diff -Naur lammps-4Dec08/doc/delete_atoms.html lammps-5Dec08/doc/delete_atoms.html --- lammps-4Dec08/doc/delete_atoms.html 2008-08-21 07:53:06.000000000 -0600 +++ lammps-5Dec08/doc/delete_atoms.html 2008-12-04 09:15:03.000000000 -0700 @@ -15,7 +15,7 @@
delete_atoms style args-
group args = group-ID region args = region-ID @@ -23,7 +23,10 @@ cutoff = delete one atom from pairs of atoms within the cutoff (distance units) group1-ID = one atom in pair must be in this group group2-ID = other atom in pair must be in this group - + porosity args = region-ID fraction seed + region-ID = region within which to perform deletions + fraction = delete this fraction of atoms + seed = random number seed (positive integer)
delete_atoms group edge delete_atoms region sphere delete_atoms overlap 0.3 all all -delete_atoms overlap 0.5 solvent colloid +delete_atoms overlap 0.5 solvent colloid +delete_atoms porosity cube 0.1
Description:
@@ -61,6 +65,13 @@ minimum number of atoms will be deleted, or that the same atoms will be deleted when running on different numbers of processors. +For style porosity a specified fraction of atoms are deleted +within the specified region. For example, if fraction is 0.1, then +10% of the atoms will be deleted. The atoms to delete are chosen +randomly. There is no guarantee that the exact fraction of atoms will +be deleted, or that the same atoms will be deleted when running on +different numbers of processors. +
After atoms are deleted, if the system is not molecular (no bonds), then atom IDs are re-assigned so that they run from 1 to the number of atoms in the system. This is not done for molecular systems, since it diff -Naur lammps-4Dec08/doc/delete_atoms.txt lammps-5Dec08/doc/delete_atoms.txt --- lammps-4Dec08/doc/delete_atoms.txt 2008-08-21 07:53:06.000000000 -0600 +++ lammps-5Dec08/doc/delete_atoms.txt 2008-12-04 09:15:03.000000000 -0700 @@ -12,14 +12,17 @@ delete_atoms style args :pre -style = {group} or {region} or {overlap} :ulb,l +style = {group} or {region} or {overlap} or {porosity} :ulb,l {group} args = group-ID {region} args = region-ID {overlap} args = cutoff group1-ID group2-ID cutoff = delete one atom from pairs of atoms within the cutoff (distance units) group1-ID = one atom in pair must be in this group group2-ID = other atom in pair must be in this group -:pre + {porosity} args = region-ID fraction seed + region-ID = region within which to perform deletions + fraction = delete this fraction of atoms + seed = random number seed (positive integer) :pre :ule [Examples:] @@ -27,7 +30,8 @@ delete_atoms group edge delete_atoms region sphere delete_atoms overlap 0.3 all all -delete_atoms overlap 0.5 solvent colloid :pre +delete_atoms overlap 0.5 solvent colloid +delete_atoms porosity cube 0.1 :pre [Description:] @@ -56,6 +60,13 @@ minimum number of atoms will be deleted, or that the same atoms will be deleted when running on different numbers of processors. +For style {porosity} a specified {fraction} of atoms are deleted +within the specified region. For example, if fraction is 0.1, then +10% of the atoms will be deleted. The atoms to delete are chosen +randomly. There is no guarantee that the exact fraction of atoms will +be deleted, or that the same atoms will be deleted when running on +different numbers of processors. + After atoms are deleted, if the system is not molecular (no bonds), then atom IDs are re-assigned so that they run from 1 to the number of atoms in the system. This is not done for molecular systems, since it diff -Naur lammps-4Dec08/doc/fix_langevin.html lammps-5Dec08/doc/fix_langevin.html --- lammps-4Dec08/doc/fix_langevin.html 2008-05-21 16:45:59.000000000 -0600 +++ lammps-5Dec08/doc/fix_langevin.html 2008-12-04 09:15:03.000000000 -0700 @@ -23,7 +23,7 @@