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<h1><a class="anchor" name="man_disp_control">fix_modify AtC transfer momentum control</a></h1><h2><a class="anchor" name="syntax">
syntax</a></h2>
fix_modify AtC transfer momentum control none <br>
<p>
fix_modify AtC transfer momentum control rescale &lt;frequency&gt;<br>
<ul>
<li>frequency (int) = time step frequency for applying displacement and velocity rescaling <br>
</li></ul>
<p>
fix_modify AtC transfer momentum control glc_displacement <br>
<p>
fix_modify AtC transfer momentum control glc_velocity <br>
<p>
fix_modify AtC transfer momentum control flux [faceset face_set_id, interpolate]<ul>
<li>face_set_id (string) = id of boundary face set, if not specified (or not possible when the atomic domain does not line up with mesh boundaries) defaults to an atomic-quadrature approximate evaulation<br>
</li></ul>
<h2><a class="anchor" name="examples">
examples</a></h2>
fix_modify AtC transfer momentum control glc_velocity <br>
fix_modify AtC transfer momentum control stress_flux faceset bndy_faces <br>
<h2><a class="anchor" name="description">
description</a></h2>
<h2><a class="anchor" name="restrictions">
restrictions</a></h2>
only for be used with specific transfers : elastic <br>
rescale not valid with time filtering activated <h2><a class="anchor" name="related">
related</a></h2>
<h2><a class="anchor" name="default">
default</a></h2>
none <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by&nbsp;
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<h1><a class="anchor" name="man_hardy_set">fix_modify AtC set</a></h1><h2><a class="anchor" name="syntax">
syntax</a></h2>
fix_modify AtC transfer set reference_potential_energy &lt;value&gt;<ul>
<li>value (double) : optional user specified zero point for PE </li></ul>
<h2><a class="anchor" name="examples">
examples</a></h2>
<code> fix_modify AtC transfer set reference_potential_energy </code> <br>
<code> fix_modify AtC transfer set reference_potential_energy -0.05 </code> <br>
<h2><a class="anchor" name="description">
description</a></h2>
Used to set various quantities for the post-processing algorithms. Currently it only 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 <h2><a class="anchor" name="restrictions">
restrictions</a></h2>
Must be used with the hardy AtC transfer ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) <h2><a class="anchor" name="related">
related</a></h2>
<h2><a class="anchor" name="default">
default</a></h2>
Defaults to lammps zero point i.e. isolated atoms <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by&nbsp;
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<h1><a class="anchor" name="man_mesh_elemset">fix_modify AtC mesh create_elementset</a></h1><h2><a class="anchor" name="syntax">
syntax</a></h2>
fix_modify AtC create_elementset &lt;id&gt; &lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt;<ul>
<li>&lt;id&gt; = id to assign to the collection of FE element</li><li>&lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt; = coordinates of the bounding box that contains only the desired elements </li></ul>
<h2><a class="anchor" name="examples">
examples</a></h2>
<code> fix_modify AtC mesh create_elementset middle -4.1 4.1 -100 100 -100 1100 </code> <h2><a class="anchor" name="description">
description</a></h2>
Command to assign an id to a set of FE elements to be used subsequently in defining material and mesh-based operations. <h2><a class="anchor" name="restrictions">
restrictions</a></h2>
Only viable for rectangular grids. Also "INF" is not currrently handled. <h2><a class="anchor" name="related">
related</a></h2>
<h2><a class="anchor" name="default">
default</a></h2>
Coordinates are assumed to be in lattice units. <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by&nbsp;
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<h1><a class="anchor" name="man_mesh_faceset">fix_modify AtC mesh create_faceset</a></h1><h2><a class="anchor" name="syntax">
syntax</a></h2>
fix_modify AtC create_faceset &lt;id&gt; &lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt; &lt;in|out&gt; [units]<ul>
<li>&lt;id&gt; = id to assign to the collection of FE faces</li><li>&lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt; = coordinates of the bounding box that is coincident with the desired FE faces</li><li>&lt;in|out&gt; = "in" gives inner faces to the box, "out" gives the outer faces to the box</li><li>units = option to specify real as opposed to lattice units </li></ul>
<h2><a class="anchor" name="examples">
examples</a></h2>
<code> fix_modify AtC mesh create_faceset obndy -4.0 4.0 -12 12 -12 12 out </code> <h2><a class="anchor" name="description">
description</a></h2>
Command to assign an id to a set of FE faces to be used subsequently in defining flux boundary conditions. <h2><a class="anchor" name="restrictions">
restrictions</a></h2>
Only viable for rectangular grids. Also "INF" is not currrently handled. <h2><a class="anchor" name="related">
related</a></h2>
<h2><a class="anchor" name="default">
default</a></h2>
The default option is units = lattice. <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by&nbsp;
