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Adding new manual documentation for ATC version 2.0 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10646 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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jzimmer 2013-08-22 01:05:36 +00:00
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<h1><a class="anchor" id="man_add_molecule">fix_modify AtC add_molecule </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify_AtC add_molecule &lt;small|large&gt; &lt;TAG&gt; &lt;GROUP_NAME&gt; <br/>
</p>
<ul>
<li>small|large = can be small if molecule size &lt; cutoff radius, must be large otherwise <br/>
</li>
<li>&lt;TAG&gt; = tag for tracking a species <br/>
</li>
<li>&lt;GROUP_NAME&gt; = name of group that tracking will be applied to <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> group WATERGROUP type 1 2 </code> <br/>
<code> fix_modify AtC add_molecule small water WATERGROUP </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Associates a tag with all molecules corresponding to a specified group. <br/>
</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>No defaults for this command. </p>
</div>
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<h1><a class="anchor" id="man_add_species">fix_modify AtC add_species </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify_AtC add_species &lt;TAG&gt; &lt;group|type&gt; &lt;ID&gt; <br/>
</p>
<ul>
<li>&lt;TAG&gt; = tag for tracking a species <br/>
</li>
<li>group|type = LAMMPS defined group or type of atoms <br/>
</li>
<li>&lt;ID&gt; = name of group or type number <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC add_species gold type 1 </code> <br/>
<code> group GOLDGROUP type 1 </code> <br/>
<code> fix_modify AtC add_species gold group GOLDGROUP </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Associates a tag with all atoms of a specified type or within a specified group. <br/>
</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>No defaults for this command. </p>
</div>
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<h1><a class="anchor" id="man_atom_weight">fix_modify AtC atom_weight </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC atom_weight &lt;method&gt; &lt;arguments&gt;</p>
<ul>
<li>&lt;method&gt; = <br/>
value: atoms in specified group assigned constant value given <br/>
lattice: volume per atom for specified lattice type (e.g. fcc) and parameter <br/>
element: element volume divided among atoms within element <br/>
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. <br/>
group: volume per atom determined based on the atom count in a group and its volume<br/>
read_in: list of values for atoms are read-in from specified file <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc atom_weight constant myatoms 11.8 </code> <br/>
<code> fix_modify atc atom_weight lattice </code> <br/>
<code> fix_modify atc atom_weight read-in atm_wt_file.txt </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command for assigning the value of atomic weights used for atomic integration in atom-continuum coupled simulations. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Use of lattice option requires a lattice type and parameter is already specified. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>lattice </p>
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<h1><a class="anchor" id="man_atomic_charge">fix_modify AtC atomic_charge </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC &lt;include | omit&gt; atomic_charge</p>
<ul>
<li>&lt;include | omit&gt; = switch to activiate/deactiviate inclusion of intrinsic atomic charge in <a class="el" href="namespaceATC.html" title="owned field/s: MASS_DENSITY">ATC</a> </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc compute include atomic_charge </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Determines whether AtC tracks the total charge as a finite element field </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Required for: electrostatics </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>if the atom charge is defined, default is on, otherwise default is off </p>
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<h1><a class="anchor" id="man_boundary">fix_modify AtC boundary </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC boundary type &lt;atom-type-id&gt;</p>
<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" id="examples">
examples</a></h2>
<p><code> fix_modify AtC boundary type ghost_atoms </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>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. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none </p>
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<h1><a class="anchor" id="man_boundary_dynamics">fix_modify AtC boundary_dynamics </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC boundary_dynamics &lt; on | damped_harmonic | prescribed | coupled | none &gt; [args] <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Sets different schemes for controlling boundary atoms. On will integrate the boundary atoms using the velocity-verlet algorithm. Damped harmonic uses a mass/spring/dashpot for the boundary atoms with added arguments of the damping and spring constants followed by the ratio of the boundary type mass to the desired mass. Prescribed forces the boundary atoms to follow the finite element displacement. Coupled does the same. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Boundary atoms must be specified. When using swaps between internal and boundary atoms, the initial configuration must have already correctly partitioned the two. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>prescribed on </p>
