final batch of converted AtC doc files

.. index:: fix_modify AtC add_molecule

fix_modify AtC add_molecule command

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

Syntax

""""""

.. parsed-literal::

   fix_modify <AtC fixID> add_molecule <small|large> <tag> <group-ID>

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

* add_molecule = name of the AtC sub-command

* *small* or *large* = can be *small* if molecule size < cutoff radius, must be *large* otherwise

* tag = tag for tracking a molecule

* *group-ID* = LAMMPS defined group-ID

Examples

""""""""

.. code-block:: LAMMPS

   group WATERGROUP type 1 2

   fix_modify AtC add_molecule small water WATERGROUP

Description

"""""""""""

Associates a tag with all molecules corresponding to a specified group.

Restrictions

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

None.

Related AtC commands

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

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

- :doc:`fix_modify AtC add_species <atc_add_species>`

- :doc:`fix_modify AtC remove_species <atc_remove_species>`

- :doc:`fix_modify AtC remove_molecule <atc_remove_molecule>`

Default

"""""""

None.

.. index:: fix_modify AtC add_species

fix_modify AtC add_species command

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

Syntax

""""""

.. parsed-literal::

   fix_modify <AtC fixID> add_species <tag> <group|type> <ID>

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

* add_species = name of the AtC sub-command

* tag = tag for tracking a species

* *group* or *type* = LAMMPS defined group or type of atoms

* ID = name of group or type number

Examples

""""""""

.. code-block:: LAMMPS

   fix_modify AtC add_species gold type 1

   group GOLDGROUP type 1

   fix_modify AtC add_species gold group GOLDGROUP

Description

"""""""""""

Associates a tag with all atoms of a specified type or within a specified group.

Restrictions

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

None.

Related AtC commands

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

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

- :doc:`fix_modify AtC add_molecule <atc_add_molecule>`

- :doc:`fix_modify AtC remove_species <atc_remove_species>`

- :doc:`fix_modify AtC remove_molecule <atc_remove_molecule>`

Default

"""""""

None.

.. index:: fix_modify AtC atomic_charge

fix_modify AtC atomic_charge command

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

Syntax

""""""

.. parsed-literal::

   fix_modify <AtC fixID> <include|omit> atomic_charge

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

* *include* or *omit* = switch to activate/deactivate inclusion of intrinsic atomic charge in ATC

* atomic_charge = name of the AtC sub-command

Examples

""""""""

.. code-block:: LAMMPS

   fix_modify AtC include atomic_charge

Description

"""""""""""

Determines whether AtC tracks the total charge as a finite element

field.

Restrictions

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

Required for: *electrostatics*

Related AtC commands

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

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

Default

"""""""

If the atom charge is defined, default is on, otherwise default is off.

.. index:: fix_modify AtC boundary_dynamics

fix_modify AtC boundary_dynamics command

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

Syntax

""""""

.. parsed-literal::

   fix_modify <AtC fixID> boundary_dynamics <on|damped_harmonic|prescribed|coupled|none>

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

* boundary_dynamics = name of the AtC sub-command

* *on* or *damped_harmonic* *prescribed* *coupled* *none*

Description

"""""""""""

Sets different schemes for controlling boundary atoms.  *on* will integrate

the boundary atoms using the velocity-verlet algorithm.  *damped_harmonic*

uses a mass/spring/dashpot for the boundary atoms with added arguments

of the damping and spring constants followed by the ratio of the

boundary type mass to the desired mass.  *prescribed* forces the boundary

atoms to follow the finite element displacement.  *coupled* does the same.

Restrictions

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

Boundary atoms must be specified.  When using swaps between internal and

boundary atoms, the initial configuration must have already correctly

partitioned the two.

Related AtC commands

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

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

Default

"""""""

*prescribed on*

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

* consistent_fe_initialization = name of the AtC sub-command

* *on* or *off* = switch to activiate/deactiviate the initial setting of FE intrinsic field to match the projected MD field

* *on* or *off* = switch to activate/deactivate the initial setting of the FE intrinsic field to match the projected MD field

Examples

""""""""