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doc/src/compute.rst
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@ -6,7 +6,7 @@ compute command
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
compute ID group-ID style args
@ -33,8 +33,8 @@ they are calculated from information about atoms on the current
timestep or iteration, though a compute may internally store some
information about a previous state of the system. Defining a compute
does not perform a computation. Instead computes are invoked by other
LAMMPS commands as needed, e.g. to calculate a temperature needed for
a thermostat fix or to generate thermodynamic or dump file output.
LAMMPS commands as needed (e.g., to calculate a temperature needed for
a thermostat fix or to generate thermodynamic or dump file output).
See the :doc:`Howto output <Howto_output>` page for a summary of
various LAMMPS output options, many of which involve computes.
@ -89,14 +89,14 @@ notation, where ID is the ID of the compute:
+-------------+--------------------------------------------+
In other words, using one bracket reduces the dimension of the
quantity once (vector -> scalar, array -> vector). Using two brackets
reduces the dimension twice (array -> scalar). Thus a command that
uses scalar compute values as input can also process elements of a
quantity once (vector :math:`\to` scalar, array :math:`\to` vector). Using two
brackets reduces the dimension twice (array :math:`\to` scalar). Thus a
command that uses scalar compute values as input can also process elements of a
vector or array.
Note that commands and :doc:`variables <variable>` which use compute
quantities typically do not allow for all kinds, e.g. a command may
require a vector of values, not a scalar. This means there is no
quantities typically do not allow for all kinds (e.g., a command may
require a vector of values, not a scalar). This means there is no
ambiguity about referring to a compute quantity as c_ID even if it
produces, for example, both a scalar and vector. The doc pages for
various commands explain the details.
@ -120,14 +120,14 @@ ways:
The results of computes that calculate global quantities can be either
"intensive" or "extensive" values. Intensive means the value is
independent of the number of atoms in the simulation,
e.g. temperature. Extensive means the value scales with the number of
atoms in the simulation, e.g. total rotational kinetic energy.
independent of the number of atoms in the simulation
(e.g., temperature). Extensive means the value scales with the number of
atoms in the simulation (e.g., total rotational kinetic energy).
:doc:`Thermodynamic output <thermo_style>` will normalize extensive
values by the number of atoms in the system, depending on the
"thermo_modify norm" setting. It will not normalize intensive values.
If a compute value is accessed in another way, e.g. by a
:doc:`variable <variable>`, you may want to know whether it is an
If a compute value is accessed in another way (e.g., by a
:doc:`variable <variable>`), you may want to know whether it is an
intensive or extensive value. See the page for individual
computes for further info.
@ -196,8 +196,8 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
* :doc:`cluster/atom <compute_cluster_atom>` - cluster ID for each atom
* :doc:`cna/atom <compute_cna_atom>` - common neighbor analysis (CNA) for each atom
* :doc:`cnp/atom <compute_cnp_atom>` - common neighborhood parameter (CNP) for each atom
* :doc:`com <compute_com>` - center-of-mass of group of atoms
* :doc:`com/chunk <compute_com_chunk>` - center-of-mass for each chunk
* :doc:`com <compute_com>` - center of mass of group of atoms
* :doc:`com/chunk <compute_com_chunk>` - center of mass for each chunk
* :doc:`contact/atom <compute_contact_atom>` - contact count for each spherical particle
* :doc:`coord/atom <compute_coord_atom>` - coordination number for each atom
* :doc:`damage/atom <compute_damage_atom>` - Peridynamic damage for each atom
@ -207,10 +207,10 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
* :doc:`dipole <compute_dipole>` - dipole vector and total dipole
* :doc:`dipole/chunk <compute_dipole_chunk>` - dipole vector and total dipole for each chunk
* :doc:`displace/atom <compute_displace_atom>` - displacement of each atom
* :doc:`dpd <compute_dpd>` -
* :doc:`dpd/atom <compute_dpd_atom>` -
* :doc:`dpd <compute_dpd>` - total values of internal conductive energy, internal mechanical energy, chemical energy, and harmonic average of internal temperature
