NAMD in Momentum Space (Hefei-NAMD-EPC)

Contents

• Overview
• Installation Guide
• Tutorials of Runing Hefei-NAMD-EPC

This program also has a python version developed by Youyou Tu

Overview

This is a program to perform non-adiabatic molecular dynamics (NAMD) simultion in momentum space, where the non-adiabatic coupling (NAC) are replaced by electron-phonon (e-ph) coupling (EPC).

The codes are based on Hefei-NAMD developed by Qijing Zheng, et al.

For theoretical details on the code, we refer the users to the manuscript accompying the source code:

Z. Zheng, Y. Shi, J. J. Zhou, O. V. Prezhdo, Q. Zheng, J. Zhao. "Ab initio real-time quantum dynamics of charge carriers in momentum space". Nat Comput Sci (2023)

For EPC calculation, we use the package Perturbo, please refer to:

J. J. Zhou, J. Park, I. T. Lu, I. Maliyov, X. Tong, M. Bernardi, “Perturbo: a software package for ab initio electron-phonon interactions, charge transport and ultrafast dynamics”. Comput. Phys. Commun. 264, 107970, (2021)

When using results from this program in your publications, please cite the paper given above and acknowledge the use of the code.

It would also be appropriate to cite the original articles:

Q. Zheng, W. A. Saidi, Y. Xie, Z. Lan, O. V. Prezhdo, H. Petek, J. Zhao. "Phonon-Assisted Ultrafast Charge Transfer at van der Waals Heterostructure Interface". Nano Lett 17, 6435-6442, (2017)

Q. Zheng, W. Chu, C. Zhao, L. Zhang, H. Guo, Y. Wang, X. Jiang, J. Zhao. "Ab initio nonadiabatic molecular dynamics investigations on the excited carriers in condensed matter systems". WIREs Comput. Mol. Sci. 9:e1411, (2019)

Installation Guide

The user can get the source files of this program from Github

$ git clone https://github.com/ZhenfaZheng/NAMDinMomentumSpace.git

Then, go into folder of source files

$ cd src

To compile this program, you should specify the path to your HDF5 library. Open the "Makefile"

$ vim Makefile

Modify the two flags "IFLAGS" and "LFLAGS"

IFLAGS = -I/${path-to-your-hdf5-dir}/include
LFLAGS = -I/${path-to-your-hdf5-dir}/lib -lhdf5 -lhdf5_fortran

After modifying the "Makefile", compile the Hefei-NAMD-EPC

$ make clean
$ make

You will get an executable file "namd-epc" for simulations of NAMD in momentum space.

Tutorials of Runing Hefei-NAMD-EPC

1. Calculate e-ph matrix elements using PERTURBO

Befor carrying out NAMD simulations in momentum space, the user needs to calculate e-ph matrix elements $g_{mn\nu}(\mathbf{k}, \mathbf{q})$ using a modified version PERTURBO. Therefore, first of all, the user needs to install and learn using PERTURBO. We recommend users to visit the home page of PERTURBO (https://perturbo-code.github.io) to get the source code and tutorials of PERTURBO.

Then, replace the source file "calc_ephmat.f90" in path of "pert-src/" with our modified file in the path of "patch" before compiling PERTURBO. It should be noted that this patch is modified by Prof. Jin-Jian Zhou and us together, and it will output files containing e-ph information (named "${prefix}_ephmat_p1.h5", "${prefix}_ephmat_p2.h5", "${prefix}_ephmat_p3.h5", ...) additionally when run "perturbo.x" with "calc_mode = 'ephmat'".

To run perturbo.x for doing e-ph coupling calculations in ultra-fine $\mathbf{k}$- and $\mathbf{q}$-points grids, one needs to prepare input file "pert.in", $\mathbf{k}$- and $\mathbf{q}$-point list files "eph.kpt", and "eph.qpt", and "${prefix}_epr.h5" file from qe2pert calculation.

The input file "pert.in" can be set as follows

&perturbo
  prefix = 'graphene'
  calc_mode = 'ephmat'
  fklist = 'eph.kpt'
  fqlist = 'eph.qpt'

  band_min = 1
  band_max = 2

  phfreq_cutoff = 0.625    ! meV

  output_yaml = .False.
 /

We provide a python script "kqgen.py" to generate $\mathbf{k}$- and $\mathbf{q}$-point list files. User needs to set nkx, nky and nkz in the first few lines of "kqgen.py" script. Then excute

$ python kqgen.py

If there are too many $\mathbf{k}$- and $\mathbf{q}$-points (nks * nqs > $10^7$), the script will separate the $\mathbf{k}$-points into several parts and save "eph.kpt" and "eph.qpt" files in differen folders ("1P", "2P", ...). Then user needs to link "pert.in" and "${prefix}_epr.h5" file into folders for different parts of $\mathbf{k}$-points to do perturbo calculations respectively.

