-Changes frame of reference from eulerian to lagrangian and sets the frequency for which the map from atoms to elements is reformed and all the attendant data is recalculated. <h2><a class="anchor" name="restrictions">
+<p>Changes frame of reference from eulerian to lagrangian and sets the frequency for which the map from atoms to elements is reformed and all the attendant data is recalculated. </p>
+<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
-Cannot change map type after initialization. <h2><a class="anchor" name="related">
+<p>Cannot change map type after initialization. </p>
+<h2><a class="anchor" id="related">
related</a></h2>
-<h2><a class="anchor" name="default">
+<h2><a class="anchor" id="default">
default</a></h2>
-lagrangian <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by
+<p>lagrangian </p>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
+ 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/>
+<p>fix_modify AtC boundary type <atom-type-id></p>
+<ul>
+<li><atom-type-id> = 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>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
+<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>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
-Calculates a surface integral of the given field dotted with the outward normal of the faces and puts output in the "GLOBALS" file <h2><a class="anchor" name="restrictions">
+<p>Calculates a surface integral of the given field dotted with the outward normal of the faces and puts output in the "GLOBALS" file </p>
+<h2><a class="anchor" id="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">
+<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" name="default">
+<h2><a class="anchor" id="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
+<p>none </p>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
+<li><on|off> = 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>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
-Calculates a surface integral of the given field dotted with the outward normal of the faces and puts output in the "GLOBALS" file <h2><a class="anchor" name="restrictions">
+<p>Calculates a surface integral of the given field dotted with the outward normal of the faces and puts output in the "GLOBALS" file </p>
+<h2><a class="anchor" id="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">
+<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" name="default">
+<h2><a class="anchor" id="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
+<p>none </p>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
+<p>fix_modify AtC transfer <physics_type> control max_iterations <max_iterations><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 <physics_type> control tolerance <tolerance> <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>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
+<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 <frequency><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>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
+<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/>
+<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>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
+<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 <max_iterations></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>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
-<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 <frequency><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
-Switches between integration scheme for the electron temperature. The number of subcyling steps used to integrate the electron temperature 1 LAMMPS timestep can be manually adjusted to capture fast electron dynamics.<h2><a class="anchor" name="restrictions">
+<p>Switches between integration scheme for the electron temperature. The number of subcyling steps used to integrate the electron temperature 1 LAMMPS timestep can be manually adjusted to capture fast electron dynamics.</p>
+<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
-For use only with two_temperature type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) <br>
- <h2><a class="anchor" name="default">
+<p>For use only with two_temperature type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) <br/>
+ </p>
+<h2><a class="anchor" id="default">
default</a></h2>
-implicit<br>
- subcycle_steps = 1 <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by
+<p>implicit<br/>
+ subcycle_steps = 1 </p>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
+<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>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
-Filters the MD dynamics to construct a more appropriate continuous field. Equilibrating first filters the time derivatives without changing the dynamics to provide a better initial condition to the filtered dynamics <h2><a class="anchor" name="restrictions">
+<p>Filters the MD dynamics to construct a more appropriate continuous field. Equilibrating first filters the time derivatives without changing the dynamics to provide a better initial condition to the filtered dynamics </p>
+<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
-only for be used with specific transfers: thermal, two_temperature<h2><a class="anchor" name="related">
+<p>only for be used with specific transfers: thermal, two_temperature</p>
+<h2><a class="anchor" id="related">
related</a></h2>
-<a class="el" href="man_time_filter.html">fix_modify AtC transfer filter</a><h2><a class="anchor" name="default">
-This fix is the beginning to creating a coupled FE/MD simulation and/or an on-the-fly estimation of continuum fields. The coupled versions of this fix do Verlet integration and the Hardy/post-processing does not. After instantiating this fix, several other fix_modify commands will be needed to set up the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions.<p>
-The following coupling example is typical, but non-exhaustive:<br>
-<p>
-<code> # ... commands to create and initialize the MD system <br>
-</code><p>
-<code> # initial fix to designate coupling type and group to apply it to <br>
- # tag group physics material_file <br>
- fix AtC internal atc thermal Ar_thermal.mat<br>
- <br>
- # create a uniform 12 x 2 x 2 mesh that covers region contain the group <br>
- # nx ny nz region periodicity <br>
- fix_modify AtC fem create mesh 12 2 2 mdRegion f p p<br>
- <br>
- # specify the control method for the type of coupling <br>
- # physics control_type <br>
- fix_modify AtC transfer thermal control flux <br>
- <br>
- # specify the initial values for the empirical field "temperature" <br>
- # field node_group value <br>
- fix_modify AtC transfer initial temperature all 30.<br>
- <br>
- # create an output stream for nodal fields <br>
- # filename output_frequency <br>
- fix_modify AtC transfer output atc_fe_output 100<br>
- <br>
-</code><p>
-<code> run 1000 <br>
- </code><p>
-likewise for this post-processing example: <br>
-<p>
-<code> # ... commands to create and initialize the MD system <br>
-</code><p>
-<code> # initial fix to designate post-processing and the group to apply it to <br>
- # no material file is allowed nor required <br>
- fix AtC internal atc hardy <br>
- <br>
- # create a uniform 1 x 1 x 1 mesh that covers region contain the group <br>
- # with periodicity this effectively creats a system average <br>
- fix_modify AtC fem create mesh 1 1 1 box p p p <br>
-<br>
- # change from default lagrangian map to eulerian <br>
- # add mass density, potential energy density, stress and temperature <br>
- fix_modify AtC transfer fields add density energy stress temperature <br>
-<br>
- # create an output stream for nodal fields <br>
- # filename output_frequency <br>
- fix_modify AtC transfer output nvtFE 100 text <br>
-</code><p>
-<code> run 1000 <br>
- </code><p>
-Note coupling and post-processing can be combined in the same simulations using separate fixes. <br>
- For detailed exposition of the theory and algorithms please see:<br>
+<p>This fix is the beginning to creating a coupled FE/MD simulation and/or an on-the-fly estimation of continuum fields. The coupled versions of this fix do Verlet integration and the /post-processing does not. After instantiating this fix, several other fix_modify commands will be needed to set up the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions.</p>
+<p>The following coupling example is typical, but non-exhaustive:<br/>
+</p>
+<p><code> # ... commands to create and initialize the MD system <br/>
+</code></p>
+<p><code> # initial fix to designate coupling type and group to apply it to <br/>
+ # add mass density, potential energy density, stress and temperature <br/>
+ fix_modify AtC fields add density energy stress temperature <br/>
+<br/>
+ # create an output stream for nodal fields <br/>
+ # filename output_frequency <br/>
+ fix_modify AtC output nvtFE 100 text <br/>
+</code></p>
+<p><code> run 1000 <br/>
+ </code></p>
+<p>the mesh's linear interpolation functions can be used as the localization function <br/>
+ by using the field option: <br/>
+</p>
+<p><code> fix AtC internal atc field <br/>
+ <br/>
+ fix_modify AtC mesh create 1 1 1 box p p p <br/>
+<br/>
+ ... <br/>
+<br/>
+ </code></p>
+<p>Note coupling and post-processing can be combined in the same simulations using separate fixes. <br/>
+ For detailed exposition of the theory and algorithms please see:<br/>
+</p>
<ul>
-<li>Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA. <em> An atomistic-to-continuum coupling method for heat transfer in solids. </em> Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351.</li><li>Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, <em> Calculation of stress in atomistic simulation </em> Special Issue of Modelling and Simulation in Materials Science and Engineering (2004), 12:S319</li></ul>
-<p>
-Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes <em> The finite element method </em>, Dover 2003, for the basics of FE simulation.<h2><a class="anchor" name="restrictions">
+<li>Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, <em> An atomistic-to-continuum coupling method for heat transfer in solids. </em> Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351. <br/>
+</li>
+<li>Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, <em> Calculation of stress in atomistic simulation. </em> Special Issue of Modelling and Simulation in Materials Science and Engineering (2004), 12:S319. <br/>
+</li>
+<li>Zimmerman, JA; Jones, RE; Templeton, JA, <em> A material frame approach for evaluating continuum variables in atomistic simulations. </em> Journal of Computational Physics (2010), 229:2364. <br/>
+</li>
+<li>Templeton, JA; Jones, RE; Wagner, GJ, <em> Application of a field-based method to spatially varying thermal transport problems in molecular dynamics. </em> Modelling and Simulation in Materials Science and Engineering (2010), 18:085007. <br/>
+</li>
+<li>Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine, JA, <em> Electron transport enhanced molecular dynamics for metals and semi-metals. </em> International Journal for Numerical Methods in Engineering (2010), 83:940. <br/>
+</li>
+<li>Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, <em> A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling. </em> Journal of Chemical Theory and Computation (2011), 7:1736. <br/>
+</li>
+<li>Mandadapu, KK; Templeton, JA; Lee, JW, <em> Polarization as a field variable from molecular dynamics simulations. </em> Journal of Chemical Physics (2013), 139:054115. <br/>
+</li>
+</ul>
+<p>Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes <em> The finite element method </em>, Dover 2003, for the basics of FE simulation.</p>
+<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
-Thermal and two_temperature (coupling) types use a Verlet time-integration algorithm. The hardy type does not contain its own time-integrator and must be used with a separate fix that does contain one, e.g. nve, nvt, etc.<p>
-Currently,<ul>
-<li>the coupling is restricted to thermal physics</li><li>the FE computations are done in serial on each processor.</li></ul>
-<h2><a class="anchor" name="related">
+<p>Thermal and two_temperature (coupling) types use a Verlet time-integration algorithm. The hardy type does not contain its own time-integrator and must be used with a separate fix that does contain one, e.g. nve, nvt, etc.</p>
+<p>Currently,</p>
+<ul>
+<li>the coupling is restricted to thermal physics</li>
+<li>the FE computations are done in serial on each processor.</li>
+</ul>
+<h2><a class="anchor" id="related">
related</a></h2>
-fix_modify commands for setup: <br>
+<p>fix_modify commands for setup: <br/>
+</p>
<ul>
-<li><a class="el" href="man_fem_mesh.html">fix_modify AtC fem create mesh</a></li><li><a class="el" href="man_mesh_nodeset.html">fix_modify AtC mesh create_nodeset</a></li><li><a class="el" href="man_mesh_faceset.html">fix_modify AtC mesh create_faceset</a></li><li><a class="el" href="man_mesh_elemset.html">fix_modify AtC mesh create_elementset</a></li><li><a class="el" href="man_transfer_internal.html">fix_modify AtC transfer internal</a></li><li><a class="el" href="man_transfer_boundary.html">fix_modify AtC transfer boundary</a></li><li><a class="el" href="man_internal_quadrature.html">fix_modify AtC transfer internal_quadrature</a></li><li><a class="el" href="man_time_integration.html">fix_modify AtC transfer pmfc</a></li><li><a class="el" href="man_electron_integration.html">fix_modify AtC extrinsic electron_integration</a></li></ul>
-<p>
-fix_modify commands for boundary and initial conditions:<br>
-fix_modify AtC transfer fix_flux <field> <face_set> <value | function><ul>
-<li><field> = field name valid for type of physics, temperature | electron_temperature</li><li><face_set> = name of set of element faces </li></ul>
+<li><field> = field name valid for type of physics, temperature | electron_temperature</li>
+<li><face_set> = name of set of element faces </li>
+</ul>
+<h2><a class="anchor" id="examples">
examples</a></h2>
-<code> fix_modify atc transfer fix_flux temperature faceSet 10.0 </code> <br>
-<h2><a class="anchor" name="description">
+<p><code> fix_modify atc fix_flux temperature faceSet 10.0 </code> <br/>
+</p>
+<h2><a class="anchor" id="description">
description</a></h2>
-Command for fixing normal fluxes e.g. heat_flux. This command only prescribes the normal component of the physical flux, e.g. heat (energy) flux. The units are in AtC units, i.e. derived from the LAMMPS length, time, and mass scales. <h2><a class="anchor" name="restrictions">
+<p>Command for fixing normal fluxes e.g. heat_flux. This command only prescribes the normal component of the physical flux, e.g. heat (energy) flux. The units are in AtC units, i.e. derived from the LAMMPS length, time, and mass scales. </p>
+<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
-Only normal fluxes (Neumann data) can be prescribed. <h2><a class="anchor" name="related">
+<p>Only normal fluxes (Neumann data) can be prescribed. </p>
+<h2><a class="anchor" id="related">
related</a></h2>
-see <a class="el" href="man_unfix_flux.html">fix_modify AtC transfer unfix_flux</a> <h2><a class="anchor" name="default">
-fix_modify AtC transfer fix <field> <nodeset> <constant | function><ul>
-<li><field> = field name valid for type of physics</li><li><nodeset> = name of set of nodes to apply boundary condition</li><li><constant | function> = value or name of function followed by its parameters </li></ul>
-<li>add | delete (keyword) = add or delete the calculation of an equivalent continuum field for the specified per-atom compute as volume or number density quantity <br>
-</li><li>per-atom compute id = name/id for per-atom compute, fields can be calculated for all per-atom computes available from LAMMPS <br>
-</li><li>volume | number (keyword) = field created is a per-unit-volume quantity or a per-atom quantity as weighted by kernel functions <br>
-</li></ul>
-<h2><a class="anchor" name="examples">
+<li>add | delete (keyword) = add or delete the calculation of an equivalent continuum field for the specified per-atom compute as volume or number density quantity <br/>
+</li>
+<li>per-atom compute id = name/id for per-atom compute, fields can be calculated for all per-atom computes available from LAMMPS <br/>
+</li>
+<li>volume | number (keyword) = field created is a per-unit-volume quantity or a per-atom quantity as weighted by kernel functions <br/>
+</li>
+</ul>
+<h2><a class="anchor" id="examples">
examples</a></h2>
-<code> compute virial all stress/atom </code> <br>
-<li>all | none (keyword) = output all or no fields <br>
-</li><li>add | delete (keyword) = add or delete the listed output fields <br>
-</li><li>fields (keyword) = <br>
- density : mass per unit volume <br>
- displacement : displacement vector <br>
- momentum : momentum per unit volume <br>
- velocity : defined by momentum divided by density <br>
- projected_velocity : simple kernel estimation of atomic velocities <br>
- temperature : temperature derived from the relative atomic kinetic energy (as done by Hardy) <br>
- kinetic_temperature : temperature derived from the full kinetic energy <br>
- energy : total energy (potential + kinetic) per unit volume <br>
- number_density : simple kernel estimation of number of atoms per unit volume <br>
- stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or 1st Piola-Kirchhoff stress tensor for lagrangian analysis <br>
- transformed_stress : 1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis <br>
- heat_flux : spatial heat flux vector for eulerian, or referential heat flux vector for lagrangian <br>
- </li></ul>
-<h2><a class="anchor" name="examples">
+<li>all | none (keyword) = output all or no fields <br/>
+</li>
+<li>add | delete (keyword) = add or delete the listed output fields <br/>
+</li>
+<li>fields (keyword) = <br/>
+ density : mass per unit volume <br/>
+ displacement : displacement vector <br/>
+ momentum : momentum per unit volume <br/>
+ velocity : defined by momentum divided by density <br/>
+ projected_velocity : simple kernel estimation of atomic velocities <br/>
+ temperature : temperature derived from the relative atomic kinetic energy (as done by ) <br/>
+ kinetic_temperature : temperature derived from the full kinetic energy <br/>
+ number_density : simple kernel estimation of number of atoms per unit volume <br/>
+ stress : Cauchy stress tensor for eulerian analysis (atom_element_map), or 1st Piola-Kirchhoff stress tensor for lagrangian analysis <br/>
+ transformed_stress : 1st Piola-Kirchhoff stress tensor for eulerian analysis (atom_element_map), or Cauchy stress tensor for lagrangian analysis <br/>
+ heat_flux : spatial heat flux vector for eulerian, or referential heat flux vector for lagrangian <br/>
+ potential_energy : potential energy per unit volume <br/>
+ kinetic_energy : kinetic energy per unit volume <br/>
+ thermal_energy : thermal energy (kinetic energy - continuum kinetic energy) per unit volume <br/>
