Todo List¶
Todo
Global todo list:
examples:
add ex_string, ex_tensor, and ex_eos_had_rmf to the documentation
integ/multip
replace the old inte_exp_sinh and inte_tanh_sinh integrators with integ_double_exp_boost_multip
fix the docs for subdivisions in inte_adapt_cern
check to see if polylog.h classes need new integrators (done, created new polylog_multip)
make a most consistent interface for the multiprecision integrators and code reuse via, e.g. a parent class?
create multiprecision versions of the GSL integrators using the coefficients in the boost headers
part
improve and calibrate fermion_rel_ld and fermion_rel_cdf25
implement fermion_rel_ld in eos_lepton
etc
implement more code reuse in funct_multip_transform
move calc_utf8 and funct_strings classes down in the header file hierarchy so we can include polylogs and other related functions in calc_utf8
acol
document the cyl_bessel functions better
implement find for more types and fix the problem (what is it?) for size_t[]
sync read generic and output
more options for acol kde to-table, including the options to change the upper and lower x limits
Todo
In class acol_manager:
(Future) Fix documentation for value-grid command.
(Future) There is quite a bit of code duplication in comm_autocorr() between the “table” and “other” types. This could be streamlined.
(Future) sum/max/min/output/interp/deriv/integ/deriv2 for hist, hist_2d, and v<c>
(Future) Commands xindex and yindex for table3d.
(Future) Fix fit for table.
(Future) Use swap instead of copy in ‘select’ for table objects.
(Future) Make sure get_input() is used more consistently.
(Future) Make sure preview, output, internal, generic, and create work consistently across all types.
(Future) Stack-like operations (push, pop, swap, stack-list, etc.)?
(Future) Add functionality to ensure that three digit exponents are still handled gracefully (do this by creating a new boolean setting which, if true, always makes three spaces for exponents?)
(Future) Fix insert and insert_full so that it automatically renames columns
(Future) Allow “insert” commands to be restrictive, avoiding extrapolation
(Future) For strings, allow selection of words or substrings
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Todo
Future: In class anneal_mt, here may be a good way to remove the function indirection here to make this class a bit faster.
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Todo
In class auto_format:
Allow user-specified table alignments
switch to columnify::add_spaces() and add more complicated table line specifications
Implement row_max
Future:
Create a replacement for std::flush
Finish automatic table detection
For automatic table detection: allow user to change the number of rows which must have the same number of ‘words’ to verify a table.
Make internal algorithm more efficient.
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Todo
In bessel_K_exp_integ_tl, better testing of accuracy.
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Todo
In bose_einstein_integ_tl, better testing of accuracy.
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Todo
In class boson_rel: Testing not completely finished.
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Todo
In class calc_utf8:
Future: Add more special functions. Add hypot(x,y,z)?
Future: There is some code duplication across the functions, especially with regard to conversion between UTF8 and char32, which could be removed.
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Todo
In class cli: - Future: Warn in run_interactive() when extra parameters are given. - Future: A replace command function, there’s already some code
in cli.cpp for this.
Future: There’s some code duplication between comm_option_run() and run_interactive().
Future: Disallow direct access to ref o2scl::cli::par_list in order to ensure parameter names do not contain whitespace.
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Todo
Future: Create a single column version of add_spaces().
Future: Create a function which accepts delimited strings (e.g. like csv) instead of vector<vector<string>>.
Future: Move the screenify() functionality from misc.h into this class?
Future: It might be better to allow the string table to be specified with iterators.
Future: Consider a function which takes a ref o2scl::table object as input?
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Todo
Future: Copy constructor
Future: Improve the algorithm to ensure that no contour line ends on an internal point. I am not sure the best way to do this, but it could be done recursively just by trying all possible links instead of just using the one that minimizes the distance.
Future: Rewrite the code which adjusts the contour levels to ensure contours don’t go through the data to adjust the internal copy of the data instead? This should be more accurate because we’re perturbing one point instead of perturbing the entire line.
Future: Change nx and ny to size_t?
Future: It would be nice to have a function which creates a set of closed regions to fill which represent the data. However, this likely requires a completely new algorithm, because it’s not easy to simply close the contours already generated by the calc_contours() function. There are, for example, several cases which are difficult to handle, such as filling a region in between several closed contours
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Todo
Future: Make this a subclass of ref o2scl::contour ? (12/12/16 Maybe not, as it is a generic concept which can be computed outside the ref o2scl::contour class.)
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Todo
In class convert_units:
(Future) Add G=1.
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Todo
In deriv_eqi::deriv_vector(): generalize to other values of npoints.
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Todo
Future: Make this a subclass of ref o2scl::contour .
