next chunk of converted html files

doc/src/Howto_viz.rst

@@ -19,7 +19,7 @@ A Python-based toolkit distributed by our group can read native LAMMPS
 dump files, including custom dump files with additional columns of
 user-specified atom information, and convert them to various formats
 or pipe them into visualization software directly.  See the `Pizza.py WWW site <pizza_>`_ for details.  Specifically, Pizza.py can convert
-LAMMPS dump files into PDB, XYZ, `Ensight <ensight_>`_, and VTK formats.
+LAMMPS dump files into PDB, XYZ, `EnSight <ensight_>`_, and VTK formats.
 Pizza.py can pipe LAMMPS dump files directly into the Raster3d and
 RasMol visualization programs.  Pizza.py has tools that do interactive
 3d OpenGL visualization and one that creates SVG images of dump file
@@ -27,6 +27,6 @@ snapshots.
 
 .. _pizza: https://pizza.sandia.gov
 
-.. _ensight: https://daac.hpc.mil/software/EnSight/
+.. _ensight: https://www.ansys.com/products/fluids/ansys-ensight
 
 .. _atomeye: http://li.mit.edu/Archive/Graphics/A/

doc/src/atc_electron_integration.rst

@@ -12,7 +12,7 @@ Syntax
 
 * AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
 * extrinsic electron_integration = name of the AtC sub-command
-* integration_type = *explicit* or *implicit* or *steadydescriptor*
+* integration_type = *explicit* or *implicit* or *steady*
 * num_subcycle_steps = number of subcycle steps for the electron time integration (optional)
 
 

doc/src/atc_equilibrium_start.rst

@@ -0,0 +1,44 @@
+.. index:: fix_modify AtC equilibrium_start
+
+fix_modify AtC equilibrium_start command
+========================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> equilibrium_start <on|off>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* equilibrium_start = name of the AtC sub-command
+* *exponential* or *step* or *no_filter* = select type of filter
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC equilibrium_start on
+
+Description
+"""""""""""
+
+Starts filtered calculations assuming they start in equilibrium,
+i.e. perfect finite element force balance.
+
+Restrictions
+""""""""""""
+
+Only for use with these specific transfers: thermal, two_temperature
+
+Related AtC commands
+""""""""""""""""""""
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+- :doc:`fix_modify AtC filter <atc_time_filter>`
+- :doc:`fix_modify AtC filter scale <atc_filter_scale>`
+
+Default
+"""""""
+
+None.

doc/src/atc_extrinsic_exchange.rst

@@ -0,0 +1,45 @@
+.. index:: fix_modify AtC extrinsic exchange
+
+fix_modify AtC extrinsic exchange command
+=========================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> extrinsic exchange <on|off>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* extrinsic exchange = name of the AtC sub-command
+* *on* or *off* = set state of energy exchange
+
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC extrinsic exchange on
+
+Description
+"""""""""""
+
+Switches energy exchange between the MD system and the electron system
+on or off
+
+Restrictions
+""""""""""""
+
+For use only with the two_temperature type of the AtC fix (see
+:doc:`fix atc <fix_atc>` command)
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+
+Default
+"""""""
+
+*on*

doc/src/atc_filter_scale.rst

@@ -0,0 +1,44 @@
+.. index:: fix_modify AtC filter scale
+
+fix_modify AtC filter scale command
+===================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> filter scale <scale>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* filter scale = name of the AtC sub-command
+* scale = characteristic times scale of the filter
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC filter scale 10.0
+
+Description
+"""""""""""
+
+Sets the time scale for MD dynamics filter to construct a more
+appropriate continuous field.
+
+Restrictions
+""""""""""""
+
+Only for use with these specific transfers: thermal, two_temperature
+
+Related AtC commands
+""""""""""""""""""""
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+- :doc:`fix_modify AtC filter <atc_time_filter>`
+- :doc:`fix_modify AtC filter type <atc_filter_type>`
+
+Default
+"""""""
+
+0.0