+ internal_energy : total internal energy (potential + thermal) per unit volume <br/>
+ energy : total energy (potential + kinetic) per unit volume <br/>
+ number_density : number of atoms per unit volume <br/>
+ eshelby_stress: configurational stress (energy-momentum) tensor defined by Eshelby [References: Philos. Trans. Royal Soc. London A, Math. Phys. Sci., Vol. 244, No. 877 (1951) pp. 87-112; J. Elasticity, Vol. 5, Nos. 3-4 (1975) pp. 321-335] <br/>
+ vacancy_concentration: volume fraction of vacancy content <br/>
+ type_concentration: volume fraction of a specific atom type <br/>
+ </li>
+</ul>
+<h2><a class="anchor" id="examples">
examples</a></h2>
-<code> fix_modify AtC transfer fields add velocity temperature </code> <h2><a class="anchor" name="description">
+<p><code> fix_modify AtC fields add velocity temperature </code> </p>
+<h2><a class="anchor" id="description">
description</a></h2>
-Allows modification of the fields calculated and output by the Hardy transfer class. The commands are cumulative, e.g.<br>
- <code> fix_modify AtC transfer fields none </code> <br>
- followed by <br>
- <code> fix_modify AtC transfer fields add velocity temperature </code> <br>
- will only output the velocity and temperature fields. <h2><a class="anchor" name="restrictions">
+<p>Allows modification of the fields calculated and output by the transfer class. The commands are cumulative, e.g.<br/>
+ <code> fix_modify AtC fields none </code> <br/>
+ followed by <br/>
+ <code> fix_modify AtC fields add velocity temperature </code> <br/>
+ will only output the velocity and temperature fields. </p>
+<h2><a class="anchor" id="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>. Currently, the stress and heat flux formulas are only correct for central force potentials, e.g. Lennard-Jones and EAM but not Stillinger-Weber. <h2><a class="anchor" name="related">
+<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>. Currently, the stress and heat flux formulas are only correct for central force potentials, e.g. Lennard-Jones and EAM but not Stillinger-Weber. </p>
+<h2><a class="anchor" id="related">
related</a></h2>
-See <a class="el" href="man_hardy_gradients.html">fix_modify AtC transfer gradients</a> , <a class="el" href="man_hardy_rates.html">fix_modify AtC transfer rates</a> and <a class="el" href="man_hardy_computes.html">fix_modify AtC transfer computes</a> <h2><a class="anchor" name="default">
-Requests calculation and ouput of gradients of the fields from the Hardy transfer class. These gradients will be with regard to spatial or material coordinate for eulerian or lagrangian analysis, respectively, as specified by atom_element_map (see <a class="el" href="man_atom_element_map.html">fix_modify AtC transfer atom_element_map</a> ) <h2><a class="anchor" name="restrictions">
+<p>Requests calculation and ouput of gradients of the fields from the transfer class. These gradients will be with regard to spatial or material coordinate for eulerian or lagrangian analysis, respectively, as specified by atom_element_map (see <a class="el" href="man_atom_element_map.html">fix_modify AtC atom_element_map</a> ) </p>
+<h2><a class="anchor" id="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">
+<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" name="default">
+<h2><a class="anchor" id="default">
default</a></h2>
-No gradients are calculated by default <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by
+<p>No gradients are calculated by default </p>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
+ <code> fix_modify AtC on_the_fly kernel off </code> <br/>
+ </p>
+<h2><a class="anchor" id="description">
description</a></h2>
-Overrides normal mode of pre-calculating and storing bond pair-to-node and kernel atom-to-node matrices. If activated, will calculate elements of these matrices during repeated calls of field computations (i.e. "on-the-fly") and not store them for future use. <br>
- on flag is optional - if omitted, on_the_fly will be activated for the specified matrix. Can be deactivated using off flag. <br>
- <h2><a class="anchor" name="restrictions">
+<p>Overrides normal mode of pre-calculating and storing bond pair-to-node a nd kernel atom-to-node matrices. If activated, will calculate elements of t hese matrices during repeated calls of field computations (i.e. "on-the-fly") and not store them for future use. <br/>
+ on flag is optional - if omitted, on_the_fly will be activated for the s pecified matrix. Can be deactivated using off flag. <br/>
+ </p>
+<h2><a class="anchor" id="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">
+<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" name="default">
+<h2><a class="anchor" id="default">
default</a></h2>
-By default, on-the-fly calculation is not active (i.e. off). However, code does a memory allocation check to determine if it can store all needed bond and kernel matrix elements. If this allocation fails, on-the-fly is activated. <br>
- <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by
+<p>By default, on-the-fly calculation is not active (i.e. off). However, code does a memory allocation check to determine if it can store all needed bond and kernel matrix ele ments. If this allocation fails, on-the-fly is activated. <br/>
+ </p>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
-Requests calculation and ouput of rates (time derivatives) of the fields from the Hardy transfer class. For eulerian analysis (see <a class="el" href="man_atom_element_map.html">fix_modify AtC transfer atom_element_map</a> ), these rates are the partial time derivatives of the nodal fields, not the full (material) time derivatives. <br>
- <h2><a class="anchor" name="restrictions">
+<p>Requests calculation and ouput of rates (time derivatives) of the fields from the transfer class. For eulerian analysis (see <a class="el" href="man_atom_element_map.html">fix_modify AtC atom_element_map</a> ), these rates are the partial time derivatives of the nodal fields, not the full (material) time derivatives. <br/>
+ </p>
+<h2><a class="anchor" id="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">
+<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" name="default">
+<h2><a class="anchor" id="default">
default</a></h2>
-No rates are calculated by default <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by
+<p>No rates are calculated by default </p>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
-fix_modify AtC transfer set reference_potential_energy <value><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
-fix_modify AtC transfer initial <field> <nodeset> <constant | function><ul>
-<li><field> = field name valid for type of physics, temperature | electron_temperature</li><li><nodeset> = name of set of nodes to apply boundary condition</li><li><constant | function> = value or name of function followed by its parameters </li></ul>
+<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>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
-<code> fix_modify atc transfer internal_quadrature off </code> <h2><a class="anchor" name="description">
+<p><code> fix_modify atc internal_quadrature off </code> </p>
+<h2><a class="anchor" id="description">
description</a></h2>
-Command use or not use atomic quadrature on internal elements fully filled with atoms. By turning the internal quadrature off these elements do not contribute to the governing PDE and the fields at the internal nodes follow the weighted averages of the atomic data. <h2><a class="anchor" name="restrictions">
+<p>Command to use or not use atomic quadrature on internal elements fully filled with atoms. By turning the internal quadrature off these elements do not contribute to the governing PDE and the fields at the internal nodes follow the weighted averages of the atomic data. </p>
+<h2><a class="anchor" id="optional">
+optional</a></h2>
+<p>Optional region tag specifies which finite element nodes will be treated as being within the MD region. This option is only valid with internal_quadrature off. </p>
+<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
-<h2><a class="anchor" name="related">
+<h2><a class="anchor" id="related">
related</a></h2>
-<h2><a class="anchor" name="default">
+<h2><a class="anchor" id="default">
default</a></h2>
-on <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by
+<p>on </p>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
+<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 <on|off> </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>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
+<li><fe | md_fe> = 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>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
+<li><id> = id of FE nodeset to be added to</li>
+<li><xmin> <xmax> <ymin> <ymax> <zmin> <zmax> = coordinates of the bounding box that contains the desired nodes to be added </li>
+<li><id> = id to assign to the collection of FE element</li>
+<li><xmin> <xmax> <ymin> <ymax> <zmin> <zmax> = coordinates of the bounding box that contains only the desired elements </li>
+<li><id> = id to assign to the collection of FE faces</li>
+<li><xmin> <xmax> <ymin> <ymax> <zmin> <zmax> = coordinates of the bounding box that is coincident with the desired FE faces</li>
+<li><in|out> = "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>
+<li><id> = id to assign to the collection of FE nodes</li>
+<li><xmin> <xmax> <ymin> <ymax> <zmin> <zmax> = coordinates of the bounding box that contains only the desired nodes </li>
-<li><id> = id to assign to the collection of FE element</li><li><xmin> <xmax> <ymin> <ymax> <zmin> <zmax> = coordinates of the bounding box that contains only the desired elements </li></ul>
-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
-<li><id> = id to assign to the collection of FE faces</li><li><xmin> <xmax> <ymin> <ymax> <zmin> <zmax> = coordinates of the bounding box that is coincident with the desired FE faces</li><li><in|out> = "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>
-<li><id> = id to assign to the collection of FE nodes</li><li><xmin> <xmax> <ymin> <ymax> <zmin> <zmax> = coordinates of the bounding box that contains only the desired nodes </li></ul>
-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
+<li><nodeset_id> = id of desired nodeset from which to create elementset</li>
+<li><elementset_id> = id to assign to the collection of FE element</li>
+<li><max/min> = 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>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
-Command to output mesh and associated data: nodesets, facesets, and elementsets. This data is only output once upon initialization since currently the mesh is static. Creates (binary, "gold" format) Ensight output of mesh data. <h2><a class="anchor" name="restrictions">
+<p>Command to output mesh and associated data: nodesets, facesets, and elementsets. This data is only output once upon initialization since currently the mesh is static. Creates (binary, "gold" format) Ensight output of mesh data. </p>
+<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
-none <h2><a class="anchor" name="related">
+<p>none </p>
+<h2><a class="anchor" id="related">
related</a></h2>
-<h2><a class="anchor" name="default">
+<h2><a class="anchor" id="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
+<p>none </p>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
+<li>quad = one of <nodal|gauss1|gauss2|gauss3|face> --- 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>
+<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/>
-<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 <frequency><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
+ <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>
-Reads the current state of the fields from a named text-based restart file. <h2><a class="anchor" name="restrictions">
+<p>Reads the current state of the fields from a named text-based restart file. </p>
+<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
-The restart file only contains fields and their time derivatives. The reference positions of the atoms and the commands that initialize the fix are not saved e.g. an identical mesh containing the same atoms will have to be recreated. <h2><a class="anchor" name="related">
+<p>The restart file only contains fields and their time derivatives. The reference positions of the atoms and the commands that initialize the fix are not saved e.g. an identical mesh containing the same atoms will have to be recreated. </p>
+<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>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
+<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>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
+<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>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
+<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 <value_or_filename(optional)></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>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
-Add domain sources to the mesh. The units are consistent with LAMMPS's units for mass, length and time and are defined by the PDE being solved, e.g. for thermal transfer the balance equation is for energy and source is energy per time. <h2><a class="anchor" name="restrictions">
+<p>Add domain sources to the mesh. The units are consistent with LAMMPS's units for mass, length and time and are defined by the PDE being solved, e.g. for thermal transfer the balance equation is for energy and source is energy per time. </p>
+<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
-keyword 'all' reserved in element_set name <h2><a class="anchor" name="related">
+<p>keyword 'all' reserved in element_set name </p>
+<h2><a class="anchor" id="related">
related</a></h2>
-see <a class="el" href="man_remove_source.html">fix_modify AtC transfer remove_source</a> <h2><a class="anchor" name="default">
+<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>
+</div>
+<hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by
-</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
+<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/>
-fix_modify AtC transfer filter <on | off | equilibrate> <br>
+<p>fix_modify AtC filter <on | off | equilibrate> <br/>
+</p>
<ul>
-<li>on | off (keyword) = turns filter on or off<br>
-</li><li>equilibrate = runs dynamics without filtering but initializes filtered quantities </li></ul>
-<h2><a class="anchor" name="examples">
+<li>on | off (keyword) = turns filter on or off<br/>
+</li>
+<li>equilibrate = runs dynamics without filtering but initializes filtered quantities </li>
+</ul>
+<h2><a class="anchor" id="examples">
examples</a></h2>
-<code> fix_modify atc transfer filter on </code> <br>
-<h2><a class="anchor" name="description">
+<p><code> fix_modify atc transfer filter on </code> <br/>
+</p>
+<h2><a class="anchor" id="description">
description</a></h2>
-Filters the MD dynamics to construct a more appropriate continuous field. Equilibrating first filters the time derivatives without changing the dynamics to provide a better initial condition to the filtered dynamics<h2><a class="anchor" name="restrictions">
+<p>Filters the MD dynamics to construct a more appropriate continuous field. Equilibrating first filters the time derivatives without changing the dynamics to provide a better initial condition to the filtered dynamics</p>
+<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
-only for be used with specific transfers: thermal, two_temperature<h2><a class="anchor" name="related">
+<p>only for be used with specific transfers: thermal, two_temperature</p>
+<h2><a class="anchor" id="related">
related</a></h2>
-<a class="el" href="man_filter_scale.html">fix_modify AtC transfer filter scale</a> <br>
- <a class="el" href="man_equilibrium_start.html">fix_modify AtC transfer equilibrium_start</a><h2><a class="anchor" name="default">
-<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 <on|off><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
-<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 <filename_prefix> <frequency> [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>
-none <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by
-<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 <atom-type-id><ul>
-<li><atom-type-id> = 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>
-none <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by
-<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 <atom-type-id><ul>
-<li><atom-type-id> = 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>
-none <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by
-<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">
-fix_modify AtC transfer fix_flux <field> <face_set> <value | function><ul>
-<li><field> = field name valid for type of physics, temperature | electron_temperature</li><li><face_set> = name of set of element faces </li></ul>
-Dumps the current state of the fields to a named text-based restart file. This done when the command is invoked and not repeated, unlike the similar lammps command. <h2><a class="anchor" name="restrictions">
+<p>Dumps the current state of the fields to a named text-based restart file. This done when the command is invoked and not repeated, unlike the similar lammps command. </p>
+<h2><a class="anchor" id="restrictions">
restrictions</a></h2>
-The restart file only contains fields and their time derivatives. The reference positions of the atoms and the commands that initialize the fix are not saved e.g. an identical mesh containing the same atoms will have to be recreated. <h2><a class="anchor" name="related">
+<p>The restart file only contains fields and their time derivatives. The reference positions of the atoms and the commands that initialize the fix are not saved e.g. an identical mesh containing the same atoms will have to be recreated. </p>
<PRE>fix ID group-ID style bodystyle args keyword values ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>style = <I>rigid</I> or <I>rigid/nve</I> or <I>rigid/nvt</I> or <I>rigid/npt</I> or <I>rigid/nph</I> or <I>rigid/small</I>
<LI>bodystyle = <I>single</I> or <I>molecule</I> or <I>group</I>
<PRE> <I>single</I> args = none
<I>molecule</I> args = none
<I>group</I> args = N groupID1 groupID2 ...
N = # of groups
groupID1, groupID2, ... = list of N group IDs
</PRE>
<LI>zero or more keyword/value pairs may be appended
<LI>keyword = <I>langevin</I> or <I>temp</I> or <I>iso</I> or <I>aniso</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>couple</I> or <I>tparam</I> or <I>pchain</I> or <I>dilate</I> or <I>force</I> or <I>torque</I> or <I>infile</I>
fix ID group-ID style bodystyle args keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
style = {rigid} or {rigid/nve} or {rigid/nvt} or {rigid/npt} or {rigid/nph} or {rigid/small} :l
bodystyle = {single} or {molecule} or {group} :l
{single} args = none
{molecule} args = none
{group} args = N groupID1 groupID2 ...
