lammps/examples/USER/atc6864dfa2d184efficient_neuronet
lammps/examples/USER/atc
6864dfa2d184efficient_neuronet
README
README
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 reponse 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 reponse 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
c4science · Help