doc/src/atc_filter_type.rst

@@ -0,0 +1,43 @@
+.. index:: fix_modify AtC filter type
+
+fix_modify AtC filter type command
+===================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> filter type <exponential|step|no_filter>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* filter type = name of the AtC sub-command
+* *exponential* or *step* or *no_filter* = select type of filter
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC filter type exponential
+
+Description
+"""""""""""
+
+Specifies the type of time filter used.
+
+Restrictions
+""""""""""""
+
+Only for use with these specific transfers: thermal, two_temperature
+
+Related AtC commands
+""""""""""""""""""""
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+- :doc:`fix_modify AtC filter <atc_time_filter>`
+- :doc:`fix_modify AtC filter scale <atc_filter_scale>`
+
+Default
+"""""""
+
+None.

doc/src/atc_lumped_lambda_solve.rst

@@ -0,0 +1,41 @@
+.. index:: fix_modify AtC control lumped_lambda_solve
+
+fix_modify AtC control lumped_lambda_solve command
+==================================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> control lumped_lambda_solve <on|off>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* control lumped_lambda_solve = name of the AtC sub-command
+* *on* or *off* = Toggles state of lumped matrix
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC control lumped_lambda_solve on
+
+Description
+"""""""""""
+
+Command select whether to use or not use lumped matrix for lambda solve.
+
+Restrictions
+""""""""""""
+
+None.
+
+Related AtC commands
+""""""""""""""""""""
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+
+Default
+"""""""
+
+off

doc/src/atc_mask_direction.rst

@@ -0,0 +1,38 @@
+.. index:: fix_modify AtC control mask_direction
+
+fix_modify AtC control mask_direction command
+=============================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> control mask_direction <direction> <on|off>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* control mask_direction = name of the AtC sub-command
+* direction = select direction
+* *on* or *off* = Toggles state
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC control mask_direction 0 on
+
+Description
+"""""""""""
+
+Command to mask out certain dimensions from the atomic regulator
+
+Restrictions
+""""""""""""
+
+None.
+
+Related AtC commands
+""""""""""""""""""""
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+

doc/src/atc_output.rst

@@ -0,0 +1,59 @@
+.. index:: fix_modify AtC output
+
+fix_modify AtC output command
+=============================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> output <filename_prefix> <frequency> [text|full_text|binary|vector_components|tensor_components]
+   fix_modify <AtC fixID> output index [step|time]
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* *output* or *output index* = name of the AtC sub-command
+* filename_prefix = prefix for data files (for *output*)
+* frequency = frequency of output in time-steps (for *output*)
+* optional keywords for *output*:
+  - text = creates text output of index, step and nodal variable values for unique nodes
+  - full_text = creates text output index, nodal id, step, nodal coordinates and nodal variable values for unique and image nodes
+  - binary = creates binary EnSight output
+  - vector_components = outputs vectors as scalar components
+  - tensor_components = outputs tensor as scalar components (for use with ParaView)
+* *step* or *time* = index output by step or by time (for *output index*)
+
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC output heatFE 100
+   fix_modify AtC output hardyFE 1 text tensor_components
+   fix_modify AtC output hardyFE 10 text binary tensor_components
+   fix_modify AtC output index step
+
+
+Description
+"""""""""""
+
+Creates text and/or binary (EnSight, "gold" format) output of nodal/mesh
+data which is transfer/physics specific. Output indexing by step or time
+is possible.
+
+Restrictions
+""""""""""""
+
+None.
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+- :doc:`fix atc command <fix_atc>`
+
+Default
+"""""""
+
+No default format. Output indexed by time.

doc/src/atc_poisson_solver.rst

@@ -0,0 +1,45 @@
+.. index:: fix_modify AtC poisson_solver
+
+fix_modify AtC poisson_solver command
+=====================================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> poisson_solver mesh create <nx> <ny> <nz> <region-ID> <f|p> <f|p> <f|p>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* poisson_solver = name of the AtC sub-command
+* *nx* *ny* *nz* = number of elements in x, y, and z
+* region-id = id of region to be meshed
+* *f* or *p* = periodicity flags for x, y, and z
+
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC poisson_solver mesh create 10 1 1 feRegion p p p
+
+Description
+"""""""""""
+
+Creates a uniform mesh in a rectangular region.
+
+Restrictions
+""""""""""""
+
+Creates only uniform rectangular grids in rectangular regions.
+
+Related AtC commands
+""""""""""""""""""""
+
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+
+Default
+"""""""
+
+None.