N = # of groups
groupID1, groupID2, ... = list of N group IDs :pre
zero or more keyword/value pairs may be appended :l
keyword = {langevin} or {temp} or {iso} or {aniso} or {x} or {y} or {z} or {couple} or {tparam} or {pchain} or {dilate} or {force} or {torque} or {infile} :l
{langevin} values = Tstart Tstop Tperiod seed
Tstart,Tstop = desired temperature at start/stop of run (temperature units)
Tdamp = temperature damping parameter (time units)
seed = random number seed to use for white noise (positive integer)
{temp} values = Tstart Tstop Tdamp
Tstart,Tstop = desired temperature at start/stop of run (temperature units)
Tdamp = temperature damping parameter (time units)
{iso} or {aniso} values = Pstart Pstop Pdamp
Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
Pdamp = pressure damping parameter (time units)
{x} or {y} or {z} values = Pstart Pstop Pdamp
Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
Pdamp = stress damping parameter (time units)
{couple} = {none} or {xyz} or {xy} or {yz} or {xz}
{tparam} values = Tchain Titer Torder
Tchain = length of Nose/Hoover thermostat chain
Titer = number of thermostat iterations performed
Torder = 3 or 5 = Yoshida-Suzuki integration parameters
{pchain} values = Pchain
Pchain = length of the Nose/Hoover thermostat chain coupled with the barostat
{dilate} value = dilate-group-ID
dilate-group-ID = only dilate atoms in this group due to barostat volume changes
{force} values = M xflag yflag zflag
M = which rigid body from 1-Nbody (see asterisk form below)
xflag,yflag,zflag = off/on if component of center-of-mass force is active
{torque} values = M xflag yflag zflag
M = which rigid body from 1-Nbody (see asterisk form below)
xflag,yflag,zflag = off/on if component of center-of-mass torque is active
{infile} filename
filename = file with per-body values of mass, center-of-mass, moments of inertia :pre
:ule
[Examples:]
fix 1 clump rigid single
fix 1 clump rigid/small molecule
fix 1 clump rigid single force 1 off off on langevin 1.0 1.0 1.0 428984
This directory contains examples run using the AtC library in LAMMPS
in its various coupling and post-processing modes. Descriptions of
the files in each are provided below. In addition to the included
output these examples will "dump" mesh-based data either in binary
(Ensight) format or simple column-based text format (for gnuplot, for
example).
-bar1d_thermal:
- input files:
- in.bar1d - Atoms comprise a subset of a 1D finite element bar,
- heated at the left end and cooled at the right end.
- A Gaussian isokinetic thermostat is used to keep the atomic
- kinetic temperature equal to the finite element temperature
- at the boundaries.
- in.bar1d_flux - Same setup and geometry as in.bar1d.
- A Gaussian isokinetic thermostat is used to transfer
- the FE heat flux to the atoms at the boundaries.
- Ar_thermal.mat - Material parameter file specifying
- the thermal properties of argon.
- temp.init - Initial set of atomic positions and velocities.
+cauchy_born:
+ input files:
+ in.cb_biaxial - Computes Hardy and Cauchy-Born metrics of energy density and stress for an lj/cut Ar system subjected to biaxial deformation equivalent to shearing
+ in.cb_shear - Computes Hardy and Cauchy-Born metrics of energy density and stress for an lj/cut Ar system subjected to shear deformation
+ in.cb_unistrain - Computes Hardy and Cauchy-Born metrics of energy density and stress for an lj/cut Ar system subjected to uniaxial strain deformation
+ in.cb_unistrain - Computes Hardy and Cauchy-Born metrics of energy density and stress for an lj/cut Ar system subjected to uniaxial strain deformation
+ in.cb_unistrain_eam - Computes Hardy and Cauchy-Born metrics of energy density and stress for an EAM Cu system subjected to uniaxial strain deformation
+ in.cb_unistrain_eam_linear - Computes Hardy and Cauchy-Born metrics of energy density and stress for an EAM Au system subjected to uniaxial strain deformation; Compares non-linear Cauchy-Born expressions with linearized versions
+ in.cb_volumetric - Computes Hardy and Cauchy-Born metrics of energy density and stress for an lj/cut Ar system subjected to volumetric stretching
+ in.flying_cube - Computes Hardy fields for a small block of LJ material undergoing translation in the x-direction through the periodic boundary
+ in.ftcb_constV - Computes Hardy and Cauchy-Born metrics of energy density and stress for an lj/cut Ar system undergoing dynamics at a finite temperature.
+ in.read_xref - Test for reading an atomic reference configuration
+
+ material files:
+ Ar_CauchyBorn.mat - Parameters used for constructing a Cauchy-Born equivalent model of a lj/cut Ar material
+ Ar_CauchyBorn_linear.mat - Parameters used for constructing a linearized Cauchy-Born equivalent model of a lj/cut Ar material
+ Au_CauchyBorn.mat - Parameters used for constructing a Cauchy-Born equivalent model of a lj/smooth/linear Au material
+ Au_CauchyBorn.mat - Parameters used for constructing a linearized Cauchy-Born equivalent model of a lj/smooth/linear Au material
+ Au_eam.mat - Parameters used for constructing a Cauchy-Born equivalent model of an EAM Au material
+ Au_eam_linear.mat - Parameters used for constructing a linearized Cauchy-Born equivalent model of an EAM Au material
+ Cu_CauchyBorn.mat - Parameters used for constructing a Cauchy-Born equivalent model of an EAM Cu material
output files:
- bar1d.log - LAMMPS log file generated by running in.bar1d.
- bar1d_flux.log - LAMMPS log file generated by running in.bar1d_flux.
+ XXX.screen - Screen/console output generated by running in.XXX
-bar1d_two_temperature:
+drift_diffusion
input files:
- in.bar1d_ttm - Atoms comprise a subset of a 1D finite element bar,
- with a high fixed electron temperature on the left end
- and low fixed phonon and electron temperatures on the right end.
- A Gaussian isokinetic thermostat is used to transfer energy
- from the electron temperature field to the atoms.
- in.gaussianIC_ttm - Atoms fully overlap an FE mesh with an initially
- elevated electron temperature having a Gaussian distribution.
- in.no_atoms - Heating followed by relaxation is simulated on a FE mesh.
- in.uniform_exchange - Electron and kinetic temperatures are initially
- spatially uniform but out of equilibrium, followed by relaxation.
- in.uniform_heating - Initially equal electron and kinetic temperatures
- are subjected to heating of the kinetic temperature only. The kinetic
- temperature is fixed at both ends while the electrons are insulated.
- Ar_ttm.mat - Material parameter file specifying
- the kinetic and electric thermal properties of argon.
- Cu_ttm.mat - Material parameter file specifying
- the kinetic and electric thermal properties of copper.
- temp.init - Initial set of atomic positions and velocities for most cases.
- uniform_exchange_init.data - Initial set of atomic positions and velocities
- for in.uniform_exchange
- uniform_heating_init.data - Initial set of atomic positions and velocities
- for in.uniform_heating
+ in.convective_pulse - 1D Haynes-Schockley pulse in copper with electron convection
+ in.ddm_schrodinger - 1D Haynes Schockley pulse in silicon using Schrodinger-Poisson model for electron density
+ in.finite_well - Quasi-static, 1D Schrodinger-Poisson electron density in a finite energy well
+ in.no_atoms_ddm - 1D Haynes--Schockley pulse in silicon with drift from an applied potential
+ in.null_material_ddm - 2D Argon drift diffusion with part of the region not including electron effects but including the electric potential
+ in.poisson1d_noatoms - Static 1D drift-diffusion model in silicon with a self consistent poisson solution for the electron density
+ in.poisson2d_noatoms - Static 2D drift-diffusion model in a CNT with a self consistent poisson solution for the electron density
+ in.schrodinger_poisson2d_XXX -Static 2D drift-diffusion model in silicon with a schrodinger-poisson solution for the elctron desntiy and electric fields and different mechanisms for drift: no-atoms (follows electric field), convective (electron convection), Jconstraint (conservation of current)
+ XXX_ddm_XXX.mat - Two-temperature and electron diffusion properties
+ XXX_cddm.mat - Two-temperaure, electron diffusion and convection properties
+ XXX_schrodinger.mat - Two-temperature, electron diffusion (and sometimes convection), and Schrodinger-Poisson parameters
+ Si_ddm_thermopower.mat -
output files:
- bar1d_ttm.log - LAMMPS log file generated by running in.bar1d_ttm.
- gaussianIC_ttm.log - log file generated by running in.gaussianIC_ttm.
- no_atoms.log - LAMMPS log file generated by running in.no_atoms.
- uniform_exchange.log - log file generated by running in.uniform_exchange.
- uniform_heating.log - LAMMPS log file generated by running in.uniform_heating.
+ XXX.screen - Screen/console output generated by running in.XXX
+
+elastic:
+ input files:
+ in.bar1d - Quasi-1D elastic wave propagation with coupling using momentum constraints
+ in.bar1d_damped - Quasi-1D elastic wave propagation with damped materials and ghost atoms for propagating waves out of MD region
+ in.bar1d_flux - Quasi-1D elastic wave propagation with coupling using boundary stresses from FEM
+ in.bar1d_frac_step - Quasi-1D elastic wave propagation with a fractional step time integrator
+ in.bar1d_ghost_flux - Quasi-1D elastic wave propagation with coupling using boundary stresses from ghost atoms
+ in.bar1d_thermo_elastic - Quasi-1D finite temperature elastic wave propagation
+ in.cnt_electrostatic - Mechanical response of CNT with fixed charge density in an electric field
+ in.cnt_electrostatic2 - Mechanical reponse of CNT with self-consistent charge density and electric field
+ in.cnt_fixed_charge - Mechancial response of CNT with fixed atomic charges in an electric field
+ in.eam_energy - Quasi-static/quasi-1D coupling and transfer extraction of energy density for EAM gold
+ in.electron_density - Mechanical response of differnt CNT models with a self-consistent electron density and electric field
+ in.electrostatic_bending_dos - Quasi-static bending of a CNT using a quantum density of states model for electron density
+ in.no_atoms - FE solution of a box subject to an initial displacement condition
+ in.no_atoms_cb - FE solution of a box subject to an initial displacement condition with a Cauchy-Born material model
+ in.no_atoms_cb_linear -FE solution of a box subject to an initial displacement condition with a linear Cauchy-Born material model
+ Ar_CauchyBornLinear.mat - Linear Cauchy Born material model for argon
+ Ar_CauchyBorn.mat - Cauchy-Born material model for argon
+ Ar_damped.mat - Argon elastic and fictitious damping material properties
+ Ar_elastic.mat - Argon elastic properties
+ Ar_thermo_elastic.mat - Argon elastic and thermal properties
+ Au_elastic.mat - Gold elastic properties
+ CNT_electrostatic2.mat - CNT elastic, electric field, and linear field/electron density properties
+ CNT_electrostatic.mat - CNT elastic and electric field properties
+ CNT_id.mat - CNT elastic and electric field properties
+ CNT.mat - Mechanical, electrical, and various field/electron density properties
+
+ output files:
+ XXX.screen - Screen/console output generated by running in.XXX
+
+fluids:
+ input_files:
+ in.bar1d_fluids - Quasi-1D FE/MD temperature coupling for liquid argon
+ in.concentration - Quasi-1D double layer with ion concentration controlled in some elements
+ in.conducting_interface - Quasi-2D double layer with a material model for a conducting solid
+ in.dielectric_interface - Quasi-2D double layer with a material model for a dielectric solid
+ in.double_layer - 3D double layer charging
+ in.liquid_electrostatic - Quasi-1D double layer with a fixed potential surface
+ in.opp_force - Computes electrostatic interactions between two oppositely charged groups in an argon lattice
+ in.poisson - Computes electrostatic interactions in a charged LJ fluid
+ in.shear_flow - Poisseuille flow
+ in.shear_no_atoms - No atom viscosity solution
+ Ar_electrostatic.mat - Liquid argon density and electrical properties
+ Ar_species_dl.mat - Faux mass density and electrical properties
+ Ar_species.mat - Electrical properties
+ Ar_thermal.mat - thermal properties of liquid argon
+ Ar_visc_no_atoms.mat - Viscous flow model
+ Ar_viscosity.mat - Viscous flow properties for liquid argon
hardy:
input files:
in.consistency - Small block of EAM Copper is used to confirm the
consistency between the atc calculations of 1st Piola-Kirchhoff (P-K)
stress, displacment gradient, and strain energy density for various
amounts of uniaxial strain.
in.eam_kernel_convergence - Block of EAM Gold is used to examine the
variation of the atc estimate of 1st P-K stress with size of localization
(averaging) volume. Volume is spherical, and kernel function
is quartic depending on radial distance from sphere center.
in.eam_unistrain_xxxx - Long block of EAM Copper is subjected to uniaxial
stretching and estimates of 1st P-K stress, energy density, displacement
and displacement gradient are calculated. The end-suffix denotes the
localization volume shape and kernel function type:
cell - 3D rectangular elements with step-functions at cell boundary
mesh - 3D rectangular elements with linear "tent" functions
qcylinder - cylindrical volume with quartic function dependent on
distance from cylinder axis
qsphere - spherical volume with quartic function dependent on
distance from sphere center
step - spherical volume with step-function at sphere boundary
in.eam_volume_stretch - Small block of EAM Copper is equitriaxially
stretched and estimates of 1st P-K stress, energy density, and mass
density are calculated.
