diff --git a/CMakeLists.txt b/CMakeLists.txt index 675f004c..5becfb10 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -145,6 +145,8 @@ endif() # Python if(PythonSupport) add_subdirectory(python/${PROJECT_NAME}) + # elk binary i/o code for wrappers + add_subdirectory(python/${PROJECT_NAME}/converters/elktools/elkwrappers) endif() # Docs diff --git a/doc/guide/transport.rst b/doc/guide/transport.rst index 69db4753..4df6b838 100644 --- a/doc/guide/transport.rst +++ b/doc/guide/transport.rst @@ -45,13 +45,17 @@ First perform a standard :ref:`DFT+DMFT calculation ` for real-frequency self energy. .. note:: - If you use a CT-QMC impurity solver you need to perform an **analytic continuation** of - self energies and Green functions from Matsubara frequencies to the real-frequency axis! - This packages does NOT provide methods to do this, but a list of options available within the TRIQS framework - is given :ref:`here `. Keep in mind that all these methods have to be used very carefully. Especially for optics calculations - it is crucial to perform the analytic continuation in such a way that the real-frequency self energy - is accurate around the Fermi energy as low-energy features strongly influence the final results. + If you use a CT-QMC impurity solver you need to perform an **analytic continuation** of + self energies and Green functions from Matsubara frequencies to the real-frequency axis! + This packages does NOT provide methods to do this, but a list of options available within the TRIQS framework + is given :ref:`here `. Keep in mind that all these methods have to be used very carefully. Especially for optics calculations + it is crucial to perform the analytic continuation in such a way that the real-frequency self energy + is accurate around the Fermi energy as low-energy features strongly influence the final results. +Below will describe the prerequisites from the different DFT codes. + +Prequisites from Wien2k +^^^^^^^^^^^^^^^^^^^^^^^ Besides the self energy the Wien2k files read by the transport converter (:meth:`convert_transport_input `) are: * :file:`.struct`: The lattice constants specified in the struct file are used to calculate the unit cell volume. * :file:`.outputs`: In this file the k-point symmetries are given. @@ -61,8 +65,22 @@ Besides the self energy the Wien2k files read by the transport converter (:meth: * :file:`.h5`: The hdf5 archive has to be present and should contain the dft_input subgroup. Otherwise :meth:`convert_dft_input ` needs to be called before :meth:`convert_transport_input `. +These Wien2k files are read and the relevant information is stored in the hdf5 archive by using the following:: + + from triqs_dft_tools.converters.wien2k import * + from triqs_dft_tools.sumk_dft_tools import * + + Converter = Wien2kConverter(filename='case', repacking=True) + Converter.convert_transport_input() + + SK = SumkDFTTools(hdf_file='case.h5', use_dft_blocks=True) + +The converter :meth:`convert_transport_input ` +reads the required data of the Wien2k output and stores it in the `dft_transp_input` subgroup of your hdf file. + + Wien2k optics package ---------------------- +^^^^^^^^^^^^^^^^^^^^^ The basics steps to calculate the matrix elements of the momentum operator with the Wien2k optics package are: 1) Perform a standard Wien2k calculation for your material. @@ -79,22 +97,39 @@ You can read off the Fermi energy from the :file:`case.scf2` file. Please do not Furthermore it is necessary to set line 6 to "ON" and put a "1" in the following line to enable the printing of the matrix elements to :file:`case.pmat`. -Using the transport code ------------------------- -First we have to read the Wien2k files and store the relevant information in the hdf5 archive:: - from triqs_dft_tools.converters.wien2k import * +Prequisites from Elk +^^^^^^^^^^^^^^^^^^^^ + +The Elk transport converter (:meth:`convert_transport_input `) reads in the following files: + * `LATTICE.OUT`: Real and reciprocal lattice structure and cell volumes. + * `SYMCRYS.OUT`: Crystal symmetries. + * `PMAT.OUT`: Fortran binary containing the velocity matrix elements. + * :file:`.h5`: The hdf5 archive has to be present and should contain the dft_input subgroup. Otherwise :meth:`convert_dft_input ` needs to be called before :meth:`convert_transport_input `. It is recommended to call :meth:`convert_dft_input ` before :meth:`convert_transport_input `. + + +Except for `PMAT.OUT`, the other files are standard outputs from Elk's groundstate calculation and are used in :meth:`convert_dft_input `. The `PMAT.OUT` file on the otherhand is generated by Elk by running **task 120**, see [#userguide2]_. Note that unlike in the Wien2k transport converter, the Elk transport converter uses the correlated band window stored in the `dft_misc_input` (which originates from running :meth:`convert_dft_input `). + +These Elk files are then read and the relevant information is stored in the hdf5 archive by using the following:: + + from triqs_dft_tools.converters.elk import * from triqs_dft_tools.sumk_dft_tools import * - Converter = Wien2kConverter(filename='case', repacking=True) + Converter = ElkConverter(filename='case', repacking=True) Converter.convert_transport_input() SK = SumkDFTTools(hdf_file='case.h5', use_dft_blocks=True) The converter :meth:`convert_transport_input ` -reads the required data of the Wien2k output and stores it in the `dft_transp_input` subgroup of your hdf file. -Additionally we need to read and set the self energy, the chemical potential and the double counting:: +reads the required data of the Elk output and stores it in the `dft_transp_input` subgroup of your hdf file. + + + +Using the transport code +------------------------ + +Once we have converted the transport data from the DFT codes (see above), we also need to read and set the self energy, the chemical potential and the double counting:: with HDFArchive('case.h5', 'r') as ar: SK.set_Sigma([ar['dmft_output']['Sigma_w']]) @@ -108,18 +143,18 @@ As next step we can calculate the transport distribution :math:`\Gamma_{\alpha\b with_Sigma=True, broadening=0.0, beta=40) Here the transport distribution is calculated in :math:`xx` direction for the frequencies :math:`\Omega=0.0` and :math:`0.1`. -To use the previously obtained self energy we set with_Sigma to True and the broadening to :math:`0.0`. +To use the previously obtained self energy we set `with_Sigma` to **True** and the broadening to :math:`0.0`. As we also want to calculate the Seebeck coefficient and the thermal conductivity we have to include :math:`\Omega=0.0` in the mesh. Note that the current version of the code repines the :math:`\Omega` values to the closest values on the self energy mesh. For complete description of the input parameters see the :meth:`transport_distribution reference `. The resulting transport distribution is not automatically saved, but this can be easily achieved with:: - SK.save(['Gamma_w','Om_meshr','omega','directions']) + SK.save(['Gamma_w','Om_mesh','omega','directions']) You can retrieve it from the archive by:: - SK.Gamma_w, SK.Om_meshr, SK.omega, SK.directions = SK.load(['Gamma_w','Om_meshr','omega','directions']) + SK.Gamma_w, SK.Om_mesh, SK.omega, SK.directions = SK.load(['Gamma_w','Om_mesh','omega','directions']) Finally the optical conductivity :math:`\sigma(\Omega)`, the Seebeck coefficient :math:`S` and the thermal conductivity :math:`\kappa^{\text{el}}` can be obtained with:: @@ -129,9 +164,44 @@ Finally the optical conductivity :math:`\sigma(\Omega)`, the Seebeck coefficient It is strongly advised to check convergence in the number of k-points! +Example +------- + +Here we present an example calculation of the DFT optical conductivity of SrVO3 comparing the results from the Elk and Wien2k inputs. The DFT codes used 4495 k-points in the +irreducible Brillouin zone with Wanner projectors generated within a correlated energy window of [-8, 7.5] eV. We assume that the required DFT files have been read and saved by the TRIQS +interface routines as discussed previously. Below is an example script to generate the conductivities:: + + from sumk_dft_tools import * + import numpy + + SK = SumkDFTTools(hdf_file=filename+'.h5', use_dft_blocks=True) + + #Generate numpy mesh for omega values + om_mesh = list(numpy.linspace(0.0,5.0,51)) + + #Generate and save the transport distribution + SK.transport_distribution(directions=['xx'], Om_mesh=om_mesh, energy_window=[-8.0, 7.5], with_Sigma=False, broadening=-0.05, beta=40, n_om=1000) + SK.save(['Gamma_w','Om_mesh','omega','directions']) + + #Generate and save conductivities + SK.conductivity_and_seebeck(beta=40) + SK.save(['seebeck','optic_cond','kappa']) + +The optic_cond variable can be loaded by using :meth:`SK.load` and then plotted to generate the following figure. + +.. image:: transport_plots/opt_comp.png + :width: 700 + :align: center + +Note that the differences between the conductivities arise from the differences in the velocities generated in the DFT codes. The DMFT optical conductivity can easily be calculated by adjusting +the above example script by setting `with_Sigma` to **True**. In this case however, the SK object will need the DMFT self-energy on the real frequency axis. + + References ---------- .. [#transp1] `V. S. Oudovenko, G. Palsson, K. Haule, G. Kotliar, S. Y. Savrasov, Phys. Rev. B 73, 035120 (2006) `_ .. [#transp2] `J. M. Tomczak, K. Haule, T. Miyake, A. Georges, G. Kotliar, Phys. Rev. B 82, 085104 (2010) `_ .. [#userguide] `P. Blaha, K. Schwarz, G. K. H. Madsen, D. Kvasnicka, J. Luitz, ISBN 3-9501031-1-2 `_ +.. [#userguide2] `J. K. Dewhurst, S. Sharma, L. Nordstrom, F. Cricchio, O. Granas, and E. K. U. Gross, The Elk Code Manual `_ + diff --git a/doc/guide/transport_plots/opt_comp.png b/doc/guide/transport_plots/opt_comp.png new file mode 100644 index 00000000..0021d478 Binary files /dev/null and b/doc/guide/transport_plots/opt_comp.png differ diff --git a/python/triqs_dft_tools/converters/elk.py b/python/triqs_dft_tools/converters/elk.py index b44ed152..42773bf1 100644 --- a/python/triqs_dft_tools/converters/elk.py +++ b/python/triqs_dft_tools/converters/elk.py @@ -310,7 +310,7 @@ class ElkConverter(ConverterTools,Elk_tools,read_Elk): mpi.report("Reading