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Todo
This function, eos_had_base::f_number_suscept(), should be overloaded for Skyrme with derivatives
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Todo
This function, eos_had_base::f_inv_number_suscept(), should be overloaded for Skyrme with derivatives
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Todo
In eos_had_ddc::calc_eq_e(): is the thermodynamic identity is satisfied even when the field equations are not solved? Check this.
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Todo
In class eos_had_rmf:
The functions fcomp_fields(), fkprime_fields(), and fesym_fields() are not quite correct if the neutron and proton masses are different. For this reason, they are currently unused by saturation().
The fix_saturation() and calc_cr() functions use mnuc, and should be modified to allow different neutron and proton masses.
Check the formulas in the “Background” section
Make sure that this class properly handles particles for which inc_rest_mass is true/false
The calc_e() function fails to converge at lower densities. See the testing code which has trouble with NL3 and RAPR.
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Todo
In class eos_had_rmf_hyp:
The couplings in the test code match the table but the maximum masses appear much smaller than GM91. I need to check that muons are added correctly, and it might be good to compare with a different reference. This also might be due to a different crust EOS.
The interpretation of the calc_e() function is a bit unclear, so I need to more clearly figure out what that function ought to do. I don’t think it’s really used at the moment.
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Todo
In eos_had_schematic::set_a_from_mstar(): This was computed in schematic_sym.nb, which might be added to the documentation?
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Todo
This function, eos_had_schematic::baryon_suscep() is untested.
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Todo
In class eos_had_skyrme:
Convert W0 to b4 and b4p everywhere
Remove use of mnuc in calparfun()?
Update reference list.
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Todo
This function, eos_had_skyrme::landau_nuclear() needs to be checked.
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Todo
This function, eos_had_skyrme::landau_neutron() needs to be checked.
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Todo
In function eos_had_skyrme::calpar():
Does this work for both ‘a’ and ‘b’ non-zero?
Compare to similar formulas in [Margueron02].
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Todo
In eos_had_skyrme::alt_params_set(): These expressions are not exactly the same as those in [Bender03], so I need to find out why and make this more clear.
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Todo
In class eos_nse_full: I don’t think inc_lept_phot=false works because then all WS cells have infinite size because of no electrons. For the moment, this variable is protected to discourage the user from changing it.
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Todo
In eos_quark_cfl::calc_eq_temp_p(): It surprises me that n3 is not -res[11]. Is there a sign error in the color densities?
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Todo
In eos_quark_cfl::gapped_eigenvalues(): In the code, the equal mass case seems to be commented out. Why?
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Todo
In class eos_quark_njl: better documentation.
future Remove the stored quark pointers if they are unnecessary?
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Todo
In class eos_sn_ls: There are still a few points for which the electron/photon EOS seems to be off, but this may be the result of small inaccuracies from finite-differencing the LS table.
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Todo
In class eos_sn_stos: Add the T=0 and Ye=0 data to this class. Separate tables for these cases have been released, but I don’t think this class can read them yet.
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Todo
In eos_tov_polytrope, document the behavior of the baryon density in the small energy density limit
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Todo
Future: There may be an issue associated with the string manipulations causing errors in the error handler.
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Todo
Future: In fermi_dirac_integ_direct, create a new function allowing arbitrary values of ‘a’ in the equation above.
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Todo
In fermi_dirac_integ_tl, better testing of accuracy.
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Todo
In class fermi_dirac_multip: implement degenerate and nondegenerate expansions.
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Todo
In class fermion_deriv_rel_tl:
Future: The option err_nonconv=false is not really implemented yet.
Future: The ref pair_density() function is a bit slow because it computes the non-derivative thermodynamic quantities twice, and this could be improved.
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Todo
Class fermion_deriv_thermo_tl
Future:
Include explicit zero-temperature calculation, maybe by making this a child of fermion_zerot or by making a new fermion_deriv_zerot? (This is done, see dndmu_zerot())
There is also a closed form for the derivatives of massless fermions with pairs at finite temperature in Constantinou et al. 2014 which could be implemented here.
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Todo
In class fermion_nonrel_tl
Future: Implement ref o2scl::fermion_nonrel_tl::pair_density() and ref o2scl::fermion_nonrel_tl::pair_mu(). [AWS, 1/23/19: it is not entirely clear to me that antiparticles will be useful.]
Future: This could be improved by performing a Chebyshev approximation (for example) to invert the density integral so that we don’t need to use a solver.
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Todo
In class fermion_rel_tl:
Future: The expressions which appear in in the integrand functions density_fun(), etc. could likely be improved, especially in the case where ref o2scl::part::inc_rest_mass is <tt>false</tt>. There should not be a need to check if <tt>ret</tt> is finite.