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<h1><a class="anchor" id="man_boundary_faceset">fix_modify AtC boundary_faceset </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC boundary_faceset &lt;is | add&gt; [args] </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p>fix_modify AtC boundary_faceset is obndy </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>This command species the faceset name when using a faceset to compute the MD/FE boundary fluxes. The faceset must already exist. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>This is only valid when fe_md_boundary is set to faceset. </p>
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related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
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<h1><a class="anchor" id="man_consistent_fe_initialization">fix_modify AtC consistent_fe_initialization </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC consistent_fe_initialization &lt;on | off&gt;</p>
<ul>
<li>&lt;on|off&gt; = switch to activiate/deactiviate the intial setting of FE intrinsic field to match the projected MD field </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc consistent_fe_initialization on </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Determines whether AtC initializes FE intrinsic fields (e.g., temperature) to match the projected MD values. This is particularly useful for fully overlapping simulations. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Can be used with: thermal, two_temperature. Cannot be used with time filtering on. Does not include boundary nodes. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>Default is off </p>
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<h1><a class="anchor" id="man_control">fix_modify AtC control </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC control &lt;physics_type&gt; &lt;solution_parameter&gt; </p>
<p><br/>
</p>
<ul>
<li>physics_type (string) = thermal | momentum<br/>
</li>
<li>solution_parameter (string) = max_iterations | tolerance<br/>
</li>
</ul>
<p>fix_modify AtC transfer &lt;physics_type&gt; control max_iterations &lt;max_iterations&gt;<br/>
</p>
<ul>
<li>max_iterations (int) = maximum number of iterations that will be used by iterative matrix solvers<br/>
</li>
</ul>
<p>fix_modify AtC transfer &lt;physics_type&gt; control tolerance &lt;tolerance&gt; <br/>
</p>
<ul>
<li>tolerance (float) = relative tolerance to which matrix equations will be solved<br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC control thermal max_iterations 10 </code> <br/>
<code> fix_modify AtC control momentum tolerance 1.e-5 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Sets the numerical parameters for the matrix solvers used in the specified control algorithm. Many solution approaches require iterative solvers, and these methods enable users to provide the maximum number of iterations and the relative tolerance. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>only for be used with specific controllers : thermal, momentum <br/>
They are ignored if a lumped solution is requested </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>max_iterations is the number of rows in the matrix<br/>
tolerance is 1.e-10 </p>
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<h1><a class="anchor" id="man_control_momentum">fix_modify AtC control momentum </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC control momentum none <br/>
</p>
<p>fix_modify AtC control momentum rescale &lt;frequency&gt;<br/>
</p>
<ul>
<li>frequency (int) = time step frequency for applying displacement and velocity rescaling <br/>
</li>
</ul>
<p>fix_modify AtC control momentum glc_displacement <br/>
</p>
<p>fix_modify AtC control momentum glc_velocity <br/>
</p>
<p>fix_modify AtC control momentum hoover <br/>
</p>
<p>fix_modify AtC control momentum flux [faceset face_set_id, interpolate]</p>
<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" id="examples">
examples</a></h2>
<p>fix_modify AtC control momentum glc_velocity <br/>
fix_modify AtC control momentum flux faceset bndy_faces <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>only to be used with specific transfers : elastic <br/>
rescale not valid with time filtering activated </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none </p>
</div>
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<h1><a class="anchor" id="man_control_thermal">fix_modify AtC control thermal </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC control thermal &lt;control_type&gt; &lt;optional_args&gt;</p>
<ul>
<li>control_type (string) = none | rescale | hoover | flux<br/>
</li>
</ul>
<p>fix_modify AtC control thermal rescale &lt;frequency&gt; <br/>
</p>
<ul>
<li>frequency (int) = time step frequency for applying velocity rescaling <br/>
</li>
</ul>
<p>fix_modify AtC control thermal hoover <br/>
</p>
<p>fix_modify AtC control thermal flux &lt;boundary_integration_type(optional)&gt; &lt;face_set_id(optional)&gt;<br/>
</p>
<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" id="examples">
examples</a></h2>
<p><code> fix_modify AtC control thermal none </code> <br/>
<code> fix_modify AtC control thermal rescale 10 </code> <br/>
<code> fix_modify AtC control thermal hoover </code> <br/>
<code> fix_modify AtC control thermal flux </code> <br/>