+ in.eshelby_static - Static calculation of eshelby stress.
in.nvt - Block of Lennard-Jones Argon is simulated at 30K for 1000 timesteps.
output files:
- consistency.log - LAMMPS log file generated by running in.consistency
- consistency.screen - Screen/console output generated by running
- in.consistency
- eam_kernel_convergence.log - LAMMPS log file generated by running
- in.eam_kernel_convergence
- eam_kernel_convergence.screen - Screen/console output generated by running
- in.eam_kernel_convergence
- eam_unistrain_xxxx.log - LAMMPS log file generated by running
- in.eam_unistrain_xxxx
- eam_unistrain_xxxx.screen - Screen/console output generated by running
ATC: WARNING: physics model: [convection drift-diffusion], material: [vacuum] does not provide all interfaces for <temperature> physics and will be treated as null
ATC: WARNING: physics model: [convection drift-diffusion], material: [vacuum] does not provide all interfaces for <electron_density> physics and will be treated as null
ATC: WARNING: physics model: [convection drift-diffusion], material: [cu] does not provide all interfaces for <electron_density> physics and will be treated as null
ATC: WARNING: physics model: [convection drift-diffusion], material: [vacuum] does not provide all interfaces for <electron_velocity> physics and will be treated as null
ATC: WARNING: physics model: [convection drift-diffusion], material: [vacuum] does not provide all interfaces for <electron_temperature> physics and will be treated as null
ATC: WARNING: physics model: [drift-diffusion], material: [vacuum] does not provide all interfaces for <temperature> physics and will be treated as null
ATC: WARNING: physics model: [drift-diffusion], material: [vacuum] does not provide all interfaces for <electron_density> physics and will be treated as null
ATC: WARNING: physics model: [drift-diffusion], material: [vacuum] does not provide all interfaces for <electron_temperature> physics and will be treated as null
+Loop time of 37.6155 on 4 procs for 2000 steps with 2304 atoms
+
+Pair time (%) = 11.5713 (30.7621)
+Neigh time (%) = 4.99228 (13.2719)
+Comm time (%) = 11.2439 (29.8916)
+Outpt time (%) = 0.0705782 (0.187631)
+Other time (%) = 9.73741 (25.8867)
Nlocal: 576 ave 864 max 288 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 5170 ave 6910 max 3430 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 178632 ave 288864 max 65670 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 357264 ave 577008 max 137520 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 1429056
Ave neighs/atom = 620.25
Neighbor list builds = 200
Dangerous builds = 0
# ATC: CB stiffness: 7.56717 Einstein freq: 0.355649 from Ar_CauchyBorn.mat
# real to metal 1 kcal/mol = 0.04336 eV
variable kCal2eV equal 0.04336
-variable k equal 1.e-3 # 7.56717*${kCal2eV} NOTE <<<
-variable g equal 0.75*0.355649e3*${kCal2eV}
-variable g equal 0.75*0.355649e3*0.043360000000000002707
-variable m equal 0.5*39.95
+variable fconv equal 1./0.000103643 # NOTE old routine was doing calculations in lammps units, not atc units, so this conversion is necessary for bmark to pass
+#variable k equal 1.e-3 # 7.56717*${kCal2eV} NOTE <<<
+#variable k equal 0.75*0.355649e3*${kCal2eV}
+variable k equal 0.5*39.95*${fconv} # NOTE it was set to above, should have been 2 above, but there was a bug so this value is here for bmark
+variable k equal 0.5*39.95*9648.5049641558034637
+#variable g equal 0.75*0.355649e3*${kCal2eV}
+variable g equal 1.e-3*${fconv} # NOTE it should be above, but there was a bug so this value is here for bmark
ATC: WARNING: physics model: [electrostatic], material: [cnt] does not provide all interfaces for <electron_density> physics and will be treated as null
Memory usage per processor = 53.947 Mbytes
Step CPU TotEng KinEng
0 0 -7315.3918 4.2386027e-06
- 1 0.31967092 -7315.3918 8.3975109e-06
- 2 0.57961583 -7315.3918 1.4120368e-05
- 3 0.73119783 -7315.3918 2.1378868e-05
- 4 0.77118993 -7315.3918 3.0172501e-05
- 5 0.81124997 -7315.3918 4.0500585e-05
- 6 0.85121584 -7315.3918 5.2362272e-05
- 7 0.89118791 -7315.3918 6.5756548e-05
- 8 0.93097782 -7315.3918 8.0682245e-05
- 9 0.97063279 -7315.3918 9.713804e-05
- 10 1.0182109 -7315.3918 0.00011512246
- 11 1.0585999 -7315.3918 0.00013463391
- 12 1.0980539 -7315.3918 0.00015567063
- 13 1.13748 -7315.3918 0.00017823074
- 14 1.177192 -7315.3918 0.00020231225
- 15 1.2165098 -7315.3918 0.00022791303
- 16 1.2559309 -7315.3918 0.00025503085
- 17 1.2955098 -7315.3918 0.00028366338
- 18 1.334971 -7315.3918 0.00031380817
- 19 1.3744769 -7315.3918 0.0003454627
- 20 1.4319949 -7315.3918 0.00037862437
- 21 1.4716878 -7315.3918 0.0004132905
- 22 1.5113468 -7315.3918 0.00044945835
- 23 1.67961 -7315.3918 0.00048712513
- 24 1.718936 -7315.3918 0.00052628798
- 25 1.75843 -7315.3918 0.00056694404
- 26 1.7989509 -7315.3918 0.00060909036
- 27 1.930331 -7315.3918 0.00065272401
- 28 1.9778998 -7315.3918 0.00069784199
- 29 2.0358789 -7315.3917 0.00074444131
- 30 2.0961409 -7315.3917 0.00079251893
- 31 2.3385279 -7315.3917 0.00084207182
- 32 2.636704 -7315.3917 0.00089309691
- 33 2.714483 -7315.3917 0.00094559113
- 34 2.9397018 -7315.3917 0.00099955142
- 35 3.2066698 -7315.3917 0.0010549747
- 36 3.2912428 -7315.3917 0.0011118579
- 37 3.4499469 -7315.3917 0.0011701978
- 38 3.609957 -7315.3917 0.0012299916
- 39 3.694387 -7315.3917 0.001291236
- 40 3.774771 -7315.3917 0.001353928
- 41 3.814693 -7315.3917 0.0014180645
- 42 3.8544669 -7315.3917 0.0014836425
- 43 3.899441 -7315.3917 0.0015506588
- 44 3.9393668 -7315.3917 0.0016191104
- 45 4.1302609 -7315.3917 0.0016889941
- 46 4.2312019 -7315.3917 0.0017603069
- 47 4.3896489 -7315.3917 0.0018330457
- 48 4.4500258 -7315.3917 0.0019072073
- 49 4.5496428 -7315.3916 0.0019827887
- 50 5.0796728 -7315.3916 0.0020597866
- 51 5.3996999 -7315.3916 0.002138198
- 52 5.7496638 -7315.3916 0.0022180196
- 53 6.0696678 -7315.3916 0.0022992484
- 54 6.1538389 -7315.3916 0.0023818813
- 55 6.1931789 -7315.3916 0.0024659149
- 56 6.232445 -7315.3916 0.0025513463
- 57 6.271626 -7315.3916 0.0026381721
- 58 6.3107619 -7315.3916 0.0027263893
- 59 6.350004 -7315.3916 0.0028159946
- 60 6.3956769 -7315.3916 0.0029069848
- 61 6.4278479 -7315.3916 0.0029993569
- 62 6.468123 -7315.3916 0.0030931075
- 63 6.5084469 -7315.3915 0.0031882335
- 64 6.5487828 -7315.3915 0.0032847318
- 65 6.588315 -7315.3915 0.0033825991
- 66 6.628861 -7315.3915 0.0034818323
- 67 6.6681879 -7315.3915 0.0035824284
- 68 6.7083828 -7315.3915 0.0036843841
- 69 6.7478988 -7315.3915 0.0037876964
- 70 6.8052649 -7315.3915 0.0038923623
- 71 6.8364089 -7315.3915 0.0039983787
- 72 6.8688459 -7315.3915 0.0041057427
- 73 6.9038498 -7315.3915 0.0042144511
- 74 6.9437559 -7315.3915 0.0043245012
- 75 6.983357 -7315.3915 0.0044358899
- 76 7.0233488 -7315.3914 0.0045486143
- 77 7.0634668 -7315.3914 0.0046626717
- 78 7.1032989 -7315.3914 0.0047780591
- 79 7.143338 -7315.3914 0.0048947738
- 80 7.2009349 -7315.3914 0.0050128131
- 81 7.2304518 -7315.3914 0.005132174
- 82 7.260041 -7315.3914 0.0052528541
- 83 7.300066 -7315.3914 0.0053748505
- 84 7.3296208 -7315.3914 0.0054981606
- 85 7.3695228 -7315.3914 0.0056227818
- 86 7.409111 -7315.3913 0.0057487114
- 87 7.4488299 -7315.3913 0.0058759467
- 88 7.4784439 -7315.3913 0.0060044851
- 89 7.498029 -7315.3913 0.006134324
- 90 7.5257208 -7315.3913 0.0062654606
- 91 7.5550458 -7315.3913 0.0063978923
- 92 7.5941949 -7315.3913 0.0065316164
- 93 7.6136239 -7315.3913 0.0066666301
- 94 7.6330369 -7315.3913 0.0068029305
- 95 7.652329 -7315.3913 0.006940515
- 96 7.671556 -7315.3912 0.0070793805
- 97 7.6908948 -7315.3912 0.0072195241
- 98 7.7102349 -7315.3912 0.0073609428
- 99 7.7295499 -7315.3912 0.0075036336
- 100 7.8130169 -7315.3912 0.0076475932
- 101 7.8324709 -7315.3912 0.0077928183
- 102 7.852021 -7315.3912 0.0079393056
- 103 7.871295 -7315.3912 0.0080870517
- 104 7.9005089 -7315.3912 0.0082360529
- 105 7.939764 -7315.3911 0.0083863055
- 106 7.9591198 -7315.3911 0.0085378058
- 107 7.9786189 -7315.3911 0.0086905498
- 108 7.998369 -7315.3911 0.0088445335
- 109 8.1596448 -7315.3911 0.0089997527
- 110 8.2999489 -7315.3911 0.0091562032
- 111 8.4596839 -7315.3911 0.0093138804
- 112 8.7796738 -7315.3911 0.00947278
- 113 8.979708 -7315.3911 0.0096328972
- 114 9.179704 -7315.391 0.0097942273
- 115 9.3797159 -7315.391 0.0099567653
- 116 9.5797029 -7315.391 0.010120506
- 117 9.7797039 -7315.391 0.010285445
- 118 10.139666 -7315.391 0.010451576
- 119 10.48775 -7315.391 0.010618895
- 120 10.909639 -7315.391 0.010787395
- 121 11.209625 -7315.391 0.010957072
- 122 11.449644 -7315.3909 0.011127918
- 123 11.689628 -7315.3909 0.01129993
- 124 11.939698 -7315.3909 0.0114731
- 125 12.139709 -7315.3909 0.011647424
- 126 12.3397 -7315.3909 0.011822894
- 127 12.53975 -7315.3909 0.011999506
- 128 12.739698 -7315.3909 0.012177252
- 129 12.959952 -7315.3908 0.012356127
- 130 13.199949 -7315.3908 0.012536125
- 131 13.40965 -7315.3908 0.012717239
- 132 13.649624 -7315.3908 0.012899462
- 133 13.859712 -7315.3908 0.01308279
- 134 14.059702 -7315.3908 0.013267215
- 135 14.259705 -7315.3908 0.01345273
- 136 14.569647 -7315.3908 0.01363933
- 137 14.800963 -7315.3907 0.013827009
- 138 15.186622 -7315.3907 0.014015759
- 139 15.626654 -7315.3907 0.014205574
- 140 15.926937 -7315.3907 0.014396449
- 141 16.141167 -7315.3907 0.014588376
- 142 16.384635 -7315.3907 0.014781349
- 143 16.829641 -7315.3907 0.014975362
- 144 17.14671 -7315.3906 0.015170409
- 145 17.339733 -7315.3906 0.015366482
- 146 17.579739 -7315.3906 0.015563577
- 147 17.779642 -7315.3906 0.015761685
- 148 17.843004 -7315.3906 0.015960802
- 149 17.882239 -7315.3906 0.01616092
- 150 17.967242 -7315.3905 0.016362034
- 151 17.99843 -7315.3905 0.016564137
- 152 18.03849 -7315.3905 0.016767223
- 153 18.077649 -7315.3905 0.016971286
- 154 18.107811 -7315.3905 0.017176319
- 155 18.126918 -7315.3905 0.017382317
- 156 18.146051 -7315.3905 0.017589273
- 157 18.165207 -7315.3904 0.01779718
- 158 18.184314 -7315.3904 0.018006034
- 159 18.203415 -7315.3904 0.018215827
- 160 18.230428 -7315.3904 0.018426554
- 161 18.249539 -7315.3904 0.018638208
- 162 18.268613 -7315.3904 0.018850784
- 163 18.287874 -7315.3903 0.019064276
- 164 18.306925 -7315.3903 0.019278677
- 165 18.326238 -7315.3903 0.019493981
- 166 18.399314 -7315.3903 0.019710184
- 167 18.418596 -7315.3903 0.019927278
- 168 18.437743 -7315.3903 0.020145259
- 169 18.456929 -7315.3902 0.02036412
- 170 18.484008 -7315.3902 0.020583855
- 171 18.503426 -7315.3902 0.02080446
- 172 18.522622 -7315.3902 0.021025928
- 173 18.541824 -7315.3902 0.021248253
- 174 18.561048 -7315.3902 0.021471431
- 175 18.580206 -7315.3901 0.021695456
- 176 18.599349 -7315.3901 0.021920323
- 177 18.618534 -7315.3901 0.022146026
- 178 18.638064 -7315.3901 0.022372559
- 179 18.657386 -7315.3901 0.022599919
- 180 18.684453 -7315.3901 0.0228281
- 181 18.724044 -7315.39 0.023057097
- 182 18.773259 -7315.39 0.023286904
- 183 18.832546 -7315.39 0.023517518
- 184 18.971291 -7315.39 0.023748934
- 185 18.997376 -7315.39 0.023981146
- 186 19.016538 -7315.3899 0.024214151
- 187 19.035734 -7315.3899 0.024447944
- 188 19.054972 -7315.3899 0.024682521
- 189 19.074098 -7315.3899 0.024917876
- 190 19.101161 -7315.3899 0.025154007
- 191 19.12035 -7315.3898 0.025390909
- 192 19.13971 -7315.3898 0.025628577
- 193 19.159221 -7315.3898 0.025867009
- 194 19.178876 -7315.3898 0.026106199
- 195 19.198877 -7315.3898 0.026346144
- 196 19.218139 -7315.3897 0.026586841
- 197 19.237305 -7315.3897 0.026828285
- 198 19.256529 -7315.3897 0.027070473
- 199 19.275746 -7315.3897 0.0273134
- 200 19.320708 -7315.3897 0.027557065
- 201 19.340115 -7315.3896 0.027801461
- 202 19.35955 -7315.3896 0.028046587
- 203 19.37881 -7315.3896 0.028292439
- 204 19.397985 -7315.3896 0.028539012
- 205 19.417365 -7315.3896 0.028786304
- 206 19.436589 -7315.3895 0.02903431
- 207 19.455744 -7315.3895 0.029283027
- 208 19.475087 -7315.3895 0.029532451
- 209 19.49439 -7315.3895 0.029782578
- 210 19.521502 -7315.3895 0.030033406
- 211 19.540793 -7315.3894 0.030284929
- 212 19.560032 -7315.3894 0.030537145
- 213 19.579251 -7315.3894 0.030790049
- 214 19.598373 -7315.3894 0.031043637
- 215 19.627613 -7315.3894 0.031297905
- 216 19.646909 -7315.3893 0.03155285
- 217 19.666108 -7315.3893 0.031808467
- 218 19.685288 -7315.3893 0.032064752
- 219 19.704805 -7315.3893 0.0323217
- 220 19.731995 -7315.3892 0.032579308
- 221 19.751148 -7315.3892 0.032837571
- 222 19.79389 -7315.3892 0.033096484
- 223 19.833547 -7315.3892 0.033356043
- 224 19.919784 -7315.3891 0.033616243
- 225 20.145626 -7315.3891 0.03387708
- 226 20.305699 -7315.3891 0.034138548
- 227 20.734641 -7315.3891 0.034400644
- 228 21.009673 -7315.3891 0.034663362
- 229 21.209665 -7315.389 0.034926696
- 230 21.489666 -7315.389 0.035190644
- 231 21.689671 -7315.389 0.035455198
- 232 21.889662 -7315.389 0.035720354
- 233 22.089666 -7315.3889 0.035986107
- 234 22.309621 -7315.3889 0.036252452
- 235 22.549627 -7315.3889 0.036519384