Future: It appears this class doesn’t compute the uncertainty in the chemical potential or density with calc_density(). This could be fixed.
Future: I’d like to change the lower limit on the entropy integration, but the value in the code at the moment (stored in <tt>ll</tt>) makes bm_part2.cpp worse.
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Todo
In class fermion_thermo_tl:
Future: Create a Chebyshev approximation for inverting the the Fermi functions for massless_calc_density() functions?
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Todo
In function massless_pair_density()
Future: This could be improved by including more terms in the expansions.
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Todo
In function calc_mu_deg()
Future: Make a function like this for dndm, dsdT, etc. for fermion_deriv .
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Todo
In class fit_nonlin:
Allow the user to specify the derivatives
Fix so that the user can specify automatic scaling of the fitting parameters, where the initial guess are used for scaling so that the fitting parameters are near unity.
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Todo
In class gen_test_number, need to test this class somehow.
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Todo
Check implementation of <tt>hist::extend_lhs</tt>.
More testing.
Future: Add a counter which counts the number of calls to update()?
Future: Add conversions back and forth from GSL histograms
Future: Create extend_lhs too?
Future: Would be nice not to have to create a new ref o2scl::search_vec object in ref o2scl::hist::get_bin_index() (make a search_vec data member?)
Future: Consider adding the analogs of the GSL histogram sampling functions (separate class?)
Future: Add a function which computes the bin sizes?
Future: Allow rebinning?
Future: Add histograms of float and integer values
Future: Allow addition and other operations for two histograms.
Future: Make the interpolation functions c const (this is a bit complicated because of ref o2scl::hist::set_reps_auto() ).
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Todo
Future: Create a copy_from_table3d() function.
Future: Write a function to create a 1-d histogram from a 2-d histogram either by selecting one bin in one axis or by marginalizing over one direction.
Future: Note that here, there is a conflict between implementing operator(size_t,size_t) to give matrix indexing of the histogram weights, and operator(double,double) to implement two-dimensional interpolation using the weights and the representatives. Currently neither is implemented, but maybe both should be implemented instead?
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Todo
In class inte_multi, the function integ_err() this class could now be made a child of the class inte in the future.
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Todo
Class inte_qawf_gsl_sin: More documentation and examples for the qawf, qawo and qawc integrators.
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Todo
Future: Convert into fewer loops over the data
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Todo
Future: In class interp_vec, make a version which copies vectors rather than storing pointers might be better and then has copy constructors.
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Todo
Use the mechanism provided by <tt>n_extra</tt> above to remove degenerate points.
Future: This function requires an extra copy from “ders” to “ders2” which could be removed.
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Todo
CLass mcarlo_vegas: Mode = importance only doesn’t give the same answer as GSL yet.
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Todo
Function mcarlo_vegas::vegas_minteg_err():
Should stage be passed by reference?
There was an update between gsl-1.12 and 1.15 which has not been implemented here yet.
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Todo
In class ref mcmc_para_base:
The main loop with the affine-invariant sampling could be
modified with a new inner loop to do many function evaluations for each thread. However, I think this would demand combining the two sequential parallel loops.
There is a little code in mcmc_init() and mcmc_cleanup()
and I should document why that code needs to be there.
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Todo
Class mroot:
Future: Change ntrial to size_t?
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Todo
In class mroot_cern:
Future:
Modify this so it handles functions which return non-zero values.
Move some of the memory allocation out of msolve()
Give the user access to the number of function calls
Rename nier6, nier7, and nier8 to something sensible.
It may be that the o2 native Householder transformations should be used here instead of the inline version given here.
Based on the CERNLIB routines RSNLEQ and DSNLEQ, which was based on [More79] and [More80] and is documented at http://wwwasdoc.web.cern.ch/wwwasdoc/shortwrupsdir/c201/top.html
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Todo
class mroot_hybrids
Future:
Is all the setting of vectors and matrices to zero really necessary? Do they need to be executed even if memory hasn’t been recently allocated?
Convert more ubvectors to vec_t.
Some more of the element-wise vector manipulation could be converted to BLAS routines.
It’s kind of strange that set() sets jac_given to false and set_de() has to reset it to true. Can this be simplified?
Many of these minpack functions could be put in their own “minpack_tools” class, or possibly moved to be linear algebra routines instead.
There are still some numbers in here which the user could have control over, for example, the
nslow2threshold which indicates failure.
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Todo
class mroot_hybrids
Future: Replace this with c dnrm2 from ref cblas_base.h
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Todo
class mroot_hybrids
Future: Replace this function with daxpy?
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Todo
class mroot_hybrids
Future: Replace this function with daxpy?
