Merge pull request #1788 from lammps/atomvec-custom (06737ce7) · Commits · 郑智淋 / lammps

doc/src/Commands_compute.rst

+3 −3

Original line number	Original line	Diff line number	Diff line
	@@ -79,9 +79,6 @@ KOKKOS, o = USER-OMP, t = OPT.
	* :doc:`ke/atom/eff <compute_ke_atom_eff>`		* :doc:`ke/atom/eff <compute_ke_atom_eff>`
	* :doc:`ke/eff <compute_ke_eff>`		* :doc:`ke/eff <compute_ke_eff>`
	* :doc:`ke/rigid <compute_ke_rigid>`		* :doc:`ke/rigid <compute_ke_rigid>`
	* :doc:`meso/e/atom <compute_meso_e_atom>`
	* :doc:`meso/rho/atom <compute_meso_rho_atom>`
	* :doc:`meso/t/atom <compute_meso_t_atom>`
	* :doc:`momentum <compute_momentum>`		* :doc:`momentum <compute_momentum>`
	* :doc:`msd <compute_msd>`		* :doc:`msd <compute_msd>`
	* :doc:`msd/chunk <compute_msd_chunk>`		* :doc:`msd/chunk <compute_msd_chunk>`
	@@ -133,6 +130,9 @@ KOKKOS, o = USER-OMP, t = OPT.
	* :doc:`sna/atom <compute_sna_atom>`		* :doc:`sna/atom <compute_sna_atom>`
	* :doc:`snad/atom <compute_sna_atom>`		* :doc:`snad/atom <compute_sna_atom>`
	* :doc:`snav/atom <compute_sna_atom>`		* :doc:`snav/atom <compute_sna_atom>`
			* :doc:`sph/e/atom <compute_sph_e_atom>`
			* :doc:`sph/rho/atom <compute_sph_rho_atom>`
			* :doc:`sph/t/atom <compute_sph_t_atom>`
	* :doc:`spin <compute_spin>`		* :doc:`spin <compute_spin>`
	* :doc:`stress/atom <compute_stress_atom>`		* :doc:`stress/atom <compute_stress_atom>`
	* :doc:`stress/mop <compute_stress_mop>`		* :doc:`stress/mop <compute_stress_mop>`

doc/src/Commands_fix.rst

+2 −2

Original line number	Original line	Diff line number	Diff line
	@@ -95,9 +95,7 @@ OPT.
	* :doc:`lb/viscous <fix_lb_viscous>`		* :doc:`lb/viscous <fix_lb_viscous>`
	* :doc:`lineforce <fix_lineforce>`		* :doc:`lineforce <fix_lineforce>`
	* :doc:`manifoldforce <fix_manifoldforce>`		* :doc:`manifoldforce <fix_manifoldforce>`
	* :doc:`meso <fix_meso>`
	* :doc:`meso/move <fix_meso_move>`		* :doc:`meso/move <fix_meso_move>`
	* :doc:`meso/stationary <fix_meso_stationary>`
	* :doc:`momentum (k) <fix_momentum>`		* :doc:`momentum (k) <fix_momentum>`
	* :doc:`move <fix_move>`		* :doc:`move <fix_move>`
	* :doc:`mscg <fix_mscg>`		* :doc:`mscg <fix_mscg>`
	@@ -202,6 +200,8 @@ OPT.
	* :doc:`smd/move_tri_surf <fix_smd_move_triangulated_surface>`		* :doc:`smd/move_tri_surf <fix_smd_move_triangulated_surface>`
	* :doc:`smd/setvel <fix_smd_setvel>`		* :doc:`smd/setvel <fix_smd_setvel>`
	* :doc:`smd/wall_surface <fix_smd_wall_surface>`		* :doc:`smd/wall_surface <fix_smd_wall_surface>`
			* :doc:`sph <fix_sph>`
			* :doc:`sph/stationary <fix_sph_stationary>`
	* :doc:`spring <fix_spring>`		* :doc:`spring <fix_spring>`
	* :doc:`spring/chunk <fix_spring_chunk>`		* :doc:`spring/chunk <fix_spring_chunk>`
	* :doc:`spring/rg <fix_spring_rg>`		* :doc:`spring/rg <fix_spring_rg>`

doc/src/Modify_atom.rst

+166 −112

Original line number	Original line	Diff line number	Diff line
	@@ -3,115 +3,169 @@ Atom styles

