From 65b6b6f2f82fcba474f5e6bd09dfd7ee717111c9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 19 Mar 2020 12:22:06 -0400 Subject: [PATCH] next batch of converted files --- doc/src/atc_atom_element_map.rst | 2 +- doc/src/atc_atom_weight.rst | 56 ++++++++++++++++++++ doc/src/atc_boundary_faceset.rst | 47 ++++++++++++++++ doc/src/atc_consistent_fe_initialization.rst | 46 ++++++++++++++++ doc/src/atc_fe_md_boundary.rst | 52 ++++++++++++++++++ doc/src/atc_hardy_on_the_fly.rst | 2 +- doc/src/atc_initial.rst | 2 +- doc/src/atc_kernel_bandwidth.rst | 47 ++++++++++++++++ doc/src/atc_pair_interactions.rst | 47 ++++++++++++++++ doc/src/atc_reset_atomic_reference.rst | 46 ++++++++++++++++ doc/src/atc_reset_time.rst | 44 +++++++++++++++ doc/src/atc_sample_frequency.rst | 44 +++++++++++++++ doc/src/atc_set_reference_pe.rst | 50 +++++++++++++++++ doc/src/atc_time_integration.rst | 2 +- doc/src/atc_write_atom_weights.rst | 45 ++++++++++++++++ doc/src/fix_atc.rst | 21 ++++---- 16 files changed, 539 insertions(+), 14 deletions(-) create mode 100644 doc/src/atc_atom_weight.rst create mode 100644 doc/src/atc_boundary_faceset.rst create mode 100644 doc/src/atc_consistent_fe_initialization.rst create mode 100644 doc/src/atc_fe_md_boundary.rst create mode 100644 doc/src/atc_kernel_bandwidth.rst create mode 100644 doc/src/atc_pair_interactions.rst create mode 100644 doc/src/atc_reset_atomic_reference.rst create mode 100644 doc/src/atc_reset_time.rst create mode 100644 doc/src/atc_sample_frequency.rst create mode 100644 doc/src/atc_set_reference_pe.rst create mode 100644 doc/src/atc_write_atom_weights.rst diff --git a/doc/src/atc_atom_element_map.rst b/doc/src/atc_atom_element_map.rst index 11f58d0841..96895acc8e 100644 --- a/doc/src/atc_atom_element_map.rst +++ b/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 """"""""""" diff --git a/doc/src/atc_atom_weight.rst b/doc/src/atc_atom_weight.rst new file mode 100644 index 0000000000..50e7ea146d --- /dev/null +++ b/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 atom_weight + +* AtC fixID = ID of :doc:`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* : 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*\ : 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 ` + +Default +""""""" + +*lattice* + diff --git a/doc/src/atc_boundary_faceset.rst b/doc/src/atc_boundary_faceset.rst new file mode 100644 index 0000000000..5198899bee --- /dev/null +++ b/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 boundary_faceset + +* AtC fixID = ID of :doc:`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 ` +- :doc:`fix_modify AtC fe_md_boundary ` +- :doc:`fix_modify AtC mesh create_faceset box ` +- :doc:`fix_modify AtC mesh create_faceset plane ` + + Default +""""""" + +None. diff --git a/doc/src/atc_consistent_fe_initialization.rst b/doc/src/atc_consistent_fe_initialization.rst new file mode 100644 index 0000000000..ed755a7239 --- /dev/null +++ b/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 consistent_fe_initialization + +* AtC fixID = ID of :doc:`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 ` + +Default +""""""" + +Default is *off* diff --git a/doc/src/atc_fe_md_boundary.rst b/doc/src/atc_fe_md_boundary.rst new file mode 100644 index 0000000000..ad66bf6d49 --- /dev/null +++ b/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 fe_md_boundary + +* AtC fixID = ID of :doc:`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 ` +- :doc:`fix_modify AtC mesh create_faceset box ` +- :doc:`fix_modify AtC mesh create_faceset plane ` + +Default +""""""" + +*interpolate* diff --git a/doc/src/atc_hardy_on_the_fly.rst b/doc/src/atc_hardy_on_the_fly.rst index 0aa186f219..fe7c688387 100644 --- a/doc/src/atc_hardy_on_the_fly.rst +++ b/doc/src/atc_hardy_on_the_fly.rst @@ -8,7 +8,7 @@ Syntax .. parsed-literal:: - fix_modify on_the_fly on_the_fly + fix_modify on_the_fly * AtC fixID = ID of :doc:`fix atc ` instance * on_the_fly = name of the AtC sub-command diff --git a/doc/src/atc_initial.rst b/doc/src/atc_initial.rst index fd45da0679..7d62251c6c 100644 --- a/doc/src/atc_initial.rst +++ b/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 """"""""""" diff --git a/doc/src/atc_kernel_bandwidth.rst b/doc/src/atc_kernel_bandwidth.rst new