$ for ip in *P
$ do
$     cd ${ip}
$     cp ../pert.in .
$     ln -sf ../../qe2pert/prefix_epr.h5 .
$     cd ..
$ done

We provide a Sbatch script "sub_pert_part" for users to run perturbo calculations for different parts of $\mathbf{k}$-points.

2. Prepare input files

To run Hefei-NAMD-EPC, the user should prepare 3 kinds of files: "${prefix}_ephmat_p${ipart}.h5" files containing e-ph information from perturbo calculations, "inp" file for input parameters setting, and "INICON" file for initial conditions setting.

First, copy or link "${prefix}_ephmat_p${ipart}.h5" files from perturbo calculations by perturbo.x, user can excute bash script "lnh5.sh" to link these files into a folder.

Then generate "inp" file, below is an example

&NAMDPARA
  BMIN       = 1       ! minimum band index
  BMAX       = 2       ! maximum band index
  KMIN       = 1       ! minimum $\mathbf{k}$-point index
  KMAX       = 40      ! maximum $\mathbf{k}$-point index
  EMIN       = -4.6    ! minimum energy, in unit of eV
  EMAX       = -1.5    ! maximum energy, in unit of eV
  NBANDS     = 2       ! number of bands
  NKPOINTS   = 81      ! number of $\mathbf{k}$-points
  NINIBS     = 1       ! number of initial states
  Np         = 81      ! number of unit cells corresponding to the $\mathbf{k}$-grid

  NSW        = 1200    ! number of time steps for the MD trajctory
  POTIM      = 1.0     ! time step for the MD trajctory, in unit of fs
  TEMP       = 300     ! MD temperature

  NSAMPLE    = 6       ! number of samples with different initial conditions
  NAMDTIME   = 1000    ! time of NAMD, in unit of fs
  NELM       = 1000    ! number of steps of electron wave propagation each POTIM
  NTRAJ      = 10000   ! number of surface hopping trajectories for each sample
  LHOLE      = .F.     ! hole or electron surface hopping
  LCPEXT     = .F.     ! whether to read TXT files or not (not available for epc version)

  LEPC       = .T.     ! whether to use e-p matrix as NA couplings
  LBASSEL    = .F.     ! whether to read BASSEL file. If not, will generate it. 
                       ! if ture, will ignore parameters: BMIN, BMAX, KMIN, KMAX, EMIN, EMAX.
  LSORT      = .T.     ! whether ot sort states in order of energy
  SIGMA      = 0.025   ! energy broadening
  EPCTYPE    = 1       ! 1: calculate EPC from average phonon populations.
                       ! 2: calculate EPC by norm mode decompositon form MD traj
  NPARTS     = 1       ! number of parts of ephmat information
  EPMDIR     = 'h5files/'    ! directory of ephmat.h5 files
  EPMPREF    = 'graphene'    ! prefix of ephmat.h5 files
/

The last file we need is "INICON" file, for example

   11     4     2
   23    10     1
   47    17     2
   51    21     2
   85    34     2
   93    38     2

Each line of "INICON" represents initial condition of each sample, the first column indicates initial time, the second and third column indicate $\mathbf{k}$ and band indices of initial electronic state. We provide a python script "gen_inicon.py" to help user generate "INICON" file, user has to set the energy and $\mathbf{k}$-point location for initial states at the first few line in "gen_inicon.py" script.

3. Run Hefei-NAMD-EPC

Copy executable file "namd-epc" to your work diretory, then execute

$ mpirun -np 16 ./namd-epc # Here, 16 is the number of processes as an example

User can also use Sbatch script "sub_namd" to submit the computational job.

4. Output files

After Hefei-NAMD-EPC calculation, we obtain files as bellow:

"BASSEL" (Selected basises in NAMD simulation)

"EPELTXT", "EPPHTXT" (e-ph couplings)

"PHPROP.${imode}" (Evolution of phonon number for each mode)

"PSICT.${initime}" (Evolution of expanding coefficients for each sample)

"SHPROP.${initime}" (Evolution of population for each sample)

5. Data processing

We provide python scripts to do the data processing, just copy the "postnamd.py" and "namdplt.py" from the folder "scripts" to your work diretory, and execute

$ python namdplt.py

You will obtain figures of results, including: COUPLE.png, COUPLE_EL.png, COUPLE_PH.png, TDEN.png, TDBAND.png, TDKPROP.png, TDPH.png, TDPHEN.png, TDPHNUM.png, TDQPROP.png et al.