git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7088 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
@ -140,43 +140,48 @@ features that can be added in the manner just described:
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10.1 Atom styles :link(mod_1),h4
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Classes that define an atom style are derived from the Atom class.
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The atom style determines what quantities are associated with an atom.
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A new atom style can be created if one of the existing atom styles
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does not define all the arrays you need to store and communicate with
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atoms.
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Classes that define an atom style are derived from the AtomVec class
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and managed by the Atom class. The atom style determines what
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quantities are associated with an atom. A new atom style can be
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created if one of the existing atom styles does not define all
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the arrays you need to store and communicate with atoms.
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Atom_vec_atomic.cpp is a simple example of an atom style.
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Here is a brief description of methods you define in your new derived
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class. See atom.h for details.
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class. See atom_vec.h for details.
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grow: re-allocate atom arrays to longer lengths
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copy: copy info for one atom to another atom's array locations
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pack_comm: store an atom's info in a buffer communicated every timestep
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pack_comm_vel: add velocity info to buffer
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pack_comm_one: store extra info unique to this atom style
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unpack_comm: retrieve an atom's info from the buffer
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unpack_comm_vel: also retrieve velocity info
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unpack_comm_one: retreive extra info unique to this atom style
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pack_reverse: store an atom's info in a buffer communicating partial forces
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pack_reverse_one: store extra info unique to this atom style
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unpack_reverse: retrieve an atom's info from the buffer
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unpack_reverse_one: retreive extra info unique to this atom style
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pack_border: store an atom's info in a buffer communicated on neighbor re-builds
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pack_border_vel: add velocity info to buffer
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pack_border_one: store extra info unique to this atom style
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unpack_border: retrieve an atom's info from the buffer
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unpack_border_vel: also retrieve velocity info
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unpack_border_one: retreive extra info unique to this atom style
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pack_exchange: store all an atom's info to migrate to another processor
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unpack_exchange: retrieve an atom's info from the buffer
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size_restart: number of restart quantities associated with proc's atoms
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pack_restart: pack atom quantities into a buffer
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unpack_restart: unpack atom quantities from a buffer
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create_atom: create an individual atom of this style
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data_atom: parse an atom line from the data file
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memory_usage: tally memory allocated by atom arrays :tb(s=:)
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init: one time setup (optional)
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grow: re-allocate atom arrays to longer lengths (required)
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grow_reset: make array pointers in Atom and AtomVec classes consistent (required)
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copy: copy info for one atom to another atom's array locations (required)
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pack_comm: store an atom's info in a buffer communicated every timestep (required)
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pack_comm_vel: add velocity info to communication buffer (required)
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pack_comm_hybrid: store extra info unique to this atom style (optional)
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unpack_comm: retrieve an atom's info from the buffer (required)
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unpack_comm_vel: also retrieve velocity info (required)
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unpack_comm_hybrid: retreive extra info unique to this atom style (optional)
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pack_reverse: store an atom's info in a buffer communicating partial forces (required)
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pack_reverse_hybrid: store extra info unique to this atom style (optional)
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unpack_reverse: retrieve an atom's info from the buffer (required)
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unpack_reverse_hybrid: retreive extra info unique to this atom style (optional)
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pack_border: store an atom's info in a buffer communicated on neighbor re-builds (required)
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pack_border_vel: add velocity info to buffer (required)
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pack_border_hybrid: store extra info unique to this atom style (optional)
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unpack_border: retrieve an atom's info from the buffer (required)
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unpack_border_vel: also retrieve velocity info (required)
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unpack_border_hybrid: retreive extra info unique to this atom style (optional)
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pack_exchange: store all an atom's info to migrate to another processor (required)
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unpack_exchange: retrieve an atom's info from the buffer (required)
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size_restart: number of restart quantities associated with proc's atoms (required)
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pack_restart: pack atom quantities into a buffer (required)
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unpack_restart: unpack atom quantities from a buffer (required)
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create_atom: create an individual atom of this style (required)
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data_atom: parse an atom line from the data file (required)
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data_atom_hybrid: parse additional atom info unique to this atom style (optional)
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data_vel: parse one line of velocity information from data file (optional)
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data_vel_hybrid: parse additional velocity data unique to this atom style (optional)
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memory_usage: tally memory allocated by atom arrays (required) :tb(s=:)
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The constructor of the derived class sets values for several variables
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that you must set when defining a new atom style, which are documented
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@ -196,15 +201,20 @@ Bond_harmonic.cpp is the simplest example of a bond style. Ditto for
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the harmonic forms of the angle, dihedral, and improper style
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commands.
