If the setting for the molecule keyword is yes, then when an atom is chosen for deletion, the entire molecule it is part of is deleted. The count of deleted atoms is incremented by the number of atoms in -the molecule. If the molecule ID of the chosen atom is 0, then it is -assumed to not be part of a molecule, and just the single atom is -deleted. +the molecule, which may make it exceed M. If the molecule ID of the +chosen atom is 0, then it is assumed to not be part of a molecule, and +just the single atom is deleted.
As an example, if you wish to delete 10 water molecules every N steps, you should set M to 30. If only the water's oxygen atoms diff --git a/doc/fix_evaporate.txt b/doc/fix_evaporate.txt index 5cc700919d..147fc14457 100644 --- a/doc/fix_evaporate.txt +++ b/doc/fix_evaporate.txt @@ -47,9 +47,9 @@ molecule ID, but does not check for this at the time of deletion. If the setting for the {molecule} keyword is {yes}, then when an atom is chosen for deletion, the entire molecule it is part of is deleted. The count of deleted atoms is incremented by the number of atoms in -the molecule. If the molecule ID of the chosen atom is 0, then it is -assumed to not be part of a molecule, and just the single atom is -deleted. +the molecule, which may make it exceed {M}. If the molecule ID of the +chosen atom is 0, then it is assumed to not be part of a molecule, and +just the single atom is deleted. As an example, if you wish to delete 10 water molecules every {N} steps, you should set {M} to 30. If only the water's oxygen atoms diff --git a/doc/thermo_modify.html b/doc/thermo_modify.html index dac12092b6..5f87f8a7c5 100644 --- a/doc/thermo_modify.html +++ b/doc/thermo_modify.html @@ -50,10 +50,17 @@ thermo_modify command after it.
The lost keyword determines whether LAMMPS checks for lost atoms each time it computes thermodynamics and what it does if atoms are -lost. If the value is ignore, LAMMPS does not check for lost atoms. -If the value is error or warn, LAMMPS checks and either issues an -error or warning. The code will exit with an error and continue with -a warning. This can be a useful debugging option. +lost. An atom can be "lost" if it moves across a non-periodic +simulation box boundary or if it moves more than a box +length outside the simulation domain (or more than a processor +sub-domain length) before reneighboring occurs. The latter case is +typically due to bad dynamics, e.g. too large a timestep or huge +forces and velocities. If the value is ignore, LAMMPS does not +check for lost atoms. If the value is error or warn, LAMMPS +checks and either issues an error or warning. The code will exit with +an error and continue with a warning. A warning will only be issued +once, the first time an atom is lost. This can be a useful debugging +option.
The norm keyword determines whether various thermodynamic output values are normalized by the number of atoms or not, depending on diff --git a/doc/thermo_modify.txt b/doc/thermo_modify.txt index 3f126ad151..eae2c31eb5 100644 --- a/doc/thermo_modify.txt +++ b/doc/thermo_modify.txt @@ -45,10 +45,17 @@ thermo_modify command after it. The {lost} keyword determines whether LAMMPS checks for lost atoms each time it computes thermodynamics and what it does if atoms are -lost. If the value is {ignore}, LAMMPS does not check for lost atoms. -If the value is {error} or {warn}, LAMMPS checks and either issues an -error or warning. The code will exit with an error and continue with -a warning. This can be a useful debugging option. +lost. An atom can be "lost" if it moves across a non-periodic +simulation box "boundary"_boundary.html or if it moves more than a box +length outside the simulation domain (or more than a processor +sub-domain length) before reneighboring occurs. The latter case is +typically due to bad dynamics, e.g. too large a timestep or huge +forces and velocities. If the value is {ignore}, LAMMPS does not +check for lost atoms. If the value is {error} or {warn}, LAMMPS +checks and either issues an error or warning. The code will exit with +an error and continue with a warning. A warning will only be issued +once, the first time an atom is lost. This can be a useful debugging +option. The {norm} keyword determines whether various thermodynamic output values are normalized by the number of atoms or not, depending on