Name: USER-EPH
Owner: Lawrence Livermore National Laboratory
Description: LAMMPS extension to capture electron-ion interaction
Created: 2018-05-10 03:38:20.0
Updated: 2018-05-10 18:32:58.0
Pushed: 2018-05-10 18:09:31.0
Homepage: null
Size: 34
Language: null
GitHub Committers
| User | Most Recent Commit | # Commits |
|---|
Other Committers
| User | Most Recent Commit | # Commits |
|---|
LAMMPS extension (LAMMPS “fix”) to capture electron-ion interaction. LLNL-CODE-750832
Artur Tamm and Alfredo A. Correa (LLNL)
In LAMMPS, a “fix” is any operation that is applied to the system during
timestepping or minimization.
We use this extension mechanism to generalize the two-temperature model to include electron-phonon coupling.
The extension is flexible enough to represent cascades, laser heating and equilibration and study energy transport with realistic electron-phonon coupling.
The theory is developed in the papers “Langevin dynamics with spatial correlations as a model for electron-phonon coupling” (https://dx.doi.org/10.1103/PhysRevLett.120.185501) and “Electron-phonon interaction within classical molecular dynamics” (https://link.aps.org/doi/10.1103/PhysRevB.94.024305).
Get LAMMPS (source code)
mywork
t clone https://github.com/lammps/lammps.git
Get USER-EPH (this plugin, you have to have access to the repository)
lammps/src
t clone https://github.com/LLNL/USER-EPH.git
Edit Makefile add string user-eph to the end of PACKUSER variable (near line 66).
Edit MAKE/Makefile.mpi and MAKE/Makefile.serial to read CCFLAGS = -g -O3 -std=c++11 (near line 10).
Execute:
ke yes-manybody yes-user-eph
ke -j 8 serial
Make sure your MPI enviroment is setup already (mpicxx compiler wrapper works), this may require for example running $ module load mpi/mpich-x86_64
ke -j 8 mpi
The executables are ./lmp_mpi (for parallel runs) ./lmp_serial (for serial runs, testing), you can copy them elsewhere.
Take your MD input file
Add a line at the correct place,
[ID] [group-ID] eph [seed] [flags] [model] [rho_e] [C_e] [kappa_e] [T_e] [NX] [NY] [NZ] [T_infile] [freq] [Te_outfile] [beta_infile] [A] [B] [C...]
Where:
ID -> user-assigned name for the fix, [string, e.g. ephttm or friction]
group-ID -> group of atoms to which this fix will be applied, [string, e.g. all]
seed -> seed for random number generator [integer, e.g. 123]
flags: control of different terms or'd together [integer or bitmask]
1 -> enable friction (only) (pure damping)
2 -> enable random force (only) (not recommended)
3 -> enable friction and random force (fixed e-temperature)
4 -> heat equation (by FDM finite difference method) (decoupled from ions)
5 -> enable friction and heat equation (no feedback from e-)
7 -> enable friction, random force, and heat equation (coupled e-ions)
model: select model for friction and random force [integer]
1 -> standard Langevin (for vanilla TTM with beta(rho))
2 -> simple e-ph model (https://link.aps.org/doi/10.1103/PhysRevB.94.024305) (not recommended)
3 -> e-ph with spatial correlations, with CM-correction only (https://arxiv.org/abs/1801.06610)
4 -> e-ph with spatial correlations, full model (https://arxiv.org/abs/1801.06610)
rho_e -> scaling parameter for the FDM grid [float, recommended 1.0] [unitless]
C_e -> electronic heat capacity per volume [float, e.g. 2.5e-6] [in eV/K/Ang^3]
kappa_e -> electronic thermal conductivity [float, ignored for single grid point] [in eV/K/Ang/ps]
T_e -> electronic temperature [float, e.g. 300] [in K]
NX, NY, NZ -> grid size in x, y, and z direction [integer, e.g. 1 1 1 sets single grid point]
T_infile -> input filename for the FDM grid parameters and initial values [string or NULL]
freq -> heat map output (T_output) frequency, 0 to disable [integer, e.g. 10]
Te_output -> output heat map filename (CUBE format) [string, e.g. Te_output.cub]
beta_infile -> beta(rho) input filename [string, e.g. NiFe.beta]
A, B, C... -> element type mapping [1 or more strings, Ni Ni Fe]
For example the following line in LAMMPS input script, will run the MD including the coupling to electrons, within the spatially correlated Langevin bath. The electronic specific heat is assumed to be 2.5e-6 eV/K/Ang^3 (400000 J/m³/K) (see LinPRB772008) which is a good approximation for a range of electronic temperatures from 500 to 1500K. Initial electron temperature is set to 300K (and not from a file). We use uniform tempetures (one grid element), therefore the heat conductivity is not relevant in this case.
