next batch of converted files

doc/src/atc_atom_element_map.rst

@@ -21,7 +21,7 @@ Examples
 
 .. code-block:: LAMMPS
 
-   fix_modify atc atom_element_map eulerian 100
+   fix_modify AtC atom_element_map eulerian 100
 
 Description
 """""""""""

doc/src/atc_atom_weight.rst

@@ -0,0 +1,56 @@
+.. index:: fix_modify AtC atom_weight
+
+fix_modify AtC atom_weight command
+==================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> atom_weight <method> <args>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* atom_weight = name of the AtC sub-command
+* method = *constant* or *lattice* or *element* or *region* or *group* or *read_in*
+
+  - *constant* <group-ID> <value>: atoms in specified group are assigned the constant value given
+  - *lattice*\ : volume per atom for specified lattice type (e.g. fcc) and parameter
+  - *element*\ : element volume divided among atoms within element
+  - *region*\ : volume per atom determined based on the atom count in the MD regions and their volumes. Note: meaningful only if atoms completely fill all the regions.
+  - *group*\ : volume per atom determined based on the atom count in a group and its volume
+  - *node*\ : (undocumented)
+  - *node_element*\ : (undocumented)
+  - *read_in*\ <filename>: list of values for atoms are read-in from specified file
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC atom_weight constant myatoms 11.8
+   fix_modify AtC atom_weight lattice
+   fix_modify AtC atom_weight read-in atm_wt_file.txt
+
+Description
+"""""""""""
+
+Command for assigning the value of atomic weights used for atomic
+integration in atom-continuum coupled simulations.
+
+
+Restrictions
+""""""""""""
+
+The use of the lattice option requires a lattice type and parameter is already specified.
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+
+Default
+"""""""
+
+*lattice*
+

doc/src/atc_boundary_faceset.rst

@@ -0,0 +1,47 @@
+.. index:: fix_modify AtC boundary_faceset
+
+fix_modify AtC boundary_faceset command
+=======================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> boundary_faceset <is|add> <faceset_name>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* boundary_faceset = name of the AtC sub-command
+* *is* or *add* = select whether to select or add a faceset
+* faceset_name = name of the faceset
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC boundary_faceset is obndy
+
+Description
+"""""""""""
+
+This command species the faceset name when using a faceset to compute
+the MD/FE boundary fluxes. The faceset must already exist.
+
+Restrictions
+""""""""""""
+
+This is only valid when *fe_md_boundary* is set to *faceset*\ .
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+- :doc:`fix_modify AtC fe_md_boundary <atc_fe_md_boundary>`
+- :doc:`fix_modify AtC mesh create_faceset box <atc_mesh_create_faceset_box>`
+- :doc:`fix_modify AtC mesh create_faceset plane <atc_mesh_create_faceset_plane>`
+
+  Default
+"""""""
+
+None.

doc/src/atc_consistent_fe_initialization.rst

@@ -0,0 +1,46 @@
+.. index:: fix_modify AtC consistent_fe_initialization
+
+fix_modify AtC consistent_fe_initialization command
+===================================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> consistent_fe_initialization <on|off>
+
+* 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
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC consistent_fe_initialization on
+
+Description
+"""""""""""
+
+Determines whether AtC initializes FE intrinsic fields (e.g.,
+temperature) to match the projected MD values. This is particularly
+useful for fully overlapping simulations.
+
+Restrictions
+""""""""""""
+
+Can be used with: *thermal*, *two_temperature*.
+Cannot be used with time filtering on.
+Does not include boundary nodes.
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+
+Default
+"""""""
+
+Default is *off*

doc/src/atc_fe_md_boundary.rst

@@ -0,0 +1,52 @@
+.. index:: fix_modify AtC fe_md_boundary
+
+fix_modify AtC fe_md_boundary command
+=====================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> fe_md_boundary <faceset|interpolate|no_boundary>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* fe_md_boundary = name of the AtC sub-command
+* *faceset* or *interpolate* or *no_boundary*
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC fe_md_boundary interpolate
+
+Description
+"""""""""""
+
+Specifies different methods for computing fluxes between between the MD
+and FE integration regions.  Faceset defines a faceset separating the MD
+and FE regions and uses finite element face quadrature to compute the
+flux.  Interpolate uses a reconstruction scheme to approximate the flux,
+which is more robust but less accurate if the MD/FE boundary does
+correspond to a faceset.  No boundary results in no fluxes between the
+systems being computed.
+
+
+Restrictions
+""""""""""""
+
+If *faceset* is used, all the AtC non-boundary atoms must lie within and
+completely fill the domain enclosed by the faceset.
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+- :doc:`fix_modify AtC mesh create_faceset box <atc_mesh_create_faceset_box>`
+- :doc:`fix_modify AtC mesh create_faceset plane <atc_mesh_create_faceset_plane>`
+
+Default
+"""""""
+
+*interpolate*

doc/src/atc_hardy_on_the_fly.rst

@@ -8,7 +8,7 @@ Syntax
 
 .. parsed-literal::
 