	Classes that define an :doc:`atom style <atom_style>` are derived from		Classes that define an :doc:`atom style <atom_style>` are derived from
	the AtomVec class and managed by the Atom class. The atom style		the AtomVec class and managed by the Atom class. The atom style
	determines what attributes are associated with an atom. A new atom		determines what attributes are associated with an atom and
	style can be created if one of the existing atom styles does not		communicated when it is a ghost atom or migrates to a new processor.
	define all the attributes you need to store and communicate with		A new atom style can be created if one of the existing atom styles
	atoms.		does not define all the attributes you need to store and communicate
			with atoms.
	Atom_vec_atomic.cpp is a simple example of an atom style.
			Atom_vec_atomic.cpp is the simplest example of an atom style.
	Here is a brief description of methods you define in your new derived		Examining the code for others will make these instructions more clear.
	class. See atom_vec.h for details.
			Note that the :doc:`atom style hybrid <atom_style>` command can be
	+-------------------------+--------------------------------------------------------------------------------+		used to define atoms or particles which have the union of properties
	\| init \| one time setup (optional) \|		of individual styles. Also the :doc:`fix property/atom <fix_property_atom>`
	+-------------------------+--------------------------------------------------------------------------------+		command can be used to add a single property (e.g. charge
	\| grow \| re-allocate atom arrays to longer lengths (required) \|		or a molecule ID) to a style that does not have it. It can also be
	+-------------------------+--------------------------------------------------------------------------------+		used to add custom properties to an atom, with options to communicate
	\| grow_reset \| make array pointers in Atom and AtomVec classes consistent (required) \|		them with ghost atoms or read them from a data file. Other LAMMPS
	+-------------------------+--------------------------------------------------------------------------------+		commands can access these custom properties, as can new pair, fix,
	\| copy \| copy info for one atom to another atom's array locations (required) \|		compute styles that are written to work with these properties. For
	+-------------------------+--------------------------------------------------------------------------------+		example, the :doc:`set <set>` command can be used to set the values of
	\| pack_comm \| store an atom's info in a buffer communicated every timestep (required) \|		custom per-atom properties from an input script. All of these methods
	+-------------------------+--------------------------------------------------------------------------------+		are less work than writing code for a new atom style.
	\| pack_comm_vel \| add velocity info to communication buffer (required) \|
	+-------------------------+--------------------------------------------------------------------------------+		If you follow these directions your new style will automatically work
	\| pack_comm_hybrid \| store extra info unique to this atom style (optional) \|		in tandem with others via the :doc:`atom_style hybrid <atom_style>`
	+-------------------------+--------------------------------------------------------------------------------+		command.
	\| unpack_comm \| retrieve an atom's info from the buffer (required) \|
	+-------------------------+--------------------------------------------------------------------------------+		The first step is to define a set of strings in the constructor of the
	\| unpack_comm_vel \| also retrieve velocity info (required) \|		new derived class. Each string will have zero or more space-separated
	+-------------------------+--------------------------------------------------------------------------------+		variable names which are identical to those used in the atom.h header
	\| unpack_comm_hybrid \| retrieve extra info unique to this atom style (optional) \|		file for per-atom properties. Note that some represent per-atom
	+-------------------------+--------------------------------------------------------------------------------+		vectors (q, molecule) while other are per-atom arrays (x,v). For all
	\| pack_reverse \| store an atom's info in a buffer communicating partial forces (required) \|		but the last 2 strings you do not need to specify any of
	+-------------------------+--------------------------------------------------------------------------------+		(id,type,x,v,f). Those are included automatically as needed in the
	\| pack_reverse_hybrid \| store extra info unique to this atom style (optional) \|		other strings.
	+-------------------------+--------------------------------------------------------------------------------+
	\| unpack_reverse \| retrieve an atom's info from the buffer (required) \|		.. list-table::
	+-------------------------+--------------------------------------------------------------------------------+
	\| unpack_reverse_hybrid \| retrieve extra info unique to this atom style (optional) \|		* - fields_grow
	+-------------------------+--------------------------------------------------------------------------------+		- full list of properties which is allocated and stored
	\| pack_border \| store an atom's info in a buffer communicated on neighbor re-builds (required) \|		* - fields_copy
	+-------------------------+--------------------------------------------------------------------------------+		- list of properties to copy atoms are rearranged on-processor
	\| pack_border_vel \| add velocity info to buffer (required) \|		* - fields_comm
	+-------------------------+--------------------------------------------------------------------------------+		- list of properties communicated to ghost atoms every step
	\| pack_border_hybrid \| store extra info unique to this atom style (optional) \|		* - fields_comm_vel
	+-------------------------+--------------------------------------------------------------------------------+		- additional properties communicated if :doc:`comm_modify vel <atom_style>` is used
	\| unpack_border \| retrieve an atom's info from the buffer (required) \|		* - fields_reverse