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<h1><a class="anchor" name="man_mesh_nodeset">fix_modify AtC mesh create_nodeset</a></h1><h2><a class="anchor" name="syntax">
syntax</a></h2>
fix_modify AtC create_nodeset &lt;id&gt; &lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt;<ul>
<li>&lt;id&gt; = id to assign to the collection of FE nodes</li><li>&lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt; = coordinates of the bounding box that contains only the desired nodes </li></ul>
<h2><a class="anchor" name="examples">
examples</a></h2>
<code> fix_modify AtC mesh create_faceset left -4.1 3.9 -100 100 -100 100 </code> <h2><a class="anchor" name="description">
description</a></h2>
Command to assign an id to a set of FE nodes to be used subsequently in defining boundary conditions. <h2><a class="anchor" name="restrictions">
restrictions</a></h2>
Only viable for rectangular grids. Also "INF" is not currrently handled. <h2><a class="anchor" name="related">
related</a></h2>
<h2><a class="anchor" name="default">
default</a></h2>
Coordinates are assumed to be in lattice units. <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by&nbsp;
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<h1><a class="anchor" name="man_neighbor_reset_frequency">fix_modify AtC transfer neighbor_reset_frequency</a></h1><h2><a class="anchor" name="syntax">
syntax</a></h2>
fix_modify AtC transfer neighbor_reset_frequency &lt;frequency&gt;<ul>
<li>frequency (int) : reset neighbor map for AtC analysis every "frequency" steps </li></ul>
<h2><a class="anchor" name="examples">
examples</a></h2>
<code> fix_modify AtC transfer neighbor_reset_frequency 1000 </code> <h2><a class="anchor" name="description">
description</a></h2>
This command allows the control of how often the lists of which atoms pairs are in the support of a node are reformed <h2><a class="anchor" name="restrictions">
restrictions</a></h2>
Only currently relevant to Hardy post-processing see <a class="el" href="man_fix_atc.html">fix atc command</a> <h2><a class="anchor" name="related">
related</a></h2>
This command is different from <a class="el" href="man_atom_element_map.html">fix_modify AtC transfer atom_element_map</a> in that it only concerns neighbor lists internal to ATC not the map of atom locations to elements which define the shape function values at atoms. <h2><a class="anchor" name="default">
default</a></h2>
The default is for the internal neighbor lists to be recalculated on the next output step (or sample step if time filtering is used). <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by&nbsp;
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<h1><a class="anchor" name="man_thermal_control">fix_modify AtC transfer thermal control</a></h1><h2><a class="anchor" name="syntax">
syntax</a></h2>
fix_modify AtC transfer thermal control &lt;control_type&gt; &lt;optional args=""&gt;<br>
<ul>
<li>control_type (string) = none | rescale | hoover | flux<br>
</li></ul>
<p>
fix_modify AtC transfer thermal control rescale &lt;frequency&gt;<br>
<ul>
<li>frequency (int) = time step frequency for applying velocity rescaling <br>
</li></ul>
<p>
fix_modify AtC transfer thermal control hoover <br>
<p>
fix_modify AtC transfer thermal control flux &lt;boundary_integration_type&gt; &lt;face_set_id(optional)&gt;<br>
<ul>
<li>boundary_integration_type (string) = faceset | interpolate<br>
</li><li>face_set_id (string), optional = id of boundary face set, if not specified (or not possible when the atomic domain does not line up with mesh boundaries) defaults to an atomic-quadrature approximate evaulation, does not work with interpolate<br>
</li></ul>
<h2><a class="anchor" name="examples">
examples</a></h2>
<code> fix_modify AtC transfer thermal control none </code> <br>
<code> fix_modify AtC transfer thermal control rescale 10 </code> <br>
<code> fix_modify AtC transfer thermal control hoover </code> <br>
<code> fix_modify AtC transfer thermal control flux bndy_faces </code> <br>
<h2><a class="anchor" name="description">
description</a></h2>
Sets the energy exchange mechansim from the finite elements to the atoms, managed through a control algorithm. Rescale computes a scale factor for each atom to match the finite element temperature. Hoover is a Gaussian least-constraint isokinetic thermostat enforces that the nodal restricted atomic temperature matches the finite element temperature. Flux is a similar mode, but rather adds energy to the atoms based on conservation of energy. Hoover and flux allows the prescription of sources or fixed temperatures on the atoms. <h2><a class="anchor" name="restrictions">
restrictions</a></h2>
only for be used with specific transfers : thermal (rescale, hoover, flux), two_temperature (flux) <br>
rescale not valid with time filtering activated <h2><a class="anchor" name="related">
related</a></h2>
<h2><a class="anchor" name="default">
default</a></h2>
none<br>
rescale frequency is 1<br>
flux boundary_integration_type is interpolate <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by&nbsp;
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<title>ATC: fix_modify AtC transfer pmfc</title>