file mode 100644 index 0000000000..02707cfd30 --- /dev/null +++ b/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 kernel_bandwidth + +* AtC fixID = ID of :doc:`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 ` + +Default +""""""" + +Number of sample locations. + diff --git a/doc/src/atc_pair_interactions.rst b/doc/src/atc_pair_interactions.rst new file mode 100644 index 0000000000..73ada09001 --- /dev/null +++ b/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 pair_interactions + fix_modify bond_interactions + +* AtC fixID = ID of :doc:`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 ` + +Default +""""""" + +*pair_interactions*\ : on, *bond_interactions*\ : off diff --git a/doc/src/atc_reset_atomic_reference.rst b/doc/src/atc_reset_atomic_reference.rst new file mode 100644 index 0000000000..8f53cbfbe9 --- /dev/null +++ b/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 reset_atomic_reference_positions + +* AtC fixID = ID of :doc:`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 ` + +Default +""""""" + +None + diff --git a/doc/src/atc_reset_time.rst b/doc/src/atc_reset_time.rst new file mode 100644 index 0000000000..147a6ab910 --- /dev/null +++ b/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 reset_time + +* AtC fixID = ID of :doc:`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 ` + +Default +""""""" + +None + diff --git a/doc/src/atc_sample_frequency.rst b/doc/src/atc_sample_frequency.rst new file mode 100644 index 0000000000..5b0da6d9dd --- /dev/null +++ b/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 sample_frequency + +* AtC fixID = ID of :doc:`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 ` and is only relevant when time filters are being used. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` + +Default +""""""" + +None. + diff --git a/doc/src/atc_set_reference_pe.rst b/doc/src/atc_set_reference_pe.rst new file mode 100644 index 0000000000..ff4d95526f --- /dev/null +++ b/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 set reference_potential_energy [] + +* AtC fixID = ID of :doc:`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 ` or :doc:`fix atc field `. + +Related AtC commands +"""""""""""""""""""" + +- :ref:`fix_modify AtC command overview ` + +Default +""""""" + +Defaults to the LAMMPS zero point i.e. isolated atoms. + diff --git a/doc/src/atc_time_integration.rst b/doc/src/atc_time_integration.rst index 382f11d459..580be0430c 100644 --- a/doc/src/atc_time_integration.rst +++ b/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 diff --git a/doc/src/atc_write_atom_weights.rst b/doc/src/atc_write_atom_weights.rst new file mode 100644 index 0000000000..ecb69b5deb --- /dev/null +++ b/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 write_atom_weights + +* AtC fixID = ID of :doc:`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 ` + +Default +""""""" + +None + diff --git a/doc/src/fix_atc.rst b/doc/src/fix_atc.rst index 902c336706..d87405632c 100644 --- a/doc/src/fix_atc.rst +++ b/doc/src/fix_atc.rst @@ -212,20 +212,21 @@ conditions. * :doc:`fix_modify AtC rates ` * :doc:`fix_modify AtC computes ` * :doc:`fix_modify AtC on_the_fly ` -* `fix_modify AtC pair_interactions/bond_interactions `_ -* `fix_modify AtC sample_frequency `_ -* `fix_modify AtC set `_ +* :doc:`fix_modify AtC pair/bond_interactions ` +* :doc:`fix_modify AtC sample_frequency ` +* :doc:`fix_modify AtC set ` miscellaneous *fix_modify* commands: * :doc:`fix_modify AtC atom_element_map ` -* `fix_modify AtC atom_weight `_ -* `fix_modify AtC write_atom_weights `_ -* `fix_modify AtC reset_time `_ -* `fix_modify AtC reset_atomic_reference_positions `_ -* `fix_modify AtC fe_md_boundary `_ -* `fix_modify AtC boundary_faceset `_ -* `fix_modify AtC consistent_fe_initialization `_ +* :doc:`fix_modify AtC atom_weight ` +* :doc:`fix_modify AtC write_atom_weights ` +* :doc:`fix_modify AtC kernel_bandwidth ` +* :doc:`fix_modify AtC reset_time ` +* :doc:`fix_modify AtC reset_atomic_reference_positions ` +* :doc:`fix_modify AtC fe_md_boundary ` +* :doc:`fix_modify AtC boundary_faceset ` +* :doc:`fix_modify AtC consistent_fe_initialization ` * `fix_modify AtC mass_matrix `_ * `fix_modify AtC material `_ * `fix_modify AtC atomic_charge `_