	+-------------------------+--------------------------------------------------------------------------------+		- list of properties summed from ghost atoms every step
	\| unpack_border_vel \| also retrieve velocity info (required) \|		* - fields_border
	+-------------------------+--------------------------------------------------------------------------------+		- list of properties communicated with ghost atoms every reneighboring step
	\| unpack_border_hybrid \| retrieve extra info unique to this atom style (optional) \|		* - fields_border_vel
	+-------------------------+--------------------------------------------------------------------------------+		- additional properties communicated if :doc:`comm_modify vel <atom_style>` is used
	\| pack_exchange \| store all an atom's info to migrate to another processor (required) \|		* - fields_exchange
	+-------------------------+--------------------------------------------------------------------------------+		- list of properties communicated when an atom migrates to another processor
	\| unpack_exchange \| retrieve an atom's info from the buffer (required) \|		* - fields_restart
	+-------------------------+--------------------------------------------------------------------------------+		- list of properties written/read to/from a restart file
	\| size_restart \| number of restart quantities associated with proc's atoms (required) \|		* - fields_create
	+-------------------------+--------------------------------------------------------------------------------+		- list of properties defined when an atom is created by :doc:`create_atoms <create_atoms>`
	\| pack_restart \| pack atom quantities into a buffer (required) \|		* - fields_data_atom
	+-------------------------+--------------------------------------------------------------------------------+		- list of properties (in order) in the Atoms section of a data file, as read by :doc:`read_data <read_data>`
	\| unpack_restart \| unpack atom quantities from a buffer (required) \|		* - fields_data_vel
	+-------------------------+--------------------------------------------------------------------------------+		- list of properties (in order) in the Velocities section of a data file, as read by :doc:`read_data <read_data>`
	\| create_atom \| create an individual atom of this style (required) \|
	+-------------------------+--------------------------------------------------------------------------------+		In these strings you can list variable names which LAMMPS already
	\| data_atom \| parse an atom line from the data file (required) \|		defines (in some other atom style), or you can create new variable
	+-------------------------+--------------------------------------------------------------------------------+		names. You should not re-use a LAMMPS variable for something with
	\| data_atom_hybrid \| parse additional atom info unique to this atom style (optional) \|		different meaning in your atom style. If the meaning is related, but
	+-------------------------+--------------------------------------------------------------------------------+		interpreted differently by your atom style, then using the same
	\| data_vel \| parse one line of velocity information from data file (optional) \|		variable name means a user should not use your style and the other
	+-------------------------+--------------------------------------------------------------------------------+		style together in a :doc:`atom_style hybrid <atom_style>` command.
	\| data_vel_hybrid \| parse additional velocity data unique to this atom style (optional) \|		Because there will only be one value of the variable and different
	+-------------------------+--------------------------------------------------------------------------------+		parts of LAMMPS will then likely use it differently. LAMMPS has
	\| memory_usage \| tally memory allocated by atom arrays (required) \|		no way of checking for this.
	+-------------------------+--------------------------------------------------------------------------------+
			If you are defining new variable names then make them descriptive and
	The constructor of the derived class sets values for several variables		unique to your new atom style. For example choosing "e" for energy is
	that you must set when defining a new atom style, which are documented		a bad choice; it is too generic. A better choice would be "e_foo",
	in atom_vec.h. New atom arrays are defined in atom.cpp. Search for		where "foo" is specific to your style.
	the word "customize" and you will find locations you will need to
	modify.		If any of the variable names in your new atom style do not exist in
			LAMMPS, you need to add them to the src/atom.h and atom.cpp files.
	.. note::
			Search for the word "customize" or "customization" in these 2 files to
	It is possible to add some attributes, such as a molecule ID, to		see where to add your variable. Adding a flag to the 2nd
	atom styles that do not have them via the :doc:`fix property/atom <fix_property_atom>` command. This command also		customization section in atom.h is only necessary if your code (e.g. a
	allows new custom attributes consisting of extra integer or		pair style) needs to check that a per-atom property is defined. These
	floating-point values to be added to atoms. See the :doc:`fix property/atom <fix_property_atom>` doc page for examples of cases		flags should also be set in the constructor of the atom style child
	where this is useful and details on how to initialize, access, and		class.
	output the custom values.
			In atom.cpp, aside from the constructor and destructor, there are 3
	New :doc:`pair styles <pair_style>`, :doc:`fixes <fix>`, or		methods that a new variable name or flag needs to be added to.
	:doc:`computes <compute>` can be added to LAMMPS, as discussed below.
	The code for these classes can use the per-atom properties defined by		In Atom::peratom_create() when using the add_peratom() method, a
	fix property/atom. The Atom class has a find_custom() method that is		final length argument of 0 is for per-atom vectors, a length > 1 is
	useful in this context:		for per-atom arrays. Note the use of an extra per-thread flag and the
			add_peratom_vary() method when last dimension of the array is
	.. code-block:: c++		variable-length.