-   fix_modify <AtC fixID> on_the_fly on_the_fly <bond|kernel> <on|off>
+   fix_modify <AtC fixID> on_the_fly <bond|kernel> <on|off>
 
 * AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
 * on_the_fly = name of the AtC sub-command

doc/src/atc_initial.rst

@@ -21,7 +21,7 @@ Examples
 
 .. code-block:: LAMMPS
 
-   fix_modify atc initial temperature groupNAME 10.
+   fix_modify AtC initial temperature groupNAME 10.
 
 Description
 """""""""""

doc/src/atc_kernel_bandwidth.rst

@@ -0,0 +1,47 @@
+.. index:: fix_modify AtC kernel_bandwidth
+
+fix_modify AtC kernel_bandwidth command
+=======================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> kernel_bandwidth <value>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* kernel_bandwidth = name of the AtC sub-command
+* value = new bandwidth value
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC kernel_bandwidth 8
+
+Description
+"""""""""""
+
+Sets a maximum parallel bandwidth for the kernel functions during
+parallel communication. If the command is not issued, the default will
+be to assume the bandwidth of the kernel matrix corresponds to the
+number of sampling locations.
+
+
+Restrictions
+""""""""""""
+
+Only is used if kernel functions are being used.
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+
+Default
+"""""""
+
+Number of sample locations.
+

doc/src/atc_pair_interactions.rst

@@ -0,0 +1,47 @@
+.. index:: fix_modify AtC pair_interactions
+
+fix_modify AtC pair_interactions command
+========================================
+
+fix_modify AtC bond_interactions command
+========================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> pair_interactions <on|off>
+   fix_modify <AtC fixID> bond_interactions <on|off>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* *pair_interactions* or *bond_interactions* = name of the AtC sub-command
+* *on* or *off* = activate or deactivate
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC pair_interactions off
+   fix_modify AtC bond_interactions on
+
+Description
+"""""""""""
+
+Include bonds and/or pairs in stress and heat flux computations.
+
+Restrictions
+""""""""""""
+
+None.
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+
+Default
+"""""""
+
+*pair_interactions*\ : on, *bond_interactions*\ : off

doc/src/atc_reset_atomic_reference.rst

@@ -0,0 +1,46 @@
+.. index:: fix_modify AtC reset_atomic_reference_positions
+
+fix_modify AtC reset_atomic_reference_positions command
+=======================================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> reset_atomic_reference_positions
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* reset_atomic_reference_positions = name of the AtC sub-command
+
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC reset_atomic_reference_positions
+
+Description
+"""""""""""
+
+Resets the atomic positions ATC uses to perform point to field
+operations. In can be used to use perfect lattice sites in ATC but a
+thermalized or deformed lattice in LAMMPS.
+
+
+Restrictions
+""""""""""""
+
+None.
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+
+Default
+"""""""
+
+None
+

doc/src/atc_reset_time.rst

@@ -0,0 +1,44 @@
+.. index:: fix_modify AtC reset_time
+
+fix_modify AtC reset_time command
+=================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> reset_time <value>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* reset_time = name of the AtC sub-command
+* value = new time value
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC reset_time 0.0
+
+Description
+"""""""""""
+
+Resets the simulation time counter.
+
+
+Restrictions
+""""""""""""
+
+None.
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+
+Default
+"""""""
+
+None
+

doc/src/atc_sample_frequency.rst

@@ -0,0 +1,44 @@
+.. index:: fix_modify AtC sample_frequency
+
+fix_modify AtC sample_frequency command
+=======================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> sample_frequency <freq>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* sample_frequency = name of the AtC sub-command
+* freq = frequency to sample fields in number of steps
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC sample_frequency 10
+
+Description
+"""""""""""
+
+Specifies a frequency at which fields are computed for the case where
+time filters are being applied.
+
+Restrictions
+""""""""""""
+
+Must be used with :doc:`fix atc hardy <fix_atc>` and is only relevant when time filters are being used.
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+
+Default
+"""""""
+
+None.
+

