A library providing a numerical implementation of the density matrix formulation of quantum transport, including inter-band coherence and scattering from multiple Fermi surface sheets.
The formalism implemented here is presented in:
Culcer, Sekine, and MacDonald, Phys. Rev. B 96, 035106 (2017)
Sekine, Culcer, and MacDonald, Phys. Rev. B 96, 235134 (2017)
A paper discussing the numerical implementation provided by this repository is in preparation.
Regression and unit tests providing examples of the use of this software are given in the test directory. The following tests have been validated against analytic results (using the "result plots" parameter sets in the test files):
- The spin accumulation and spin Hall conductivity for the Rashba model calculated by the
Rashba_electrictest intest/Rashba_Hamiltonian_test.cpp. - The chiral magnetic effect current for a single Weyl node calculated by the
wsm_continuum_cme_nodetest intest/wsm_continuum_Hamiltonian_test.cpp.
Additionally the following tests are expected to be correct, but have not been fully validated:
- The anomalous Hall conductivity of the Rashba model with exchange field calculated by the
Rashba_magnetized_electrictest intest/Rashba_magnetic_Hamiltonian_test.cppyields the expected cancellation of the intrinsic and extrinsic contributions, but the absolute value of these contributions has not been checked. - The anomalous Hall conductivity of the Weyl semimetal calculated by the
wsm_continuum_ahetest intest/wsm_continuum_Hamiltonian_test.cppappears to converge toward the correct result as the k-point density and sampling volume are increased, but this convergence has not been fully checked.
This software is distributed under the MIT license to allow maximum freedom of use. However we ask that any publication making use of this software or derivative software cite the two papers listed above and acknowledge use of this repository, providing a link to it (after the numerical paper is available, we will ask that such publications cite that paper as well). This software is in active development, and while we are confident in the cases which have been validated as noted above, we make no general guarantee of correctness. We encourage users or potential users of this software to contact us via mailing list at anomtrans@googlegroups.com, or to file issues in this repository with specific bug reports or feature suggestions.
These instructions are based on a fresh Linux Mint 18.1 installation. They should work for any Debian-based distribution.
Get git, g++, gfortran, CMake, OpenMPI, valgrind, boost, doxygen, matplotlib, scipy:
sudo apt-get install git g++ gfortran cmake libopenmpi-dev openmpi-bin valgrind libboost-all-dev doxygen graphviz python-matplotlib python-tk python3-matplotlib python3-tk python3-setuptools python3-scipy libubsan0 lib64ubsan0 curl
Note that the Boost package is Boost 1.58.
PETSc 3.8 is not available from the package manager. We'll need to build it. (download page) (install instructions)
cd ~
git clone -b maint https://bitbucket.org/petsc/petsc petsc
cd ~/petsc
./configure PETSC_ARCH=arch-linux2-cxx-complex-debug --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 --download-fblaslapack --with-clanguage=cxx --with-scalar-type=complex
make PETSC_DIR=$HOME/petsc PETSC_ARCH=arch-linux2-cxx-complex-debug all
make PETSC_DIR=$HOME/petsc PETSC_ARCH=arch-linux2-cxx-complex-debug test
make PETSC_DIR=$HOME/petsc PETSC_ARCH=arch-linux2-cxx-complex-debug streams
anomtrans regression test data is stored in Git LFS. Install this:
cd ~
curl -L -o git-lfs-linux-amd64-2.3.4.tar.gz https://github.com/git-lfs/git-lfs/releases/download/v2.3.4/git-lfs-linux-amd64-2.3.4.tar.gz
tar -xvzf git-lfs-linux-amd64-2.3.4.tar.gz
cd git-lfs-2.3.4
PREFIX=$HOME ./install.sh
export PATH=$HOME/bin:$PATH
To keep git lfs accessible, add its location to your default PATH. In the file ~/.bashrc, add:
export PATH=$HOME/bin:$PATH
With Git LFS installed, we can now clone the anomtrans repository and get the test data.
cd ~
git clone https://github.com/tflovorn/anomtrans.git
(If this repository was cloned before Git LFS was installed, the test data will not have been fetched. To remedy this, run git lfs fetch in the anomtrans directory.)