	int index = atom->find_custom(char *name, int &flag);		Adding the variable name to Atom::extract() enable the per-atom data
			to be accessed through the :doc:`LAMMPS library interface
	The "name" of a custom attribute, as specified in the :doc:`fix property/atom <fix_property_atom>` command, is checked to verify		<Howto_library>` by a calling code, including from :doc:`Python
	that it exists and its index is returned. The method also sets flag =		<Python_head>`.
	0/1 depending on whether it is an integer or floating-point attribute.
	The vector of values associated with the attribute can then be		The constructor of the new atom style will also typically set a few
	accessed using the returned index as		flags which are defined at the top of atom_vec.h. If these are
			unclear, see how other atom styles use them.
	.. code-block:: c++
			The grow_pointers() method is also required to make
	int *ivector = atom->ivector[index];		a copy of peratom data pointers, as explained in the code.
	double *dvector = atom->dvector[index];
			There are a number of other optional methods which your atom style can
	Ivector or dvector are vectors of length Nlocal = # of owned atoms,		implement. These are only needed if you need to do something
	which store the attributes of individual atoms.		out-of-the-ordinary which the default operation of the AtomVec parent
			class does not take care of. The best way to figure out why they are
			sometimes useful is to look at how other atom styles use them.

			* process_args = use if the atom style has arguments
			* init = called before each run
			* force_clear = called before force computations each timestep

			A few atom styles define "bonus" data associated with some or all of
			their particles, such as :doc:`atom_style ellipsoid or tri
			<atom_style>`. These methods work with that data:

			* copy_bonus
			* clear_bonus
			* pack_comm_bonus
			* unpack_comm_bonus
			* pack_border_bonus
			* unpack_border_bonus
			* pack_exchange_bonus
			* unpack_exchange_bonus
			* size_restart_bonus
			* pack_restart_bonus
			* unpack_restart_bonus
			* data_atom_bonus
			* memory_usage_bonus

			The :doc:`atom_style body <atom_style>` command can define a particle
			geometry with an arbitrary number of values. This method reads it
			from a data file:

			* data_body

			These methods are called before or after operations handled by the
			parent AtomVec class. They allow an atom style to do customized
			operations on the per-atom values. For example :doc:`atom_style
			sphere <atom_style>` reads a diameter and density of each particle
			from a data file. But these need to be converted internally to a
			radius and mass. That operation is done in the data_atom_post()
			method.

			* pack_restart_pre
			* pack_restart_post
			* unpack_restart_init
			* create_atom_post
			* data_atom_post
			* pack_data_pre
			* pack_data_post

			These methods enable the :doc:`compute property/atom <compute_property_atom>`
			command to access per-atom variables it does not
			already define as arguments, so that they can be written to a dump
			file or used by other LAMMPS commands.

