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.

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.

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