Our First-prinicples DMC(FEP-DMC) is a module of the open-source package of Perturbo. For more information of Perturbo, please visit our github website https://perturbo-code.github.io/ .
The minimal RAM is 64GB to run the full example.
This package is supported for Linux only. It has been tested on the following systems.
Linux: Ubuntu 20.04
PERTURBO currently uses a small number of subroutines from the Quantum Espresso (QE) packages. Therefore, it needs to be compiled on top of QE. We assume that the users have already compiled QE successfully.
FEP-DMC is built on top of QE version 6.5. See the downloading link https://gitlab.com/QEF/q-e/-/tags/qe-6.5. Other versions of QE are not supported currently. Please note that QE should be compiled with the Intel Fortran compiler and HDF5 (recommended version >= 1.8.5). HDF5 should be compiled with the same Intel Fortran compiler. HDF5 should be configured with --enable-fortran --enable-fortran2003. The website https://perturbo-code.github.io/MB-group-resource-sharing/docs/compile-codes/ is useful for installation of HDF5 and QE on your own HPC or Ubuntu, although it is for our own HPC.
In addition, the installation of QE also requires the Intel Fortran compiler, BLAS, and LAPACK. We recommend Intel oneAPI https://www.intel.com/content/www/us/en/developer/tools/oneapi/fortran-compiler.html, which includes BLAS and LAPACK via the MKL in oneAPI.
On my ubuntu workstation, this whole installation, including compiling QE and perturbo, takes around 15 mins.
Assume that HDF5 and Intel oneAPI have been installed and activated.
Go to the directory of QE and copy the perturbo-fep-dmc there.
$ cd QE_direcroty/
$ cp -rf /some_directory/perturbo-fep-dmc .
$ ls
archive Doc KS_Solvers perturbo-fep-dmc TDDFPT
atomic environment_variables LAXlib PHonon test-suite
clib EPW License PlotPhon upftools
configure FFTXlib logo.jpg PP UtilXlib
CONTRIBUTING.md GUI LR_Modules pseudo XSpectra
COUPLE GWW Makefile PW
CPV HP make.inc PWCOND
dev-tools include Modules QHA
dft-d3 install NEB README.md
$
In an Ubuntu 20.04 OS system, I compile QE with the following commands:
# my HDF is installed in /home/yaoluo/software/hdf5-1.8.18-ifort
$ ./configure MPIF90=mpiifort --with-hdf5=/home/yaoluo/software/hdf5-1.8.18-ifort
$ make pw ph pp
Perturbo uses the config file make.inc of QE for most of the compiler options. In the perturbo-fep-dmc/ directory, we provide you with a make.sys for setting up the compilation.
$ cd perturbo-fep-dmc
# modify the file make.sys
>> vim make.sys
------------------------------------------------------------------------------------------
......
# modify the paths for HDF5 library
# my HDF is installed in /home/yaoluo/software/hdf5-1.8.18-ifort
......
IFLAGS += -I/home/yaoluo/software/hdf5-1.8.18-ifort/include
HDF5_LIB = -L/home/yaoluo/software/hdf5-1.8.18-ifort/lib -lhdf5 -lhdf5_fortran
......
------------------------------------------------------------------------------------------
and make the necessary changes to it. You will then be ready to compile PERTURBO:
$ make perturbo
#add perturbo bin to the path for the example
$ export PATH="<QE-directory>/perturbo-fep-dmc/bin:$PATH"
After the compiling, a directory called "bin" is generated, which contains one executable, perturbo.x
This whole process takes around 20 mins on my workstation.
We are going to calculate the formation energy of electron polarons in LiF with compressed electron-phonon interactions.
This example is dedicated to reproducing some points of Fig.2(b) in the main text.
Before calculation, one should download the "lif-sp3_epwan.h5" file via this link " https://www.dropbox.com/scl/fi/40djsz04bkrdyrr8pmzf2/DMC-Demo.zip?rlkey=kyil1w6j7f5tt5ii84ii5oi4o&dl=0 ".
This file contains the electron-phonon interactions.
There are three steps.
$ cd example/pert-svd
$ ln -sf ../lif-sp3_epwan.h5
$ ./run.sh
$ cd example/pert-Htable
$ ln -sf ../lif-sp3_epwan.h5
$ ./run-nk.sh
$ cd example/E-nk
# caluclate polaron binding energy for different size of grid
# 20^3, 40^3, 60^3, 80^3
$ ./loop-nk.sh
$ ls
20 40 60 loop-nk.sh
# 20 for 20^3 grid; 40 for 40^3 grid; 60 for 60^3 grid
$ cd 20
$ ls
chemical_pot.dat orderStat.dat-1 pert.in sign.dat-1
diagMC.in parameter.dat PolaronLat.dat-1 temper.in
lif-sp3_epwan.h5 parameter.dat-1 PolaronWF.dat-1 Znph.dat-1
# parameter.dat-1 contains polaron ground state energy
# expected output for 20^3 grid
$ cat parameter.1
#mu =
0.00000E+00
#alpha =
0.10000E+01
#Ep =
0.93549E+01
#Etrue =
0.9107056695E+01
#<g/Z> =
0.9400030978E+00
#<Z0> =
0.2238440137E+00
# Here, Ep = the band electron energy, Etrue = polaron ground state energy;
# The polaron binding energy equals `Etrue - Ep = -0.25 eV` for 20^3 grid.
# Znph.dat-1 contains the n phonon amplitude, the last two lines are polaron ground state energy
# PolaronWF.dat-1 contains the reduced density matrix in electron basis
#
For more details on the code structure of Perturbo, we refer the users to the manuscript accompying the source code:
When using results from PERTURBO in your publications, please cite the PERTURBO paper given above and acknowledge the use of the code.