next chunk of converted atc doc files

doc/src/atc_hardy_computes.rst

@@ -0,0 +1,54 @@
+.. 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.

doc/src/atc_hardy_fields.rst

@@ -0,0 +1,86 @@
+.. 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]

doc/src/atc_hardy_gradients.rst

@@ -0,0 +1,74 @@
+.. 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.

doc/src/atc_hardy_kernel.rst

@@ -0,0 +1,64 @@
+.. 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.

doc/src/atc_hardy_rates.rst

@@ -0,0 +1,74 @@
+.. 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.

doc/src/fix_atc.rst

@@ -206,11 +206,11 @@ conditions.
 
 *fix_modify* commands for post-processing:
 
-* `fix_modify AtC kernel <USER/atc/man_hardy_kernel.html>`_
-* `fix_modify AtC fields <USER/atc/man_hardy_fields.html>`_
-* `fix_modify AtC grdients <USER/atc/man_hardy_gradients.html>`_
-* `fix_modify AtC rates <USER/atc/man_hardy_rates.html>`_
-* `fix_modify AtC computes <USER/atc/man_hardy_computes.html>`_
+* :doc:`fix_modify AtC kernel <atc_hardy_kernel>`
+* :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>`
 * `fix_modify AtC on_the_fly <USER/atc/man_hardy_on_the_fly.html>`_
 * `fix_modify AtC pair_interactions/bond_interactions <USER/atc/man_pair_interactions.html>`_
 * `fix_modify AtC sample_frequency <USER/atc/man_sample_frequency.html>`_

doc/utils/sphinx-config/false_positives.txt

@@ -820,6 +820,8 @@ erotate
 Ertas
 ervel
 Espanol
+Eshelby
+eshelby
 eskm
 esu
 esub
@@ -1166,6 +1168,8 @@ Hugoniot
 Hura
 hux
 hwloc
+hx
+hy
 hydrophobicity
 hydrostatic
 hydrostatically
@@ -1175,6 +1179,7 @@ hyperdynamics
 hyperradius
 hyperspherical
 hysteretic
+hz
 Ibanez
 ibar
 ibm