* :doc:`dpd/atom <compute_dpd_atom>` - per-particle values of internal conductive energy, internal mechanical energy, chemical energy, and internal temperature
* :doc:`edpd/temp/atom <compute_edpd_temp_atom>` - per-atom temperature for each eDPD particle in a group
* :doc:`efield/atom <compute_efield_atom>` -
* :doc:`efield/atom <compute_efield_atom>` - electric field at each atom
* :doc:`entropy/atom <compute_entropy_atom>` - pair entropy fingerprint of each atom
* :doc:`erotate/asphere <compute_erotate_asphere>` - rotational energy of aspherical particles
* :doc:`erotate/rigid <compute_erotate_rigid>` - rotational energy of rigid bodies
@ -222,7 +222,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
* :doc:`fep/ta <compute_fep_ta>` - compute free energies for a test area perturbation
* :doc:`force/tally <compute_tally>` - force between two groups of atoms via the tally callback mechanism
* :doc:`fragment/atom <compute_cluster_atom>` - fragment ID for each atom
* :doc:`global/atom <compute_global_atom>` -
* :doc:`global/atom <compute_global_atom>` - assign global values to each atom from arrays of global values
* :doc:`group/group <compute_group_group>` - energy/force between two groups of atoms
* :doc:`gyration <compute_gyration>` - radius of gyration of group of atoms
* :doc:`gyration/chunk <compute_gyration_chunk>` - radius of gyration for each chunk
@ -241,7 +241,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
* :doc:`ke/atom/eff <compute_ke_atom_eff>` - per-atom translational and radial kinetic energy in the electron force field model
* :doc:`ke/eff <compute_ke_eff>` - kinetic energy of a group of nuclei and electrons in the electron force field model
* :doc:`ke/rigid <compute_ke_rigid>` - translational kinetic energy of rigid bodies
* :doc:`mliap <compute_mliap>` - gradients of energy and forces w.r.t. model parameters and related quantities for training machine learning interatomic potentials
* :doc:`mliap <compute_mliap>` - gradients of energy and forces with respect to model parameters and related quantities for training machine learning interatomic potentials
* :doc:`momentum <compute_momentum>` - translational momentum
* :doc:`msd <compute_msd>` - mean-squared displacement of group of atoms
* :doc:`msd/chunk <compute_msd_chunk>` - mean-squared displacement for each chunk
@ -264,35 +264,35 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
* :doc:`property/grid <compute_property_grid>` - convert per-grid attributes to per-grid vectors/arrays
* :doc:`property/local <compute_property_local>` - convert local attributes to local vectors/arrays
* :doc:`ptm/atom <compute_ptm_atom>` - determines the local lattice structure based on the Polyhedral Template Matching method
* :doc:`rdf <compute_rdf>` - radial distribution function g(r) histogram of group of atoms
* :doc:`rdf <compute_rdf>` - radial distribution function :math:`g(r)` histogram of group of atoms
* :doc:`reduce <compute_reduce>` - combine per-atom quantities into a single global value
* :doc:`reduce/chunk <compute_reduce_chunk>` - reduce per-atom quantities within each chunk
* :doc:`reduce/region <compute_reduce>` - same as compute reduce, within a region
* :doc:`rigid/local <compute_rigid_local>` - extract rigid body attributes
* :doc:`saed <compute_saed>` - electron diffraction intensity on a mesh of reciprocal lattice nodes
* :doc:`slice <compute_slice>` - extract values from global vector or array
* :doc:`smd/contact/radius <compute_smd_contact_radius>` -
* :doc:`smd/contact/radius <compute_smd_contact_radius>` - contact radius for Smooth Mach Dynamics
* :doc:`smd/damage <compute_smd_damage>` - damage status of SPH particles in Smooth Mach Dynamics
* :doc:`smd/hourglass/error <compute_smd_hourglass_error>` -
* :doc:`smd/hourglass/error <compute_smd_hourglass_error>` - error associated with approximated relative separation in Smooth Mach Dynamics
* :doc:`smd/internal/energy <compute_smd_internal_energy>` - per-particle enthalpy in Smooth Mach Dynamics
* :doc:`smd/plastic/strain <compute_smd_plastic_strain>` - equivalent plastic strain per particle in Smooth Mach Dynamics
* :doc:`smd/plastic/strain/rate <compute_smd_plastic_strain_rate>` - time rate of the equivalent plastic strain in Smooth Mach Dynamics
* :doc:`smd/rho <compute_smd_rho>` - per-particle mass density in Smooth Mach Dynamics
* :doc:`smd/tlsph/defgrad <compute_smd_tlsph_defgrad>` - deformation gradient in Smooth Mach Dynamics