ephttm all eph 123 7 4 1.0 2.5e-6 1.0 300.0 1 1 1 NULL 10 Te_output.cub Ni.beta Ni
This fix produces two types of Lammps-internal results in addition to the normal MD:
vector with the energy and temperature of the electronic system
f_ID[1] -> Net energy transfer between electronic and ionic system
f_ID[2] -> Average electronic temperature
per atom values:
f_ID[i][1] -> site density
f_ID[i][2] -> coupling parameter
To access them in the output file add this to the LAMMPS input script:
out all print 1000 "$(step) $(time) $(temp) $(f_ephttm[1]) $(f_ephtmm[2])" file out.data screen no
out all custom 10 strucs_out.dump.gz type x y z f_ephttm[1] f_ephttm[2]
This file provides the electronic densities and beta(rho) functions for individual species (see https://dx.doi.org/10.1103/PhysRevLett.120.185501).
The format is described in Doc/Beta/input.beta.
The file is similar to EAM setfl format.
The beta(rho) function has units of [eV ps/Ang^2].
An example is provided in Examples/Beta/Ni_model_4.beta.
This file is used to initialise FDM grid for the electronic system.
The format is described in Doc/FDM/T_input.fdm.
This allows fine control of the properties at various grid points.
Also, the grid can be larger than ionic system if energy reservoir far away is needed.
Grid points can act as energy sources, sinks or walls (individual grid points updates can be deactivated).
An example of input file is provided in Examples/FDM/T.in.
Units are [Kelvin], [eV/Ang3/ps], [unitless], [in eV/K/Ang3] [eV/K/Ang/ps] for T, local source term, rho_e, Ce, kappa_e respectively.
C_e, rho_e, and kappa_e are constants at the moment (not temperature dependent).T_infile is not NULL then C_e, rho_e, kappa_e, T_e, NX, NY, NZ are ignored and are read from the filename supplied.
If NULL is provided as the filename then the FDM grid is initialised with the parameters provided in the command.Examples can be found in Examples/ directory.
To run them type lmp_serial -i run.lmp in the appropriate example directory and assuming executable is in PATH.
Some of the examples may take long on older machines, so tweak the input file (run.lmp) accordingly. Every example contains a README file that describes what the runscript does.
Examples/Example_1/:
In this example a crystal structure is created and the model is applied with both the friction and random force terms.
The electrons are kept at constant temperature (300K).
This example illustrates the thermalisation process from 0K to the target temperature through electron-ion interaction only.
Examples/Example_1
path/lmp_serial -i run.lmp
The run will write to the file out.data, column 2 has the time (in ps), columns 3 and 5 have the ionic and the electronic temperature respectively.
uplot
ot "out.data" u 2:3 w lp lw 2 t "Tion", "out.data" u 2:5 w lp lw 2 t "Te"
You will see that the ionic temperature increases and approaches the (fixed) electronic temperature (300K).
Examples/Example_2/:
This example illustrates the use cooling of the ionic systems due to electrons only.
This means that only the friction term acts on atoms and removes energy.
This is equivalent to having electrons at 0K.
Examples/Example_3/:
In this example the full model with electronic heat equation FDM grid is used.
The crystal is created at equilibrium positions (0K) and it is heated by electrons.
During the simulation the electronic system will cool and the ionic system heat.
At equilibrium both systems end up at the same temperature on average.
Also, this example illustrates the automatic initialisation of the FDM grid with constant parameters.
The electronic temperature at various grid points is written to files (one per step) (T_out_XXXXXX).
Final state of the grid is stored and can be reused in later simulations (T.restart).
Although you can run in serial mode (like above),
you can try to run this example with in parallel, for example in 4 processes.
Make sure your MPI environment works, for example you may need $ module load mpi/mpich-x86_64
irun -np 4 mypath/lmp_mpi -i run.lmp
uplot
ot "out.data" u 2:3 w lp lw 2 t "Tion", "out.data" u 2:5 w lp lw 2 t "Te"
Examples/Example_4/:
This example reads the FDM grid parameters from a file (T.in).
In this file a source term is added at line in the grid representing the energy dumped by swift ion.
During the simulation the ionic system will heat while electron temperature will diffuse and due to gradient in the electronic system forces acting on atoms at different grid points will 'feel' different random forces in magnitude.
After a few MD-TTM steps the electronic temperature field will look like this:
USER-EPH is licensed under the terms of the GPL v3 License.
USER-EPH is not part of the LAMMPS code https://github.com/lammps/lammps
If you have any questions contact Artur Tamm tamm3@llnl.gov or Alfredo Correa correaa@llnl.gov
LLNL-CODE-750832