SYMCRYS.OUT") [n_symm,spinmat,symmat,tr] = read_Elk.readsym(self) mpi.report("Reading LATTICE.OUT") - [amat,amatinv,bmat,bmatinv] = read_Elk.readlat(self) + [amat,amatinv,bmat,bmatinv,cell_vol] = read_Elk.readlat(self) #calculating atom permutations perm = Elk_tools.gen_perm(self,n_symm,ns,na,n_atoms,symmat,tr,atpos) #determine the cartesian lattice symmetries and the spin axis rotations @@ -388,9 +388,12 @@ class ElkConverter(ConverterTools,Elk_tools,read_Elk): #remove "spatom" del shells[ish]['spatom'] n_orbits=len(orbits) - #Note that the T numpy array is defined for all shells. + #new variable: dft_code - this determines which DFT code the inputs come from. + #used for certain routines within dft_tools if treating the inputs differently is required. + dft_code = 'elk' + # Save it to the HDF: ar = HDFArchive(self.hdf_file, 'a') if not (self.dft_subgrp in ar): @@ -400,7 +403,7 @@ class ElkConverter(ConverterTools,Elk_tools,read_Elk): things_to_save = ['energy_unit', 'n_k', 'k_dep_projection', 'SP', 'SO', 'charge_below', 'density_required', 'symm_op', 'n_shells', 'shells', 'n_corr_shells', 'corr_shells', 'use_rotations', 'rot_mat', 'rot_mat_time_inv', 'n_reps', 'dim_reps', 'T', 'n_orbitals', 'proj_mat', 'bz_weights', 'hopping', - 'n_inequiv_shells', 'corr_to_inequiv', 'inequiv_to_corr'] + 'n_inequiv_shells', 'corr_to_inequiv', 'inequiv_to_corr', 'dft_code'] for it in things_to_save: ar[self.dft_subgrp][it] = locals()[it] del ar @@ -647,3 +650,110 @@ class ElkConverter(ConverterTools,Elk_tools,read_Elk): del ar mpi.report('Converted the band character data') + + def convert_transport_input(self): + """ + Reads the necessary information for transport calculations on: + + - the optical band window and the velocity matrix elements from :file:`case.pmat` + + and stores the data in the hdf5 archive. + + """ + + if not (mpi.is_master_node()): + return + + # get needed data from hdf file + with HDFArchive(self.hdf_file, 'r') as ar: + if not (self.dft_subgrp in ar): + raise IOError("convert_transport_input: No %s subgroup in hdf file found! Call convert_dft_input first." % self.dft_subgrp) + things_to_read = ['SP', 'SO','n_k','n_orbitals'] + for it in things_to_read: + if not hasattr(self, it): + setattr(self, it, ar[self.dft_subgrp][it]) + #from misc info + things_to_read = ['band_window','vkl','nstsv'] + for it in things_to_read: + if not hasattr(self, it): + setattr(self, it, ar[self.misc_subgrp][it]) + + #unlike in WIEN2k, Elk writes the velocities (momentum) matrix elements for all bands. + #Therefore, we can use the indices in the n_orbitals array to extract the desired elements. + #However, the PMAT.OUT file is in Fortran-binary, so the file is read in by python wrappers + #around the reading fortran code. + + # Read relevant data from PMAT.OUT binary file + ########################################### + # band_window_optics: same as Elk converter's band_window, but rearranged to be compatible + # for the transport calculations. + # velocities_k: velocity (momentum) matrix elements between all bands in band_window_optics + # and each k-point. + + #load fortran wrapper module + import triqs_dft_tools.converters.elktools.elkwrappers.getpmatelk as et + #elk velocities for all bands + pmat=numpy.zeros([self.nstsv,self.nstsv,3],dtype=complex) + + n_spin_blocks = self.SP + 1 - self.SO + #TRIQS' velocities array used in its transport routines + velocities_k = [[] for isp in range(n_spin_blocks)] + #TRIQS' band_window array used in its transport routines + band_window_optics = [] + + + mpi.report("Reading PMAT.OUT") + #read velocities for each k-point + for ik in range(self.n_k): + #need to use a fortran array for wrapper + f_vkl = numpy.asfortranarray(self.vkl[ik,:]) + #read the ik velocity using the wrapper + pmat[:,:,:]=et.getpmatelk(ik+1,self.nstsv,f_vkl) + #loop over spin + for isp in range(n_spin_blocks): + #no. correlated bands at ik + nu1=self.band_window[isp][ik,0]-1 + nu2=self.band_window[isp][ik,1]-1 + n_bands=nu2-nu1+1 + #put into velocity array (code similar to that in wien.py. + if n_bands <= 0: + velocity_xyz = numpy.zeros((1, 1, 3), dtype=complex) + else: + velocity_xyz = numpy.zeros( + (n_bands, n_bands, 3), dtype=complex) + #CHECK these lines + velocity_xyz[:,:,:]=pmat[nu1:nu2+1,nu1:nu2+1,:] + velocities_k[isp].append(velocity_xyz) + + #rearrange Elk's band_window array into band_window_optics array format + for isp in range(n_spin_blocks): + band_window_optics_isp = [] + for ik in range(self.n_k): + nu1=self.band_window[isp][ik,0] + nu2=self.band_window[isp][ik,1] + band_window_optics_isp.append((nu1, nu2)) + n_bands=nu2-nu1+1 + band_window_optics.append(numpy.array(band_window_optics_isp)) + + #read in the cell volume from LATTICE.OUT + mpi.report("Reading LATTICE.OUT") + [amat,amatinv,bmat,bmatinv,cell_vol] = read_Elk.readlat(self) + + #read in the crystal symmetries + mpi.report("Reading SYMCRYS.OUT") + [n_symmetries,spinmat,rot_symmetries,tr] = read_Elk.readsym(self) + + + # Put data to HDF5 file + with HDFArchive(self.hdf_file, 'a') as ar: + if not (self.transp_subgrp in ar): + ar.create_group(self.transp_subgrp) + # The subgroup containing the data. If it does not exist, it