* :doc:`smd/tlsph/dt <compute_smd_tlsph_dt>` - CFL-stable time increment per particle in Smooth Mach Dynamics
* :doc:`smd/tlsph/num/neighs <compute_smd_tlsph_num_neighs>` -
* :doc:`smd/tlsph/shape <compute_smd_tlsph_shape>` -
* :doc:`smd/tlsph/strain <compute_smd_tlsph_strain>` -
* :doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>` -
* :doc:`smd/tlsph/num/neighs <compute_smd_tlsph_num_neighs>` - number of particles inside the smoothing kernel radius for Smooth Mach Dynamics
* :doc:`smd/tlsph/shape <compute_smd_tlsph_shape>` - current shape of the volume of a particle for Smooth Mach Dynamics
* :doc:`smd/tlsph/strain <compute_smd_tlsph_strain>` - Green--Lagrange strain tensor for Smooth Mach Dynamics
* :doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>` - rate of strain for Smooth Mach Dynamics
* :doc:`smd/tlsph/stress <compute_smd_tlsph_stress>` - per-particle Cauchy stress tensor for SPH particles
* :doc:`smd/triangle/vertices <compute_smd_triangle_vertices>` -
* :doc:`smd/triangle/vertices <compute_smd_triangle_vertices>` - coordinates of vertices corresponding to the triangle elements of a mesh for Smooth Mach Dynamics
* :doc:`smd/ulsph/effm <compute_smd_ulsph_effm>` - per-particle effective shear modulus
* :doc:`smd/ulsph/num/neighs <compute_smd_ulsph_num_neighs>` -
* :doc:`smd/ulsph/strain <compute_smd_ulsph_strain>` -
* :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>` -
* :doc:`smd/ulsph/num/neighs <compute_smd_ulsph_num_neighs>` - number of neighbor particles inside the smoothing kernel radius for Smooth Mach Dynamics
* :doc:`smd/ulsph/strain <compute_smd_ulsph_strain>` - logarithmic strain tensor for Smooth Mach Dynamics
* :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>` - logarithmic strain rate for Smooth Mach Dynamics
* :doc:`smd/ulsph/stress <compute_smd_ulsph_stress>` - per-particle Cauchy stress tensor and von Mises equivalent stress in Smooth Mach Dynamics
* :doc:`smd/vol <compute_smd_vol>` - per-particle volumes and their sum in Smooth Mach Dynamics
* :doc:`snap <compute_sna_atom>` - gradients of SNAP energy and forces w.r.t. linear coefficients and related quantities for fitting SNAP potentials
* :doc:`snap <compute_sna_atom>` - gradients of SNAP energy and forces with respect to linear coefficients and related quantities for fitting SNAP potentials
* :doc:`sna/atom <compute_sna_atom>` - bispectrum components for each atom
* :doc:`sna/grid <compute_sna_atom>` - global array of bispectrum components on a regular grid
* :doc:`sna/grid/local <compute_sna_atom>` - local array of bispectrum components on a regular grid
@ -318,7 +318,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
* :doc:`temp/cs <compute_temp_cs>` - temperature based on the center-of-mass velocity of atom pairs that are bonded to each other
* :doc:`temp/deform <compute_temp_deform>` - temperature excluding box deformation velocity
* :doc:`temp/deform/eff <compute_temp_deform_eff>` - temperature excluding box deformation velocity in the electron force field model
* :doc:`temp/drude <compute_temp_drude>` - temperature of Core-Drude pairs
* :doc:`temp/drude <compute_temp_drude>` - temperature of Core--Drude pairs
* :doc:`temp/eff <compute_temp_eff>` - temperature of a group of nuclei and electrons in the electron force field model
* :doc:`temp/partial <compute_temp_partial>` - temperature excluding one or more dimensions of velocity
* :doc:`temp/profile <compute_temp_profile>` - temperature excluding a binned velocity profile
@ -334,7 +334,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
* :doc:`vcm/chunk <compute_vcm_chunk>` - velocity of center-of-mass for each chunk
* :doc:`viscosity/cos <compute_viscosity_cos>` - velocity profile under cosine-shaped acceleration
* :doc:`voronoi/atom <compute_voronoi_atom>` - Voronoi volume and neighbors for each atom
* :doc:`xrd <compute_xrd>` - x-ray diffraction intensity on a mesh of reciprocal lattice nodes
* :doc:`xrd <compute_xrd>` - X-ray diffraction intensity on a mesh of reciprocal lattice nodes
Restrictions
""""""""""""
@ -343,7 +343,9 @@ Restrictions
Related commands
""""""""""""""""
:doc:`uncompute <uncompute>`, :doc:`compute_modify <compute_modify>`, :doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/time <fix_ave_time>`, :doc:`fix ave/histo <fix_ave_histo>`
:doc:`uncompute <uncompute>`, :doc:`compute_modify <compute_modify>`,
:doc:`fix ave/atom <fix_ave_atom>`, :doc:`fix ave/time <fix_ave_time>`,
:doc:`fix ave/histo <fix_ave_histo>`
Default
"""""""