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Here is a brief description of methods you define in your new derived
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bond class. See bond.h, angle.h, dihedral.h, and improper.h for
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details.
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Here is a brief description of common methods you define in your
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new derived class. See bond.h, angle.h, dihedral.h, and improper.h
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for details and specific additional methods.
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compute: compute the molecular interactions
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coeff: set coefficients for one bond type
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equilibrium_distance: length of bond, used by SHAKE
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write & read_restart: writes/reads coeffs to restart files
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single: force and energy of a single bond :tb(s=:)
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init: check if all coefficients are set, calls {init_style} (optional)
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init_style: check if style specific conditions are met (optional)
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compute: compute the molecular interactions (required)
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settings: apply global settings for all types (optional)
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coeff: set coefficients for one type (required)
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equilibrium_distance: length of bond, used by SHAKE (required, bond only)
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equilibrium_angle: opening of angle, used by SHAKE (required, angle only)
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write & read_restart: writes/reads coeffs to restart files (required)
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single: force and energy of a single bond or angle (required, bond or angle only)
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memory_usage: tally memory allocated by the style (optional) :tb(s=:)
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:line
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@ -223,14 +233,21 @@ per-atom kinetic energy.
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Here is a brief description of methods you define in your new derived
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class. See compute.h for details.
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compute_scalar: compute a scalar quantity
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compute_vector: compute a vector of quantities
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compute_peratom: compute one or more quantities per atom
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pack_comm: pack a buffer with items to communicate
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unpack_comm: unpack the buffer
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pack_reverse: pack a buffer with items to reverse communicate
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unpack_reverse: unpack the buffer
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memory_usage: tally memory usage :tb(s=:)
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init: perform one time setup (required)
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init_list: neighbor list setup, if needed (optional)
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compute_scalar: compute a scalar quantity (optional)
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compute_vector: compute a vector of quantities (optional)
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compute_peratom: compute one or more quantities per atom (optional)
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compute_local: compute one or more quantities per processor (optional)
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pack_comm: pack a buffer with items to communicate (optional)
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unpack_comm: unpack the buffer (optional)
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pack_reverse: pack a buffer with items to reverse communicate (optional)
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unpack_reverse: unpack the buffer (optional)
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remove_bias: remove velocity bias from one atom (optional)
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remove_bias_all: remove velocity bias from all atoms in group (optional)
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restore_bias: restore velocity bias for one atom after remove_bias (optional)
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restore_bias_all: same as before, but for all atoms in group (optional)
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memory_usage: tally memory usage (optional) :tb(s=:)
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:line
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@ -283,34 +300,59 @@ implement.
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Here is a brief description of methods you can define in your new
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derived class. See fix.h for details.