<code> fix_modify AtC control thermal flux faceset bndy_faces </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>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. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>only for be used with specific transfers : thermal (rescale, hoover, flux), two_temperature (flux) <br/>
rescale not valid with time filtering activated </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none<br/>
rescale frequency is 1<br/>
flux boundary_integration_type is interpolate </p>
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<h1><a class="anchor" id="man_control_thermal_correction_max_iterations">fix_modify AtC control thermal correction_max_iterations </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC control thermal correction_max_iterations &lt;max_iterations&gt;</p>
<ul>
<li>max_iterations (int) = maximum number of iterations that will be used by iterative matrix solvers<br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC control thermal correction_max_iterations 10 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Sets the maximum number of iterations to compute the 2nd order in time correction term for lambda with the fractional step method. The method uses the same tolerance as the controller's matrix solver. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>only for use with thermal physics using the fractional step method. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>correction_max_iterations is 20 </p>
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<h1><a class="anchor" id="man_decomposition">fix_modify AtC decomposition </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC decomposition &lt;type&gt;</p>
<ul>
<li>&lt;type&gt; = <br/>
replicated_memory: nodal information replicated on each processor <br/>
distributed_memory: only owned nodal information on processor <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc decomposition distributed_memory </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command for assigning the distribution of work and memory for parallel runs. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>replicated_memory is appropriate for simulations were the number of nodes &lt;&lt; number of atoms </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>replicated_memory </p>
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<h1><a class="anchor" id="man_fe_md_boundary">fix_modify AtC fe_md_boundary </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC fe_md_boundary &lt;faceset | interpolate | no_boundary&gt; [args] </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc fe_md_boundary interpolate </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>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. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>If faceset is used, all the AtC non-boundary atoms must lie within and completely fill the domain enclosed by the faceset. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<p>see for how to specify the faceset name. </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>Interpolate. </p>
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<h1><a class="anchor" id="man_filter_type">fix_modify AtC filter type </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC filter type &lt;exponential | step | no_filter&gt; <br/>
</p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC filter type exponential </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Specifies the type of time filter used. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>only for be used with specific transfers: thermal, two_temperature</p>
<h2><a class="anchor" id="related">
related</a></h2>
<p><a class="el" href="man_time_filter.html">fix_modify AtC filter</a> <a class="el" href="man_filter_scale.html">fix_modify AtC filter scale</a></p>
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default</a></h2>
<p>No default. </p>
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<h1><a class="anchor" id="man_internal_atom_integrate">fix_modify AtC internal_atom_integrate </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC internal_atom_integrate &lt;on | off&gt; <code> fix_modify AtC internal_atom_integrate on </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Has AtC perform time integration for the atoms in the group on which it operates. This does not include boundary atoms. </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>on for coupling methods, off for post-processors off </p>
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<h1><a class="anchor" id="man_internal_element_set">fix_modify AtC internal_element_set </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC internal_element_set &lt;element-set-name&gt;</p>
<ul>
<li>&lt;element-set-name&gt; = name of element set defining internal region, or off </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC internal_element_set myElementSet </code> <code> fix_modify AtC internal_element_set off </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Enables AtC to base the region for internal atoms to be an element set. If no ghost atoms are used, all the AtC atoms must be constrained to remain in this element set by the user, e.g., with walls. If boundary atoms are used in conjunction with Eulerian atom maps AtC will partition all atoms of a boundary or internal type to be of type internal if they are in the internal region or to be of type boundary otherwise. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>If boundary atoms are used in conjunction with Eulerian atom maps, the Eulerian reset frequency must be an integer multiple of the Lammps reneighbor frequency </p>
<h2><a class="anchor" id="related">
