2006-09-22 00:22:34 +08:00
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<HR>
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<H3>delete_atoms command
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</H3>
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<P><B>Syntax:</B>
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</P>
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2010-08-04 07:38:55 +08:00
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<PRE>delete_atoms style args keyword value ...
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2006-09-22 00:22:34 +08:00
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</PRE>
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2008-12-05 00:15:03 +08:00
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<UL><LI>style = <I>group</I> or <I>region</I> or <I>overlap</I> or <I>porosity</I>
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2006-09-22 00:22:34 +08:00
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<PRE> <I>group</I> args = group-ID
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<I>region</I> args = region-ID
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2008-01-25 06:33:02 +08:00
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<I>overlap</I> args = cutoff group1-ID group2-ID
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cutoff = delete one atom from pairs of atoms within the cutoff (distance units)
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group1-ID = one atom in pair must be in this group
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group2-ID = other atom in pair must be in this group
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2008-12-05 00:15:03 +08:00
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<I>porosity</I> args = region-ID fraction seed
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region-ID = region within which to perform deletions
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fraction = delete this fraction of atoms
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seed = random number seed (positive integer)
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2006-09-22 00:22:34 +08:00
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</PRE>
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2010-08-04 07:38:55 +08:00
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<LI>zero or more keyword/value pairs may be appended
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2013-05-24 06:50:14 +08:00
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<LI>keyword = <I>compress</I> or <I>mol</I>
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2010-08-04 07:38:55 +08:00
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2013-05-24 06:50:14 +08:00
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<PRE> <I>compress</I> value = <I>no</I> or <I>yes</I>
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<I>mol</I> value = <I>no</I> or <I>yes</I>
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2010-08-04 07:38:55 +08:00
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</PRE>
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2006-09-22 00:22:34 +08:00
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>delete_atoms group edge
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2010-08-04 07:38:55 +08:00
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delete_atoms region sphere compress no
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2008-01-25 06:33:02 +08:00
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delete_atoms overlap 0.3 all all
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2008-12-05 00:15:03 +08:00
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delete_atoms overlap 0.5 solvent colloid
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2011-06-20 22:11:32 +08:00
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delete_atoms porosity cube 0.1 482793
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2006-09-22 00:22:34 +08:00
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</PRE>
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<P><B>Description:</B>
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</P>
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2006-09-29 03:55:36 +08:00
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<P>Delete the specified atoms. This command can be used to carve out
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2006-09-22 00:22:34 +08:00
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voids from a block of material or to delete created atoms that are too
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close to each other (e.g. at a grain boundary).
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</P>
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<P>For style <I>group</I>, all atoms belonging to the group are deleted.
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</P>
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<P>For style <I>region</I>, all atoms in the region volume are deleted.
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2013-05-24 06:50:14 +08:00
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Additional atoms can be deleted if they are in a molecule for which
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one or more atoms were deleted within the region; see the <I>mol</I>
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keyword discussion below.
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2006-09-22 00:22:34 +08:00
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</P>
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2008-01-25 06:33:02 +08:00
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<P>For style <I>overlap</I> pairs of atoms whose distance of separation is
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within the specified cutoff distance are searched for, and one of the
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2 atoms is deleted. Only pairs where one of the two atoms is in the
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first group specified and the other atom is in the second group are
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considered. The atom that is in the first group is the one that is
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deleted.
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</P>
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<P>Note that it is OK for the two group IDs to be the same (e.g. group
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<I>all</I>), or for some atoms to be members of both groups. In these
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cases, either atom in the pair may be deleted. Also note that if
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there are atoms which are members of both groups, the only guarantee
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is that at the end of the deletion operation, enough deletions will
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have occurred that no atom pairs within the cutoff will remain
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(subject to the group restriction). There is no guarantee that the
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minimum number of atoms will be deleted, or that the same atoms will
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be deleted when running on different numbers of processors.
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2006-09-22 00:22:34 +08:00
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</P>
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2008-12-05 00:15:03 +08:00
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<P>For style <I>porosity</I> a specified <I>fraction</I> of atoms are deleted
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within the specified region. For example, if fraction is 0.1, then
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10% of the atoms will be deleted. The atoms to delete are chosen
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randomly. There is no guarantee that the exact fraction of atoms will
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be deleted, or that the same atoms will be deleted when running on
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different numbers of processors.
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</P>
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2010-08-04 07:38:55 +08:00
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<P>If the <I>compress</I> keyword is set to <I>yes</I>, then after atoms are
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deleted, then atom IDs are re-assigned so that they run from 1 to the
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number of atoms in the system. This is not done for molecular systems
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(see the <A HREF = "atom_style.html">atom_style</A> command), regardless of the
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<I>compress</I> setting, since it would foul up the bond connectivity that
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has already been assigned.
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2006-09-22 00:22:34 +08:00
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</P>
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2013-05-24 06:50:14 +08:00
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<P>It the <I>mol</I> keyword is set to <I>yes</I>, then for every atom that is
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deleted, all other atoms in the same molecule will also be deleted.
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2014-05-01 04:58:58 +08:00
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This is a way to insure that entire molecules are deleted instead of
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only a subset of atoms in the molecule which will typically lead to
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errors because of bond, angle, or dihedral interactions stored by
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remaining atoms which reference deleted atoms.
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</P>
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<P>IMPORTANT NOTE: The molecule deletion operation in invoked after all
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individual atoms have been deleted using the rules described above for
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each style. This means additional atoms may be deleted that are not
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in the group or region, that are not required by the overlap cutoff
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criterion, or that will create a higher fraction of porosity than was
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requested.
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2013-05-24 06:50:14 +08:00
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</P>
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2006-09-22 00:22:34 +08:00
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<P><B>Restrictions:</B>
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</P>
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2008-01-25 06:33:02 +08:00
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<P>The <I>overlap</I> styles requires inter-processor communication to acquire
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ghost atoms and build a neighbor list. This means that your system
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2006-09-22 00:22:34 +08:00
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must be ready to perform a simulation before using this command (force
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2008-08-21 21:53:06 +08:00
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fields setup, atom masses set, etc). Since a neighbor list is used to
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find overlapping atom pairs, it also means that you must define a
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<A HREF = "pair_style.html">pair style</A> with force cutoffs greater than or equal
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to the desired overlap cutoff between pairs of relevant atom types,
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even though the pair potential will not be evaluated.
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2006-09-22 00:22:34 +08:00
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</P>
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<P>If the <A HREF = "special_bonds.html">special_bonds</A> command is used with a
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setting of 0, then a pair of bonded atoms (1-2, 1-3, or 1-4) will not
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appear in the neighbor list, and thus will not be considered for
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2008-01-25 06:33:02 +08:00
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deletion by the <I>overlap</I> styles. You probably don't want to be
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2006-09-22 00:22:34 +08:00
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deleting one atom in a bonded pair anyway.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "create_atoms.html">create_atoms</A>
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</P>
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2010-08-04 07:38:55 +08:00
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<P><B>Default:</B>
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</P>
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2013-05-24 06:50:14 +08:00
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<P>The option defaults are compress = yes and mol = no.
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2006-09-22 00:22:34 +08:00
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</P>
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</HTML>
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