- 236 22.789619 -7315.3889 0.036786897
- 237 23.02962 -7315.3888 0.037054986
- 238 23.269627 -7315.3888 0.037323645
- 239 23.509621 -7315.3888 0.03759287
- 240 23.789619 -7315.3888 0.037862655
- 241 24.019911 -7315.3887 0.038132995
- 242 24.23991 -7315.3887 0.038403884
- 243 24.459904 -7315.3887 0.038675316
- 244 24.679905 -7315.3887 0.038947288
- 245 24.899904 -7315.3886 0.039219793
- 246 25.139919 -7315.3886 0.039492825
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- 1000 92.330713 -7315.3517 0.22357286
-Loop time of 92.3283 on 4 procs for 1000 steps with 1008 atoms
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+ 844 19.12374 -7315.3609 0.20681066
+ 845 19.142759 -7315.3609 0.20698878
+ 846 19.161746 -7315.3608 0.20716611
+ 847 19.180769 -7315.3608 0.20734266
+ 848 19.199737 -7315.3607 0.20751842
+ 849 19.218653 -7315.3606 0.20769339
+ 850 19.26317 -7315.3606 0.20786757
+ 851 19.282135 -7315.3605 0.20804095
+ 852 19.301106 -7315.3605 0.20821353
+ 853 19.319999 -7315.3604 0.2083853
+ 854 19.338916 -7315.3604 0.20855628
+ 855 19.357791 -7315.3603 0.20872644
+ 856 19.376703 -7315.3602 0.20889579
+ 857 19.395673 -7315.3602 0.20906433
+ 858 19.414558 -7315.3601 0.20923205
+ 859 19.433471 -7315.3601 0.20939895
+ 860 19.46011 -7315.36 0.20956503
+ 861 19.479016 -7315.3599 0.20973029
+ 862 19.497875 -7315.3599 0.20989472
+ 863 19.516764 -7315.3598 0.21005832
+ 864 19.535746 -7315.3598 0.21022108
+ 865 19.554725 -7315.3597 0.21038301
+ 866 19.57361 -7315.3597 0.21054411
+ 867 19.592541 -7315.3596 0.21070436
+ 868 19.61148 -7315.3595 0.21086378
+ 869 19.630452 -7315.3595 0.21102234
+ 870 19.657153 -7315.3594 0.21118007
+ 871 19.676267 -7315.3594 0.21133694
+ 872 19.695157 -7315.3593 0.21149296
+ 873 19.714083 -7315.3593 0.21164813
+ 874 19.733065 -7315.3592 0.21180245
+ 875 19.752064 -7315.3591 0.2119559
+ 876 19.771032 -7315.3591 0.2121085
+ 877 19.789993 -7315.359 0.21226024
+ 878 19.808899 -7315.359 0.21241111
+ 879 19.827757 -7315.3589 0.21256112
+ 880 19.854376 -7315.3588 0.21271026
+ 881 19.873263 -7315.3588 0.21285853
+ 882 19.892182 -7315.3587 0.21300594
+ 883 19.911193 -7315.3587 0.21315246
+ 884 19.93017 -7315.3586 0.21329812
+ 885 19.949208 -7315.3586 0.2134429
+ 886 19.968188 -7315.3585 0.2135868
+ 887 19.987239 -7315.3584 0.21372982
+ 888 20.006231 -7315.3584 0.21387196
+ 889 20.025123 -7315.3583 0.21401322
+ 890 20.051774 -7315.3583 0.21415359
+ 891 20.070805 -7315.3582 0.21429308
+ 892 20.089726 -7315.3581 0.21443167
+ 893 20.108651 -7315.3581 0.21456938
+ 894 20.127602 -7315.358 0.2147062
+ 895 20.146634 -7315.358 0.21484212
+ 896 20.165667 -7315.3579 0.21497714
+ 897 20.184613 -7315.3579 0.21511127
+ 898 20.203754 -7315.3578 0.2152445
+ 899 20.222864 -7315.3577 0.21537683
+ 900 20.267447 -7315.3577 0.21550825
+ 901 20.286617 -7315.3576 0.21563876
+ 902 20.305708 -7315.3576 0.21576837
+ 903 20.324854 -7315.3575 0.21589707
+ 904 20.344024 -7315.3574 0.21602485
+ 905 20.363072 -7315.3574 0.21615172
+ 906 20.382092 -7315.3573 0.21627767
+ 907 20.401062 -7315.3573 0.2164027
+ 908 20.420153 -7315.3572 0.21652681
+ 909 20.43911 -7315.3572 0.21664999
+ 910 20.465801 -7315.3571 0.21677224
+ 911 20.484821 -7315.357 0.21689356
+ 912 20.50384 -7315.357 0.21701394
+ 913 20.52275 -7315.3569 0.21713339
+ 914 20.541703 -7315.3569 0.21725189
+ 915 20.56072 -7315.3568 0.21736946
+ 916 20.579674 -7315.3567 0.21748607
+ 917 20.598622 -7315.3567 0.21760173
+ 918 20.617603 -7315.3566 0.21771644
+ 919 20.636576 -7315.3566 0.21783019
+ 920 20.663315 -7315.3565 0.21794298
+ 921 20.682282 -7315.3564 0.2180548
+ 922 20.70654 -7315.3564 0.21816566
+ 923 20.725513 -7315.3563 0.21827554
+ 924 20.74449 -7315.3563 0.21838445
+ 925 20.763508 -7315.3562 0.21849238
+ 926 20.782488 -7315.3561 0.21859933
+ 927 20.801631 -7315.3561 0.21870529
+ 928 20.82058 -7315.356 0.21881025
+ 929 20.839487 -7315.356 0.21891423
+ 930 20.866125 -7315.3559 0.2190172
+ 931 20.885039 -7315.3558 0.21911918
+ 932 20.903956 -7315.3558 0.21922015
+ 933 20.922894 -7315.3557 0.21932011
+ 934 20.942382 -7315.3557 0.21941906
+ 935 20.961498 -7315.3556 0.21951699
+ 936 20.980532 -7315.3556 0.2196139
+ 937 21.000184 -7315.3555 0.21970979
+ 938 21.019062 -7315.3554 0.21980465
+ 939 21.037983 -7315.3554 0.21989848
+ 940 21.064886 -7315.3553 0.21999128
+ 941 21.084159 -7315.3553 0.22008304
+ 942 21.103302 -7315.3552 0.22017376
+ 943 21.122323 -7315.3551 0.22026344
+ 944 21.16113 -7315.3551 0.22035207
+ 945 21.199809 -7315.355 0.22043965
+ 946 21.260737 -7315.355 0.22052618
+ 947 21.340589 -7315.3549 0.22061165
+ 948 21.3995 -7315.3548 0.22069606
+ 949 21.43873 -7315.3548 0.22077941
+ 950 21.582494 -7315.3547 0.2208617
+ 951 21.793692 -7315.3547 0.22094292
+ 952 21.962676 -7315.3546 0.22102306
+ 953 22.202676 -7315.3545 0.22110214
+ 954 22.382995 -7315.3545 0.22118014
+ 955 22.602677 -7315.3544 0.22125706
+ 956 22.639823 -7315.3544 0.2213329
+ 957 22.663705 -7315.3543 0.22140765
+ 958 22.682609 -7315.3542 0.22148132
+ 959 22.701568 -7315.3542 0.22155391
+ 960 22.728795 -7315.3541 0.2216254
+ 961 22.747851 -7315.3541 0.2216958
+ 962 22.76681 -7315.354 0.2217651
+ 963 22.785828 -7315.3539 0.22183331
+ 964 22.804818 -7315.3539 0.22190042
+ 965 22.82372 -7315.3538 0.22196643
+ 966 22.842705 -7315.3538 0.22203133
+ 967 22.861784 -7315.3537 0.22209513
+ 968 22.880756 -7315.3536 0.22215783
+ 969 22.899779 -7315.3536 0.22221941
+ 970 22.926919 -7315.3535 0.22227989
+ 971 22.945984 -7315.3535 0.22233925
+ 972 22.965121 -7315.3534 0.2223975
+ 973 22.98439 -7315.3533 0.22245464
+ 974 23.003614 -7315.3533 0.22251066
+ 975 23.022739 -7315.3532 0.22256556
+ 976 23.041785 -7315.3532 0.22261935
+ 977 23.060875 -7315.3531 0.22267201
+ 978 23.079938 -7315.353 0.22272356
+ 979 23.098936 -7315.353 0.22277398
+ 980 23.126245 -7315.3529 0.22282328
+ 981 23.145234 -7315.3529 0.22287146
+ 982 23.16423 -7315.3528 0.22291852
+ 983 23.183107 -7315.3527 0.22296445
+ 984 23.20206 -7315.3527 0.22300925
+ 985 23.221019 -7315.3526 0.22305293
+ 986 23.240034 -7315.3526 0.22309548
+ 987 23.259107 -7315.3525 0.2231369
+ 988 23.278317 -7315.3524 0.2231772
+ 989 23.29729 -7315.3524 0.22321637
+ 990 23.324356 -7315.3523 0.22325442
+ 991 23.343342 -7315.3523 0.22329133
+ 992 23.362212 -7315.3522 0.22332712
+ 993 23.381156 -7315.3521 0.22336179
+ 994 23.40012 -7315.3521 0.22339532
+ 995 23.419104 -7315.352 0.22342773
+ 996 23.43806 -7315.352 0.22345901
+ 997 23.457105 -7315.3519 0.22348916
+ 998 23.476011 -7315.3518 0.22351819
+ 999 23.494921 -7315.3518 0.22354609
+ 1000 23.540198 -7315.3517 0.22357286
+Loop time of 23.5402 on 4 procs for 1000 steps with 1008 atoms
ATC: WARNING: physics model: [electrostatic], material: [cnt0] does not provide all interfaces for <electron_density> physics and will be treated as null
ATC: WARNING: physics model: [electrostatic], material: [cnt0] does not provide all interfaces for <electron_density> physics and will be treated as null
ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt-exp] does not provide all interfaces for <velocity> physics and will be treated as null
ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt] does not provide all interfaces for <velocity> physics and will be treated as null
Memory usage per processor = 0.432442 Mbytes
Step CPU TotEng KinEng
0 0 0 -0
- 1 0.01880908 0 -0
-Loop time of 0.018833 on 4 procs for 1 steps with 0 atoms
+ 1 0.0019478798 0 -0
+Loop time of 0.00196469 on 4 procs for 1 steps with 0 atoms
ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt-exp] does not provide all interfaces for <velocity> physics and will be treated as null
ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt] does not provide all interfaces for <velocity> physics and will be treated as null
Memory usage per processor = 0.432442 Mbytes
Step CPU TotEng KinEng
1 0 0 -0
- 2 0.11045408 0 -0
-Loop time of 0.110485 on 4 procs for 1 steps with 0 atoms
+ 2 0.0016391277 0 -0
+Loop time of 0.00165129 on 4 procs for 1 steps with 0 atoms
ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt-exp] does not provide all interfaces for <velocity> physics and will be treated as null
ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt] does not provide all interfaces for <velocity> physics and will be treated as null
Memory usage per processor = 0.432442 Mbytes
Step CPU TotEng KinEng
2 0 0 -0
- 3 0.10601687 0 -0
-Loop time of 0.123864 on 4 procs for 1 steps with 0 atoms
+ 3 0.0016679764 0 -0
+Loop time of 0.00168163 on 4 procs for 1 steps with 0 atoms
ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt-exp] does not provide all interfaces for <velocity> physics and will be treated as null
ATC: WARNING: physics model: [equilibrium electrostatic], material: [cnt] does not provide all interfaces for <velocity> physics and will be treated as null
Memory usage per processor = 0.432442 Mbytes
Step CPU TotEng KinEng
3 0 0 -0
- 4 0.0015778542 0 -0
-Loop time of 0.00159025 on 4 procs for 1 steps with 0 atoms
+ 4 0.0016648769 0 -0
+Loop time of 0.00167871 on 4 procs for 1 steps with 0 atoms
ATC: WARNING: physics model: [electrostatic], material: [cnt0] does not provide all interfaces for <electron_density> physics and will be treated as null
ATC: WARNING: physics model: [electrostatic], material: [cnt0] does not provide all interfaces for <electron_density> physics and will be treated as null
variable EI equal $F*${Lfree}*${Lfree}*${Lfree}/3./$u
variable EI equal 1.9116216109081213915e-08*${Lfree}*${Lfree}*${Lfree}/3./$u
variable EI equal 1.9116216109081213915e-08*90*${Lfree}*${Lfree}/3./$u
variable EI equal 1.9116216109081213915e-08*90*90*${Lfree}/3./$u
variable EI equal 1.9116216109081213915e-08*90*90*90/3./$u
variable EI equal 1.9116216109081213915e-08*90*90*90/3./-1.4672651617664272549e-11
variable EI equal ${EI}*${eV2J}*${A2m}
variable EI equal -316591754.20715177059*${eV2J}*${A2m}
variable EI equal -316591754.20715177059*1.6021764600000000642e-19*${A2m}
variable EI equal -316591754.20715177059*1.6021764600000000642e-19*1.0000000000000000364e-10
#print "flexural rigidity ${EI} [Nm^2] NOTE z force"
print ">> V $b $a F $F ${Fz} u $u ${uz} c $c phi 0 EI ${EI} R $R ${Rz}"
>> V 0 0 F 1.9116216109081213915e-08 -3.2008125606681979403e-05 u -1.4672651617664272549e-11 96.935507997738042718 c -0.0027777777777777778838 phi 0 EI -5.072358560208045613e-21 R 1.9116216109081213915e-08 -3.2008125606681979403e-05
next i
jump SELF loop_i
variable b equal ($i-1)*${Vg}/(${ng}-1)/${Lx}
variable b equal (2-1)*${Vg}/(${ng}-1)/${Lx}
variable b equal (2-1)*0.10000000000000000555/(${ng}-1)/${Lx}
variable b equal (2-1)*0.10000000000000000555/(4-1)/${Lx}
variable b equal (2-1)*0.10000000000000000555/(4-1)/1
fix_modify AtC fix electric_potential all linear 0 0 0 $b 0 $a 0
fix_modify AtC fix electric_potential all linear 0 0 0 0.033333333333333332871 0 $a 0
fix_modify AtC fix electric_potential all linear 0 0 0 0.033333333333333332871 0 0 0
ATC: created function : 0 + 0.0333333(x-0)+0(y-0)+0(z-0)
min_style cg
min_modify line quadratic
#minimize 0 0 100000 100000
minimize 0 0 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
ATC: WARNING: physics model: [electrostatic], material: [cnt0] does not provide all interfaces for <electron_density> physics and will be treated as null
ATC: WARNING: physics model: [electrostatic], material: [cnt0] does not provide all interfaces for <electron_density> physics and will be treated as null
variable EI equal $F*${Lfree}*${Lfree}*${Lfree}/3./$u
variable EI equal 0.0025877461923070671154*${Lfree}*${Lfree}*${Lfree}/3./$u
variable EI equal 0.0025877461923070671154*90*${Lfree}*${Lfree}/3./$u
variable EI equal 0.0025877461923070671154*90*90*${Lfree}/3./$u
variable EI equal 0.0025877461923070671154*90*90*90/3./$u
variable EI equal 0.0025877461923070671154*90*90*90/3./0.0093585293597155689432
variable EI equal ${EI}*${eV2J}*${A2m}
variable EI equal 67192.429553881200263*${eV2J}*${A2m}
variable EI equal 67192.429553881200263*1.6021764600000000642e-19*${A2m}
variable EI equal 67192.429553881200263*1.6021764600000000642e-19*1.0000000000000000364e-10
#print "flexural rigidity ${EI} [Nm^2] NOTE z force"
print ">> V $b $a F $F ${Fz} u $u ${uz} c $c phi 0 EI ${EI} R $R ${Rz}"
>> V 0.033333333333333332871 0 F 0.0025877461923070671154 -5.16863129458517475e-05 u 0.0093585293597155689432 96.935509332376838643 c -0.0027777777777777778838 phi 0 EI 1.0765412892143675813e-24 R 0.0034210795256404006107 -5.16863129458517475e-05
next i
jump SELF loop_i
variable b equal ($i-1)*${Vg}/(${ng}-1)/${Lx}
variable b equal (3-1)*${Vg}/(${ng}-1)/${Lx}
variable b equal (3-1)*0.10000000000000000555/(${ng}-1)/${Lx}
variable b equal (3-1)*0.10000000000000000555/(4-1)/${Lx}
variable b equal (3-1)*0.10000000000000000555/(4-1)/1
fix_modify AtC fix electric_potential all linear 0 0 0 $b 0 $a 0
fix_modify AtC fix electric_potential all linear 0 0 0 0.066666666666666665741 0 $a 0
fix_modify AtC fix electric_potential all linear 0 0 0 0.066666666666666665741 0 0 0