			* property_atom
			* pack_property_atom

doc/src/atom_style.rst

+24 −14

Original line number	Original line	Diff line number	Diff line
	@@ -10,7 +10,7 @@ Syntax

	atom_style style args		atom_style style args

	* style = angle or atomic or body or bond or charge or dipole or dpd or edpd or mdpd or tdpd or electron or ellipsoid or full or line or meso or molecular or peri or smd or sphere or spin or tri or template or hybrid		* style = angle or atomic or body or bond or charge or dipole or dpd or edpd or electron or ellipsoid or full or line or mdpd or molecular or peri or smd or sph or sphere or spin or tdpd or tri or template or hybrid

	.. parsed-literal::		.. parsed-literal::

	@@ -18,7 +18,9 @@ Syntax
	body args = bstyle bstyle-args		body args = bstyle bstyle-args
	bstyle = style of body particles		bstyle = style of body particles
	bstyle-args = additional arguments specific to the bstyle		bstyle-args = additional arguments specific to the bstyle
	see the :doc:`Howto body <Howto_body>` doc page for details		see the :doc:`Howto body <Howto_body>` doc
			page for details
			sphere arg = 0/1 (optional) for static/dynamic particle radii
	tdpd arg = Nspecies		tdpd arg = Nspecies
	Nspecies = # of chemical species		Nspecies = # of chemical species
	template arg = template-ID		template arg = template-ID
	@@ -91,10 +93,6 @@ quantities.
	+--------------+-----------------------------------------------------+--------------------------------------+		+--------------+-----------------------------------------------------+--------------------------------------+
	\| edpd \| temperature and heat capacity \| eDPD particles \|		\| edpd \| temperature and heat capacity \| eDPD particles \|
	+--------------+-----------------------------------------------------+--------------------------------------+		+--------------+-----------------------------------------------------+--------------------------------------+
	\| mdpd \| density \| mDPD particles \|
	+--------------+-----------------------------------------------------+--------------------------------------+
	\| tdpd \| chemical concentration \| tDPD particles \|
	+--------------+-----------------------------------------------------+--------------------------------------+
	\| electron \| charge and spin and eradius \| electronic force field \|		\| electron \| charge and spin and eradius \| electronic force field \|
	+--------------+-----------------------------------------------------+--------------------------------------+		+--------------+-----------------------------------------------------+--------------------------------------+
	\| ellipsoid \| shape, quaternion, angular momentum \| aspherical particles \|		\| ellipsoid \| shape, quaternion, angular momentum \| aspherical particles \|
	@@ -103,7 +101,7 @@ quantities.
	+--------------+-----------------------------------------------------+--------------------------------------+		+--------------+-----------------------------------------------------+--------------------------------------+
	\| line \| end points, angular velocity \| rigid bodies \|		\| line \| end points, angular velocity \| rigid bodies \|
	+--------------+-----------------------------------------------------+--------------------------------------+		+--------------+-----------------------------------------------------+--------------------------------------+
	\| meso \| rho, e, cv \| SPH particles \|		\| mdpd \| density \| mDPD particles \|
	+--------------+-----------------------------------------------------+--------------------------------------+		+--------------+-----------------------------------------------------+--------------------------------------+
	\| molecular \| bonds, angles, dihedrals, impropers \| uncharged molecules \|		\| molecular \| bonds, angles, dihedrals, impropers \| uncharged molecules \|
	+--------------+-----------------------------------------------------+--------------------------------------+		+--------------+-----------------------------------------------------+--------------------------------------+
	@@ -111,10 +109,14 @@ quantities.
	+--------------+-----------------------------------------------------+--------------------------------------+		+--------------+-----------------------------------------------------+--------------------------------------+
	\| smd \| volume, kernel diameter, contact radius, mass \| solid and fluid SPH particles \|		\| smd \| volume, kernel diameter, contact radius, mass \| solid and fluid SPH particles \|
	+--------------+-----------------------------------------------------+--------------------------------------+		+--------------+-----------------------------------------------------+--------------------------------------+
			\| sph \| rho, esph, cv \| SPH particles \|
			+--------------+-----------------------------------------------------+--------------------------------------+
	\| sphere \| diameter, mass, angular velocity \| granular models \|		\| sphere \| diameter, mass, angular velocity \| granular models \|
	+--------------+-----------------------------------------------------+--------------------------------------+		+--------------+-----------------------------------------------------+--------------------------------------+
	\| spin \| magnetic moment \| system with magnetic particles \|		\| spin \| magnetic moment \| system with magnetic particles \|
	+--------------+-----------------------------------------------------+--------------------------------------+		+--------------+-----------------------------------------------------+--------------------------------------+
			\| tdpd \| chemical concentration \| tDPD particles \|
			+--------------+-----------------------------------------------------+--------------------------------------+
	\| template \| template index, template atom \| small molecules with fixed topology \|		\| template \| template index, template atom \| small molecules with fixed topology \|
	+--------------+-----------------------------------------------------+--------------------------------------+		+--------------+-----------------------------------------------------+--------------------------------------+
	\| tri \| corner points, angular momentum \| rigid bodies \|		\| tri \| corner points, angular momentum \| rigid bodies \|
	@@ -144,9 +146,16 @@ basis.
	For the sphere style, the particles are spheres and each stores a		For the sphere style, the particles are spheres and each stores a
	per-particle diameter and mass. If the diameter > 0.0, the particle		per-particle diameter and mass. If the diameter > 0.0, the particle
	is a finite-size sphere. If the diameter = 0.0, it is a point		is a finite-size sphere. If the diameter = 0.0, it is a point
	particle. Note that by use of the disc keyword with the :doc:`fix nve/sphere <fix_nve_sphere>`, :doc:`fix nvt/sphere <fix_nvt_sphere>`,		particle. Note that by use of the disc keyword with the :doc:`fix
	:doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix npt/sphere <fix_npt_sphere>` commands, spheres can be effectively		nve/sphere <fix_nve_sphere>`, :doc:`fix nvt/sphere <fix_nvt_sphere>`,
	treated as 2d discs for a 2d simulation if desired. See also the :doc:`set density/disc <set>` command.		:doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix npt/sphere
			<fix_npt_sphere>` commands, spheres can be effectively treated as 2d
			discs for a 2d simulation if desired. See also the :doc:`set
			density/disc <set>` command. The sphere style takes an optional 0
			or 1 argument. A value of 0 means the radius of each sphere is
			constant for the duration of the simulation. A value of 1 means the
			radii may vary dynamically during the simulation, e.g. due to use of
			the :doc:`fix adapt <fix_adapt>` command.