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setmask: determines when the fix is called during the timestep
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init: initialization before a run
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setup: called immediately before the 1st timestep
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initial_integrate: called at very beginning of each timestep
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pre_exchange: called before atom exchange on re-neighboring steps
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pre_neighbor: called before neighbor list build
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post_force: called after pair & molecular forces are computed
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final_integrate: called at end of each timestep
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end_of_step: called at very end of timestep
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write_restart: dumps fix info to restart file
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restart: uses info from restart file to re-initialize the fix
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grow_arrays: allocate memory for atom-based arrays used by fix
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copy_arrays: copy atom info when an atom migrates to a new processor
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memory_usage: report memory used by fix
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pack_exchange: store atom's data in a buffer
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unpack_exchange: retrieve atom's data from a buffer
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pack_restart: store atom's data for writing to restart file
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unpack_restart: retrieve atom's data from a restart file buffer
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size_restart: size of atom's data
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maxsize_restart: max size of atom's data
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initial_integrate_respa: same as initial_integrate, but for rRESPA
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post_force_respa: same as post_force, but for rRESPA
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final_integrate_respa: same as final_integrate, but for rRESPA
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pack_comm: pack a buffer to communicate a per-atom quantity
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unpack_comm: unpack a buffer to communicate a per-atom quantity
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pack_reverse_comm: pack a buffer to reverse communicate a per-atom quantity
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unpack_reverse_comm: unpack a buffer to reverse communicate a per-atom quantity
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thermo: compute quantities for thermodynamic output :tb(s=:)
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setmask: determines when the fix is called during the timestep (required)
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init: initialization before a run (optional)
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setup_pre_exchange: called before atom exchange in setup (optional)
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setup_pre_force: called before force computation in setup (optional)
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setup: called immediately before the 1st timestep and after forces are computed (optional)
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min_setup_pre_force: like setup_pre_force, but for minimizations instead of MD runs (optional)
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min_setup: like setup, but for minimizations instead of MD runs (optional)
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initial_integrate: called at very beginning of each timestep (optional)
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pre_exchange: called before atom exchange on re-neighboring steps (optional)
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pre_neighbor: called before neighbor list build (optional)
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pre_force: called after pair & molecular forces are computed (optional)
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post_force: called after pair & molecular forces are computed and communicated (optional)
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final_integrate: called at end of each timestep (optional)
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end_of_step: called at very end of timestep (optional)
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write_restart: dumps fix info to restart file (optional)
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restart: uses info from restart file to re-initialize the fix (optional)
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grow_arrays: allocate memory for atom-based arrays used by fix (optional)
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copy_arrays: copy atom info when an atom migrates to a new processor (optional)
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pack_exchange: store atom's data in a buffer (optional)
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unpack_exchange: retrieve atom's data from a buffer (optional)
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pack_restart: store atom's data for writing to restart file (optional)
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unpack_restart: retrieve atom's data from a restart file buffer (optional)
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size_restart: size of atom's data (optional)
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maxsize_restart: max size of atom's data (optional)
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setup_pre_force_respa: same as setup_pre_force, but for rRESPA (optional)
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initial_integrate_respa: same as initial_integrate, but for rRESPA (optional)
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post_integrate_respa: called after the first half integration step is done in rRESPA (optional)
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pre_force_respa: same as pre_force, but for rRESPA (optional)
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post_force_respa: same as post_force, but for rRESPA (optional)
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final_integrate_respa: same as final_integrate, but for rRESPA (optional)
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min_pre_force: called after pair & molecular forces are computed in minimizer (optional)
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min_post_force: called after pair & molecular forces are computed and communicated in minmizer (optional)
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min_store: store extra data for linesearch based minimization on a LIFO stack (optional)
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min_pushstore: push the minimization LIFO stack one element down (optional)
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min_popstore: pop the minimization LIFO stack one element up (optional)
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min_clearstore: clear minimization LIFO stack (optional)
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min_step: reset or move forward on line search minimization (optional)
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min_dof: report number of degrees of freedom {added} by this fix in minimization (optional)
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max_alpha: report maximum allowed step size during linesearch minimization (optional)
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pack_comm: pack a buffer to communicate a per-atom quantity (optional)
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unpack_comm: unpack a buffer to communicate a per-atom quantity (optional)
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pack_reverse_comm: pack a buffer to reverse communicate a per-atom quantity (optional)
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unpack_reverse_comm: unpack a buffer to reverse communicate a per-atom quantity (optional)
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dof: report number of degrees of freedom {removed} by this fix during MD (optional)
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compute_scalar: return a global scalar property that the fix computes (optional)
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compute_vector: return a component of a vector property that the fix computes (optional)
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compute_array: return a component of an array property that the fix computes (optional)
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deform: called when the box size is changed (optional)
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reset_target: called when a change of the target temperature is requested during a run (optional)
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reset_dt: is called when a change of the time step is requested during a run (optional)
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modify_param: called when a fix_modify request is executed (optional)
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memory_usage: report memory used by fix (optional)
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thermo: compute quantities for thermodynamic output (optional) :tb(s=:)
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Typically, only a small fraction of these methods are defined for a
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particular fix. Setmask is mandatory, as it determines when the fix
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