd neighbors of each atom (within the bond +topology of the system). If new bonds are created (or molecules added +containing atoms with more special neighbors), the size of this list +needs to grow. Note that adding a single bond always adds a new 1st +neighbor but may also induce *many* new 2nd and 3rd neighbors, +depending on the molecular topology of your syste. Using the {extra} +keyword leaves empty space in the list for this N additional 1st, 2nd, +or 3rd neighbors to be added. If you do not do this, you may get an +error when bonds (or molecules) are added. IMPORTANT NOTE: If you reuse this command in an input script, you should set all the options you need each time. This command cannot be