is + # created. If it exists, the data is overwritten!!! + things_to_save = ['band_window_optics', 'velocities_k'] + for it in things_to_save: + ar[self.transp_subgrp][it] = locals()[it] + things_to_save_misc = ['n_symmetries', 'rot_symmetries','cell_vol'] + for it in things_to_save_misc: + ar[self.misc_subgrp][it] = locals()[it] + mpi.report("Reading complete!") diff --git a/python/triqs_dft_tools/converters/elktools/elkwrappers/CMakeLists.txt b/python/triqs_dft_tools/converters/elktools/elkwrappers/CMakeLists.txt new file mode 100644 index 00000000..c548777d --- /dev/null +++ b/python/triqs_dft_tools/converters/elktools/elkwrappers/CMakeLists.txt @@ -0,0 +1,34 @@ + +# List the sources +set(module_name "getpmatelk") +set(fortran_src_file "${CMAKE_CURRENT_SOURCE_DIR}/getpmatelk.f90") + +set(generated_module_file ${module_name}${TRIQS_PYTHON_MODULE_EXT}) + +add_custom_target(${module_name} ALL + DEPENDS ${generated_module_file} + ) + +##generate the fortran python wrapper shared library +add_custom_command( + OUTPUT ${generated_module_file} + COMMAND ${TRIQS_PYTHON_EXECUTABLE} -m numpy.f2py --f90exec=${CMAKE_Fortran_COMPILER} -c ${fortran_src_file} -m ${module_name} > elk_f2py.log + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + ) + +# where to install +install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} DESTINATION +${TRIQS_PYTHON_LIB_DEST_ROOT}/${PROJECT_NAME}/converters/elktools FILES_MATCHING PATTERN "*.so" +PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE +WORLD_READ WORLD_EXECUTE PATTERN "CMakeFiles" EXCLUDE) +message(STATUS "foo include dir: ${CMAKE_CURRENT_BINARY_DIR}") +message(STATUS "foo include dir: ${CMAKE_BINARY_DIR}") +message(STATUS "foo include dir: ${TRIQS_PYTHON_LIB_DEST_ROOT}/${PROJECT_NAME}") + +# user warning +message(STATUS "-----------------------------------------------------------------------------") +message(STATUS " ******** USER NOTE ******** ") +message(STATUS " This version of DFTTools contains interface routines to read Elk's binary ") +message(STATUS " files. ") +message(STATUS "-----------------------------------------------------------------------------") + diff --git a/python/triqs_dft_tools/converters/elktools/elkwrappers/getpmatelk.f90 b/python/triqs_dft_tools/converters/elktools/elkwrappers/getpmatelk.f90 new file mode 100644 index 00000000..64156c79 --- /dev/null +++ b/python/triqs_dft_tools/converters/elktools/elkwrappers/getpmatelk.f90 @@ -0,0 +1,65 @@ + +! Copyright (C) 2010 S. Sharma, J. K. Dewhurst and E. K. U. Gross. +! This file is distributed under the terms of the GNU General Public License. + +! version 6.2.8 file modified by A. D. N. James for interface with TRIQS + +subroutine getpmatelk(ik,nstsv,vkl,pmat) +!use modmain +implicit none +! arguments +integer, intent(in) :: ik !Need to read this in for the interface +integer, intent(in) :: nstsv !Need to read this in for the interface +real(8), intent(in) :: vkl(3) !TRIQS uses reduced kpts set +complex(8), intent(out) :: pmat(nstsv,nstsv,3) +! local variables +integer recl,nstsv_,i +real(8) vkl_(3),t1 + +!adnj - set up tolerance for lattice vectors, although this is an input in Elk, +! it is not advised to change this in Elk. Therefore, it should be fine to set +!it as a constant here. +real(8) epslat +epslat=1.d-6 + +! find the record length +inquire(iolength=recl) vkl_,nstsv_,pmat +!$OMP CRITICAL(u150) +do i=1,2 + open(150,file='PMAT.OUT',form='UNFORMATTED',access='DIRECT',recl=recl,err=10) + read(150,rec=ik,err=10) vkl_,nstsv_,pmat + exit +10 continue + if (i.eq.2) then + write(*,*) + write(*,'("Error(getpmat): unable to read from PMAT.OUT")') + write(*,*) + stop + end if + close(150) +end do +!$OMP END CRITICAL(u150) +!adnj edit - updated for vkl array from TRIQS +t1=abs(vkl(1)-vkl_(1))+abs(vkl(2)-vkl_(2))+abs(vkl(3)-vkl_(3)) +if (t1.gt.epslat) then + write(*,*) + write(*,'("Error(getpmat): differing vectors for k-point ",I8)') ik + !write(*,'(" current : ",3G18.10)') vkl(:,ik) + write(*,'(" current : ",3G18.10)') vkl(:) + write(*,'(" PMAT.OUT : ",3G18.10)') vkl_ + write(*,*) + stop +end if +if (nstsv.ne.nstsv_) then + write(*,*) + write(*,'("Error(getpmat): differing nstsv for k-point ",I8)') ik + write(*,'(" current : ",I8)') nstsv + write(*,'(" PMAT.OUT : ",I8)') nstsv_ + write(*,*) + stop +end if + +return + +end subroutine + diff --git a/python/triqs_dft_tools/converters/elktools/readElkfiles.py b/python/triqs_dft_tools/converters/elktools/readElkfiles.py index 5c9cd41d..60ebfb62 100644 --- a/python/triqs_dft_tools/converters/elktools/readElkfiles.py +++ b/python/triqs_dft_tools/converters/elktools/readElkfiles.py @@ -527,7 +527,7 @@ class readElkfiles: def readlat(self): """ - Read in the symmetries in lattice coordinates + Read in information about the lattice. """ dft_file='LATTICE.OUT' R = self.read_elk_file2( dft_file, self.fortran_to_replace) @@ -552,9 +552,11 @@ class readElkfiles: x = next(R) for j in range(3): amatinv[i,j] = atof(x[j]) - #reciprocal lattice matrices + #read in cell volume (for transport) + x = next(R) + cell_vol = atof(x[-1]) #cycling through information which is not needed - for i in