diff --git a/doc/fix_evaporate.html b/doc/fix_evaporate.html index 210b51fc0a..ff23f194bd 100644 --- a/doc/fix_evaporate.html +++ b/doc/fix_evaporate.html @@ -15,29 +15,59 @@
fix ID group-ID evaporate N M region-ID seed-
molecule value = no or yes ++
Examples:
-fix 1 solvent evaporate 1000 10 surface 49892 +fix 1 solvent evaporate 1000 10 surface 49892 +fix 1 solvent evaporate 1000 10 surface 38277 molecule yesDescription:
Remove M atoms from the simulation every N steps. This can be used, -for example, to model evaporation of solvent particles (i.e. drying) -of a system. Every N steps, the number of atoms in the fix group and -within the specifed region are counted. M of these are chosen at -random and deleted. If there are less than M eligible particles, then -all of them are deleted. +for example, to model evaporation of solvent particles or moleclues +(i.e. drying) of a system. Every N steps, the number of atoms in the +fix group and within the specifed region are counted. M of these are +chosen at random and deleted. If there are less than M eligible +particles, then all of them are deleted.
-Note that you cannot currently delete solvent molecules with this -command, only individual atoms. If you delete only one atom in a -molecule, an error will result. +
If the setting for the molecule keyword is no, then only single +atoms are deleted. In this case, you should insure you do not delete +only a portion of a molecule (only some of its atoms), or LAMMPS will +soon generate an error when it tries to find those atoms. LAMMPS will +warn you if any of the atoms eligible for deletion have a non-zero +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. +
+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 +were in the fix group, then two hydrogen atoms would be deleted when +an oxygen atom is selected for deletion, whether the hydrogens are +inside the evaporation region or not.
Note that neighbor lists are re-built on timesteps that atoms are removed. Thus you should not remove atoms too frequently or you will @@ -64,6 +94,8 @@ minimization.
-Default: none +
Default: +
+The option defaults are molecule = no.