updating args and D2min calculation in nonaffine fix
This commit is contained in:
jtclemm
@ -254,6 +254,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
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* :doc:`property/chunk <compute_property_chunk>` - extract various per-chunk attributes
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* :doc:`property/local <compute_property_local>` - convert local attributes to localvectors/arrays
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* :doc:`ptm/atom <compute_ptm_atom>` - determines the local lattice structure based on the Polyhedral Template Matching method
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* :doc:`rattlers <compute_rattlers>` - identify undercoordinated rattler atoms
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* :doc:`rdf <compute_rdf>` - radial distribution function g(r) histogram of group of atoms
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* :doc:`reduce <compute_reduce>` - combine per-atom quantities into a single global value
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* :doc:`reduce/chunk <compute_reduce_chunk>` - reduce per-atom quantities within each chunk
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@ -8,10 +8,11 @@ Syntax
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.. parsed-literal::
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compute ID group-ID contact/atom
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compute ID group-ID contact/atom group2-ID
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* contact/atom = style name of this compute command
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* group2-ID = optional argument select group-ID to restrict which atoms to consider for contacts (see below)
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Examples
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""""""""
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@ -19,6 +20,7 @@ Examples
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.. code-block:: LAMMPS
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compute 1 all contact/atom
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compute 1 all contact/atom mygroup
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Description
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"""""""""""
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@ -34,6 +36,9 @@ sum of the radii of the two particles.
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The value of the contact number will be 0.0 for atoms not in the
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specified compute group.
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The optional *group2-ID* argument allows to specify from which group atoms
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contribute to the coordination number. Default setting is group 'all'.
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Output info
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"""""""""""
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@ -63,4 +68,7 @@ Related commands
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Default
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"""""""
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*group2-ID* = all
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none
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74
doc/src/compute_rattlers.rst
Normal file
74
doc/src/compute_rattlers.rst
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@ -0,0 +1,74 @@
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.. index:: compute contact/atom
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compute contact/atom command
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============================
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Syntax
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""""""
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.. parsed-literal::
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compute ID group-ID contact/atom group2-ID
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* contact/atom = style name of this compute command
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* group2-ID = optional argument select group-ID to restrict which atoms to consider for contacts (see below)
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Examples
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""""""""
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.. code-block:: LAMMPS
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compute 1 all contact/atom
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compute 1 all contact/atom mygroup
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Description
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"""""""""""
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Define a computation that calculates the number of contacts
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for each atom in a group.
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The contact number is defined for finite-size spherical particles as
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the number of neighbor atoms which overlap the central particle,
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meaning that their distance of separation is less than or equal to the
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sum of the radii of the two particles.
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The value of the contact number will be 0.0 for atoms not in the
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specified compute group.
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The optional *group2-ID* argument allows to specify from which group atoms
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contribute to the coordination number. Default setting is group 'all'.
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Output info
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"""""""""""
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This compute calculates a per-atom vector, whose values can be
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accessed by any command that uses per-atom values from a compute as
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input. See the :doc:`Howto output <Howto_output>` page for an
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overview of LAMMPS output options.
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The per-atom vector values will be a number >= 0.0, as explained
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above.
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Restrictions
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""""""""""""
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This compute is part of the GRANULAR package. It is only enabled if
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LAMMPS was built with that package. See the
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:doc:`Build package <Build_package>` page for more info.
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This compute requires that atoms store a radius as defined by the
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:doc:`atom_style sphere <atom_style>` command.
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Related commands
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""""""""""""""""
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:doc:`compute coord/atom <compute_coord_atom>`
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Default
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"""""""
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*group2-ID* = all
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none
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@ -259,6 +259,7 @@ accelerated styles exist.