doc/src/atc_time_filter.rst

@@ -0,0 +1,46 @@
+.. index:: fix_modify AtC filter
+
+fix_modify AtC filter command
+=============================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix_modify <AtC fixID> filter <on|off|equilibrate>
+
+* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
+* filter = name of the AtC sub-command
+* *on* or *off* or *equilibrate* = Select state of filter
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix_modify AtC filter on
+
+Description
+"""""""""""
+
+Filters the MD dynamics to construct a more appropriate continuous
+field. Equilibrating first filters the time derivatives without changing
+the dynamics to provide a better initial condition to the filtered
+dynamics.
+
+Restrictions
+""""""""""""
+
+Only for use with these specific transfers: thermal, two_temperature
+
+Related AtC commands
+""""""""""""""""""""
+- :ref:`fix_modify AtC command overview <atc_fix_modify>`
+- :doc:`fix_modify AtC filter scale <atc_filter_scale>`
+- :doc:`fix_modify AtC equilibrium_start <atc_equilibrium_start>`
+
+Default
+"""""""
+
+off

doc/src/fix_atc.rst

@@ -184,18 +184,18 @@ conditions.
 * :doc:`fix_modify AtC control thermal <atc_control_thermal>`
 * :doc:`fix_modify AtC control momentum <atc_control_momentum>`
 * :doc:`fix_modify AtC control localized_lambda <atc_control_localized_lambda>`
-* `fix_modify AtC control lumped_lambda_solve <USER/atc/man_lumped_lambda_solve.html>`_
-* `fix_modify AtC control mask_direction <USER/atc/man_mask_direction.html>`_ control
-* `fix_modify AtC filter <USER/atc/man_time_filter.html>`_
-* `fix_modify AtC filter scale <USER/atc/man_filter_scale.html>`_
-* `fix_modify AtC filter type <USER/atc/man_filter_type.html>`_
-* `fix_modify AtC equilibrium_start <USER/atc/man_equilibrium_start.html>`_
-* `fix_modify AtC extrinsic exchange <USER/atc/man_extrinsic_exchange.html>`_
-* `fix_modify AtC poisson_solver <USER/atc/man_poisson_solver.html>`_
+* :doc:`fix_modify AtC control lumped_lambda_solve <atc_lumped_lambda_solve>`
+* :doc:`fix_modify AtC control mask_direction <atc_mask_direction>`
+* :doc:`fix_modify AtC filter <atc_time_filter>`
+* :doc:`fix_modify AtC filter scale <atc_filter_scale>`
+* :doc:`fix_modify AtC filter type <atc_filter_type>`
+* :doc:`fix_modify AtC equilibrium_start <atc_equilibrium_start>`
+* :doc:`fix_modify AtC extrinsic exchange <atc_extrinsic_exchange>`
+* :doc:`fix_modify AtC poisson_solver <atc_poisson_solver>`
 
 *fix_modify* commands for output:
 
-* `fix_modify AtC output <USER/atc/man_output.html>`_
+* :doc:`fix_modify AtC output <atc_output>`
 * `fix_modify AtC output nodeset <USER/atc/man_output_nodeset.html>`_
 * `fix_modify AtC output elementset <USER/atc/man_output_elementset.html>`_
 * `fix_modify AtC output boundary_integral <USER/atc/man_boundary_integral.html>`_

doc/utils/sphinx-config/false_positives.txt

@@ -772,6 +772,7 @@ engrot
 engtrans
 engvib
 enobonds
+EnSight
 enthalpy
 enums
 envoke
@@ -2164,6 +2165,7 @@ parameterizations
 parameterize
 parameterized
 params
+ParaView
 parmin
 Parrinello
 Partay
@@ -2255,6 +2257,7 @@ pN
 png
 Podhorszki
 Poiseuille
+poisson
 Polak
 polarizabilities
 polarizability