fix ttm command¶
fix ttm/mod command¶
fix ID group-ID ttm seed C_e rho_e kappa_e gamma_p gamma_s v_0 Nx Ny Nz T_infile N T_outfile fix ID group-ID ttm/mod seed init_file Nx Ny Nz T_infile N T_outfile
ID, group-ID are documented in fix command
style = ttm or ttm_mod
seed = random number seed to use for white noise (positive integer)
remaining arguments for fix ttm:
C_e = electronic specific heat (energy/(electron*temperature) units) rho_e = electronic density (electrons/volume units) kappa_e = electronic thermal conductivity (energy/(time*distance*temperature) units) gamma_p = friction coefficient due to electron-ion interactions (mass/time units) gamma_s = friction coefficient due to electronic stopping (mass/time units) v_0 = electronic stopping critical velocity (velocity units) Nx = number of thermal solve grid points in the x-direction (positive integer) Ny = number of thermal solve grid points in the y-direction (positive integer) Nz = number of thermal solve grid points in the z-direction (positive integer) T_infile = filename to read initial electronic temperature from N = dump TTM temperatures every this many timesteps, 0 = no dump T_outfile = filename to write TTM temperatures to (only needed if N > 0)
remaining arguments for fix ttm/mod:
init_file = file with the parameters to TTM Nx = number of thermal solve grid points in the x-direction (positive integer) Ny = number of thermal solve grid points in the y-direction (positive integer) Nz = number of thermal solve grid points in the z-direction (positive integer) T_infile = filename to read initial electronic temperature from N = dump TTM temperatures every this many timesteps, 0 = no dump T_outfile = filename to write TTM temperatures to (only needed if N > 0)
fix 2 all ttm 699489 1.0 1.0 10 0.1 0.0 2.0 1 12 1 initialTs 1000 T.out fix 2 all ttm 123456 1.0 1.0 1.0 1.0 1.0 5.0 5 5 5 Te.in 1 Te.out fix 2 all ttm/mod 34277 parameters.txt 5 5 5 T_init 10 T_out
Use a two-temperature model (TTM) to represent heat transfer through and between electronic and atomic subsystems. LAMMPS models the atomic subsystem as usual with a molecular dynamics model and the classical force field specified by the user, but the electronic subsystem is modeled as a continuum, or a background “gas”, on a regular grid. Energy can be transferred spatially within the grid representing the electrons. Energy can also be transferred between the electronic and the atomic subsystems. The algorithm underlying this fix was derived by D. M. Duffy and A. M. Rutherford and is discussed in two J Physics: Condensed Matter papers: (Duffy) and (Rutherford). They used this algorithm in cascade simulations where a primary knock-on atom (PKA) was initialized with a high velocity to simulate a radiation event.
The description in this sub-section applies to both fix ttm and fix ttm/mod. Fix ttm/mod adds options to account for external heat sources (e.g. at a surface) and for specifying parameters that allow the electronic heat capacity to depend strongly on electronic temperature. It is more expensive computationally than fix ttm because it treats the thermal diffusion equation as non-linear. More details on fix ttm/mod are given below.
Heat transfer between the electronic and atomic subsystems is carried out via an inhomogeneous Langevin thermostat. This thermostat differs from the regular Langevin thermostat (fix langevin) in three important ways. First, the Langevin thermostat is applied uniformly to all atoms in the user-specified group for a single target temperature, whereas the TTM fix applies Langevin thermostatting locally to atoms within the volumes represented by the user-specified grid points with a target temperature specific to that grid point. Second, the Langevin thermostat couples the temperature of the atoms to an infinite heat reservoir, whereas the heat reservoir for fix TTM is finite and represents the local electrons. Third, the TTM fix allows users to specify not just one friction coefficient, but rather two independent friction coefficients: one for the electron-ion interactions (gamma_p), and one for electron stopping (gamma_s).
