next chunk of converted atc doc files

.. index:: fix_modify AtC computes

fix_modify AtC computes command

===============================

Syntax

""""""

.. parsed-literal::

   fix_modify <AtC fixID> computes <add|delete> <per-atom compute-ID> <volume|number>

* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance

* computes = name of the AtC sub-command

* *add* or *delete* = add or delete the calculation of an equivalent continuum field for the specified per-atom compute as volume or number density quantity

* per-atom compute-ID = ID of a per-atom compute; fields can be calculated for all per-atom computes available in LAMMPS

* *volume* or *number* = select whether the created field is a per-unit-volume quantity or a per-atom quantity as weighted by kernel functions

Examples

""""""""

.. code-block:: LAMMPS

   compute virial all stress/atom

   fix_modify AtC computes add virial volume

   fix_modify AtC computes delete virial

   compute centrosymmetry all centro/atom

   fix_modify AtC computes add centrosymmetry number

Description

"""""""""""

Calculates continuum fields corresponding to specified per-atom

:doc:`computes <compute>` created by LAMMPS.

Restrictions

""""""""""""

Must be used with :doc:`fix atc hardy <fix_atc>`.  The per-atom compute

must be specified before the corresponding continuum field can be

requested.

Related AtC commands

""""""""""""""""""""

- :ref:`fix_modify AtC command overview <atc_fix_modify>`

- :doc:`fix_modify AtC fields <atc_hardy_fields>`

- :doc:`compute <compute>`

Default

"""""""

None.

.. index:: fix_modify AtC fields

fix_modify AtC fields command

=============================

Syntax

""""""

.. parsed-literal::

   fix_modify <AtC fixID> fields <all|none>

   fix_modify <AtC fixID> fields <add|delete> <list_of_fields>

* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance

* fields = name of the AtC sub-command

* *all* or *none* = output all or no fields

* *add* or *delete* = add or delete the listed output fields

* list_of_fields = one or more of the fields listed below:

  - density : mass per unit volume

  - displacement : displacement vector

  - momentum : momentum per unit volume

  - velocity : defined by momentum divided by density

  - projected_velocity : simple kernel estimation of atomic velocities

  - temperature : temperature derived from the relative atomic kinetic energy

  - kinetic_temperature : temperature derived from the full kinetic energy

  - number_density : simple kernel estimation of number of atoms per unit volume

  - stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or 1st Piola-Kirchhoff stress tensor for lagrangian analysis

  - transformed_stress : 1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis

  - heat_flux : spatial heat flux vector for eulerian, or referential heat flux vector for lagrangian

  - potential_energy : potential energy per unit volume

  - kinetic_energy : kinetic energy per unit volume

  - thermal_energy : thermal energy (kinetic energy - continuum kinetic energy) per unit volume

  - internal_energy : total internal energy (potential + thermal) per unit volume

  - energy : total energy (potential + kinetic) per unit volume

  - number_density : number of atoms per unit volume

  - eshelby_stress : configurational stress (energy-momentum) tensor defined by [Eshelby]_

  - vacancy_concentration : volume fraction of vacancy content

  - type_concentration : volume fraction of a specific atom type

Examples

""""""""

.. code-block:: LAMMPS

   fix_modify AtC fields add velocity temperature

Description

"""""""""""

Allows modification of the fields calculated and output by the AtC

transfer class.  The commands are cumulative, e.g.:

.. code-block:: LAMMPS

   fix_modify AtC fields none

   fix_modify AtC fields add velocity temperature

will only output the velocity and temperature fields.

Restrictions

""""""""""""

Must be used with :doc:`fix atc hardy <fix_atc>`.  Currently, the stress

and heat flux formulas are only correct for central force potentials,

e.g. Lennard-Jones and EAM but not Stillinger-Weber.

Related AtC commands

""""""""""""""""""""

- :ref:`fix_modify AtC command overview <atc_fix_modify>`

- :doc:`fix_modify AtC gradients <atc_hardy_gradients>`

- :doc:`fix_modify AtC rates <atc_hardy_rates>`

- :doc:`fix_modify AtC computes <atc_hardy_computes>`

Default

"""""""

By default, no fields are output.

References

""""""""""

.. [Eshelby] J.D. Eshelby, Philos. Trans. Royal Soc. London A, Math. Phys. Sci., Vol. 244, No. 877 (1951) pp. 87-112; J. Elasticity, Vol. 5, Nos. 3-4 (1975) pp. 321-335]

.. index:: fix_modify AtC gradients

fix_modify AtC gradients command

================================

Syntax

""""""

.. parsed-literal::

   fix_modify <AtC fixID> gradients <add|delete> <list_of_fields>

* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance

* gradients = name of the AtC sub-command

* *add* or *delete* = select whether to add or delete calculation of gradients for the listed output fields

* list_of_fields = one or more of the fields listed below:

  - density : mass per unit volume

  - displacement : displacement vector

  - momentum : momentum per unit volume

  - velocity : defined by momentum divided by density

  - projected_velocity : simple kernel estimation of atomic velocities

  - temperature : temperature derived from the relative atomic kinetic energy

  - kinetic_temperature : temperature derived from the full kinetic energy

  - number_density : simple kernel estimation of number of atoms per unit volume

  - stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or 1st Piola-Kirchhoff stress tensor for lagrangian analysis

  - transformed_stress : 1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis

  - heat_flux : spatial heat flux vector for eulerian, or referential heat flux vector for lagrangian

  - potential_energy : potential energy per unit volume

  - kinetic_energy : kinetic energy per unit volume

  - thermal_energy : thermal energy (kinetic energy - continuum kinetic energy) per unit volume

