ATC (Atom To Continuum methods)

Reese Jones, Jeremy Templeton, Jonathan Zimmerman 
rjones@sandia.gov
September 2009

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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.

  output files:
    bar1d.log - LAMMPS log file generated by running in.bar1d.
    bar1d_flux.log - LAMMPS log file generated by running in.bar1d_flux.

bar1d_two_temperature:
  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

  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.

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.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 
      in.eam_unistrain_xxxx ( xxxx = cell, mesh, qcylinder, qsphere, step )
    eam_volume_stretch.log - LAMMPS log file generated by running 
      in.eam_volume_stretch
    eam_volume_stretchscreen - Screen/console output generated by running 
      in.eam_volume_stretch
    nvt.log - LAMMPS log file generated by running in.nvt
    nvt.screen - Screen/console output generated by running in.nvt