	For the ellipsoid style, the particles are ellipsoids and each		For the ellipsoid style, the particles are ellipsoids and each
	stores a flag which indicates whether it is a finite-size ellipsoid or		stores a flag which indicates whether it is a finite-size ellipsoid or
	@@ -189,8 +198,8 @@ particles which store a set of chemical concentration. An integer
	"cc_species" is required to specify the number of chemical species		"cc_species" is required to specify the number of chemical species
	involved in a tDPD system.		involved in a tDPD system.

	The meso style is for smoothed particle hydrodynamics (SPH)		The sph style is for smoothed particle hydrodynamics (SPH)
	particles which store a density (rho), energy (e), and heat capacity		particles which store a density (rho), energy (esph), and heat capacity
	(cv).		(cv).

	The smd style is for a general formulation of Smooth Particle		The smd style is for a general formulation of Smooth Particle
	@@ -335,7 +344,7 @@ for energy-conserving dissipative particle dynamics (eDPD), many-body
	dissipative particle dynamics (mDPD), and transport dissipative particle		dissipative particle dynamics (mDPD), and transport dissipative particle
	dynamics (tDPD), respectively.		dynamics (tDPD), respectively.

	The meso style is part of the USER-SPH package for smoothed particle		The sph style is part of the USER-SPH package for smoothed particle
	hydrodynamics (SPH). See `this PDF guide <USER/sph/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS.		hydrodynamics (SPH). See `this PDF guide <USER/sph/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS.

	The spin style is part of the SPIN package.		The spin style is part of the SPIN package.
	@@ -351,7 +360,8 @@ Related commands
	Default		Default
	"""""""		"""""""

	atom_style atomic		The default atom style is atomic. If atom_style sphere is used its
			default argument is 0.

	----------		----------

doc/src/compute.rst

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