  - internal_energy : total internal energy (potential + thermal) per unit volume

  - energy : total energy (potential + kinetic) per unit volume

  - number_density : number of atoms per unit volume

  - eshelby_stress : configurational stress (energy-momentum) tensor defined by [Eshelby]_

  - vacancy_concentration : volume fraction of vacancy content

  - type_concentration : volume fraction of a specific atom type

Examples

""""""""

.. code-block:: LAMMPS

   fix_modify AtC gradients add temperature velocity stress

   fix_modify AtC gradients delete velocity

Description

"""""""""""

Requests calculation and output of gradients of the fields from the AtC

transfer class.  These gradients will be with regard to spatial or

material coordinate for Eulerian or Lagrangian analysis, respectively,

as specified by :doc:`fix_modify AtC atom_element_map <atc_atom_element_map>`

Restrictions

""""""""""""

Must be used with :doc:`fix atc hardy <fix_atc>`.

Related AtC commands

""""""""""""""""""""

- :ref:`fix_modify AtC command overview <atc_fix_modify>`

- :doc:`fix_modify AtC atom_element_map <atc_atom_element_map>`

- :doc:`fix_modify AtC fields <atc_hardy_fields>`

- :doc:`fix_modify AtC rates <atc_hardy_rates>`

Default

"""""""

None.

.. index:: fix_modify AtC kernel

fix_modify AtC kernel command

=============================

Syntax

""""""

.. parsed-literal::

   fix_modify <AtC fixID> kernel <type> <parameters>

* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance

* kernel = name of the AtC sub-command

* type = *step* or *cell* or *cubic_bar* or *cubic_cylinder* or

  *cubic_sphere* or *quartic_bar* or *quartic_cylinder* or

  *quartic_sphere*

* the following parameter(s) are required for each kernel:

  - *step* : <radius>

  - *cell* : <hx> <hy> <hz> or <h>

  - *cubic_bar* : <half_width>

  - *cubic_cylinder* : <radius>

  - *cubic_sphere* : <radius>

  - *quartic_bar* : <half_width>

  - *quartic_cylinder* : <radius>

  - *quartic_sphere* : <radius>

Examples

""""""""

.. code-block:: LAMMPS

   fix_modify AtC kernel cell 1.0 1.0 1.0

   fix_modify AtC kernel quartic_sphere 10.0

Description

"""""""""""

Sets the localization kernel type and parameters for :doc:`fix atc hardy <fix_atc>`.

Restrictions

""""""""""""

Must be used with :doc:`fix atc hardy <fix_atc>`.  For bar kernel types,

half-width oriented along x-direction.  For cylinder kernel types,

cylindrical axis is assumed to be in z-direction.

Related AtC commands

""""""""""""""""""""

- :ref:`fix_modify AtC command overview <atc_fix_modify>`

- :doc:`fix_modify AtC fields <atc_hardy_fields>`

- :doc:`fix_modify AtC gradients <atc_hardy_gradients>`

- :doc:`fix_modify AtC rates <atc_hardy_rates>`

- :doc:`fix_modify AtC computes <atc_hardy_computes>`

Default

"""""""

None.

.. index:: fix_modify AtC rates

fix_modify AtC rates command

================================

Syntax

""""""

.. parsed-literal::

   fix_modify <AtC fixID> rates <add|delete> <list_of_fields>

* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance

* rates = name of the AtC sub-command

* *add* or *delete* = select whether to add or delete calculation of rates for the listed output fields

* list_of_fields = one or more of the fields listed below:

  - density : mass per unit volume

  - displacement : displacement vector

  - momentum : momentum per unit volume

  - velocity : defined by momentum divided by density

  - projected_velocity : simple kernel estimation of atomic velocities

  - temperature : temperature derived from the relative atomic kinetic energy

  - kinetic_temperature : temperature derived from the full kinetic energy

  - number_density : simple kernel estimation of number of atoms per unit volume

  - stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or 1st Piola-Kirchhoff stress tensor for lagrangian analysis

  - transformed_stress : 1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis

  - heat_flux : spatial heat flux vector for eulerian, or referential heat flux vector for lagrangian

  - potential_energy : potential energy per unit volume

  - kinetic_energy : kinetic energy per unit volume

  - thermal_energy : thermal energy (kinetic energy - continuum kinetic energy) per unit volume

  - internal_energy : total internal energy (potential + thermal) per unit volume

  - energy : total energy (potential + kinetic) per unit volume

  - number_density : number of atoms per unit volume

  - eshelby_stress : configurational stress (energy-momentum) tensor defined by [Eshelby]_

  - vacancy_concentration : volume fraction of vacancy content

  - type_concentration : volume fraction of a specific atom type

Examples

""""""""

.. code-block:: LAMMPS

   fix_modify AtC rates add temperature velocity stress

   fix_modify AtC rates delete stress

Description

"""""""""""

Requests calculation and output of rates (time derivatives) of the

fields from the AtC transfer class.  For Eulerian analysis (see

:doc:`fix_modify AtC atom_element_map <atc_atom_element_map>`) these

rates are the partial time derivatives of the nodal fields, not the full

(material) time derivatives.

Restrictions

""""""""""""

Must be used with :doc:`fix atc hardy <fix_atc>`.

Related AtC commands

""""""""""""""""""""

- :ref:`fix_modify AtC command overview <atc_fix_modify>`

- :doc:`fix_modify AtC atom_element_map <atc_atom_element_map>`

- :doc:`fix_modify AtC fields <atc_hardy_fields>`

- :doc:`fix_modify AtC fields <atc_hardy_gradients>`

Default

"""""""

None.