For all styles, an interaction is only turned off (or on) if all the -atoms involved are in the specified group. For style multi this is -the only criterion applied - all types of bonds, angles, dihedrals, -impropers in the group turned off. +
For all styles, by default, an interaction is only turned off (or on) +if all the atoms involved are in the specified group. See the any +keyword to change the behavior.
-For style atom, one or more of the atoms involved must also be of -the specified type. +
For style multi all bond, angle, dihedral, and improper interactions +of any type, involving atoms in the group, are turned off. +
+Style atom is the same as style multi except that in addition, one +or more of the atoms involved in the bond, angle, dihedral, or +improper interaction must also be of the specified atom type.
For style bond, only bonds are candidates for turn-off, and the bond must also be of the specified type. Styles angle, dihedral, and @@ -84,13 +87,13 @@ force and energy calculations. This means that pairwise computations will proceed as if the bond (or angle, etc) were still turned on.
Several keywords can be appended to the argument list to alter the -default behavior. +default behaviors.
The any keyword changes the requirement that all atoms in the bond (angle, etc) must be in the specified group in order to turn-off the -interaction. If any of the atoms in the interaction are in the -specified group, it will be turned off (or on if the undo keyword is -used). +interaction. Instead, if any of the atoms in the interaction are in +the specified group, it will be turned off (or on if the undo +keyword is used).
The undo keyword inverts the delete_bonds command so that the specified bonds, angles, etc are turned on if they are currently diff --git a/doc/delete_bonds.txt b/doc/delete_bonds.txt index 1ddcd049cb..9e47faba25 100644 --- a/doc/delete_bonds.txt +++ b/doc/delete_bonds.txt @@ -43,13 +43,16 @@ off via the "neigh_modify exclude"_neigh_modify.html command. The "fix shake"_fix_shake.html command also effectively turns off certain bond and angle interactions. -For all styles, an interaction is only turned off (or on) if all the -atoms involved are in the specified group. For style {multi} this is -the only criterion applied - all types of bonds, angles, dihedrals, -impropers in the group turned off. +For all styles, by default, an interaction is only turned off (or on) +if all the atoms involved are in the specified group. See the {any} +keyword to change the behavior. -For style {atom}, one or more of the atoms involved must also be of -the specified type. +For style {multi} all bond, angle, dihedral, and improper interactions +of any type, involving atoms in the group, are turned off. + +Style {atom} is the same as style {multi} except that in addition, one +or more of the atoms involved in the bond, angle, dihedral, or +improper interaction must also be of the specified atom type. For style {bond}, only bonds are candidates for turn-off, and the bond must also be of the specified type. Styles {angle}, {dihedral}, and @@ -76,13 +79,13 @@ force and energy calculations. This means that pairwise computations will proceed as if the bond (or angle, etc) were still turned on. Several keywords can be appended to the argument list to alter the -default behavior. +default behaviors. The {any} keyword changes the requirement that all atoms in the bond (angle, etc) must be in the specified group in order to turn-off the -interaction. If any of the atoms in the interaction are in the -specified group, it will be turned off (or on if the {undo} keyword is -used). +interaction. Instead, if any of the atoms in the interaction are in +the specified group, it will be turned off (or on if the {undo} +keyword is used). The {undo} keyword inverts the delete_bonds command so that the specified bonds, angles, etc are turned on if they are currently diff --git a/doc/fix_rigid.html b/doc/fix_rigid.html index 73ef295382..ba508effd1 100644 --- a/doc/fix_rigid.html +++ b/doc/fix_rigid.html @@ -135,13 +135,17 @@ numbers of rigid bodies are simulated. number of small rigid bodies. Each body is assigned to the atom closest to the geometrical center of the body. The fix operates using local lists of rigid bodies owned by each processor and information is -summed and exchanged via local communication between neighboring -processors when ghost atom info is accumlated. This means that the -ghost atom cutoff be large enough to cover the distance between the -atom that owns the body and every other atom in the body. If the -pair_style cutoff is not of sufficient extent to -insure this, then the communicate cutoff command -can be used. +exchanged and summed via local communication between neighboring +processors when ghost atom info is accumlated. +
+IMPORTANT NOTE: To use rigid/small the ghost atom cutoff must be +large enough to span the distance between the atom that owns the body +and every other atom in the body. This distance value is printed out +when the rigid bodies are defined. If the +pair_style cutoff plus neighbor skin does not span +this distance, then you should use the communicate +cutoff command with a setting epsilon larger than +the distance.
Which of the two variants is faster for a particular problem is hard to predict. The best way to decide is to perform a short test run. diff --git a/doc/fix_rigid.txt b/doc/fix_rigid.txt index 6792a84b11..524cb948a3 100644 --- a/doc/fix_rigid.txt +++ b/doc/fix_rigid.txt @@ -121,13 +121,17 @@ The {rigid/small} variant is typically best for a system with a large number of small rigid bodies. Each body is assigned to the atom closest to the geometrical center of the body. The fix operates using local lists of rigid bodies owned by each processor and information is -summed and exchanged via local communication between neighboring -processors when ghost atom info is accumlated. This means that the -ghost atom cutoff be large enough to cover the distance between the -atom that owns the body and every other atom in the body. If the -"pair_style"_pair_style.html cutoff is not of sufficient extent to -insure this, then the "communicate cutoff"_communicate.html command -can be used. +exchanged and summed via local communication between neighboring +processors when ghost atom info is accumlated. + +IMPORTANT NOTE: To use {rigid/small} the ghost atom cutoff must be +large enough to span the distance between the atom that owns the body +and every other atom in the body. This distance value is printed out +when the rigid bodies are defined. If the +"pair_style"_pair_style.html cutoff plus neighbor skin does not span +this distance, then you should use the "communicate +cutoff"_communicate.html command with a setting epsilon larger than +the distance. Which of the two variants is faster for a particular problem is hard to predict. The best way to decide is to perform a short test run.