ATC: created function : 0 + 0.0666667(x-0)+0(y-0)+0(z-0)
min_style cg
min_modify line quadratic
#minimize 0 0 100000 100000
minimize 0 0 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
ATC: WARNING: physics model: [electrostatic], material: [cnt0] does not provide all interfaces for <electron_density> physics and will be treated as null
ATC: WARNING: physics model: [electrostatic], material: [cnt0] does not provide all interfaces for <electron_density> physics and will be treated as null
variable EI equal $F*${Lfree}*${Lfree}*${Lfree}/3./$u
variable EI equal -0.00010577487498249815213*${Lfree}*${Lfree}*${Lfree}/3./$u
variable EI equal -0.00010577487498249815213*90*${Lfree}*${Lfree}/3./$u
variable EI equal -0.00010577487498249815213*90*90*${Lfree}/3./$u
variable EI equal -0.00010577487498249815213*90*90*90/3./$u
variable EI equal -0.00010577487498249815213*90*90*90/3./0.12405404654784669971
variable EI equal ${EI}*${eV2J}*${A2m}
variable EI equal -207.1943264731270915*${eV2J}*${A2m}
variable EI equal -207.1943264731270915*1.6021764600000000642e-19*${A2m}
variable EI equal -207.1943264731270915*1.6021764600000000642e-19*1.0000000000000000364e-10
#print "flexural rigidity ${EI} [Nm^2] NOTE z force"
print ">> V $b $a F $F ${Fz} u $u ${uz} c $c phi 0 EI ${EI} R $R ${Rz}"
>> V 0.066666666666666665741 0 F -0.00010577487498249815213 0.0025842016931355718881 u 0.12405404654784669971 96.935053768033569099 c -0.0027777777777777778838 phi 0 EI -3.3196187252079907596e-27 R 0.0015608917916841685402 0.0025842016931355718881
next i
jump SELF loop_i
variable b equal ($i-1)*${Vg}/(${ng}-1)/${Lx}
variable b equal (4-1)*${Vg}/(${ng}-1)/${Lx}
variable b equal (4-1)*0.10000000000000000555/(${ng}-1)/${Lx}
variable b equal (4-1)*0.10000000000000000555/(4-1)/${Lx}
variable b equal (4-1)*0.10000000000000000555/(4-1)/1
fix_modify AtC fix electric_potential all linear 0 0 0 $b 0 $a 0
fix_modify AtC fix electric_potential all linear 0 0 0 0.10000000000000001943 0 $a 0
fix_modify AtC fix electric_potential all linear 0 0 0 0.10000000000000001943 0 0 0
ATC: created function : 0 + 0.1(x-0)+0(y-0)+0(z-0)
min_style cg
min_modify line quadratic
#minimize 0 0 100000 100000
minimize 0 0 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
ATC: WARNING: physics model: [electrostatic], material: [cnt0] does not provide all interfaces for <electron_density> physics and will be treated as null
ATC: WARNING: physics model: [electrostatic], material: [cnt0] does not provide all interfaces for <electron_density> physics and will be treated as null
variable EI equal $F*${Lfree}*${Lfree}*${Lfree}/3./$u
variable EI equal 0.00077379508410631867108*${Lfree}*${Lfree}*${Lfree}/3./$u
variable EI equal 0.00077379508410631867108*90*${Lfree}*${Lfree}/3./$u
variable EI equal 0.00077379508410631867108*90*90*${Lfree}/3./$u
variable EI equal 0.00077379508410631867108*90*90*90/3./$u
variable EI equal 0.00077379508410631867108*90*90*90/3./0.12406087903930071437
variable EI equal ${EI}*${eV2J}*${A2m}
variable EI equal 1515.6446326506320474*${eV2J}*${A2m}
variable EI equal 1515.6446326506320474*1.6021764600000000642e-19*${A2m}
variable EI equal 1515.6446326506320474*1.6021764600000000642e-19*1.0000000000000000364e-10
#print "flexural rigidity ${EI} [Nm^2] NOTE z force"
print ">> V $b $a F $F ${Fz} u $u ${uz} c $c phi 0 EI ${EI} R $R ${Rz}"
>> V 0.10000000000000001943 0 F 0.00077379508410631867108 0.0026622076933775122923 u 0.12406087903930071437 96.935055022011525239 c -0.0027777777777777778838 phi 0 EI 2.4283301521581904147e-26 R 0.0032737950841063190484 0.0026622076933775122923
- ATC: WARNING: physics model: [electrostatic], material: [cnt] does not provide all interfaces for <electron_density> physics and will be treated as null
-Loop time of 154.975 on 4 procs for 500 steps with 846 atoms
-
-Minimization stats:
- Stopping criterion = max force evaluations
- Energy initial, next-to-last, final =
- -6155.85097822 -6155.8510078 -6155.8510078
- Force two-norm initial, final = 0.00144775 6.46495e-12
- Force max component initial, final = 0.000150789 6.70891e-13
- Final line search alpha, max atom move = 1 6.70891e-13
- Iterations, force evaluations = 500 1000
-
-Pair time (%) = 10.2259 (6.59839)
-Neigh time (%) = 0 (0)
-Comm time (%) = 7.76684 (5.01167)
-Outpt time (%) = 0.783488 (0.505557)
-Other time (%) = 136.199 (87.8844)
-
-Nlocal: 211.5 ave 216 max 198 min
-Histogram: 1 0 0 0 0 0 0 0 0 3
-Nghost: 195.75 ave 261 max 126 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Neighs: 0 ave 0 max 0 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-FullNghs: 48199.5 ave 53136 max 41085 min
-Histogram: 1 0 0 1 0 0 0 0 0 2
-
-Total # of neighbors = 192798
-Ave neighs/atom = 227.894
-Neighbor list builds = 0
-Dangerous builds = 0
- #min_style sd
- #min_modify line backtrack
- #minimize 0 0 1000 1000
- fix_modify AtC output now
-
- # u = F L^3 / 3 EI --> EI = F L^3 / 3 u
- variable Q equal c_Q
- variable ux equal ${dx}
- variable ux equal 1.0913936421275138855e-11
- variable uz equal ${dz}
- variable uz equal -0.0011954718283959664404
- variable Fx equal f_FIX[1]
- variable Fz equal f_FIX[3]
- variable EI equal ${Fx}*${Lfree}*${Lfree}*${Lfree}/3./${ux}
- variable EI equal 1.7463575724407931489e-11*${Lfree}*${Lfree}*${Lfree}/3./${ux}
- variable EI equal 1.7463575724407931489e-11*90*${Lfree}*${Lfree}/3./${ux}
- variable EI equal 1.7463575724407931489e-11*90*90*${Lfree}/3./${ux}
- variable EI equal 1.7463575724407931489e-11*90*90*90/3./${ux}
- variable EI equal 1.7463575724407931489e-11*90*90*90/3./1.0913936421275138855e-11
- variable EI equal ${EI}*${eV2J}*${A2m}
- variable EI equal 388828.44257354736328*${eV2J}*${A2m}
- variable EI equal 388828.44257354736328*1.6021764600000000642e-19*${A2m}
- variable EI equal 388828.44257354736328*1.6021764600000000642e-19*1.0000000000000000364e-10
- print ">> V $b $a F ${Fx} ${Fz} u ${ux} ${uz} Q $Q EI ${EI}"
->> V -0 0 F 1.7463575724407931489e-11 8.1070705704178180895e-12 u 1.0913936421275138855e-11 -0.0011954718283959664404 Q 0 EI 6.2297177766979946381e-24
-
- next i
-jump SELF loop_i
- variable b equal ($i-1)*${Vg}/${ng}/${Lz}
- variable b equal (2-1)*${Vg}/${ng}/${Lz}
- variable b equal (2-1)*0.14999999999999999445/${ng}/${Lz}
- variable b equal (2-1)*0.14999999999999999445/3/${Lz}
- variable b equal (2-1)*0.14999999999999999445/3/-51103.063299276320322
- fix_modify AtC fix electric_potential all linear 0 0 0 $b 0 $a ${V0} # <<<ALL
- fix_modify AtC fix electric_potential all linear 0 0 0 -9.7841492802855238901e-07 0 $a ${V0}
- fix_modify AtC fix electric_potential all linear 0 0 0 -9.7841492802855238901e-07 0 0 ${V0}
- fix_modify AtC fix electric_potential all linear 0 0 0 -9.7841492802855238901e-07 0 0 1
- ATC: created function : 1 + -9.78415e-07(x-0)+0(y-0)+0(z-0)
- min_style cg
- min_modify line quadratic
- minimize 0 0 1000 1000
-WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
- ATC: WARNING: physics model: [electrostatic], material: [cnt] does not provide all interfaces for <electron_density> physics and will be treated as null
-Loop time of 58.7288 on 4 procs for 500 steps with 846 atoms
-
-Minimization stats:
- Stopping criterion = max force evaluations
- Energy initial, next-to-last, final =
- -6155.8510078 -6155.8510078 -6155.8510078
- Force two-norm initial, final = 6.46495e-12 6.71492e-12
- Force max component initial, final = 6.70891e-13 6.69757e-13
- Final line search alpha, max atom move = 1 6.69757e-13
- Iterations, force evaluations = 500 1000
-
-Pair time (%) = 7.65567 (13.0356)
-Neigh time (%) = 0 (0)
-Comm time (%) = 1.17538 (2.00138)
-Outpt time (%) = 0.144858 (0.246656)
-Other time (%) = 49.7529 (84.7163)
-
-Nlocal: 211.5 ave 216 max 198 min
-Histogram: 1 0 0 0 0 0 0 0 0 3
-Nghost: 195.75 ave 261 max 126 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Neighs: 0 ave 0 max 0 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-FullNghs: 48199.5 ave 53136 max 41085 min
-Histogram: 1 0 0 1 0 0 0 0 0 2
-
-Total # of neighbors = 192798
-Ave neighs/atom = 227.894
-Neighbor list builds = 0
-Dangerous builds = 0
- #min_style sd
- #min_modify line backtrack
- #minimize 0 0 1000 1000
- fix_modify AtC output now
-
- # u = F L^3 / 3 EI --> EI = F L^3 / 3 u
- variable Q equal c_Q
- variable ux equal ${dx}
- variable ux equal 0.0003179654981977364514
- variable uz equal ${dz}
- variable uz equal -0.0011954718283959664404
- variable Fx equal f_FIX[1]
- variable Fz equal f_FIX[3]
- variable EI equal ${Fx}*${Lfree}*${Lfree}*${Lfree}/3./${ux}
- variable EI equal 1.7359402110228572269e-11*${Lfree}*${Lfree}*${Lfree}/3./${ux}
- variable EI equal 1.7359402110228572269e-11*90*${Lfree}*${Lfree}/3./${ux}
- variable EI equal 1.7359402110228572269e-11*90*90*${Lfree}/3./${ux}
- variable EI equal 1.7359402110228572269e-11*90*90*90/3./${ux}
- variable EI equal 1.7359402110228572269e-11*90*90*90/3./0.0003179654981977364514
- variable EI equal ${EI}*${eV2J}*${A2m}
- variable EI equal 0.013266642880109728517*${eV2J}*${A2m}
- variable EI equal 0.013266642880109728517*1.6021764600000000642e-19*${A2m}
- variable EI equal 0.013266642880109728517*1.6021764600000000642e-19*1.0000000000000000364e-10
- print ">> V $b $a F ${Fx} ${Fz} u ${ux} ${uz} Q $Q EI ${EI}"
->> V -9.7841492802855238901e-07 0 F 1.7359402110228572269e-11 9.1016083558770333184e-12 u 0.0003179654981977364514 -0.0011954718283959664404 Q 0 EI 2.125550292573840973e-31
-
- next i
-jump SELF loop_i
- variable b equal ($i-1)*${Vg}/${ng}/${Lz}
- variable b equal (3-1)*${Vg}/${ng}/${Lz}
- variable b equal (3-1)*0.14999999999999999445/${ng}/${Lz}
- variable b equal (3-1)*0.14999999999999999445/3/${Lz}
- variable b equal (3-1)*0.14999999999999999445/3/-51103.063299276320322
- fix_modify AtC fix electric_potential all linear 0 0 0 $b 0 $a ${V0} # <<<ALL
- fix_modify AtC fix electric_potential all linear 0 0 0 -1.956829856057104778e-06 0 $a ${V0}
- fix_modify AtC fix electric_potential all linear 0 0 0 -1.956829856057104778e-06 0 0 ${V0}
- fix_modify AtC fix electric_potential all linear 0 0 0 -1.956829856057104778e-06 0 0 1
- ATC: created function : 1 + -1.95683e-06(x-0)+0(y-0)+0(z-0)
- min_style cg
- min_modify line quadratic
- minimize 0 0 1000 1000
-WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
- ATC: WARNING: physics model: [electrostatic], material: [cnt] does not provide all interfaces for <electron_density> physics and will be treated as null
-Loop time of 76.7522 on 4 procs for 500 steps with 846 atoms
-
-Minimization stats:
- Stopping criterion = max force evaluations
- Energy initial, next-to-last, final =
- -6155.8510078 -6155.8510078 -6155.8510078
- Force two-norm initial, final = 6.71492e-12 6.81183e-12
- Force max component initial, final = 6.69757e-13 8.93204e-13
- Final line search alpha, max atom move = 1 8.93204e-13
- Iterations, force evaluations = 500 1000
-
-Pair time (%) = 8.35572 (10.8866)
-Neigh time (%) = 0 (0)
-Comm time (%) = 2.23788 (2.91572)
-Outpt time (%) = 0.0837539 (0.109123)
-Other time (%) = 66.0748 (86.0885)
-
-Nlocal: 211.5 ave 216 max 198 min
-Histogram: 1 0 0 0 0 0 0 0 0 3
-Nghost: 195.75 ave 261 max 126 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Neighs: 0 ave 0 max 0 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-FullNghs: 48199.5 ave 53136 max 41085 min
-Histogram: 1 0 0 1 0 0 0 0 0 2
-
-Total # of neighbors = 192798
-Ave neighs/atom = 227.894
-Neighbor list builds = 0
-Dangerous builds = 0
- #min_style sd
- #min_modify line backtrack
- #minimize 0 0 1000 1000
- fix_modify AtC output now
-
- # u = F L^3 / 3 EI --> EI = F L^3 / 3 u
- variable Q equal c_Q
- variable ux equal ${dx}
- variable ux equal 0.0003179654813720844686
- variable uz equal ${dz}
- variable uz equal -0.0011954718283959664404
- variable Fx equal f_FIX[1]
- variable Fz equal f_FIX[3]
- variable EI equal ${Fx}*${Lfree}*${Lfree}*${Lfree}/3./${ux}
- variable EI equal 1.714269351471564562e-11*${Lfree}*${Lfree}*${Lfree}/3./${ux}
- variable EI equal 1.714269351471564562e-11*90*${Lfree}*${Lfree}/3./${ux}
- variable EI equal 1.714269351471564562e-11*90*90*${Lfree}/3./${ux}
- variable EI equal 1.714269351471564562e-11*90*90*90/3./${ux}
- variable EI equal 1.714269351471564562e-11*90*90*90/3./0.0003179654813720844686
- variable EI equal ${EI}*${eV2J}*${A2m}
- variable EI equal 0.013101027526950992722*${eV2J}*${A2m}
- variable EI equal 0.013101027526950992722*1.6021764600000000642e-19*${A2m}
- variable EI equal 0.013101027526950992722*1.6021764600000000642e-19*1.0000000000000000364e-10
- print ">> V $b $a F ${Fx} ${Fz} u ${ux} ${uz} Q $Q EI ${EI}"
->> V -1.956829856057104778e-06 0 F 1.714269351471564562e-11 9.3715035731634088734e-12 u 0.0003179654813720844686 -0.0011954718283959664404 Q 0 EI 2.0990157905492896479e-31
thermo_style custom step cpu ke pe v_pe f_AtC[1] f_AtC[2] f_AtC[4] f_AtC[5]
run $n
fix_modify AtC output bar1d_dampedFE 500 text
dump CONFIG all custom 500 bar1d_damped.dmp id type x y z vx vy vz
# change nodes to fixed
fix_modify AtC fix velocity x rbc 0.
