forked from lijiext/lammps
next batch of converted files
This commit is contained in:
Axel Kohlmeyer
parent
84f89134d9
commit
65b6b6f2f8
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@ -21,7 +21,7 @@ Examples
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.. code-block:: LAMMPS
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fix_modify atc atom_element_map eulerian 100
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fix_modify AtC atom_element_map eulerian 100
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Description
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"""""""""""
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@ -0,0 +1,56 @@
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.. index:: fix_modify AtC atom_weight
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fix_modify AtC atom_weight command
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==================================
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Syntax
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""""""
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.. parsed-literal::
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fix_modify <AtC fixID> atom_weight <method> <args>
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* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
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* atom_weight = name of the AtC sub-command
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* method = *constant* or *lattice* or *element* or *region* or *group* or *read_in*
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- *constant* <group-ID> <value>: atoms in specified group are assigned the constant value given
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- *lattice*\ : volume per atom for specified lattice type (e.g. fcc) and parameter
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- *element*\ : element volume divided among atoms within element
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- *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.
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- *group*\ : volume per atom determined based on the atom count in a group and its volume
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- *node*\ : (undocumented)
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- *node_element*\ : (undocumented)
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- *read_in*\ <filename>: list of values for atoms are read-in from specified file
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Examples
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""""""""
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.. code-block:: LAMMPS
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fix_modify AtC atom_weight constant myatoms 11.8
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fix_modify AtC atom_weight lattice
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fix_modify AtC atom_weight read-in atm_wt_file.txt
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Description
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"""""""""""
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Command for assigning the value of atomic weights used for atomic
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integration in atom-continuum coupled simulations.
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Restrictions
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""""""""""""
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The use of the lattice option requires a lattice type and parameter is already specified.
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Related AtC commands
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""""""""""""""""""""
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- :ref:`fix_modify AtC command overview <atc_fix_modify>`
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Default
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"""""""
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*lattice*
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@ -0,0 +1,47 @@
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.. index:: fix_modify AtC boundary_faceset
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fix_modify AtC boundary_faceset command
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=======================================
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Syntax
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""""""
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.. parsed-literal::
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fix_modify <AtC fixID> boundary_faceset <is|add> <faceset_name>
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* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
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* boundary_faceset = name of the AtC sub-command
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* *is* or *add* = select whether to select or add a faceset
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* faceset_name = name of the faceset
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Examples
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""""""""
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.. code-block:: LAMMPS
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fix_modify AtC boundary_faceset is obndy
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Description
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"""""""""""
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This command species the faceset name when using a faceset to compute
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the MD/FE boundary fluxes. The faceset must already exist.
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Restrictions
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""""""""""""
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This is only valid when *fe_md_boundary* is set to *faceset*\ .
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Related AtC commands
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""""""""""""""""""""
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- :ref:`fix_modify AtC command overview <atc_fix_modify>`
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- :doc:`fix_modify AtC fe_md_boundary <atc_fe_md_boundary>`
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- :doc:`fix_modify AtC mesh create_faceset box <atc_mesh_create_faceset_box>`
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- :doc:`fix_modify AtC mesh create_faceset plane <atc_mesh_create_faceset_plane>`
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Default
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"""""""
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None.
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@ -0,0 +1,46 @@
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.. index:: fix_modify AtC consistent_fe_initialization
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fix_modify AtC consistent_fe_initialization command
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===================================================
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Syntax
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""""""
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.. parsed-literal::
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fix_modify <AtC fixID> consistent_fe_initialization <on|off>
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* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
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* consistent_fe_initialization = name of the AtC sub-command
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* *on* or *off* = switch to activiate/deactiviate the initial setting of FE intrinsic field to match the projected MD field
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Examples
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""""""""
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.. code-block:: LAMMPS
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fix_modify AtC consistent_fe_initialization on
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Description
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"""""""""""
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Determines whether AtC initializes FE intrinsic fields (e.g.,
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temperature) to match the projected MD values. This is particularly
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useful for fully overlapping simulations.
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Restrictions
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""""""""""""
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Can be used with: *thermal*, *two_temperature*.
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Cannot be used with time filtering on.
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Does not include boundary nodes.
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Related AtC commands
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""""""""""""""""""""
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- :ref:`fix_modify AtC command overview <atc_fix_modify>`
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Default
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"""""""
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Default is *off*
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@ -0,0 +1,52 @@
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.. index:: fix_modify AtC fe_md_boundary
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fix_modify AtC fe_md_boundary command
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=====================================
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Syntax
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""""""
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.. parsed-literal::
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fix_modify <AtC fixID> fe_md_boundary <faceset|interpolate|no_boundary>
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* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
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* fe_md_boundary = name of the AtC sub-command
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* *faceset* or *interpolate* or *no_boundary*
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Examples
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""""""""
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.. code-block:: LAMMPS
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fix_modify AtC fe_md_boundary interpolate
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Description
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"""""""""""
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Specifies different methods for computing fluxes between between the MD
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and FE integration regions. Faceset defines a faceset separating the MD
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and FE regions and uses finite element face quadrature to compute the
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flux. Interpolate uses a reconstruction scheme to approximate the flux,
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which is more robust but less accurate if the MD/FE boundary does
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correspond to a faceset. No boundary results in no fluxes between the
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systems being computed.