related</a></h2>
<p>see atom_element_map_type and boundary </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>off </p>
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<h1><a class="anchor" id="man_kernel_function">fix_modify AtC kernel </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC kernel &lt;type&gt; &lt;parameters&gt;</p>
<ul>
<li>type (keyword) = step, cell, cubic_bar, cubic_cylinder, cubic_sphere, quartic_bar, quartic_cylinder, quartic_sphere <br/>
</li>
<li>parameters :<br/>
step = radius (double) <br/>
cell = hx, hy, hz (double) or h (double) <br/>
cubic_bar = half-width (double) <br/>
cubic_cylinder = radius (double) <br/>
cubic_sphere = radius (double) <br/>
quartic_bar = half-width (double) <br/>
quartic_cylinder = radius (double) <br/>
quartic_sphere = radius (double) <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p>fix_modify AtC kernel cell 1.0 1.0 1.0 fix_modify AtC kernel quartic_sphere 10.0 </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Must be used with the hardy AtC fix <br/>
For bar kernel types, half-width oriented along x-direction <br/>
For cylinder kernel types, cylindrical axis is assumed to be in z-direction <br/>
( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>No default </p>
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<h1><a class="anchor" id="man_localized_lambda">fix_modify AtC control localized_lambda </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC control localized_lambda &lt;on|off&gt; </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc control localized_lambda on </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Turns on localization algorithms for control algorithms to restrict the influence of FE coupling or boundary conditions to a region near the boundary of the MD region. Control algorithms will not affect atoms in elements not possessing faces on the boundary of the region. Flux-based control is localized via row-sum lumping while quantity control is done by solving a truncated matrix equation. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>Default is off. </p>
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<h1><a class="anchor" id="man_lumped_lambda_solve">fix_modify AtC control lumped_lambda_solve </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC control lumped_lambda_solve &lt;on|off&gt; </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc control lumped_lambda_solve on </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command to use or not use lumped matrix for lambda solve </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
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default</a></h2>
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<h1><a class="anchor" id="man_mask_direction">fix_modify AtC control mask_direction </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC control mask_direction &lt;direction&gt; &lt;on|off&gt; </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc control mask_direction 0 on </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command to mask out certain dimensions from the atomic regulator </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
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default</a></h2>
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<h1><a class="anchor" id="man_mass_matrix">fix_modify AtC mass_matrix </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC mass_matrix &lt;fe | md_fe&gt;</p>
<ul>
<li>&lt;fe | md_fe&gt; = activiate/deactiviate using the FE mass matrix in the MD region </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc mass_matrix fe </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Determines whether AtC uses the FE mass matrix based on Gaussian quadrature or based on atomic quadrature in the MD region. This is useful for fully overlapping simulations to improve efficiency. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Should not be used unless the FE region is contained within the MD region, otherwise the method will be unstable and inaccurate </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>Default is off </p>
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<h1><a class="anchor" id="man_material">fix_modify AtC material </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC material [elementset_name] [material_id] <br/>
</p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC material gap_region 2</code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Sets the material model in elementset_name to be of type material_id. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>The element set must already be created and the material must be specified in the material file given the the atc fix on construction </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>All elements default to the first material in the material file. </p>
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<h1><a class="anchor" id="man_mesh_add_to_nodeset">fix_modify AtC mesh add_to_nodeset </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC mesh add_to_nodeset &lt;id&gt; &lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt;</p>
<ul>
<li>&lt;id&gt; = id of FE nodeset to be added to</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 the desired nodes to be added </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC mesh add_to_nodeset lbc -11.9 -11 -12 12 -12 12 </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command to add nodes to an already existing FE nodeset. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>Coordinates are assumed to be in lattice units. </p>
