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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
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