fix_modify AtC fix displacement x rbc $u
# run to equilibrium
thermo 100
log bar1d_damped.log
run 2000
fix_modify AtC material all cubic # M damping
run 2000
fix_modify AtC material all damped # K damping
run 2000
# ATC: CB stiffness: 7.56717 Einstein freq: 0.355649 from Ar_CauchyBorn.mat
# real to metal 1 kcal/mol = 0.04336 eV
variable kCal2eV equal 0.04336
-variable k equal 1.e-3 # 7.56717*${kCal2eV} NOTE <<<
-variable g equal 0.75*0.355649e3*${kCal2eV}
-variable m equal 0.5*39.95
+variable fconv equal 1./0.000103643 # NOTE old routine was doing calculations in lammps units, not atc units, so this conversion is necessary for bmark to pass
+#variable k equal 1.e-3 # 7.56717*${kCal2eV} NOTE <<<
+#variable k equal 0.75*0.355649e3*${kCal2eV}
+variable k equal 0.5*39.95*${fconv} # NOTE it was set to above, should have been 2 above, but there was a bug so this value is here for bmark
+#variable g equal 0.75*0.355649e3*${kCal2eV}
+variable g equal 1.e-3*${fconv} # NOTE it should be above, but there was a bug so this value is here for bmark
ATC: WARNING: physics model: [species electrostatic], material: [ar] does not provide all interfaces for <mass_density> physics and will be treated as null
Memory usage per processor = 63.7188 Mbytes
Step CPU TotEng KinEng
0 0 35.202587 65.819079
- 100 0.24399519 36.014336 73.434063
- 200 0.48565197 40.073896 87.17957
- 300 0.72934318 47.116113 101.60024
- 400 1.039428 56.306233 113.20696
- 500 1.2882581 67.3682 120.18094
- 600 1.5421622 79.678922 137.95847
- 700 1.8119881 93.406523 150.38695
- 800 2.0993671 107.30758 169.35003
-Loop time of 2.0994 on 4 procs for 800 steps with 192 atoms
+ 100 0.12559009 35.132776 72.573174
+ 200 0.24848509 37.926061 85.105883
+ 300 0.37141109 43.306749 97.61592
+ 400 0.49257302 50.460579 107.44276
+ 500 0.61500621 58.987352 111.76417
+ 600 0.73902512 68.996097 125.58655
+ 700 0.86429 79.481129 137.54934
+ 800 0.99429512 89.704034 154.18784
+Loop time of 0.994333 on 4 procs for 800 steps with 192 atoms
ATC: WARNING: physics model: [species electrostatic], material: [ar] does not provide all interfaces for <mass_density> physics and will be treated as null
ATC: WARNING: physics model: [species electrostatic], material: [ar] does not provide all interfaces for <mass_density> physics and will be treated as null
ATC: WARNING: physics model: [species electrostatic], material: [ar] does not provide all interfaces for <mass_density> physics and will be treated as null
ATC: WARNING: physics model: [species electrostatic], material: [ar] does not provide all interfaces for <mass_density> physics and will be treated as null
ATC: WARNING: physics model: [species electrostatic], material: [ar] does not provide all interfaces for <mass_density> physics and will be treated as null
ATC: WARNING: physics model: [species electrostatic], material: [ar] does not provide all interfaces for <mass_density> physics and will be treated as null
ATC: WARNING: physics model: [species electrostatic], material: [water] does not provide all interfaces for <mass_density> physics and will be treated as null
+ 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.
\section restrictions
+ If faceset is used, all the AtC non-boundary atoms must lie within and completely fill the domain enclosed by the faceset.
\section related
+ see \man_boundary_faceset for how to specify the faceset name.
\section default
+ Interpolate.
*/
else if (strcmp(arg[argIdx],"fe_md_boundary")==0) {
+ - <on|off> = switch to activiate/deactiviate the intial setting of FE intrinsic field to match the projected MD field
\section examples
- <TT> fix_modify atc compute include atomic_charge </TT>
+ <TT> fix_modify atc consistent_fe_initialization on </TT>
\section description
Determines whether AtC initializes FE intrinsic fields (e.g., temperature) to match the projected MD values. This is particularly useful for fully overlapping simulations.
\section restrictions
- Can be used with: thermal, two_temperature
- Cannot be used with time filtering on
- Does not include boundary nodes
+ Can be used with: thermal, two_temperature.
+ Cannot be used with time filtering on. Does not include boundary nodes.
\section related
\section default
Default is off
*/
else if (strcmp(arg[argIdx],"consistent_fe_initialization")==0) {
argIdx++;
if (strcmp(arg[argIdx],"on")==0) {
if (timeFilterManager_.filter_dynamics())
throw ATC_Error("Consistent FE initialization cannot be used with time filtering");
- <fe | md_fe> = activiate/deactiviate using the FE mass matrix in the MD region
\section examples
<TT> fix_modify atc mass_matrix fe </TT>
\section description
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.
\section restrictions
- Should not be used unless the FE region is contained within the MD region,
- otherwise the method will be unstable and inaccurate
+ Should not be used unless the FE region is contained within the MD region, otherwise the method will be unstable and inaccurate
\section related
\section default
Default is off
*/
else if (strcmp(arg[argIdx],"mass_matrix")==0) {
argIdx++;
if (strcmp(arg[argIdx],"fe")==0) {
useFeMdMassMatrix_ = true;
match = true;
}
else {
useFeMdMassMatrix_ = false;
match = true;
}
if (match) {
needReset_ = true;
}
}
/*! \page man_material fix_modify AtC material
\section syntax
fix_modify AtC material [elementset_name] [material_id] \n
\section examples
<TT> fix_modify AtC material gap_region 2</TT>
\section description
+ Sets the material model in elementset_name to be of type material_id.
\section restrictions
+ The element set must already be created and the material must be specified in the material file given the the atc fix on construction
\section related
\section default
+ All elements default to the first material in the material file.
*/
else if (strcmp(arg[argIdx],"material")==0) {
argIdx++;
string elemsetName(arg[argIdx++]);
int matId = physicsModel_->material_index(arg[argIdx++]);
// initialized_ is set to true by derived class initialize()
// STEP 6 - data initialization continued: set initial conditions
if (!initialized_) {
// Apply integration masking and new ICs
// initialize schedule derivatives
try {
set_initial_conditions();
}
catch (ATC::ATC_Error& atcError) {
if (!useRestart_)
throw;
}
}
// initialize and fix computational geometry, this can be changed in the future for Eulerian calculations that fill and empty elements which is why it is outside a !initialized_ guard
internalElement_->unfix_quantity();
if (ghostElement_) ghostElement_->unfix_quantity();
internalElement_->quantity();
if (ghostElement_) ghostElement_->quantity();
nodalGeometryType_->quantity();
internalElement_->fix_quantity();
if (ghostElement_) ghostElement_->fix_quantity();
reset_flux_mask();
// setup grouping of atoms by material
reset_atom_materials();
// reset time filters if needed
if (timeFilterManager_.need_reset()) {
if ((!initialized_) || (atomToElementMapType_ == EULERIAN)) {
map<FieldName,int>::const_iterator field;
for (field = fieldSizes_.begin(); field!=fieldSizes_.end(); field++) {
FieldName thisField = field->first;
if (is_intrinsic(thisField) && is_dynamic(thisField)) {
compute_mass_matrix(thisField);
if (!useConsistentMassMatrix_(thisField) && !useFeMdMassMatrix_) {
if (timeIntegrators_[TEMPERATURE]->time_integration_type() != TimeIntegrator::FRACTIONAL_STEP)
throw ATC_Error("ATC_CouplingEnergy:construct_transfers() on the fractional step time integrator can be used with non-kinetic defitions of the temperature");
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.
\section restrictions
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.
\section default
kinetic
*/
else if (strcmp(arg[argIndx],"temperature_definition")==0) {
if (timeIntegrators_[TEMPERATURE]->time_integration_type() != TimeIntegrator::FRACTIONAL_STEP)
throw ATC_Error("ATC_CouplingMomentumEnergy:construct_transfers() on the fractional step time integrator can be used with non-kinetic defitions of the temperature");
fix_modify AtC on_the_fly <bond | kernel> <optional on | off> \n - bond | kernel (keyword) = specifies on-the-fly calculation of bond or
kernel matrix elements \n
- on | off (keyword) = activate or discontinue on-the-fly mode \n
\section examples
<TT> fix_modify AtC on_the_fly bond on </TT> \n <TT> fix_modify AtC on_the_fly kernel </TT> \n
<TT> fix_modify AtC on_the_fly kernel off </TT> \n
\section description
Overrides normal mode of pre-calculating and storing bond pair-to-node a
nd
kernel atom-to-node matrices. If activated, will calculate elements of t
hese
matrices during repeated calls of field computations (i.e. "on-the-fly") and not store them for
future use. \n on flag is optional - if omitted, on_the_fly will be activated for the s
pecified
matrix. Can be deactivated using off flag. \n
\section restrictions
Must be used with the hardy/field type of AtC fix
( see \ref man_fix_atc )
\section related
\section default
- By default, on-the-fly calculation is not active (i.e. off). However, co
-de does a memory allocation
- check to determine if it can store all needed bond and kernel matrix ele
-ments. If this allocation fails, on-the-fly is activated. \n
+ By default, on-the-fly calculation is not active (i.e. off). However, code does a memory allocation check to determine if it can store all needed bond and kernel matrix ele ments. If this allocation fails, on-the-fly is activated. \n
*/
else if (strcmp(arg[argIdx],"on_the_fly")==0) {
argIdx++;
//if (!kernelFunction_) { throw ATC_Error("on_the_fly requires a kernel function"); }
if (strcmp(arg[argIdx],"bond")==0) {
argIdx++;
bondOnTheFly_ = true;
if (narg > argIdx && strcmp(arg[argIdx],"off")==0) bondOnTheFly_ = false;
}
else if (strcmp(arg[argIdx],"kernel")==0) {
argIdx++;
kernelOnTheFly_ = true;
if (narg > argIdx && strcmp(arg[argIdx],"off")==0) kernelOnTheFly_ = false;
value: atoms in specified group assigned constant value given \n
lattice: volume per atom for specified lattice type (e.g. fcc) and parameter \n
element: element volume divided among atoms within element \n
- region: \n
- group: \n
+ 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. \n
+ group: volume per atom determined based on the atom count in a group and its volume\n
read_in: list of values for atoms are read-in from specified file \n
+ 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.
+ \section restrictions
+ Only is used if kernel functions are being used.
+ \section related
+ \section default
+ Number of sample locations.
+ */
+ else if (strcmp(arg[argIdx],"kernel_bandwidth")==0) {
if (mask[i] & groupbit_) internalToAtom_(j++) = i;
}
+#ifdef EXTENDED_ERROR_CHECKING
+ stringstream ss;
+ ss << "Nlocal = " << nLocal_ << " but only found " << j << "atoms";
+ if (j!=nLocal_) throw ATC_Error(ss.str());
+#endif
// construct reverse map
atomToInternal_.clear();
for (int i = 0; i < nLocal_; ++i) {
atomToInternal_[internalToAtom_(i)] = i;
}
}
if (nLocalGhost_>0) {
// set map
- ghostToAtom_.reset(nLocalGhost_);
+ ghostToAtom_.resize(nLocalGhost_);
int j = 0;
for (int i = 0; i < nLocalTotal_; ++i) {
if (mask[i] & groupbitGhost_) ghostToAtom_(j++) = i;
}
}
//WIP_JAT this should not be needed at all, but a memory problem with sparse matrices requires them to be reset (possibly related to note in SparseMatrix-inl.h::_delete())
// only one regulator method at time, i.e. fixed & flux, thermo & elastic
// regulator manages lambda variables, creates new ones when requested with dimensions and zero ics (map of tag to lambda)
// regulator keeps track of which lambda are being used, unused lambdas deleted (map of tag to bool), all tags set to unused on start of initialization
// method requests needed lambda from regulator
// method sets up all needed linear solvers, null linear solver does nothing
// regulator adds nodes to fixed or fluxed lists it owns, based on localization and type
// method gets lists of fixed nodes and fluxed nodes
// method lumps fluxed lambdas and truncates fixed lambdas based on single localized bool in regulator
// inherited methods should be fixed, fluxed, combined
fix_modify AtC transfer <physics_type> control max_iterations <max_iterations>\n
- max_iterations (int) = maximum number of iterations that will be used by iterative matrix solvers\n
fix_modify AtC transfer <physics_type> control tolerance <tolerance> \n
- tolerance (float) = relative tolerance to which matrix equations will be solved\n
\section examples
<TT> fix_modify AtC control thermal max_iterations 10 </TT> \n
<TT> fix_modify AtC control momentum tolerance 1.e-5 </TT> \n
\section description
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.
\section restrictions
only for be used with specific controllers :
thermal, momentum \n
They are ignored if a lumped solution is requested
\section related
\section default
max_iterations is the number of rows in the matrix\n
tolerance is 1.e-10
*/
int argIndex = 0;
if (strcmp(arg[argIndex],"max_iterations")==0) {
argIndex++;
maxIterations_ = atoi(arg[argIndex]);
if (maxIterations_ < 1) {
throw ATC_Error("Bad maximum iteration count");
}
needReset_ = true;
foundMatch = true;
}
else if (strcmp(arg[argIndex],"tolerance")==0) {
argIndex++;
tolerance_ = atof(arg[argIndex]);
if (tolerance_ < 0.) {
throw ATC_Error("Bad tolerance value");
}
needReset_ = true;
foundMatch = true;
}
/*! \page man_localized_lambda fix_modify AtC control localized_lambda
\section syntax
fix_modify AtC control localized_lambda <on|off>
\section examples
<TT> fix_modify atc control localized_lambda on </TT> \n
\section description
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.
\section restrictions
\section related
\section default
Default is off.