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* :doc:`mvv/tdpd <fix_mvv_dpd>` - constant temperature DPD using the modified velocity-Verlet algorithm
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* :doc:`neb <fix_neb>` - nudged elastic band (NEB) spring forces
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* :doc:`neb/spin <fix_neb_spin>` - nudged elastic band (NEB) spring forces for spins
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* :doc:`nonaffine/displacement <fix_nonaffine_displacement>` - calculate nonaffined displacement of atoms
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* :doc:`nph <fix_nh>` - constant NPH time integration via Nose/Hoover
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* :doc:`nph/asphere <fix_nph_asphere>` - NPH for aspherical particles
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* :doc:`nph/body <fix_nph_body>` - NPH for body particles
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140
doc/src/fix_nonaffine_displacement.rst
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140
doc/src/fix_nonaffine_displacement.rst
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@ -0,0 +1,140 @@
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.. index:: fix gravity
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.. index:: fix gravity/omp
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.. index:: fix gravity/kk
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fix gravity command
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===================
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Accelerator Variants: *gravity/omp*, *gravity/kk*
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Syntax
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""""""
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.. parsed-literal::
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fix ID group gravity magnitude style args
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* ID, group are documented in :doc:`fix <fix>` command
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* gravity = style name of this fix command
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* magnitude = size of acceleration (force/mass units)
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* magnitude can be a variable (see below)
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* style = *chute* or *spherical* or *gradient* or *vector*
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.. parsed-literal::
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*chute* args = angle
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angle = angle in +x away from -z or -y axis in 3d/2d (in degrees)
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angle can be a variable (see below)
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*spherical* args = phi theta
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phi = azimuthal angle from +x axis (in degrees)
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theta = angle from +z or +y axis in 3d/2d (in degrees)
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phi or theta can be a variable (see below)
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*vector* args = x y z
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x y z = vector direction to apply the acceleration
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x or y or z can be a variable (see below)
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Examples
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""""""""
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.. code-block:: LAMMPS
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fix 1 all gravity 1.0 chute 24.0
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fix 1 all gravity v_increase chute 24.0
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fix 1 all gravity 1.0 spherical 0.0 -180.0
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fix 1 all gravity 10.0 spherical v_phi v_theta
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fix 1 all gravity 100.0 vector 1 1 0
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Description
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"""""""""""
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Impose an additional acceleration on each particle in the group. This
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fix is typically used with granular systems to include a "gravity"
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term acting on the macroscopic particles. More generally, it can
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represent any kind of driving field, e.g. a pressure gradient inducing
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a Poiseuille flow in a fluid. Note that this fix operates differently
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than the :doc:`fix addforce <fix_addforce>` command. The addforce fix
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adds the same force to each atom, independent of its mass. This
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command imparts the same acceleration to each atom (force/mass).
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The *magnitude* of the acceleration is specified in force/mass units.
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For granular systems (LJ units) this is typically 1.0. See the
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:doc:`units <units>` command for details.
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Style *chute* is typically used for simulations of chute flow where
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the specified *angle* is the chute angle, with flow occurring in the +x
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direction. For 3d systems, the tilt is away from the z axis; for 2d
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systems, the tilt is away from the y axis.
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Style *spherical* allows an arbitrary 3d direction to be specified for
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the acceleration vector. *Phi* and *theta* are defined in the usual
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spherical coordinates. Thus for acceleration acting in the -z
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direction, *theta* would be 180.0 (or -180.0). *Theta* = 90.0 and
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*phi* = -90.0 would mean acceleration acts in the -y direction. For
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2d systems, *phi* is ignored and *theta* is an angle in the xy plane
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where *theta* = 0.0 is the y-axis.
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Style *vector* imposes an acceleration in the vector direction given
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by (x,y,z). Only the direction of the vector is important; it's
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length is ignored. For 2d systems, the *z* component is ignored.
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Any of the quantities *magnitude*, *angle*, *phi*, *theta*, *x*, *y*,
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*z* which define the gravitational magnitude and direction, can be
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specified as an equal-style :doc:`variable <variable>`. If the value is
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a variable, it should be specified as v_name, where name is the
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variable name. In this case, the variable will be evaluated each
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timestep, and its value used to determine the quantity. You should
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insure that the variable calculates a result in the appropriate units,
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e.g. force/mass or degrees.
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Equal-style variables can specify formulas with various mathematical
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functions, and include :doc:`thermo_style <thermo_style>` command
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keywords for the simulation box parameters and timestep and elapsed
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time. Thus it is easy to specify a time-dependent gravitational
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field.
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----------
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.. include:: accel_styles.rst
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----------
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Restart, fix_modify, output, run start/stop, minimize info
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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No information about this fix is written to :doc:`binary restart files <restart>`.
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The :doc:`fix_modify <fix_modify>` *energy* option is supported by
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this fix to add the gravitational potential energy of the system to
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the global potential energy of the system as part of
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:doc:`thermodynamic output <thermo_style>`. The default setting for
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this fix is :doc:`fix_modify energy no <fix_modify>`.
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The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
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fix. This allows to set at which level of the :doc:`r-RESPA
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<run_style>` integrator the fix is adding its forces. Default is the
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outermost level.
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This fix computes a global scalar which can be accessed by various
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:doc:`output commands <Howto_output>`. This scalar is the
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gravitational potential energy of the particles in the defined field,
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namely mass \* (g dot x) for each particles, where x and mass are the
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particles position and mass, and g is the gravitational field. The
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scalar value calculated by this fix is "extensive".
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No parameter of this fix can be used with the *start/stop* keywords of
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the :doc:`run <run>` command. This fix is not invoked during
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:doc:`energy minimization <minimize>`.
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Restrictions
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""""""""""""
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none
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Related commands
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""""""""""""""""
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:doc:`atom_style sphere <atom_style>`, :doc:`fix addforce <fix_addforce>`
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Default
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"""""""
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none
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