range(5): + for i in range(4): x = next(R) #reading in the reciprocal lattice vectors as matrix for i in range(3): @@ -572,7 +574,7 @@ class readElkfiles: except StopIteration: # a more explicit error if the file is corrupted. raise IOError("Elk_converter : reading PROJ.OUT file failed!") R.close() - return amat,amatinv,bmat,bmatinv + return amat,amatinv,bmat,bmatinv,cell_vol def read_geometry(self): """ diff --git a/python/triqs_dft_tools/converters/hk.py b/python/triqs_dft_tools/converters/hk.py index 02a881ae..fa56b834 100644 --- a/python/triqs_dft_tools/converters/hk.py +++ b/python/triqs_dft_tools/converters/hk.py @@ -261,6 +261,10 @@ class HkConverter(ConverterTools): R.close() + #new variable: dft_code - this determines which DFT code the inputs come from. + #used for certain routines within dft_tools if treating the inputs differently is required. + dft_code = 'hk' + # Save to the HDF5: with HDFArchive(self.hdf_file, 'a') as ar: if not (self.dft_subgrp in ar): @@ -268,6 +272,6 @@ class HkConverter(ConverterTools): things_to_save = ['energy_unit', 'n_k', 'k_dep_projection', 'SP', 'SO', 'charge_below', 'density_required', 'symm_op', 'n_shells', 'shells', 'n_corr_shells', 'corr_shells', 'use_rotations', 'rot_mat', 'rot_mat_time_inv', 'n_reps', 'dim_reps', 'T', 'n_orbitals', 'proj_mat', 'bz_weights', 'hopping', - 'n_inequiv_shells', 'corr_to_inequiv', 'inequiv_to_corr'] + 'n_inequiv_shells', 'corr_to_inequiv', 'inequiv_to_corr', 'dft_code'] for it in things_to_save: ar[self.dft_subgrp][it] = locals()[it] diff --git a/python/triqs_dft_tools/converters/vasp.py b/python/triqs_dft_tools/converters/vasp.py index 93f770a7..fb78e0c2 100644 --- a/python/triqs_dft_tools/converters/vasp.py +++ b/python/triqs_dft_tools/converters/vasp.py @@ -386,6 +386,10 @@ class VaspConverter(ConverterTools): proj_or_hk = self.proj_or_hk + #new variable: dft_code - this determines which DFT code the inputs come from. + #used for certain routines within dft_tools if treating the inputs differently is required. + dft_code = 'vasp' + # Save it to the HDF: with HDFArchive(self.hdf_file,'a') as ar: if not (self.dft_subgrp in ar): ar.create_group(self.dft_subgrp) @@ -394,7 +398,7 @@ class VaspConverter(ConverterTools): 'symm_op','n_shells','shells','n_corr_shells','corr_shells','use_rotations','rot_mat', 'rot_mat_time_inv','n_reps','dim_reps','T','n_orbitals','proj_mat','bz_weights', 'hopping','n_inequiv_shells', 'corr_to_inequiv', 'inequiv_to_corr','proj_or_hk', - 'kpts','kpt_weights', 'kpt_basis'] + 'kpts','kpt_weights', 'kpt_basis', 'dft_code'] if self.proj_or_hk == 'hk' or self.proj_or_hk == True: things_to_save.append('proj_mat_csc') for it in things_to_save: ar[self.dft_subgrp][it] = locals()[it] diff --git a/python/triqs_dft_tools/converters/wannier90.py b/python/triqs_dft_tools/converters/wannier90.py index 56b0b4bc..c97fc611 100644 --- a/python/triqs_dft_tools/converters/wannier90.py +++ b/python/triqs_dft_tools/converters/wannier90.py @@ -300,6 +300,10 @@ class Wannier90Converter(ConverterTools): # n_orbitals required by triqs h5 standard, which actually contains the number of bands n_orbitals = np.full((n_k, n_spin_blocks), n_bands) + #new variable: dft_code - this determines which DFT code the inputs come from. + #used for certain routines within dft_tools if treating the inputs differently is required. + dft_code = 'w90' + # Finally, save all required data into the HDF archive: if mpi.is_master_node(): with HDFArchive(self.hdf_file, 'a') as archive: @@ -310,7 +314,7 @@ class Wannier90Converter(ConverterTools): things_to_save = ['energy_unit', 'n_k', 'k_dep_projection', 'SP', 'SO', 'charge_below', 'density_required', 'symm_op', 'n_shells', 'shells', 'n_corr_shells', 'corr_shells', 'use_rotations', 'rot_mat', 'rot_mat_time_inv', 'n_reps', 'dim_reps', 'T', 'n_orbitals', 'proj_mat', 'bz_weights', 'hopping', - 'n_inequiv_shells', 'corr_to_inequiv', 'inequiv_to_corr', 'kpt_weights', 'kpts'] + 'n_inequiv_shells', 'corr_to_inequiv', 'inequiv_to_corr', 'kpt_weights', 'kpts', 'dft_code'] if self.bloch_basis: np.append(things_to_save, 'kpt_basis') for it in things_to_save: diff --git a/python/triqs_dft_tools/converters/wien2k.py b/python/triqs_dft_tools/converters/wien2k.py index 72387594..06c3eb66 100644 --- a/python/triqs_dft_tools/converters/wien2k.py +++ b/python/triqs_dft_tools/converters/wien2k.py @@ -259,6 +259,10 @@ class Wien2kConverter(ConverterTools): R.close() # Reading done! + #new variable: dft_code - this determines which DFT code the inputs come from. + #used for certain routines within dft_tools if treating the inputs differently is required. + dft_code = 'wien2k' + # Save it to the HDF: with HDFArchive(self.hdf_file, 'a') as ar: if not (self.dft_subgrp in ar): @@ -268,7 +272,7 @@ class Wien2kConverter(ConverterTools): things_to_save = ['energy_unit', 'n_k', 'k_dep_projection', 'SP', 'SO', 'charge_below', 'density_required', 'symm_op', 'n_shells', 'shells', 'n_corr_shells', 'corr_shells', 'use_rotations', 'rot_mat', 'rot_mat_time_inv', 'n_reps', 'dim_reps', 'T', 'n_orbitals', 'proj_mat', 'bz_weights', 'hopping', - 'n_inequiv_shells', 'corr_to_inequiv', 'inequiv_to_corr'] + 