+Syntax: +
+fix ID group-ID ttm seed e_specific_heat e_density e_thermal_conductivity gamma_p gamma_s v_0 nxnodes nynodes nznodes T_infile N T_outfile ++
Examples: +
+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 ++
Description: +
+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. +
+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, whereas the TTM fix applies Langevin +thermostatting locally within the volumes represented by the +user-specified grid points. 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 and one for +electron stopping. +
+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 is the specific heat, rho is the density, kappa is the thermal +conductivity, and the "e" and "a" subscripts represent the 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. 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 reprensented, +rather than being part of the the specific heat parameter. +
+Currently, this fix assumes that none of the user-supplied parameters +will vary with temperature. This assumption can be relaxed by +modifying the source code to include the desired temperature +dependency and functional form for any of the parameters. 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. +
+This fix requires 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 (nxnodes*nynodes*nznodes). 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 nynodes=0 plane have been +set to 1.0, and the electronic temperatures along the nynodes=1 plane +have been set to 2.0. The order of lines in this file is unimportant. +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 nxnodes*nynodes*nznodes columns contain the temperatures for +the atomic subsystem, and the final nxnodes*nynodes*nznodes columns +contain the temperatures for the electronic subsystem. The ordering +of the nxnodes*nynodes*nznodes columns is with the z index varing +fastest, y the next fastest, and x the slowest. +
+This fix does not change the coordinates of its atoms; it only scales +their velocities. Thus a time integration fix (e.g. fix +nve) should still be used to time integrate the affected +atoms. This fix should not normally be used on atoms that have their +temperature controlled by another fix - e.g. fix nvt or +fix langevin. +
+Restart, fix_modify, output, run start/stop, minimize info: +
+No information about this fix is written to binary restart +files. None of the fix_modify options +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various output +commands. No parameter of this fix can be +used with the start/stop keywords of the run command. +This fix is not invoked during energy minimization. +
+Restrictions: +
+This fix can only be used for 3d simulations and orthogonal +simlulation boxes. You must use periodic boundary +conditions with this fix. +
+Related commands: +
+ +Default: none +
+ + +(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). +
+ diff --git a/doc/fix_ttm.txt b/doc/fix_ttm.txt new file mode 100644 index 0000000000..9937bf78cc --- /dev/null +++ b/doc/fix_ttm.txt @@ -0,0 +1,171 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +fix ttm command :h3 + +[Syntax:] + +fix ID group-ID ttm seed e_specific_heat e_density e_thermal_conductivity gamma_p gamma_s v_0 nxnodes nynodes nznodes T_infile N T_outfile :pre + +ID, group-ID are documented in "fix"_fix.html command +ttm = style name of this fix command +seed = random number seed to use for white noise (positive integer) +e_specific_heat = electronic specific heat (energy/(electron*temperature) units) +e_density = electronic density (electrons/volume units) +e_thermal_conductivity = 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) +nxnodes = number of thermal solve grid points in the x-direction (positive integer) +nynodes = number of thermal solve grid points in the y-direction (positive integer) +nznodes = 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) :ul + +[Examples:] + +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 :pre + +[Description:] + +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)"_#Duffy +and "(Rutherford)"_#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. + +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"_fix_langevin.html) in three important ways. First, the +Langevin thermostat is applied uniformly to all atoms in the +user-specified group, whereas the TTM fix applies Langevin +thermostatting locally within the volumes represented by the +user-specified grid points. 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 and one for +electron stopping. + +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)"_#Duffy and +"(Rutherford)"_#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: + +:c,image(Eqs/fix_ttm.jpg) + +where C is the specific heat, rho is the density, kappa is the thermal +conductivity, and the "e" and "a" subscripts represent the 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. The form of the heat diffusion equation used here +is almost the same as that in equation 6 of "(Duffy)"_#Duffy, with the +exception that the electronic density is explicitly reprensented, +rather than being part of the the specific heat parameter. + +Currently, this fix assumes that none of the user-supplied parameters +will vary with temperature. This assumption can be relaxed by +modifying the source code to include the desired temperature +dependency and functional form for any of the parameters. Note that +"(Duffy)"_#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. + +This fix requires 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)"_#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 (nxnodes*nynodes*nznodes). 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 :pre + +where the electronic temperatures along the nynodes=0 plane have been +set to 1.0, and the electronic temperatures along the nynodes=1 plane +have been set to 2.0. The order of lines in this file is unimportant. +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 nxnodes*nynodes*nznodes columns contain the temperatures for +the atomic subsystem, and the final nxnodes*nynodes*nznodes columns +contain the temperatures for the electronic subsystem. The ordering +of the nxnodes*nynodes*nznodes columns is with the z index varing +fastest, y the next fastest, and x the slowest. + +This fix does not change the coordinates of its atoms; it only scales +their velocities. Thus a time integration fix (e.g. "fix +nve"_fix_nve.html) should still be used to time integrate the affected +atoms. This fix should not normally be used on atoms that have their +temperature controlled by another fix - e.g. "fix nvt"_fix_nvt.html or +"fix langevin"_fix_langevin.html. + +[Restart, fix_modify, output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. None of the "fix_modify"_fix_modify.html options +are relevant to this fix. No global scalar or vector or per-atom +quantities are stored by this fix for access by various "output +commands"_Section_howto.html#4_15. No parameter of this fix can be +used with the {start/stop} keywords of the "run"_run.html command. +This fix is not invoked during "energy minimization"_minimize.html. + +[Restrictions:] + +This fix can only be used for 3d simulations and orthogonal +simlulation boxes. You must use periodic "boundary"_doc/boundary.html +conditions with this fix. + +[Related commands:] + +"fix langevin"_fix_langevin.html, "fix dt/reset"_fix_dt_reset.html + +[Default:] none + +:link(Duffy) +[(Duffy)] D M Duffy and A M Rutherford, J. Phys.: Condens. Matter, 19, +016207-016218 (2007). + +:link(Rutherford) +[(Rutherford)] A M Rutherford and D M Duffy, J. Phys.: +Condens. Matter, 19, 496201-496210 (2007).