When the friction coefficient due to electron stopping, gamma_s, is non-zero, electron stopping effects are included for atoms moving faster than the electron stopping critical velocity, v_0. For further details about this algorithm, see (Duffy) and (Rutherford).
Energy transport within the electronic subsystem is solved according to the heat diffusion equation with added source terms for heat transfer between the subsystems:
where C_e is the specific heat, rho_e is the density, kappa_e is the thermal conductivity, T is temperature, the “e” and “a” subscripts represent electronic and atomic subsystems respectively, g_p is the coupling constant for the electron-ion interaction, and g_s is the electron stopping coupling parameter. C_e, rho_e, and kappa_e are specified as parameters to the fix. The other quantities are derived. The form of the heat diffusion equation used here is almost the same as that in equation 6 of (Duffy), with the exception that the electronic density is explicitly represented, rather than being part of the specific heat parameter.
Currently, fix ttm assumes that none of the user-supplied parameters will vary with temperature. Note that (Duffy) used a tanh() functional form for the temperature dependence of the electronic specific heat, but ignored temperature dependencies of any of the other parameters. See more discussion below for fix ttm/mod.
These fixes require use of periodic boundary conditions and a 3D simulation. Periodic boundary conditions are also used in the heat equation solve for the electronic subsystem. This varies from the approach of (Rutherford) where the atomic subsystem was embedded within a larger continuum representation of the electronic subsystem.
The initial electronic temperature input file, T_infile, is a text file LAMMPS reads in with no header and with four numeric columns (ix,iy,iz,Temp) and with a number of rows equal to the number of user-specified grid points (Nx by Ny by Nz). The ix,iy,iz are node indices from 0 to nxnodes-1, etc. For example, the initial electronic temperatures on a 1 by 2 by 3 grid could be specified in a T_infile as follows:
0 0 0 1.0 0 0 1 1.0 0 0 2 1.0 0 1 0 2.0 0 1 1 2.0 0 1 2 2.0
where the electronic temperatures along the y=0 plane have been set to 1.0, and the electronic temperatures along the y=1 plane have been set to 2.0. The order of lines in this file is no important. If all the nodal values are not specified, LAMMPS will generate an error.
The temperature output file, T_oufile, is created and written by this fix. Temperatures for both the electronic and atomic subsystems at every node and every N timesteps are output. If N is specified as zero, no output is generated, and no output filename is needed. The format of the output is as follows. One long line is written every output timestep. The timestep itself is given in the first column. The next Nx*Ny*Nz columns contain the temperatures for the atomic subsystem, and the final Nx*Ny*Nz columns contain the temperatures for the electronic subsystem. The ordering of the Nx*Ny*Nz columns is with the z index varying fastest, y the next fastest, and x the slowest.
These fixes do not change the coordinates of their atoms; they only scales their velocities. Thus a time integration fix (e.g. fix nve) should still be used to time integrate the affected atoms. The fixes should not normally be used on atoms that have their temperature controlled by another fix - e.g. fix nvt or fix langevin.
The current implementations of these fixes create a copy of the electron grid that overlays the entire simulation domain, for each processor. Values on the grid are summed across all processors. Thus you should insure that this grid is not too large, else your simulation could incur high memory and communication costs.
Additional details for fix ttm/mod
Fix ttm/mod uses the heat diffusion equation with possible external heat sources (e.g. laser heating in ablation simulations):
where theta is the Heaviside step function, I_0 is the (absorbed) laser pulse intensity for ablation simulations, l_skin is the depth of skin-layer, and all other designations have the same meaning as in the former equation. The duration of the pulse is set by the parameter tau in the init_file.
Fix ttm/mod also allows users to specify the dependencies of C_e and kappa_e on the electronic temperature. The specific heat is expressed as
where X = T_e/1000, and the thermal conductivity is defined as kappa_e = D_e*rho_e*C_e, where D_e is the thermal diffusion coefficient.