'n_inequiv_shells', 'corr_to_inequiv', 'inequiv_to_corr', 'dft_code'] for it in things_to_save: ar[self.dft_subgrp][it] = locals()[it] diff --git a/python/triqs_dft_tools/sumk_dft.py b/python/triqs_dft_tools/sumk_dft.py index fdce25a8..eddb2385 100644 --- a/python/triqs_dft_tools/sumk_dft.py +++ b/python/triqs_dft_tools/sumk_dft.py @@ -126,7 +126,7 @@ class SumkDFT(object): req_things_to_read = ['energy_unit', 'n_k', 'k_dep_projection', 'SP', 'SO', 'charge_below', 'density_required', 'symm_op', 'n_shells', 'shells', 'n_corr_shells', 'corr_shells', 'use_rotations', 'rot_mat', 'rot_mat_time_inv', 'n_reps', 'dim_reps', 'T', 'n_orbitals', 'proj_mat', 'bz_weights', 'hopping', - 'n_inequiv_shells', 'corr_to_inequiv', 'inequiv_to_corr'] + 'n_inequiv_shells', 'corr_to_inequiv', 'inequiv_to_corr', 'dft_code'] self.subgroup_present, self.values_not_read = self.read_input_from_hdf( subgrp=self.dft_data, things_to_read=req_things_to_read) # test if all required properties have been found @@ -1986,7 +1986,7 @@ class SumkDFT(object): return self.chemical_potential - def calc_density_correction(self, filename=None, dm_type='wien2k', spinave=False, kpts_to_write=None): + def calc_density_correction(self, filename=None, dm_type=None, spinave=False, kpts_to_write=None): r""" Calculates the charge density correction and stores it into a file. @@ -2004,7 +2004,10 @@ class SumkDFT(object): Name of the file to store the charge density correction. dm_type : string DFT code to write the density correction for. Options: - 'vasp', 'wien2k', 'elk' + 'vasp', 'wien2k', 'elk' or 'qe'. Needs to be set for 'qe' + spinave : logical + Elk specific and for magnetic calculations in DMFT only. + It averages the spin to keep the DFT part non-magnetic. kpts_to_write : iterable of int Indices of k points that are written to file. If None (default), all k points are written. Only implemented for dm_type 'vasp' @@ -2016,6 +2019,10 @@ class SumkDFT(object): the corresponing total charge `dens`. """ + #automatically set dm_type if required + if dm_type==None: + dm_type = self.dft_code + assert dm_type in ('vasp', 'wien2k','elk', 'qe'), "'dm_type' must be either 'vasp', 'wienk', 'elk' or 'qe'" #default file names if filename is None: diff --git a/python/triqs_dft_tools/sumk_dft_tools.py b/python/triqs_dft_tools/sumk_dft_tools.py index 5527902b..e9c58ad0 100644 --- a/python/triqs_dft_tools/sumk_dft_tools.py +++ b/python/triqs_dft_tools/sumk_dft_tools.py @@ -962,6 +962,7 @@ class SumkDFTTools(SumkDFT): dens_mat : list of numpy array A list of density matrices projected to all shells provided in the input. """ + assert self.dft_code in ('wien2k'), "This routine has only been implemented for wien2k inputs" things_to_read = ['dens_mat_below', 'n_parproj', 'proj_mat_all', 'rot_mat_all', 'rot_mat_all_time_inv'] @@ -1063,13 +1064,20 @@ class SumkDFTTools(SumkDFT): r""" Reads the data for transport calculations from the hdf5 archive. """ + assert self.dft_code in ('wien2k','elk'), "Transport has only been implemented for wien2k and elk inputs" thingstoread = ['band_window_optics', 'velocities_k'] self.read_input_from_hdf( subgrp=self.transp_data, things_to_read=thingstoread) - thingstoread = ['band_window', 'lattice_angles', 'lattice_constants', - 'lattice_type', 'n_symmetries', 'rot_symmetries'] + if(self.dft_code=="wien2k"): + thingstoread = ['band_window', 'lattice_angles', 'lattice_constants', + 'lattice_type', 'n_symmetries', 'rot_symmetries'] + elif(self.dft_code=="elk"): + thingstoread = ['band_window', 'n_symmetries', + 'rot_symmetries','cell_vol'] self.read_input_from_hdf( subgrp=self.misc_data, things_to_read=thingstoread) + if(self.dft_code=="wien2k"): + self.cell_vol = self.cellvolume(self.lattice_type, self.lattice_constants, self.lattice_angles)[1] def cellvolume(self, lattice_type, lattice_constants, latticeangle): r""" @@ -1222,8 +1230,8 @@ class SumkDFTTools(SumkDFT): assert broadening != 0.0 and broadening is not None, "transport_distribution: Broadening necessary to calculate transport distribution!" self.omega = numpy.linspace( energy_window[0] - max(Om_mesh), energy_window[1] + max(Om_mesh), n_om) - mesh = [energy_window[0] - - max(Om_mesh), energy_window[1] + max(Om_mesh), n_om] + mesh = MeshReFreq(energy_window[0] - + max(Om_mesh), energy_window[1] + max(Om_mesh), n_om) mu = 0.0 # Define mesh for optic conductivity @@ -1291,8 +1299,8 @@ class SumkDFTTools(SumkDFT): A_kw[isp][A_i, A_i, iw]).trace().real * self.bz_weights[ik]) for direction in self.directions: - self.Gamma_w[direction] = (mpi.all_reduce(mpi.world, self.Gamma_w[direction], lambda x, y: x + y) - / self.cellvolume(self.lattice_type, self.lattice_constants, self.lattice_angles)[1] / self.n_symmetries) + self.Gamma_w[direction] = (mpi.all_reduce(mpi.world, self.Gamma_w[direction], lambda x, y: x + y) / self.cell_vol / self.n_symmetries) + def transport_coefficient(self, direction, iq, n, beta, method=None): r""" diff --git a/test/python/SrIrO3_rot.h5 b/test/python/SrIrO3_rot.h5 index 5ea92a78..3586df16 100644 Binary files a/test/python/SrIrO3_rot.h5 and b/test/python/SrIrO3_rot.h5 differ diff --git