doc/src/atc_set_reference_pe.rst

@@ -0,0 +1,50 @@
+.. index:: fix_modify AtC set reference_potential_energy
+
+fix_modify AtC set reference_potential_energy command
+=====================================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> set reference_potential_energy [<value|filename>]
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* set reference_potential_energy = name of the AtC sub-command
+* value = optional user specified zero point for PE in native LAMMPS energy units
+* filename = optional user specified string for file of nodal PE values to be read-in
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC set reference_potential_energy
+   fix_modify AtC set reference_potential_energy -0.05
+   fix_modify AtC set reference_potential_energy myPEvalues 
+
+Description
+"""""""""""
+
+Used to set various quantities for the post-processing algorithms. It
+sets the zero point for the potential energy density using the value
+provided for all nodes, or from the current configuration of the lattice
+if no value is provided, or values provided within the specified
+filename.
+
+Restrictions
+""""""""""""
+
+Must be used with :doc:`fix atc hardy <fix_atc>` or :doc:`fix atc field <fix_atc>`.
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+
+Default
+"""""""
+
+Defaults to the LAMMPS zero point i.e. isolated atoms.
+

doc/src/atc_time_integration.rst

@@ -20,7 +20,7 @@ Examples
 
 .. code-block:: LAMMPS
 
-   fix_modify atc time_integration fractional_step
+   fix_modify AtC time_integration fractional_step
 
 
 Description

doc/src/atc_write_atom_weights.rst

@@ -0,0 +1,45 @@
+.. index:: fix_modify AtC write_atom_weights
+
+fix_modify AtC write_atom_weights command
+=========================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> write_atom_weights <filename> <frequency>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* write_atom_weights = name of the AtC sub-command
+* filename = name of file that atomic weights are written to
+* frequency = how often writes will occur
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC write_atom_weights atm_wt_file.txt 10
+
+Description
+"""""""""""
+
+Command for writing the values of atomic weights to a specified file.
+
+
+Restrictions
+""""""""""""
+
+None.
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+
+Default
+"""""""
+
+None
+

doc/src/fix_atc.rst

@@ -212,20 +212,21 @@ conditions.
 * :doc:`fix_modify AtC rates <atc_hardy_rates>`
 * :doc:`fix_modify AtC computes <atc_hardy_computes>`
 * :doc:`fix_modify AtC on_the_fly <atc_hardy_on_the_fly>`
-* `fix_modify AtC pair_interactions/bond_interactions <USER/atc/man_pair_interactions.html>`_
+* :doc:`fix_modify AtC pair/bond_interactions <atc_pair_interactions>`
-* `fix_modify AtC sample_frequency <USER/atc/man_sample_frequency.html>`_
+* :doc:`fix_modify AtC sample_frequency <atc_sample_frequency>`
-* `fix_modify AtC set <USER/atc/man_set.html>`_
+* :doc:`fix_modify AtC set <atc_set_reference_pe>`
 
 miscellaneous *fix_modify* commands:
 
 * :doc:`fix_modify AtC atom_element_map <atc_atom_element_map>`
-* `fix_modify AtC atom_weight <USER/atc/man_atom_weight.html>`_
+* :doc:`fix_modify AtC atom_weight <atc_atom_weight>`
-* `fix_modify AtC write_atom_weights <USER/atc/man_write_atom_weights.html>`_
+* :doc:`fix_modify AtC write_atom_weights <atc_write_atom_weights>`
-* `fix_modify AtC reset_time <USER/atc/man_reset_time.html>`_
+* :doc:`fix_modify AtC kernel_bandwidth <atc_kernel_bandwidth>`
-* `fix_modify AtC reset_atomic_reference_positions <USER/atc/man_reset_atomic_reference_positions.html>`_
+* :doc:`fix_modify AtC reset_time <atc_reset_time>`
-* `fix_modify AtC fe_md_boundary <USER/atc/man_fe_md_boundary.html>`_
+* :doc:`fix_modify AtC reset_atomic_reference_positions <atc_reset_atomic_reference>`
-* `fix_modify AtC boundary_faceset <USER/atc/man_boundary_faceset.html>`_
+* :doc:`fix_modify AtC fe_md_boundary <atc_fe_md_boundary>`
-* `fix_modify AtC consistent_fe_initialization <USER/atc/man_consistent_fe_initialization.html>`_
+* :doc:`fix_modify AtC boundary_faceset <atc_boundary_faceset>`
+* :doc:`fix_modify AtC consistent_fe_initialization <atc_consistent_fe_initialization>`
 * `fix_modify AtC mass_matrix <USER/atc/man_mass_matrix.html>`_
 * `fix_modify AtC material <USER/atc/man_material.html>`_
 * `fix_modify AtC atomic_charge <USER/atc/man_atomic_charge.html>`_