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Restrictions
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""""""""""""
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If *faceset* is used, all the AtC non-boundary atoms must lie within and
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completely fill the domain enclosed by the faceset.
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Related AtC commands
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""""""""""""""""""""
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- :ref:`fix_modify AtC command overview <atc_fix_modify>`
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- :doc:`fix_modify AtC mesh create_faceset box <atc_mesh_create_faceset_box>`
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- :doc:`fix_modify AtC mesh create_faceset plane <atc_mesh_create_faceset_plane>`
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Default
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"""""""
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*interpolate*
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.. parsed-literal::
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fix_modify <AtC fixID> on_the_fly on_the_fly <bond|kernel> <on|off>
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fix_modify <AtC fixID> on_the_fly <bond|kernel> <on|off>
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* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
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* on_the_fly = name of the AtC sub-command
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@ -21,7 +21,7 @@ Examples
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.. code-block:: LAMMPS
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fix_modify atc initial temperature groupNAME 10.
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fix_modify AtC initial temperature groupNAME 10.
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Description
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"""""""""""
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@ -0,0 +1,47 @@
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.. index:: fix_modify AtC kernel_bandwidth
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fix_modify AtC kernel_bandwidth command
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=======================================
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Syntax
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""""""
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.. parsed-literal::
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fix_modify <AtC fixID> kernel_bandwidth <value>
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* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
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* kernel_bandwidth = name of the AtC sub-command
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* value = new bandwidth value
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Examples
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""""""""
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.. code-block:: LAMMPS
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fix_modify AtC kernel_bandwidth 8
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Description
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"""""""""""
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Sets a maximum parallel bandwidth for the kernel functions during
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parallel communication. If the command is not issued, the default will
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be to assume the bandwidth of the kernel matrix corresponds to the
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number of sampling locations.
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Restrictions
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""""""""""""
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Only is used if kernel functions are being used.
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Related AtC commands
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""""""""""""""""""""
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- :ref:`fix_modify AtC command overview <atc_fix_modify>`
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Default
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"""""""
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Number of sample locations.
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.. index:: fix_modify AtC pair_interactions
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fix_modify AtC pair_interactions command
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========================================
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fix_modify AtC bond_interactions command
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========================================
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Syntax
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""""""
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.. parsed-literal::
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fix_modify <AtC fixID> pair_interactions <on|off>
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fix_modify <AtC fixID> bond_interactions <on|off>
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* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
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* *pair_interactions* or *bond_interactions* = name of the AtC sub-command
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* *on* or *off* = activate or deactivate
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Examples
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""""""""
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.. code-block:: LAMMPS
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fix_modify AtC pair_interactions off
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fix_modify AtC bond_interactions on
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Description
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"""""""""""
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Include bonds and/or pairs in stress and heat flux computations.
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Restrictions
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""""""""""""
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None.
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Related AtC commands
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""""""""""""""""""""
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- :ref:`fix_modify AtC command overview <atc_fix_modify>`
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Default
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"""""""
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*pair_interactions*\ : on, *bond_interactions*\ : off
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@ -0,0 +1,46 @@
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.. index:: fix_modify AtC reset_atomic_reference_positions
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fix_modify AtC reset_atomic_reference_positions command
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=======================================================
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Syntax
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""""""
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.. parsed-literal::
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fix_modify <AtC fixID> reset_atomic_reference_positions
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* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
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* reset_atomic_reference_positions = name of the AtC sub-command
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Examples
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""""""""
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.. code-block:: LAMMPS
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fix_modify AtC reset_atomic_reference_positions
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Description
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"""""""""""
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Resets the atomic positions ATC uses to perform point to field
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operations. In can be used to use perfect lattice sites in ATC but a
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thermalized or deformed lattice in LAMMPS.
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Restrictions
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""""""""""""
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None.
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Related AtC commands
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""""""""""""""""""""
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- :ref:`fix_modify AtC command overview <atc_fix_modify>`
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Default
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"""""""
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None
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@ -0,0 +1,44 @@
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.. index:: fix_modify AtC reset_time
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fix_modify AtC reset_time command
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=================================
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Syntax
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""""""
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.. parsed-literal::
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fix_modify <AtC fixID> reset_time <value>
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* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
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* reset_time = name of the AtC sub-command
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* value = new time value
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Examples
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""""""""
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.. code-block:: LAMMPS
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fix_modify AtC reset_time 0.0
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Description
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"""""""""""
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Resets the simulation time counter.
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Restrictions
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""""""""""""
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None.