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<h1><a class="anchor" id="man_mesh_create">fix_modify AtC mesh create </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC mesh create &lt;nx&gt; &lt;ny&gt; &lt;nz&gt; &lt;region-id&gt; &lt;f|p&gt; &lt;f|p&gt; &lt;f|p&gt; <br/>
</p>
<ul>
<li>nx ny nz = number of elements in x, y, z</li>
<li>region-id = id of region that is to be meshed</li>
<li>f p p = periodicity flags for x, y, z </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC mesh create 10 1 1 feRegion p p p </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Creates a uniform mesh in a rectangular region </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Creates only uniform rectangular grids in a rectangular region </p>
<h2><a class="anchor" id="related">
related</a></h2>
<p><a class="el" href="man_mesh_quadrature.html">fix_modify AtC mesh quadrature</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>When created, mesh defaults to gauss2 (2-point Gaussian) quadrature. Use "mesh quadrature" command to change quadrature style. </p>
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<h1><a class="anchor" id="man_mesh_create_elementset">fix_modify AtC mesh create_elementset </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>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;</p>
<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" id="examples">
examples</a></h2>
<p><code> fix_modify AtC mesh create_elementset middle -4.1 4.1 -100 100 -100 1100 </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command to assign an id to a set of FE elements to be used subsequently in defining material and mesh-based operations. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Only viable for rectangular grids. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>Coordinates are assumed to be in lattice units. </p>
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<h1><a class="anchor" id="man_mesh_create_faceset_box">fix_modify AtC mesh create_faceset box </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC mesh create_faceset &lt;id&gt; box &lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt; &lt;in|out&gt; [units]</p>
<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" id="examples">
examples</a></h2>
<p><code> fix_modify AtC mesh create_faceset obndy box -4.0 4.0 -12 12 -12 12 out </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command to assign an id to a set of FE faces. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Only viable for rectangular grids. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>The default options are units = lattice and the use of outer faces </p>
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<h1><a class="anchor" id="man_mesh_create_faceset_plane">fix_modify AtC mesh create_faceset plane </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC mesh create_faceset &lt;id&gt; plane &lt;x|y|z&gt; &lt;val1&gt; &lt;x|y|z&gt; &lt;lval2&gt; &lt;uval2&gt; [units]</p>
<ul>
<li>&lt;id&gt; = id to assign to the collection of FE faces</li>
<li>&lt;x|y|z&gt; = coordinate directions that define plane on which faceset lies</li>
<li>&lt;val1&gt;,&lt;lval2&gt;,&lt;uval2&gt; = plane is specified as the x|y|z=val1 plane bounded by the segments x|y|z = [lval2,uval2]</li>
<li>units = option to specify real as opposed to lattice units </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC mesh create_faceset xyplane plane y 0 x -4 0 </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command to assign an id to a set of FE faces. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Only viable for rectangular grids. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>The default option is units = lattice. </p>
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<h1><a class="anchor" id="man_mesh_create_nodeset">fix_modify AtC mesh create_nodeset </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC mesh create_nodeset &lt;id&gt; &lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt;</p>
<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" id="examples">
examples</a></h2>
<p><code> fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -12 12 -12 12 </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command to assign an id to a set of FE nodes to be used subsequently in defining boundary conditions. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>Coordinates are assumed to be in lattice units. </p>
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<h1><a class="anchor" id="man_mesh_nodeset_to_elementset">fix_modify AtC mesh nodeset_to_elementset </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC nodeset_to_elementset &lt;nodeset_id&gt; &lt;elementset_id&gt; &lt;max/min&gt;</p>
<ul>
<li>&lt;nodeset_id&gt; = id of desired nodeset from which to create elementset</li>
<li>&lt;elementset_id&gt; = id to assign to the collection of FE element</li>
<li>&lt;max/min&gt; = flag to choose either the maximal or minimal elementset </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC mesh nodeset_to_elementset myNodeset myElementset min </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command to create an elementset from an existing nodeset. Either the minimal element set of elements with all nodes in the set, or maximal element set with all elements with at least one node in the set, can be created </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>None. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>Unless specified, the maximal element set is created </p>