Electronic pressure effects are included in the TTM model to account for the blast force acting on ions because of electronic pressure gradient (see (Chen), (Norman)). The total force acting on an ion is:
where F_langevin is a force from Langevin thermostat simulating electron-phonon coupling, and nabla P_e/n_ion is the electron blast force.
The electronic pressure is taken to be P_e = B*rho_e*C_e*T_e
The current fix ttm/mod implementation allows TTM simulations with a vacuum. The vacuum region is defined as the grid cells with zero electronic temperature. The numerical scheme does not allow energy exchange with such cells. Since the material can expand to previously unoccupied region in some simulations, the vacuum border can be allowed to move. It is controlled by the surface_movement parameter in the init_file. If it is set to 1, then “vacuum” cells can be changed to “electron-filled” cells with the temperature T_e_min if atoms move into them (currently only implemented for the case of 1-dimensional motion of flat surface normal to the X axis). The initial borders of vacuum can be set in the init_file via lsurface and rsurface parameters. In this case, electronic pressure gradient is calculated as
The fix ttm/mod parameter file init_file has the following syntax/ Every line with the odd number is considered as a comment and ignored. The lines with the even numbers are treated as follows:
a_0, energy/(temperature*electron) units a_1, energy/(temperature^2*electron) units a_2, energy/(temperature^3*electron) units a_3, energy/(temperature^4*electron) units a_4, energy/(temperature^5*electron) units C_0, energy/(temperature*electron) units A, 1/temperature units rho_e, electrons/volume units D_e, length^2/time units gamma_p, mass/time units gamma_s, mass/time units v_0, length/time units I_0, energy/(time*length^2) units lsurface, electron grid units (positive integer) rsurface, electron grid units (positive integer) l_skin, length units tau, time units B, dimensionless lambda, length units n_ion, ions/volume units surface_movement: 0 to disable tracking of surface motion, 1 to enable T_e_min, temperature units
Restart, fix_modify, output, run start/stop, minimize info¶
These fixes write the state of the electronic subsystem and the energy exchange between the subsystems to binary restart files. See the read_restart command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion.
Because the state of the random number generator is not saved in the restart files, this means you cannot do “exact” restarts with this fix, where the simulation continues on the same as if no restart had taken place. However, in a statistical sense, a restarted simulation should produce the same behavior.
None of the fix_modify options are relevant to these fixes.
Both fixes compute 2 output quantities stored in a vector of length 2, which can be accessed by various output commands. The first quantity is the total energy of the electronic subsystem. The second quantity is the energy transferred from the electronic to the atomic subsystem on that timestep. Note that the velocity verlet integrator applies the fix ttm forces to the atomic subsystem as two half-step velocity updates: one on the current timestep and one on the subsequent timestep. Consequently, the change in the atomic subsystem energy is lagged by half a timestep relative to the change in the electronic subsystem energy. As a result of this, users may notice slight fluctuations in the sum of the atomic and electronic subsystem energies reported at the end of the timestep.
The vector values calculated are “extensive”.
Fix ttm is part of the MISC package. It is only enabled if LAMMPS was built with that package. Fix ttm/mod is part of the USER-MISC package. It is only enabled if LAMMPS was built with that package. See the Build package doc page for more info.
These fixes can only be used for 3d simulations and orthogonal simulation boxes. You must also use periodic boundary conditions.
(Duffy) D M Duffy and A M Rutherford, J. Phys.: Condens. Matter, 19, 016207-016218 (2007).
(Rutherford) A M Rutherford and D M Duffy, J. Phys.: Condens. Matter, 19, 496201-496210 (2007).
(Chen) J Chen, D Tzou and J Beraun, Int. J. Heat Mass Transfer, 49, 307-316 (2006).
(Norman) G E Norman, S V Starikov, V V Stegailov et al., Contrib. Plasma Phys., 53, 129-139 (2013).
(Pisarev) V V Pisarev and S V Starikov, J. Phys.: Condens. Matter, 26, 475401 (2014).