diff --git a/examples/USER/atc/README b/examples/USER/atc/README index 87820bbb9f..afe8329c28 100644 --- a/examples/USER/atc/README +++ b/examples/USER/atc/README @@ -13,55 +13,90 @@ 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: +cauchy_born: 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 + in.cb_biaxial + in.cb_shear + in.cb_unistrain_XXX + in.cb_volumetric + in.flying_cube + in.ftcb_constV + in.read_xref + Ar_CauchyBornXXX.mat + Au_CauchyBornXXX.mat + Au_eamXXX.mat + Cu_CauchyBorn.mat 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. + 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: @@ -87,23 +122,116 @@ hardy: 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: - 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 + 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