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Related AtC commands
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""""""""""""""""""""
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- :ref:`fix_modify AtC command overview <atc_fix_modify>`
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Default
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"""""""
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None
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@ -0,0 +1,44 @@
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.. index:: fix_modify AtC sample_frequency
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fix_modify AtC sample_frequency command
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=======================================
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Syntax
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""""""
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.. parsed-literal::
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fix_modify <AtC fixID> sample_frequency <freq>
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* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
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* sample_frequency = name of the AtC sub-command
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* freq = frequency to sample fields in number of steps
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Examples
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""""""""
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.. code-block:: LAMMPS
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fix_modify AtC sample_frequency 10
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Description
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"""""""""""
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Specifies a frequency at which fields are computed for the case where
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time filters are being applied.
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Restrictions
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""""""""""""
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Must be used with :doc:`fix atc hardy <fix_atc>` and is only relevant when time filters are being used.
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Related AtC commands
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""""""""""""""""""""
|
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- :ref:`fix_modify AtC command overview <atc_fix_modify>`
|
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Default
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"""""""
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None.
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@ -0,0 +1,50 @@
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.. index:: fix_modify AtC set reference_potential_energy
|
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fix_modify AtC set reference_potential_energy command
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=====================================================
|
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Syntax
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""""""
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.. parsed-literal::
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fix_modify <AtC fixID> set reference_potential_energy [<value|filename>]
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* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
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* set reference_potential_energy = name of the AtC sub-command
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* value = optional user specified zero point for PE in native LAMMPS energy units
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* filename = optional user specified string for file of nodal PE values to be read-in
|
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Examples
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||||
""""""""
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.. code-block:: LAMMPS
|
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fix_modify AtC set reference_potential_energy
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fix_modify AtC set reference_potential_energy -0.05
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fix_modify AtC set reference_potential_energy myPEvalues
|
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Description
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"""""""""""
|
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Used to set various quantities for the post-processing algorithms. It
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sets the zero point for the potential energy density using the value
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provided for all nodes, or from the current configuration of the lattice
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if no value is provided, or values provided within the specified
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filename.
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||||
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||||
Restrictions
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||||
""""""""""""
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||||
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Must be used with :doc:`fix atc hardy <fix_atc>` or :doc:`fix atc field <fix_atc>`.
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Related AtC commands
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""""""""""""""""""""
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- :ref:`fix_modify AtC command overview <atc_fix_modify>`
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Default
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"""""""
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Defaults to the LAMMPS zero point i.e. isolated atoms.
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@ -20,7 +20,7 @@ Examples
|
|||
|
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.. code-block:: LAMMPS
|
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|
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fix_modify atc time_integration fractional_step
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fix_modify AtC time_integration fractional_step
|
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Description
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|
|
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|
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@ -0,0 +1,45 @@
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.. index:: fix_modify AtC write_atom_weights
|
||||
|
||||
fix_modify AtC write_atom_weights command
|
||||
=========================================
|
||||
|
||||
Syntax
|
||||
""""""
|
||||
|
||||
.. parsed-literal::
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||||
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||||
fix_modify <AtC fixID> write_atom_weights <filename> <frequency>
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||||
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||||
* AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
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||||
* write_atom_weights = name of the AtC sub-command
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* filename = name of file that atomic weights are written to
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* frequency = how often writes will occur
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Examples
|
||||
""""""""
|
||||
|
||||
.. code-block:: LAMMPS
|
||||
|
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fix_modify AtC write_atom_weights atm_wt_file.txt 10
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||||
|
||||
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
|
||||
|
||||
|
|
@ -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>`_
|
||||
* `fix_modify AtC sample_frequency <USER/atc/man_sample_frequency.html>`_
|
||||
* `fix_modify AtC set <USER/atc/man_set.html>`_
|
||||
* :doc:`fix_modify AtC pair/bond_interactions <atc_pair_interactions>`
|
||||
* :doc:`fix_modify AtC sample_frequency <atc_sample_frequency>`
|
||||
* :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>`_
|
||||
* `fix_modify AtC write_atom_weights <USER/atc/man_write_atom_weights.html>`_
|
||||
* `fix_modify AtC reset_time <USER/atc/man_reset_time.html>`_
|
||||
* `fix_modify AtC reset_atomic_reference_positions <USER/atc/man_reset_atomic_reference_positions.html>`_
|
||||
* `fix_modify AtC fe_md_boundary <USER/atc/man_fe_md_boundary.html>`_
|
||||
* `fix_modify AtC boundary_faceset <USER/atc/man_boundary_faceset.html>`_
|
||||
* `fix_modify AtC consistent_fe_initialization <USER/atc/man_consistent_fe_initialization.html>`_
|
||||
* :doc:`fix_modify AtC atom_weight <atc_atom_weight>`
|
||||
* :doc:`fix_modify AtC write_atom_weights <atc_write_atom_weights>`
|
||||
* :doc:`fix_modify AtC kernel_bandwidth <atc_kernel_bandwidth>`
|
||||
* :doc:`fix_modify AtC reset_time <atc_reset_time>`
|
||||
* :doc:`fix_modify AtC reset_atomic_reference_positions <atc_reset_atomic_reference>`
|
||||
* :doc:`fix_modify AtC fe_md_boundary <atc_fe_md_boundary>`
|
||||
* :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>`_
|
||||
|
|
|
|||
Loading…
Reference in New Issue