Merge remote-tracking branch 'github/reset-ids-sort' into move-ubuf-to-lmptype (006f7956) · Commits · 郑智淋 / lammps

doc/src/reset_ids.rst

+40 −8

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		@@ -8,7 +8,14 @@ Syntax

		.. code-block:: LAMMPS

		reset_ids
		reset_ids keyword values ...

		* zero or more keyword/value pairs may be appended
		* keyword = sort

		.. parsed-literal::

		sort value = yes or no

		Examples
		""""""""
		@@ -16,6 +23,7 @@ Examples
		.. code-block:: LAMMPS

		reset_ids
		reset_ids sort yes

		Description
		"""""""""""
		@@ -33,11 +41,32 @@ e.g. due to atoms moving outside a simulation box with fixed
		boundaries (see the "boundary command"), or due to evaporation (see
		the "fix evaporate" command).

		Note that the resetting of IDs is not really a compression, where gaps
		in atom IDs are removed by decrementing atom IDs that are larger.
		Instead the IDs for all atoms are erased, and new IDs are assigned so
		that the atoms owned by an individual processor have consecutive IDs,
		as the :doc:`create_atoms <create_atoms>` command explains.
		If the sort keyword is used with a setting of yes, then the
		assignment of new atom IDs will be the same no matter how many
		processors LAMMPS is running on. This is done by first doing a
		spatial sort of all the atoms into bins and sorting them within each
		bin. Because the set of bins is independent of the number of
		processors, this enables a consistent assignment of new IDs to each
		atom.

		This can be useful to do after using the "create_atoms" command and/or
		"replicate" command. In general those commands do not guarantee
		assignment of the same atom ID to the same physical atom when LAMMPS
		is run on different numbers of processors. Enforcing consistent IDs
		can be useful for debugging or comparing output from two different
		runs.

		Note that the spatial sort requires communication of atom IDs and
		coordinates bewteen processors in an all-to-all manner. This is done
		efficiently in LAMMPS, but it is more expensive than how atom IDs are
		reset without sorting.

		Note that whether sorting or not, the resetting of IDs is not a
		compression, where gaps in atom IDs are removed by decrementing atom
		IDs that are larger. Instead the IDs for all atoms are erased, and
		new IDs are assigned so that the atoms owned by an individual
		processor have consecutive IDs, as the :doc:`create_atoms
		<create_atoms>` command explains.

		.. note::

		@@ -59,4 +88,7 @@ Related commands

		:doc:`delete_atoms <delete_atoms>`

		Default: none
		Default
		"""""""

		By default, sort is no.

src/RIGID/fix_rigid_small.cpp

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		@@ -72,6 +72,7 @@ FixRigidSmall::FixRigidSmall(LAMMPS lmp, int narg, char *arg) :
		create_attribute = 1;
		dof_flag = 1;
		enforce2d_flag = 1;
		stores_ids = 1;

		MPI_Comm_rank(world,&me);
		MPI_Comm_size(world,&nprocs);

src/RIGID/fix_shake.cpp

+2 −1

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		@@ -64,6 +64,7 @@ FixShake::FixShake(LAMMPS lmp, int narg, char *arg) :
		thermo_virial = 1;
		create_attribute = 1;
		dof_flag = 1;
		stores_ids = 1;

		// error check

src/fix.cpp

+2 −1

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		@@ -80,6 +80,7 @@ Fix::Fix(LAMMPS lmp, int /narg/, char *arg) :
		maxexchange = 0;
		maxexchange_dynamic = 0;
		pre_exchange_migrate = 0;
		stores_ids = 0;

		scalar_flag = vector_flag = array_flag = 0;
		peratom_flag = local_flag = 0;

src/fix.h

+1 −0

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		@@ -64,6 +64,7 @@ class Fix : protected Pointers {
		int maxexchange; // max # of per-atom values for Comm::exchange()
		int maxexchange_dynamic; // 1 if fix sets maxexchange dynamically
		int pre_exchange_migrate; // 1 if fix migrates atoms in pre_exchange()
		int stores_ids; // 1 if fix stores atom IDs

		int scalar_flag; // 0/1 if compute_scalar() function exists
		int vector_flag; // 0/1 if compute_vector() function exists

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