Get Google Test submodule:
cd ~/anomtrans
git submodule init
git submodule update
To allow for generation of result plots, install pyanomtrans:
cd ~/anomtrans
python3 setup.py develop --user
To build documentation:
cd ~/anomtrans
doxygen
To build and run tests (should be done from the anomtrans root directory):
cd ~/anomtrans
./build_test_local
cd Obj_test
ctest -V
To generate plots from tests:
cd ~/anomtrans/pyanomtrans
python3 plot_Rashba.py "Rashba_Hamiltonian_test_out" "../Obj_test/src"
python3 plot_wsm.py "wsm_continuum_cme_test_out" "../Obj_test/src"
python3 plot_series.py (other test output file here) "../Obj_test/src"
python3 plot_2d_bz.py (other test output file here) "../Obj_test/src"
Build PETSc with:
cd ~/petsc
./configure PETSC_ARCH=arch-linux2-cxx-complex-opt --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 --download-fblaslapack --with-clanguage=cxx --with-scalar-type=complex --with-debugging=0 COPTFLAGS='-O3 -march=native -mtune=native' CXXOPTFLAGS='-O3 -march=native -mtune=native' FOPTFLAGS='-O3 -march=native -mtune=native'
make PETSC_DIR=$HOME/petsc PETSC_ARCH=arch-linux2-cxx-complex-opt all
make PETSC_DIR=$HOME/petsc PETSC_ARCH=arch-linux2-cxx-complex-opt test
make PETSC_DIR=$HOME/petsc PETSC_ARCH=arch-linux2-cxx-complex-opt streams
Build and run tests:
cd ~/anomtrans
./build_release_local
cd Obj
ctest -V
TODO - MKL BLAS/LAPACK support?
Assumes the intel/16.0.1 module is loaded on Lonestar5.
Add module dependencies to ~/.bashrc just under "PLACE MODULE COMMANDS HERE and ONLY HERE.":
module load cmake boost petsc/3.7-cxxcomplexdebug
Replace petsc/3.7-cxxcomplexdebug with petsc/3.7-cxxcomplex for release mode.
Also add to ~/.bashrc just under "PLACE Environment Variables including PATH here.":
export PATH=$HOME/bin:$PATH
On Lonestar5, it is not necessary to set LIBRARY_PATH or LD_LIBRARY_PATH for boost or petsc.
The correct LD_LIBRARY_PATH is set by module load.
anomtrans regression test data is stored in Git LFS. Install this:
cd ~
curl -L -o git-lfs-linux-amd64-2.3.4.tar.gz https://github.com/git-lfs/git-lfs/releases/download/v2.3.4/git-lfs-linux-amd64-2.3.4.tar.gz
tar -xvzf git-lfs-linux-amd64-2.3.4.tar.gz
cd git-lfs-2.3.4
PREFIX=$HOME ./install.sh
export PATH=$HOME/bin:$PATH
With Git LFS installed, we can now clone the anomtrans repository and get the test data.
cd ~
git clone https://github.com/tflovorn/anomtrans.git
(If this repository was cloned before Git LFS was installed, the test data will not have been fetched. To remedy this, run git lfs fetch in the anomtrans directory.)
Get Google Test submodule:
cd ~/anomtrans
git submodule init
git submodule update
To build documentation:
doxygen
To build and run tests (should be done from the anomtrans root directory):
./build_test_ls5
idev
cd Obj_test
ctest -V
exit
Or to submit a job to test:
./build_test_ls5
sbatch run_tests_ls5
To build and test in release mode:
./build_release_ls5
idev
cd Obj
ctest -V
exit
Exceptions thrown by anomtrans functions are intended to be a 'panic' type of error.
They should not be caught unless explicitly noted as being safe to catch.
The lack of RAII for PETSc objects makes exception safety cumbersome, and in general
it is not attempted here to provide this type of safety.
Whitespace conventions of the code are satisfied by the following ~/.vimrc:
filetype plugin indent on
set tabstop=4
set shiftwidth=4
set expandtab
syntax on
au BufRead,BufNewFile Makefile* set noexpandtab
au BufRead,BufNewFile *.cpp,*.h,CMakeLists.txt set tabstop=2
au BufRead,BufNewFile *.cpp,*.h,CMakeLists.txt set shiftwidth=2
This implementation has been developed at the University of Texas at Austin with support from the Department of Energy, Office of Basic Energy Sciences, under Contract No. DE-FG02-ER45958, and from the Welch foundation, under Grant No. TBF1473.