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<h1><a class="anchor" id="man_mesh_quadrature">fix_modify AtC mesh quadrature </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC mesh quadrature &lt;quad&gt;</p>
<ul>
<li>quad = one of &lt;nodal|gauss1|gauss2|gauss3|face&gt; --- when a mesh is created it defaults to gauss2, use this call to change it after the fact </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC mesh quadrature face </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>(Re-)assigns the quadrature style for the existing mesh. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<p><a class="el" href="man_mesh_create.html">fix_modify AtC mesh create</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none </p>
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<h1><a class="anchor" id="man_mesh_read">fix_modify AtC mesh read </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC mesh read &lt;filename&gt; &lt;f|p&gt; &lt;f|p&gt; &lt;f|p&gt;</p>
<ul>
<li>filename = name of file containing mesh to be read</li>
<li>f p p = periodicity flags for x, y, z </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC mesh read myComponent.mesh p p p </code> <br/>
<code> fix_modify AtC mesh read myOtherComponent.exo </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Reads a mesh from a text or exodus file, and assigns periodic boundary conditions if needed. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>periodicity flags are false by default </p>
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<h1><a class="anchor" id="man_mesh_write">fix_modify AtC mesh write </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC mesh write &lt;filename&gt;</p>
<ul>
<li>filename = name of file to write mesh </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC mesh write myMesh.mesh </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Writes a mesh to a text file. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
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<h1><a class="anchor" id="man_momentum_time_integration">fix_modify AtC time_integration (momentum) </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC time_integration &lt;descriptor&gt; <br/>
</p>
<ul>
<li>descriptor (string) = time integration type <br/>
</li>
</ul>
<p>various time integration methods for the finite elements<br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>verlet - atomic velocity update with 2nd order Verlet, nodal temperature update with 2nd order Verlet, kinetostats based on controlling force <br/>
fractional_step - atomic velocity update with 2nd order Verlet, mixed nodal momentum update, 2nd order Verlet for continuum and exact 2nd order Verlet for atomic contributions, kinetostats based on controlling discrete momentum changes<br/>
gear - atomic velocity update with 2nd order Verlet, nodal temperature update with 3rd or 4th order Gear, kinetostats based on controlling power <br/>
</p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc time_integration verlet </code> <br/>
<code> fix_modify atc time_integration fractional_step </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<p>see <a class="el" href="man_fix_atc.html">fix atc command</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none </p>
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<h1><a class="anchor" id="man_output">fix_modify AtC output </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC output &lt;filename_prefix&gt; &lt;frequency&gt; [text | full_text | binary | vector_components | tensor_components ] fix_modify AtC output index [step | time ]</p>
<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 of index, step and nodal variable values for unique nodes <br/>
full_text = creates text output index, nodal id, step, nodal coordinates and nodal variable values for unique and image nodes <br/>
binary = creates 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" id="examples">
examples</a></h2>
<p><code> fix_modify AtC output heatFE 100 </code> <br/>
<code> fix_modify AtC output hardyFE 1 text tensor_components </code> <br/>
<code> fix_modify AtC output hardyFE 10 text binary tensor_components </code> <br/>
<code> fix_modify AtC output index step </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Creates text and/or binary (Ensight, "gold" format) output of nodal/mesh data which is transfer/physics specific. Output indexed by step or time is possible. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<p>see <a class="el" href="man_fix_atc.html">fix atc command</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>no default format output indexed by time </p>
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<h1><a class="anchor" id="man_output_elementset">fix_modify AtC output elementset </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC output volume_integral &lt;eset_name&gt; &lt;field&gt; {`</p>
<ul>
<li>set_name (string) = name of elementset to be integrated over</li>
<li>fieldname (string) = name of field to integrate csum = creates nodal sum over nodes in specified nodeset <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC output eset1 mass_density </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Performs volume integration of specified field over elementset and outputs resulting variable values to GLOBALS file. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<p>see <a class="el" href="man_fix_atc.html">fix atc command</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none </p>
</div>