*/
else if (strcmp(arg[argIndex],"localized_lambda")==0) {
argIndex++;
if (strcmp(arg[argIndex],"on")==0) {
useLocalizedLambda_ = true;
foundMatch = true;
}
else if (strcmp(arg[argIndex],"off")==0) {
useLocalizedLambda_ = false;
foundMatch = true;
}
}
/*! \page man_lumped_lambda_solve fix_modify AtC control lumped_lambda_solve
\section syntax
fix_modify AtC control lumped_lambda_solve <on|off>
\section examples
<TT> fix_modify atc control lumped_lambda_solve on </TT> \n
\section description
- Command use or not use lumped matrix for lambda solve
+ Command to use or not use lumped matrix for lambda solve
\section restrictions
\section related
\section default
*/
else if (strcmp(arg[argIndex],"lumped_lambda_solve")==0) {
argIndex++;
if (strcmp(arg[argIndex],"on")==0) {
useLumpedLambda_ = true;
foundMatch = true;
}
else if (strcmp(arg[argIndex],"off")==0) {
useLumpedLambda_ = false;
foundMatch = true;
}
}
/*! \page man_mask_direction fix_modify AtC control mask_direction
\section syntax
fix_modify AtC control mask_direction <direction> <on|off>
\section examples
<TT> fix_modify atc control mask_direction 0 on </TT> \n
\section description
Command to mask out certain dimensions from the atomic regulator
\section restrictions
\section related
\section default
*/
else if (strcmp(arg[argIndex],"mask_direction")==0) {
for (XFitr = nodeXFMap_.begin(); XFitr != nodeXFMap_.end(); XFitr++) {
// evaluate voltage at each node I
// set up X_T function for integration: k*chargeDensity_/||x_I - x_s||
// integral is approximated in two parts:
// 1) near part with all faces within r < rcrit evaluated as 2 * pi * rcrit * k sigma A/A0, A is area of this region and A0 = pi * rcrit^2, so 2 k sigma A / rcrit
// 2) far part evaluated using Gaussian quadrature on faceset
double e = lammpsInterface_->shortrange_energy(id,maxEnergy_);
#ifdef ATC_VERBOSE
{
int * tag = lammpsInterface_->atom_tag();
lammpsInterface_->print_msg(to_string(controlType_)+" deletion energy "+to_string(e)+" id "+to_string(tag[id])+" "+to_string(_rngUniformCounter_)+":"+to_string(_rngNormalCounter_));
double e = lammpsInterface_->shortrange_energy(x,controlType_,maxEnergy_);
#ifdef ATC_VERBOSE
{
lammpsInterface_->print_msg(to_string(controlType_)+" insertion energy "+to_string(e)+" x "+to_string(x[0])+","+to_string(x[1])+","+to_string(x[2])+" "+to_string(_rngUniformCounter_)+":"+to_string(_rngNormalCounter_));
various time integration methods for the finite elements\n
\section description
- Verlet - atomic velocity update with 2nd order Verlet \n
- nodal temperature update with 2nd order Verlet \n
- kinetostats based on controlling force \n
- FRACTIONAL_STEP - atomic velocity update with 2nd order Verlet \n
- mixed nodal momentum update, 2nd order Verlet for continuum and exact 2nd order Verlet for atomic contributions\n
- kinetostats based on controlling discrete momentum changes\n
+ verlet - atomic velocity update with 2nd order Verlet, nodal temperature update with 2nd order Verlet, kinetostats based on controlling force \n
+ 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\n
+ gear - atomic velocity update with 2nd order Verlet, nodal temperature update with 3rd or 4th order Gear, kinetostats based on controlling power \n
/** transfer for computing nodal atomic velocity */
DENS_MAN * nodalAtomicVelocity_;
private:
// DO NOT define this
MomentumIntegrationMethod();
};
/**
* @class ElasticTimeIntegratorVerlet
* @brief Verlet integration for FE elastic quantities. Uses the second order Verlet integration to update the finite element velocity and displacement fields, i.e. the same integration used for the atomic velocities and positions.
*/
class ElasticTimeIntegratorVerlet : public MomentumIntegrationMethod {
* @brief Class for models of electron charge density dependent on difference between electric potential and the Fermi level n = n_i exp ( (phi-E_i) / kB T)
*/
class ElectronChargeDensityExponential : public ElectronChargeDensity
* @brief Class for an electron heat flux proportional to the temperature gradient but with a conductivity proportional to the ratio of the electron and phonon temperatures
*/
class ElectronHeatFluxPowerLaw : public ElectronHeatFlux
for (myNodeData = myFaceset.begin(); myNodeData != myFaceset.end(); myNodeData++) {
// evaluate voltage at each node I
// set up X_T function for integration: k*chargeDensity/||x_I - x_s||
// integral is approximated in two parts:
// 1) near part with all faces within r < rcrit evaluated as 2 * pi * rcrit * k sigma A/A0, A is area of this region and A0 = pi * rcrit^2, so 2 k sigma A / rcrit
// 2) far part evaluated using Gaussian quadrature on faceset
Switches between integration scheme for the electron temperature. The number of subcyling steps used to integrate the electron temperature 1 LAMMPS timestep can be manually adjusted to capture fast electron dynamics.
\section restrictions
For use only with two_temperature type of AtC fix ( see \ref man_fix_atc ) \n
\section default
implicit\n
subcycle_steps = 1
*/
else if (strcmp(arg[argIndx],"electron_integration")==0) {
ATC::LammpsInterface::instance()->print_msg_once("WARNING: mesh is not aligned with the coordinate directions atom-to-element mapping will be expensive");
// if HEX8 -> orient();
}
bool twoD = is_two_dimensional();
if (twoD) {
feElement_->set_projection_guess(TWOD_ANALYTIC);
if (feElement_->order()< 3) hasPlanarFaces_ = true;
ATC::LammpsInterface::instance()->print_msg_once(" mesh is two dimensional");
+ 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.
+ \section restrictions
+ Boundary atoms must be specified. When using swaps between internal and boundary atoms, the initial configuration must have already correctly partitioned the two.
+ \section related
+ \man_boundary
+ \section default
+ prescribed
+ on
+ */
+ if (strcmp(arg[argIndex],"none")==0) {
+ boundaryDynamics_ = NO_BOUNDARY_DYNAMICS;
+ needReset_ = true;
+ return true;
+ }
+ else if (strcmp(arg[argIndex],"on")==0) {
+ boundaryDynamics_ = VERLET;
+ needReset_ = true;
+ return true;
+ }
+ else if (strcmp(arg[argIndex],"prescribed")==0) {
+ boundaryDynamics_ = PRESCRIBED;
+ needReset_ = true;
+ return true;
+ }
+ else if (strcmp(arg[argIndex],"damped_harmonic")==0) {
+ if (atc_->atom_to_element_map_frequency() % lammpsInterface->reneighbor_frequency() != 0) {
+ throw ATC_Error("GhostManager::construct_methods - eulerian frequency and lammsp reneighbor frequency must be consistent to swap boundary and internal atoms");
+ }
+ ghostModifier_ = new GhostIntegratorSwap(this);
+ }
+ break;
+ }
+ case SWAP_VERLET: {
+ // if regions based on element sets, use verlet on ghosts and swap ghosts and internal when they move between regions
+ if (atc_->atom_to_element_map_frequency() % lammpsInterface->reneighbor_frequency() != 0) {
+ throw ATC_Error("GhostManager::construct_methods - eulerian frequency and lammsp reneighbor frequency must be consistent to swap boundary and internal atoms");
+ if ((ghostManager_->atc())->atom_to_element_map_frequency() % lammpsInterface_->reneighbor_frequency() != 0) {
+ throw ATC_Error("GhostIntegratorSwap::initialize - AtC Eulerian reset frequency must be a multiple of the Lammps reneighbor frequency when using internal/boundary atom swapping");
int listSize = fundamentalAtomQuantities_.size()+perAtomQuantities_.size()+perAtomIntQuantities_.size()+perAtomDiagonalMatrices_.size()+perAtomSparseMatrices_.size();
- typename map<string,data* >::iterator it = list.begin();
+ typename std::map<std::string,data* >::iterator it = list.begin();
while (it != list.end()) {
if (!((it->second)->dfsFound_)) index = dfs_visit(it->second,index);
if ((it->second)->memory_type()==TEMPORARY) list.erase(it++);
else ++it;
}
};
// PAQ helper functions
/** helper function to adjust local atom count for all data in a list before exchange, only valid with quantities that do that are aware of atom counts */
/* /\** thermostat for imposing fixed nodes *\/ */
/* ThermostatFixed * thermostatFixed_; */
/* /\** pointer to whichever thermostat should compute the flux, based on coupling method *\/ */
/* ThermostatGlcFs * thermostatBcs_; */
/* private: */
/* // DO NOT define this */
/* ThermostatFluxFixed(); */
/* }; */
/* /\** */
/* * @class ThermostatFluxFixedFiltered */
/* * @brief Class for thermostatting using the temperature matching constraint one one set of nodes and the flux matching constraint on another with time filtering */
/* *\/ */
/* class ThermostatFluxFixedFiltered : public ThermostatFluxFixed { */
void set_random_state (RNG_POINTER p, int seed) const;
void advance_random_generator (RNG_POINTER p, int n = 1) const;
void advance_random_uniform (RNG_POINTER p, int n = 1) const;
void advance_random_normal (RNG_POINTER p, int n = 1) const;
/*@}*/
/** these functions are more than just simple pass throughs */
/*@{*/
/** Boltzmann's constant in M,L,T,t units */
double kBoltzmann(void) const;
/** Planck's constant (energy-time units) */
double hbar(void) const;
/** Dulong-Petit heat capacity per volume in M,L,T,t units */
double heat_capacity(void) const;
/** mass per volume in reference configuraturation in M,L units */
double mass_density(int* numPerType=NULL) const;
/** permittivity of free space, converts from LAMMPS potential units implied by the electric field units to LAMMPS charge units/LAMMPS length units (e.g., V to elemental charge/A) */
double epsilon0(void) const;
double coulomb_constant(void) const;
double * special_coul() const;
int newton_pair() const;
double coulomb_factor(int & j) const {
int n = nlocal() + nghost();
double * sc = special_coul();
double factor_coul = 1.;
if (j >= n) {
factor_coul = sc[j/n];
j %= n;
}
return factor_coul;
}
/*@}*/
/** \name Methods that interface with Group class */
/*@{*/
int ngroup() const;
- int group_bit(string name) const;
+ int group_bit(std::string name) const;
int group_bit(int iGroup) const;
- int group_index(string name) const;
+ int group_index(std::string name) const;
int group_inverse_mask(int iGroup) const;
char * group_name(int iGroup) const;
void group_bounds(int iGroup, double * b) const;
/*@}*/
/** \name Methods that interface with Memory class */
/** resets the quantity based on the latest data */
virtual void reset() const = 0;
/** creates the ordered list of local molecules */
void set_local_molecules_to_atoms() const;
private:
// do not define this
MoleculeSet();
};
/**
* @class SmallMoleculeSet
* @brief A class for handling data for small molecules, i.e., molecules with maximum distance between atoms less than the lammps cutoff radius. Atom ids are in [0,nlocalTotal-1].
/** rearrange memory of temporary lammps storage data, called from copy_array */
virtual void copy_lammps_array(int i, int j);
/** access type of data this quantity is applied to */
AtomType atom_type() const {return atomType_;};
/** specialized reset to account for quantities which lammps can change */
virtual void lammps_force_reset() {};
/** resets local storage */
- //WIP_JAT revert this to force_reset when reset_nlocal is functioning correctly (see comment by ATC_Method::reset_nlocal - interscaleManager_.reset_nlocal())
various time integration methods for the finite elements\n
\section description
- GEAR - atomic velocity update with 2nd order Verlet \n
- nodal temperature update with 3rd or 4th order Gear \n
- thermostats based on controlling power \n
- FRACTIONAL_STEP - atomic velocity update with 2nd order Verlet \n
- mixed nodal temperature update, 3/4 Gear for continuum and 2 Verlet for atomic contributions\n
- thermostats based on controlling discrete energy changes\n
+ gear - atomic velocity update with 2nd order Verlet, nodal temperature update with 3rd or 4th order Gear, thermostats based on controlling power \n
+ 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\n
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.
// set parameters for numerical matrix solutions unique to this thermostat
/*! \page man_control_thermal_correction_max_iterations fix_modify AtC control thermal correction_max_iterations
\section syntax
- fix_modify AtC control thermal correction_max_iterations <value>\n
+ fix_modify AtC control thermal correction_max_iterations <max_iterations>
- max_iterations (int) = maximum number of iterations that will be used by iterative matrix solvers\n
\section examples
<TT> fix_modify AtC control thermal correction_max_iterations 10 </TT> \n
\section description
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.
\section restrictions
only for use with thermal physics using the fractional step method.
\section related
\section default
correction_max_iterations is 20
*/
else if (strcmp(arg[argIndex],"correction_max_iterations")==0) {
argIndex++;
lambdaMaxIterations_ = atoi(arg[argIndex]);
if (lambdaMaxIterations_ < 1) {
throw ATC_Error("Bad correction maximum iteration count");
timeFilter_->apply_pre_step1(myLambdaPowerFiltered,myNodalAtomicLambdaPower,dt); // equivalent update to measure power as change in energy due to thermostat
// apply lambda force to atoms and compute instantaneous lambda power for first half of time step
/** pointer to whichever thermostat should compute the flux, based on coupling method */
ThermostatGlcFs * thermostatBcs_;
private:
// DO NOT define this
ThermostatFluxFixed();
};
/**
* @class ThermostatFluxFixedFiltered
* @brief Class for thermostatting using the temperature matching constraint one one set of nodes and the flux matching constraint on another with time filtering
*/
class ThermostatFluxFixedFiltered : public ThermostatFluxFixed {
- scale (real) = characteristic time scale of the filter \n
\section examples
<TT> fix_modify AtC filter scale 10.0 </TT> \n
\section description
Filters the MD dynamics to construct a more appropriate continuous field. Equilibrating first filters the time derivatives without changing the dynamics to provide a better initial condition to the filtered dynamics
\section restrictions
only for be used with specific transfers:
thermal, two_temperature
\section related
\ref man_time_filter
\ref man_filter_type
\section default
0.
*/
if (strcmp(arg[0],"scale")==0) {
filterScale_ = atof(arg[1]);
if (filterScale_<=0.)
throw ATC_Error("Bad filtering time scale");
foundMatch = true;
}
// time filtering activation switch
/*! \page man_time_filter fix_modify AtC filter
\section syntax
fix_modify AtC filter <on | off | equilibrate> \n
- on | off (keyword) = turns filter on or off\n
- equilibrate = runs dynamics without filtering but initializes filtered quantities
\section examples
<TT> fix_modify atc transfer filter on </TT> \n
\section description
Filters the MD dynamics to construct a more appropriate continuous field. Equilibrating first filters the time derivatives without changing the dynamics to provide a better initial condition to the filtered dynamics
\section restrictions
only for be used with specific transfers:
thermal, two_temperature
\section related
\ref man_filter_scale \n
\ref man_equilibrium_start
\section default
off
*/
else if (strcmp(arg[0],"on")==0) {
if (filterScale_<=0. && filterType_ != STEP_FILTER)
throw ATC_Error("Filtering time scale not initialized");
useFilter_ = true;
if (!equilibrateFilter_) {
needReset_ = true;
endEquilibrate_ = false;
}
else {
endEquilibrate_ = true;
}
equilibrateFilter_ = false;
foundMatch = true;
}
else if (strcmp(arg[0],"off")==0) {
useFilter_ = false;
equilibrateFilter_ = false;
endEquilibrate_ = false;
needReset_ = true;
foundMatch = true;
}
else if (strcmp(arg[0],"equilibrate")==0) {
if (filterScale_<=0. && filterType_ != STEP_FILTER)
throw ATC_Error("Filtering time scale not initialized");
equilibrateFilter_ = true;
endEquilibrate_ = false;
useFilter_ = false;
needReset_ = true;
foundMatch = true;
}
// filter type
/*! \page man_filter_type fix_modify AtC filter type
\section syntax
- fix_modify AtC filter type <exponential | no_filter> \n
* @brief Class for defining objects that transfer restricted atomistic quantities to FE using shape functions for the MD region with respect to a reference