a/test/python/SrVO3.ref.h5 b/test/python/SrVO3.ref.h5 index 1d923255..4150e050 100644 Binary files a/test/python/SrVO3.ref.h5 and b/test/python/SrVO3.ref.h5 differ diff --git a/test/python/SrVO3_spectral.h5 b/test/python/SrVO3_spectral.h5 index 455e5962..9e385909 100644 Binary files a/test/python/SrVO3_spectral.h5 and b/test/python/SrVO3_spectral.h5 differ diff --git a/test/python/blockstructure.in.h5 b/test/python/blockstructure.in.h5 index f4d2cada..1a0af3f5 100644 Binary files a/test/python/blockstructure.in.h5 and b/test/python/blockstructure.in.h5 differ diff --git a/test/python/elk/CMakeLists.txt b/test/python/elk/CMakeLists.txt index 7f734cf0..dc2eb6eb 100644 --- a/test/python/elk/CMakeLists.txt +++ b/test/python/elk/CMakeLists.txt @@ -4,6 +4,7 @@ set(all_tests elk_equiv_convert elk_bands_convert elk_bandcharacter_convert + elk_transport_convert ) file(GLOB all_test_files RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} *.py) diff --git a/test/python/elk/elk_bandcharacter_convert/elk_bc_convert.ref.h5 b/test/python/elk/elk_bandcharacter_convert/elk_bc_convert.ref.h5 index 8d8f86f5..f3aa74ea 100644 Binary files a/test/python/elk/elk_bandcharacter_convert/elk_bc_convert.ref.h5 and b/test/python/elk/elk_bandcharacter_convert/elk_bc_convert.ref.h5 differ diff --git a/test/python/elk/elk_bands_convert/elk_bands_convert.ref.h5 b/test/python/elk/elk_bands_convert/elk_bands_convert.ref.h5 index b028ff6a..5355aca9 100644 Binary files a/test/python/elk/elk_bands_convert/elk_bands_convert.ref.h5 and b/test/python/elk/elk_bands_convert/elk_bands_convert.ref.h5 differ diff --git a/test/python/elk/elk_convert/elk_convert.ref.h5 b/test/python/elk/elk_convert/elk_convert.ref.h5 index 8a100766..5bf9c233 100644 Binary files a/test/python/elk/elk_convert/elk_convert.ref.h5 and b/test/python/elk/elk_convert/elk_convert.ref.h5 differ diff --git a/test/python/elk/elk_equiv_convert/elk_equiv_convert.ref.h5 b/test/python/elk/elk_equiv_convert/elk_equiv_convert.ref.h5 index e5a53578..a51f9f1d 100644 Binary files a/test/python/elk/elk_equiv_convert/elk_equiv_convert.ref.h5 and b/test/python/elk/elk_equiv_convert/elk_equiv_convert.ref.h5 differ diff --git a/test/python/elk/elk_transport_convert.py b/test/python/elk/elk_transport_convert.py new file mode 100644 index 00000000..f193a6f5 --- /dev/null +++ b/test/python/elk/elk_transport_convert.py @@ -0,0 +1,24 @@ +import os +from h5 import * +from triqs.utility.comparison_tests import * +from triqs.utility.h5diff import h5diff +import triqs.utility.mpi as mpi + +from triqs_dft_tools.converters import ElkConverter +#get current working directory path +cwd = format(os.getcwd()) +#location of test directory +testdir = cwd+'/elk_transport_convert' +#change to test directory +os.chdir(testdir) + +Converter = ElkConverter(filename='SrVO3', repacking=True) +Converter.hdf_file = 'elk_transport_convert.out.h5' +Converter.convert_dft_input() +Converter.convert_transport_input() + +if mpi.is_master_node(): + h5diff('elk_transport_convert.out.h5','elk_transport_convert.ref.h5') + +#return to cwd +os.chdir(cwd) diff --git a/test/python/elk/elk_transport_convert/EFERMI.OUT b/test/python/elk/elk_transport_convert/EFERMI.OUT new file mode 100644 index 00000000..f020fc13 --- /dev/null +++ b/test/python/elk/elk_transport_convert/EFERMI.OUT @@ -0,0 +1 @@ + 0.3195858311 diff --git a/test/python/elk/elk_transport_convert/EIGVAL.OUT b/test/python/elk/elk_transport_convert/EIGVAL.OUT new file mode 100644 index 00000000..4a82286a --- /dev/null +++ b/test/python/elk/elk_transport_convert/EIGVAL.OUT @@ -0,0 +1,452 @@ + 10 : nkpt + 41 : nstsv + + 1 0.000000000 0.000000000 0.000000000 : k-point, vkl + (state, eigenvalue and occupancy below) + 1 -2.080512267 2.000000000 + 2 -1.131321703 2.000000000 + 3 -1.131321703 2.000000000 + 4 -1.131321703 2.000000000 + 5 -0.9440995962 2.000000000 + 6 -0.4008824873 2.000000000 + 7 -0.3552791000 2.000000000 + 8 -0.3552791000 2.000000000 + 9 -0.2842140945 2.000000000 + 10 -0.2842140945 2.000000000 + 11 -0.2842140945 2.000000000 + 12 0.1240445701 2.000000000 + 13 0.1240445701 2.000000000 + 14 0.1240445701 2.000000000 + 15 0.1963657132 2.000000000 + 16 0.1963657132 2.000000000 + 17 0.1963657132 2.000000000 + 18 0.2274578760 1.999999992 + 19 0.2274578760 1.999999992 + 20 0.2274578760 1.999999992 + 21 0.2789989931 1.999610736 + 22 0.2789989931 1.999610736 + 23 0.2789989931 1.999610736 + 24 0.3630465670 0.2125849074E-03 + 25 0.3630465670 0.2125849074E-03 + 26 0.4679515512 0.5451436638E-13 + 27 0.4679515512 0.5451436638E-13 + 28 0.4816851639 0.3026205990E-14 + 29 0.6363678094 0.000000000 + 30 0.6363678094 0.000000000 + 31 0.6363678094 0.000000000 + 32 0.7998166430 0.000000000 + 33 0.8808469236 0.000000000 + 34 0.8808469236 0.000000000 + 35 0.8808469236 0.000000000 + 36 1.065275448 0.000000000 + 37 1.106537298 0.000000000 + 38 1.106537298 0.000000000 + 39 1.106537298 0.000000000 + 40 1.114329639 0.000000000 + 41 1.114329639 0.000000000 + + + 2 0.2500000000 0.000000000 0.000000000 : k-point, vkl + (state, eigenvalue and occupancy below) + 1 -2.080514726 2.000000000 + 2 -1.131961789 2.000000000 + 3 -1.131259898 2.000000000 + 4 -1.131259898 2.000000000 + 5 -0.9434733782 2.000000000 + 6 -0.4030932930 2.000000000 + 7 -0.3558005147 2.000000000 + 8 -0.3545784259 2.000000000 + 9 -0.2829968758 2.000000000 + 10 -0.2829968758 2.000000000 + 11 -0.2705339640 2.000000000 + 12 0.9562813155E-01 2.000000000 + 13 0.1229027827 2.000000000 + 14 0.1229027827 2.000000000 + 15 0.1683668952 2.000000000 + 16 0.1683668952 2.000000000 + 17 0.1776091949 2.000000000 + 18 0.1784639199 2.000000000 + 19 0.2167716847 1.999999999 + 20 0.2167716847 1.999999999 + 21 0.2813385282 1.999363080 + 22 0.3214745569 0.8037742202 + 23 0.3214745569 0.8037742202 + 24 0.3633365372 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Path for species files +sppath + '/home/elk-6.2.8/species/' + +! Maximum length for G+k vectors +rgkmax + 7.0 + +avec + 7.260500000 0.000000000 0.000000000 + 0.000000000 7.260500000 0.000000000 + 0.000000000 0.000000000 7.260500000 + +atoms + 3 : nspecies +'Sr.in' : spfname + 1 : natoms; atposl, bfcmt below + 0.50000000 0.50000000 0.50000000 0.00000000 0.00000000 0.00000000 +'V.in' : spfname + 1 : natoms; atposl, bfcmt below + 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 +'O.in' : spfname + 3 : natoms; atposl, bfcmt below + 0.50000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 + 0.00000000 0.50000000 0.00000000 0.00000000 0.00000000 0.00000000 + 0.00000000 0.00000000 0.50000000 0.00000000 0.00000000 0.00000000 + + +!Wannier projectors +wanproj !projector flag + 1 !number of projectors - next 3 lines are repeated for each projector + 2 2 3 !species, l, reduced max lm (rlmmax) value + 7 8 9 !the lm quanties which will be projected (vector length eq. rlmmax) +-0.294 0.27562 ![-8.0, 7.5] eV energy window diff --git a/test/python/elk/elk_transport_convert/elk_transport_convert.out.h5 b/test/python/elk/elk_transport_convert/elk_transport_convert.out.h5 new file mode 100644 index 00000000..a32aaef9 Binary files /dev/null and b/test/python/elk/elk_transport_convert/elk_transport_convert.out.h5 differ diff --git a/test/python/elk/elk_transport_convert/elk_transport_convert.ref.h5 b/test/python/elk/elk_transport_convert/elk_transport_convert.ref.h5 new file mode 100644 index 00000000..a9097e5a Binary files /dev/null and b/test/python/elk/elk_transport_convert/elk_transport_convert.ref.h5 differ diff --git a/test/python/hk_convert.ref.h5 b/test/python/hk_convert.ref.h5 index 8dcfc7d2..e4c924a2 100644 Binary files a/test/python/hk_convert.ref.h5 and b/test/python/hk_convert.ref.h5 differ diff --git a/test/python/plovasp/converter/lunio3.ref.h5 b/test/python/plovasp/converter/lunio3.ref.h5 index 50abe7a8..5c2f49fa 100644 Binary files a/test/python/plovasp/converter/lunio3.ref.h5 and b/test/python/plovasp/converter/lunio3.ref.h5 differ diff --git a/test/python/plovasp/converter/pg_output.ref.h5 b/test/python/plovasp/converter/pg_output.ref.h5 index c69199e1..4018eaf5 100644 Binary files a/test/python/plovasp/converter/pg_output.ref.h5 and b/test/python/plovasp/converter/pg_output.ref.h5 differ diff --git a/test/python/w90_convert/LaVO3-Pbnm_hloc_diag.ref.h5 b/test/python/w90_convert/LaVO3-Pbnm_hloc_diag.ref.h5 index 06e26e5f..7a72e473 100644 Binary files a/test/python/w90_convert/LaVO3-Pbnm_hloc_diag.ref.h5 and b/test/python/w90_convert/LaVO3-Pbnm_hloc_diag.ref.h5 differ diff --git a/test/python/w90_convert/LaVO3-Pnma_lambda.ref.h5 b/test/python/w90_convert/LaVO3-Pnma_lambda.ref.h5 index 5b82f552..51c56cde 100644 Binary files a/test/python/w90_convert/LaVO3-Pnma_lambda.ref.h5 and b/test/python/w90_convert/LaVO3-Pnma_lambda.ref.h5 differ diff --git a/test/python/w90_convert/LaVO3-Pnma_wannier.ref.h5 b/test/python/w90_convert/LaVO3-Pnma_wannier.ref.h5 index 5a4407e2..3c643db7 100644 Binary files a/test/python/w90_convert/LaVO3-Pnma_wannier.ref.h5 and b/test/python/w90_convert/LaVO3-Pnma_wannier.ref.h5 differ diff --git a/test/python/w90_convert/SrVO3_col_blochbasis.ref.h5 b/test/python/w90_convert/SrVO3_col_blochbasis.ref.h5 index ea1eebb4..c9cf9dd7 100644 Binary files a/test/python/w90_convert/SrVO3_col_blochbasis.ref.h5 and b/test/python/w90_convert/SrVO3_col_blochbasis.ref.h5 differ diff --git a/test/python/w90_convert/SrVO3_col_wannierbasis.ref.h5 b/test/python/w90_convert/SrVO3_col_wannierbasis.ref.h5 index 42566d21..a376ec77 100644 Binary files a/test/python/w90_convert/SrVO3_col_wannierbasis.ref.h5 and b/test/python/w90_convert/SrVO3_col_wannierbasis.ref.h5 differ diff --git a/test/python/w90_convert/SrVO3_soc.ref.h5 b/test/python/w90_convert/SrVO3_soc.ref.h5 index 2b6a5661..50174cef 100644 Binary files a/test/python/w90_convert/SrVO3_soc.ref.h5 and b/test/python/w90_convert/SrVO3_soc.ref.h5 differ diff --git a/test/python/w90_convert/SrVO3_t2g_col_lambda.ref.h5 b/test/python/w90_convert/SrVO3_t2g_col_lambda.ref.h5 index 2bb5e66f..93cdc7be 100644 Binary files a/test/python/w90_convert/SrVO3_t2g_col_lambda.ref.h5 and b/test/python/w90_convert/SrVO3_t2g_col_lambda.ref.h5 differ diff --git a/test/python/wien2k_convert.ref.h5 b/test/python/wien2k_convert.ref.h5 index a5729cae..f837d178 100644 Binary files a/test/python/wien2k_convert.ref.h5 and b/test/python/wien2k_convert.ref.h5 differ