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<h1><a class="anchor" id="man_output_nodeset">fix_modify AtC output nodeset </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC output nodeset &lt;nodeset_name&gt; &lt;operation&gt;</p>
<ul>
<li>nodeset_name (string) = name of nodeset to be operated on</li>
<li>operation (keyword/s): <br/>
sum = creates nodal sum over nodes in specified nodeset <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC output nodeset nset1 sum </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Performs operation over the nodes belonging to specified nodeset and outputs resulting variable values to GLOBALS file. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<p>see <a class="el" href="man_fix_atc.html">fix atc command</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none </p>
</div>
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<h1><a class="anchor" id="man_pair_interactions">fix_modify AtC pair_interactions/bond_interactions </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC pair_interactions &lt;on|off&gt; <br/>
fix_modify AtC bond_interactions &lt;on|off&gt; <br/>
</p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC bond_interactions on </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>include bonds and/or pairs in the stress and heat flux computations </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>pair interactions: on, bond interactions: off </p>
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<h1><a class="anchor" id="man_poisson_solver">fix_modify AtC poisson_solver </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC poisson_solver mesh create &lt;nx&gt; &lt;ny&gt; &lt;nz&gt; &lt;region-id&gt; &lt;f|p&gt; &lt;f|p&gt; &lt;f|p&gt;</p>
<ul>
<li>nx ny nz = number of elements in x, y, z</li>
<li>region-id = id of region that is to be meshed</li>
<li>f p p = perioidicity flags for x, y, z </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC poisson_solver mesh create 10 1 1 feRegion p p p </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Creates a uniform mesh in a rectangular region </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>creates only uniform rectangular grids in a rectangular region </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none </p>
</div>
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<h1><a class="anchor" id="man_remove_molecule">fix_modify AtC remove_molecule </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify_AtC remove_molecule &lt;TAG&gt; <br/>
</p>
<ul>
<li>&lt;TAG&gt; = tag for tracking a molecule type <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC remove_molecule water </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Removes tag designated for tracking a specified set of molecules. <br/>
</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>No defaults for this command. </p>
</div>
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<h1><a class="anchor" id="man_remove_species">fix_modify AtC remove_species </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify_AtC delete_species &lt;TAG&gt; <br/>
</p>
<ul>
<li>&lt;TAG&gt; = tag for tracking a species <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC remove_species gold </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Removes tag designated for tracking a specified species. <br/>
</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>No defaults for this command. </p>
</div>
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<h1><a class="anchor" id="man_reset_atomic_reference_positions">fix_modify AtC reset_atomic_reference_positions </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC reset_atomic_reference_positions </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc reset_atomic_reference_positions </code></p>
<h2><a class="anchor" id="description">
description</a></h2>
<p><code> Resets the atomic positions <a class="el" href="namespaceATC.html" title="owned field/s: MASS_DENSITY">ATC</a> uses to perform point to field operations. In can be used to use perfect lattice sites in <a class="el" href="namespaceATC.html" title="owned field/s: MASS_DENSITY">ATC</a> but a thermalized or deformed lattice in LAMMPS. </code></p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p><code> </code></p>
<h2><a class="anchor" id="related">
related</a></h2>
<p><code> </code></p>
<h2><a class="anchor" id="default">
default</a></h2>
<p><code> Default is off </code></p>
</div>
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<h1><a class="anchor" id="man_reset_time">fix_modify AtC reset_time </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC reset_time </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc reset_time 0.0 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Resets the simulation time counter. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC kernel_bandwidth </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc reset_time 8 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>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. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Only is used if kernel functions are being used. </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>Number of sample locations. </p>
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<h1><a class="anchor" id="man_sample_frequency">fix_modify AtC sample_frequency </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC sample_frequency [freq]</p>
<ul>
<li>freq (int) : frequency to sample field in number of steps </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC sample_frequency 10 </code></p>
<h2><a class="anchor" id="description">
