Skip to content

Commit

Permalink
move parameter tables to CSV and read into MD
Browse files Browse the repository at this point in the history
  • Loading branch information
jimustafa committed May 8, 2024
1 parent 7806b3f commit fe54a7f
Show file tree
Hide file tree
Showing 9 changed files with 141 additions and 139 deletions.
12 changes: 12 additions & 0 deletions docs/docs/parameters/w90-disentanglement-parameters.csv
Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
Keyword ,Type ,Description
dis_win_min ,P ,"Bottom of the outer energy window"
dis_win_max ,P ,"Top of the outer energy window"
dis_froz_min ,P ,"Bottom of the inner (frozen) energy window"
dis_froz_max ,P ,"Top of the inner (frozen) energy window"
dis_num_iter ,I ,"Number of iterations for the minimisation of $\\Omega_{\\mathrm{I}}$"
dis_mix_ratio ,R ,"Mixing ratio during the minimisation of $\\Omega_{\\mathrm{I}}$"
dis_conv_tol ,R ,"The convergence tolerance for finding $\\Omega_{\\mathrm{I}}$"
dis_conv_window ,I ,"The number of iterations over which convergence of $\\Omega_{\\mathrm{I}}$ is assessed."
dis_spheres_num ,I ,"Number of spheres in k-space where disentaglement is performed"
dis_spheres_first_wann ,I ,"Index of the first band to be considered a Wannier function"
dis_spheres ,R ,"List of centres and radii, for disentanglement only in spheres"
17 changes: 17 additions & 0 deletions docs/docs/parameters/w90-job-control-parameters.csv
Original file line number Diff line number Diff line change
@@ -0,0 +1,17 @@
Keyword ,Type ,Description
postproc_setup ,L ,"To output the `seedname.nnkp` file"
exclude_bands ,I ,"List of bands to exclude from the calculation"
select_projections ,I ,"List of projections to use in Wannierisation"
auto_projections ,L ,"To automatically generate initial projections"
restart ,S ,"Restart from checkpoint file"
iprint ,I ,"Output verbosity level"
length_unit ,S ,"System of units to output lengths"
wvfn_formatted ,L ,"Read the wavefunctions from a (un)formatted file"
spin ,S ,"Which spin channel to read"
devel_flag ,S ,"Flag for development use"
timing_level ,I ,"Determines amount of timing information written to output"
optimisation ,I ,"Optimisation level"
translate_home_cell ,L ,"To translate final Wannier centres to home unit cell when writing xyz file"
write_xyz ,L ,"To write atomic positions and final centres in xyz file format"
write_vdw_data ,L ,"To write data for futher processing by w90vdw utility"
write_hr_diag ,L ,"To write the diagonal elements of the Hamiltonian in the Wannier basis to `seedname.wout` (in eV)"
37 changes: 37 additions & 0 deletions docs/docs/parameters/w90-plot-parameters.csv
Original file line number Diff line number Diff line change
@@ -0,0 +1,37 @@
Keyword ,Type ,"Description"
wannier_plot ,L ,"Plot the WF"
wannier_plot_list ,I ,"List of WF to plot"
wannier_plot_supercell ,I ,"Size of the supercell for plotting the WF"
wannier_plot_format ,S ,"File format in which to plot the WF"
wannier_plot_mode ,S ,"Mode in which to plot the WF, molecule or crystal"
wannier_plot_radius ,R ,"Cut-off radius of WF\*"
wannier_plot_scale ,R ,"Scaling parameter for cube files"
wannier_plot_spinor_mode ,S ,"Quantity to plot for spinor WF"
wannier_plot_spinor_phase ,L ,"Include the “phase” when plotting spinor WF"
bands_plot ,L ,"Plot interpolated band structure"
kpoint_path ,P ,"K-point path for the interpolated band structure"
bands_num_points ,I ,"Number of points along the first section of the k-point path"
bands_plot_format ,S ,"File format in which to plot the interpolated bands"
bands_plot_project ,I ,"WF to project the band structure onto"
bands_plot_mode ,S ,"Slater-Koster type interpolation or Hamiltonian cut-off"
bands_plot_dim ,I ,"Dimension of the system"
fermi_surface_plot ,L ,"Plot the Fermi surface"
fermi_surface_num_points ,I ,"Number of points in the Fermi surface plot"
fermi_energy ,P ,"The Fermi energy"
fermi_energy_min ,P ,"Lower limit of the Fermi energy range"
fermi_energy_max ,P ,"Upper limit of the Fermi energy range"
fermi_energy_step ,R ,"Step for increasing the Fermi energy in the specified range"
fermi_surface_plot_format ,S ,"File format for the Fermi surface plot"
hr_plot ,L ,"This parameter is not used anymore. Use write_hr instead."
write_hr ,L ,"Write the Hamiltonian in the WF basis"
write_rmn ,L ,"Write the position operator in the WF basis"
write_bvec ,L ,"Write to file the matrix elements of the bvectors and their weights"
write_tb ,L ,"Write lattice vectors, Hamiltonian, and position operator in WF basis"
hr_cutoff ,P ,"Cut-off for the absolute value of the Hamiltonian"
dist_cutoff ,P ,"Cut-off for the distance between WF"
dist_cutoff_mode ,S ,"Dimension in which the distance between WF is calculated"
translation_centre_frac ,R ,"Centre of the unit cell to which final WF are translated"
use_ws_distance ,L ,"Improve interpolation using minimum distance between WFs, see Chap. [Some notes on the interpolation](notes_interpolations.md)"
ws_distance_tol ,R ,"Absolute tolerance for the distance to equivalent positions."
