ATC (Atom To Continuum methods)

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

--------------

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).

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

drift_diffusion
  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

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 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

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

mesh:
  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

molecule:
  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

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_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

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.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