description</a></h2>
<p><code> Specifies a frequency at which fields are computed for the case where time filters are being applied. </code></p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p><code> Must be used with the hardy/field AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) and is only relevant when time filters are being used. </code></p>
<h2><a class="anchor" id="related">
related</a></h2>
<p><code> </code></p>
<h2><a class="anchor" id="default">
default</a></h2>
<p><code> none </code></p>
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<h1><a class="anchor" id="man_set">fix_modify AtC set </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC set reference_potential_energy &lt;value_or_filename(optional)&gt;</p>
<ul>
<li>value (double) : optional user specified zero point for PE in native LAMMPS energy units <br/>
</li>
<li>filename (string) : optional user specified string for file of nodal PE values to be read-in </li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify AtC set reference_potential_energy </code> <br/>
<code> fix_modify AtC set reference_potential_energy -0.05 </code> <br/>
<code> fix_modify AtC set reference_potential_energy myPEvalues </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>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. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>Defaults to lammps zero point i.e. isolated atoms </p>
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<h1><a class="anchor" id="man_source_integration">fix_modify AtC source_integration </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC source_integration &lt; fe | atom&gt; </p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc source_integration atom </code> </p>
<h2><a class="anchor" id="description">
description</a></h2>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
<p>Default is fe </p>
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<h1><a class="anchor" id="man_temperature_definition">fix_modify AtC temperature_definition </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC temperature_definition &lt;kinetic|total&gt;</p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc temperature_definition kinetic </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Change the definition for the atomic temperature used to create the finite element temperature. The kinetic option is based only on the kinetic energy of the atoms while the total option uses the total energy (kinetic + potential) of an atom.</p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>This command is only valid when using thermal coupling. Also, while not a formal restriction, the user should ensure that associating a potential energy with each atom makes physical sense for the total option to be meaningful.</p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>kinetic </p>
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<h1><a class="anchor" id="man_thermal_time_integration">fix_modify AtC time_integration (thermal) </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC time_integration &lt;descriptor&gt; <br/>
</p>
<ul>
<li>descriptor (string) = time integration type <br/>
</li>
</ul>
<p>various time integration methods for the finite elements<br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>gear - atomic velocity update with 2nd order Verlet, nodal temperature update with 3rd or 4th order Gear, thermostats based on controlling power <br/>
fractional_step - atomic velocity update with 2nd order Verlet, mixed nodal temperature update, 3/4 Gear for continuum and 2 Verlet for atomic contributions, thermostats based on controlling discrete energy changes<br/>
</p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc time_integration gear </code> <br/>
<code> fix_modify atc time_integration fractional_step </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<p>see <a class="el" href="man_fix_atc.html">fix atc command</a> </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>none </p>
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<h1><a class="anchor" id="man_track_displacement">fix_modify AtC track_displacement </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC track_displacement &lt;on/off&gt; <br/>
</p>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc track_displacement on </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Determines whether displacement is tracked or not. For solids problems this is a useful quantity, but for fluids it is not relevant. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<p>Some constitutive models require the displacement field </p>
<h2><a class="anchor" id="default">
default</a></h2>
<p>on </p>
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<h1><a class="anchor" id="man_write_atom_weights">fix_modify AtC write_atom_weights </a></h1><h2><a class="anchor" id="syntax">
syntax</a></h2>
<p>fix_modify AtC write_atom_weights &lt;filename&gt; &lt;frequency&gt;</p>
<ul>
<li>&lt;filename&gt; = name of file that atomic weights are written to <br/>
</li>
<li>&lt;frequency&gt; = how often writes will occur <br/>
</li>
</ul>
<h2><a class="anchor" id="examples">
examples</a></h2>
<p><code> fix_modify atc write_atom_weights atm_wt_file.txt 10 </code> <br/>
</p>
<h2><a class="anchor" id="description">
description</a></h2>
<p>Command for writing the values of atomic weights to a specified file. </p>
<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
<h2><a class="anchor" id="related">
related</a></h2>
<h2><a class="anchor" id="default">
default</a></h2>
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