ws_search_size ,I ,"Maximum extension in each direction of the super-cell of the Born-von Karmann cell to search for points inside the Wigner-Seitz cell"
write_u_matrices ,L ,"Write $U^{(\\bm{k})}$ and $U^{dis(\\bm{k})}$ matrices to files"
15 changes: 15 additions & 0 deletions docs/docs/parameters/w90-system-parameters.csv
Original file line number Diff line number Diff line change
@@ -0,0 +1,15 @@
Keyword ,Type ,Description
num_wann ,I ,"Number of WF"
num_bands ,I ,"Number of bands passed to the code"
unit_cell_cart ,P ,"Unit cell vectors in Cartesian coordinates"
atoms_cart \* ,P ,"Positions of atoms in Cartesian coordinates"
atoms_frac \* ,R ,"Positions of atoms in fractional coordinates with respect to the lattice vectors"
mp_grid ,I ,"Dimensions of the Monkhorst-Pack grid of k-points"
kpoints ,R ,"List of k-points in the Monkhorst-Pack grid"
gamma_only ,L ,"Wavefunctions from underlying ab initio calculation are manifestly real"
spinors ,L ,"WF are spinors"
shell_list ,I ,"Which shells to use in finite difference formula"
search_shells ,I ,"The number of shells to search when determining finite difference formula"
skip_B1_tests ,L ,"Check the condition B1 of Ref [@marzari-prb97]"
nnkpts ,I ,"Explicit list of nearest-neighbour k-points"
kmesh_tol ,R ,"The tolerance to control if two kpoint belong to the same shell"
25 changes: 25 additions & 0 deletions docs/docs/parameters/w90-transport-parameters.csv
Original file line number Diff line number Diff line change
@@ -0,0 +1,25 @@
Keyword ,Type ,"Description"
transport ,L ,"Calculate quantum conductance and density of states"
transport_mode ,S ,"Bulk or left-lead_conductor_right-lead calculation"
tran_win_min ,P ,"Bottom of the energy window for transport calculation"
tran_win_max ,P ,"Top of the energy window for transport calculation"
tran_energy_step ,R ,"Sampling interval of the energy values"
fermi_energy ,R ,"The Fermi energy"
tran_num_bb ,I ,"Size of a bulk Hamiltonian"
tran_num_ll ,I ,"Size of a left-lead Hamiltonian"
tran_num_rr ,I ,"Size of a right-lead Hamiltonian"
tran_num_cc ,I ,"Size of a conductor Hamiltonian"
tran_num_lc ,I ,"Number of columns in a left-lead_conductor Hamiltonian"
tran_num_cr ,I ,"Number of rows in a conductor_right-lead Hamiltonian"
tran_num_cell_ll ,I ,"Number of unit cells in PL of left lead"
tran_num_cell_rr ,I ,"Number of unit cells in PL of right lead"
tran_num_bandc ,I ,"Half-bandwidth+1 of a band-diagonal conductor Hamiltonian"
tran_write_ht ,L ,"Write the Hamiltonian for transport calculation"
tran_read_ht ,L ,"Read the Hamiltonian for transport calculation"
tran_use_same_lead ,L ,"Left and right leads are the same"
tran_group_threshold ,R ,"Distance that determines the grouping of WFs"
hr_cutoff ,P ,"Cut-off for the absolute value of the Hamiltonian"
dist_cutoff ,P ,"Cut-off for the distance between WF"
dist_cutoff_mode ,S ,"Dimension in which the distance between WF is calculated"
one_dim_axis ,S ,"Extended direction for a one-dimensional system"
translation_centre_frac ,R ,"Centre of the unit cell to which final WF are translated"
23 changes: 23 additions & 0 deletions docs/docs/parameters/w90-wannierise-parameters.csv
Original file line number Diff line number Diff line change
@@ -0,0 +1,23 @@
Keyword ,Type ,Description
num_iter ,I ,"Number of iterations for the minimisation of $\\Omega$"
num_cg_steps ,I ,"During the minimisation of $\\Omega$ the number of Conjugate Gradient steps before resetting to Steepest Descents"
conv_window ,I ,"The number of iterations over which convergence of $\\Omega$ is assessed"
conv_tol ,P ,"The convergence tolerance for finding $\\Omega$"
precond ,L ,"Use preconditioning"
conv_noise_amp ,R ,"The amplitude of random noise applied towards end of minimisation procedure"
conv_noise_num ,I ,"The number of times random noise is applied"
num_dump_cycles ,I ,"Control frequency of check-pointing"
num_print_cycles ,I ,"Control frequency of printing"
write_r2mn ,L ,"Write matrix elements of $r^2$ between WF to file"
guiding_centres ,L ,"Use guiding centres"
num_guide_cycles ,I ,"Frequency of guiding centres"
num_no_guide_iter ,I ,"The number of iterations after which guiding centres are used"
trial_step \* ,R ,"The trial step length for the parabolic line search during the minimisation of $\\Omega$"
fixed_step \* ,R ,"The fixed step length to take during the minimisation of $\\Omega$, instead of doing a parabolic line search"
use_bloch_phases \*\* ,L ,"To use phases for initial projections"
site_symmetry\*\*\* ,L ,"To construct symmetry-adapted Wannier functions"
symmetrize_eps\*\*\* ,R ,"The convergence tolerance used in the symmetry-adapted mode"
slwf_num ,I ,"The number of objective WFs for selective localization"
slwf_constrain ,L ,"Whether to constrain the centres of the objective WFs"
slwf_lambda ,R ,"Value of the Lagrange multiplier for constraining the objective WFs"
slwf_centres ,P ,"The centres to which the objective WFs are to be constrained"
Loading

0 comments on commit fe54a7f

Please sign in to comment.