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<h1><a class="anchor" name="man_time_integration">fix_modify AtC transfer pmfc</a></h1><h2><a class="anchor" name="syntax">
syntax</a></h2>
fix_modify AtC transfer pmfc &lt;on|off&gt;<h2><a class="anchor" name="examples">
examples</a></h2>
<code> fix_modify atc transfer pmfc on </code><h2><a class="anchor" name="description">
description</a></h2>
Switches the poor man's fractional step algorithm on where the finite element data lags the exact atomic data by one time step for overlap nodes<h2><a class="anchor" name="restrictions">
restrictions</a></h2>
<h2><a class="anchor" name="related">
related</a></h2>
<h2><a class="anchor" name="default">
default</a></h2>
off <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by&nbsp;
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<h1><a class="anchor" name="man_transfer_atomic_output">fix_modify AtC transfer atomic_output</a></h1><h2><a class="anchor" name="syntax">
syntax</a></h2>
fix_modify AtC transfer atomic_output &lt;filename_prefix&gt; &lt;frequency&gt; [text]<ul>
<li>filename_prefix (string) = prefix for data files</li><li>frequency (integer) = frequency of output in time-steps</li><li>option "text" = creates a text version of the output as well as the binary Ensight output </li></ul>
<h2><a class="anchor" name="examples">
examples</a></h2>
<code> fix_modify AtC transfer atomic_output heatMD 100 </code> <br>
<code> fix_modify AtC transfer atomic_output nanoMD 1 text </code> <br>
<h2><a class="anchor" name="description">
description</a></h2>
Creates (binary, "gold" format) Ensight output of atom (point) data which is transfer/physics specific. <h2><a class="anchor" name="restrictions">
restrictions</a></h2>
<h2><a class="anchor" name="related">
related</a></h2>
<h2><a class="anchor" name="default">
default</a></h2>
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<h1><a class="anchor" name="man_transfer_boundary">fix_modify AtC transfer boundary</a></h1><h2><a class="anchor" name="syntax">
syntax</a></h2>
fix_modify AtC transfer boundary type &lt;atom-type-id&gt;<ul>
<li>&lt;atom-type-id&gt; = type id for atoms that represent a ficticious boundary internal to the FE mesh </li></ul>
<h2><a class="anchor" name="examples">
examples</a></h2>
<code> fix_modify AtC transfer boundary type ghost_atoms </code> <h2><a class="anchor" name="description">
description</a></h2>
Command to define the atoms that represent the ficticious boundary internal to the FE mesh. For fully overlapped MD/FE domains with periodic boundary conditions no boundary atoms should be defined. <h2><a class="anchor" name="restrictions">
restrictions</a></h2>
<h2><a class="anchor" name="related">
related</a></h2>
see <a class="el" href="man_transfer_internal.html">fix_modify AtC transfer internal</a> <h2><a class="anchor" name="default">
default</a></h2>
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<h1><a class="anchor" name="man_transfer_internal">fix_modify AtC transfer internal</a></h1><h2><a class="anchor" name="syntax">
syntax</a></h2>
fix_modify AtC transfer internal type &lt;atom-type-id&gt;<ul>
<li>&lt;atom-type-id&gt; = type id for non-fixed atoms internal to the FE mesh </li></ul>
<h2><a class="anchor" name="examples">
examples</a></h2>
<code> fix_modify AtC transfer internal type internal_atoms </code> <h2><a class="anchor" name="description">
description</a></h2>
Command to define the atoms to couple to finite elements. This definition is required for a AtC simulation. <h2><a class="anchor" name="restrictions">
restrictions</a></h2>
<h2><a class="anchor" name="related">
related</a></h2>
see <a class="el" href="man_transfer_boundary.html">fix_modify AtC transfer boundary</a> <h2><a class="anchor" name="default">
default</a></h2>
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<h1><a class="anchor" name="man_transfer_output">fix_modify AtC transfer output</a></h1><h2><a class="anchor" name="syntax">
syntax</a></h2>
fix_modify AtC transfer output &lt;filename_prefix&gt; &lt;frequency&gt; [text | vector_components | tensor_components ]<ul>
<li>filename_prefix (string) = prefix for data files</li><li>frequency (integer) = frequency of output in time-steps</li><li>options (keyword/s): <br>
text = creates text output as well as binary Ensight output <br>
vector_components = outputs vectors as scalar components <br>
tensor_components = outputs tensor as scalar components (use this for Paraview)<br>
</li></ul>
<h2><a class="anchor" name="examples">
examples</a></h2>
<code> fix_modify AtC transfer output heatFE 100 </code> <br>
<code> fix_modify AtC transfer output hardyFE 1 text tensor_components </code> <br>
<h2><a class="anchor" name="description">
description</a></h2>
Creates (binary, "gold" format) Ensight output of nodal/mesh data which is transfer/physics specific. <h2><a class="anchor" name="restrictions">
restrictions</a></h2>
<h2><a class="anchor" name="related">
related</a></h2>
see <a class="el" href="man_fix_atc.html">fix atc command</a> <h2><a class="anchor" name="default">
default</a></h2>
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<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.3.9.1 </small></address>
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