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:
  XXX.screen - Screen/console output generated by running in.XXX

input files:
  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:
  XXX.screen - Screen/console output generated by running in.XXX

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 response 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

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

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:
  XXX.log - LAMMPS log file generated by running in.XXX
  XXX.screen - Screen/console output generated by running in.XXX

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 response 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

input_files:
  in.gaussianICXd_YYY - Initial Gaussian temperature profile in X dimensions (1/2) decay using a YYY mesh type (hex, hex20, hex27, tet
  in.kernel2d_YYY - hardy post-processing of initial Gaussian temperature profiles using a YYY mesh type (hex,tet)
  in.mesh2d_tet - field-based hardy post-processing of initial Gaussian temperature profile using a 2d tet mesh
  in.semicircle - heated semi-cicular domain using an unstructured 2d hex mesh
  Ar_ttm.mat - two-temperature material model for argon

output files:
  XXX.screen - Screen/console output generated by running in.XXX

input_files:
  in.harmonic_bonds - Stress and heat flux calculation for a bonded lattice
  in.polarize - Polarization calculation for water subject to an electric field
  in.quartic_bonds - Stress and energy calculation for a system with bonds and pairs
  in.water - Water polarization from an applied field using multiscale-based atomic weights
  water.mat - Electrical properties for water cases

output files:
  XXX.screen - Screen/console output generated by running in.XXX

 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_all_atoms - Fixed temperature and fixed flux boundary conditions are applied to a quasi-1D bar of atoms
 in.bar1d_combined - Quasi-1D coupled heat flux using the kinetic + potential energy definition
 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.
 in.bar1d_frac_step - Quasi-1D all atom heat flux with fixed temperature boundaries using fractional step time integration
 in.bar1d_hoover - Quasi-1D coupled heat flux using the kinetic + potential energy definition and fixed-temperature coupling mode
 in.bar1d_interpolate - Quasi-1D coupled heat flux using the interpolation-based reconstruction to estimate the heat flux
 in.bar1d_lumped - Quasi-1D coupled heat flux using localized heat flux control and time filtering
 in.no_atoms - FE solution to a heat source temperature distribution
 Ar_thermal.mat - Material parameter file specifying
   the thermal properties of argon.
 temp.init - Initial set of atomic positions and velocities.

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

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.cutout - demonstrates how to delete elements from an intrinsic atc mesh.
  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.restart - Demonstrates how to use atc restart commands.
  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:
  XXX.log - LAMMPS log file generated by running in.XXX