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Todo
class mroot_hybrids
Future: This function is just right-multiplication, so we could use the O2scl cblas routines instead.
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Todo
In class nstar_rot:
Better documentation is needed everywhere.
Test the resize() function
It appears that KAPPA and KSCALE contant an arbitrary constant, try changing it and see if we get identical results. Try to ensure that the values are consistent between the eos_nstar_rot class and the nstar_rot class.
Variables r_is_gp, p_center, h_center, and others only occur in spherical_star(), integrate(), and make_center(), and can be moved to function parameters or otherwise reorganized.
Directly compare spherical_star() output with tov_solve results
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Todo
In class nucmass_dz_fit: Document each field.
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Todo
In class nucmass_dz_fit_33: Document each field.
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Todo
In nucmass_fit::eval_isospin_beta(): More documentation and compute uncertainty.
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Todo
In class nucmass_frdm:
Fix pairing energy and double vs. int
Document drip_binding_energy(), etc.
Decide on number of fit parameters (10 or 12?) or let the user decide
Document the protected variables
Set the neutron and proton masses and hbarc to Moller et al.’s values
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Todo
In class nucmass_hfb:
Mg40 is present in some tables but not others. Compare hfb14-plain with hfb14-plain_v0. This may be related to the fact that the mass excess of Mg40 differs significantly between the 2003 and 2013 Audi et al. tables?
Update to include hfb17.
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Todo
In class nucmass_ldrop, 12/4/14: This doesn’t gracefully handle negative values of n0 and n1 as then the neutron and proton densities become negative. This needs to be addressed. For now, there is a fix at line 246 in nucmass_ldrop.cpp .
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Todo
In class nucmass_ldrop_skin:
This is based on LPRL, but it’s a little different in Lattimer and Swesty. I should document what the difference is.
The testing could be updated.
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Todo
Class nucmass_sdnp is unfinished.
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Todo
Class nucmass_wlw is unfinished.
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Todo
Future: The form of solve_final_value() is very similar to that of astep_base::astep_full(), but not quite the same. Maybe these functions should be consistent with each other?
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Todo
In class polylog, test with higher accuracy floating point types.
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Todo
In class prob_cond_mdim_gaussian:
This should be a symmetric conditional probability, i.e. f$ P(x|y) = P(y|x) f$. Test this.
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Todo
Future: Give functions for mean, median, mode, variance, etc?
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Todo
Future: The storage required by the mesh is larger than necessary, and could be replaced by a tree-like structure which uses less storage, but that might demand longer lookup times.
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Todo
Future: Make v[] zero-indexed as well.
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Todo
class root
Future:
Maybe consider allowing the user to specify the stream to which ‘verbose’ information is sent.
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Todo
class root
Future: Return early if the bracketing procedure finds a root early?
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Todo
class root_brent_gsl
Future:
There is some duplication in the variables c x_lower,
c x_upper, c a, and c b, which could be removed. Some better variable names would also be helpful. - Create a meaningful enum list for ref o2scl::root_brent_gsl::test_form. - There is code duplication between the test_interval here and in root_toms748.
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Todo
class root_cern
Future:
Double-check this class to make sure it cannot fail while returning 0 for success.
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Todo
class root
Future: Implement the functions solve() and solve_bkt() for derivative solvers.
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Todo
class root_stef
Future:
There’s some extra copying here which can probably be removed.
Compare directly to GSL
This can probably be modified to shorten the step if the function goes out of bounds as in exc_mroot_hybrids.
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Todo
Future: Move the workspaces to classes? Future: Create an example
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Todo
Future: Move memory allocation outside of ref o2scl::smooth_func::operator()() .
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Todo
In function pair_density():
Needs a bit more error checking and more documentation.
Future: Generalize to generic vector types. (Does this require reworking the GSL linear fitting routines? Doesn’t matter now, the GSL linear fitting routines are now reworked.)
Future: Possibly create a new gsl_bspline class which replaces the GSL bspline workspace
Future: Allow user to probe chi squared and the covariance?
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Todo
In class table:
Future: Create a sort_column_names() or a function to arbitrarily rearrange the columns
The present structure, std::map<std::string,col,string_comp> atree and c std::vector<aiter> alist; could be replaced with c std::vector<col> list and c std::map<std::string,int> tree where the map just stores the index of the the column in the list.
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Todo
In table::function_vector(): FIXME: there may be a problem with the OpenMP code if an exception is thrown in the calculator class and there is not a unique error handler for each thread.
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Todo
In class table3d:
Future: Improve interpolation and derivative caching, possibly through non-const versions of the interpolation functions.
Future: Should there be a clear_grid() function separate from clear_data() and clear()?
Future: Allow the user to more clearly probe ‘size_set’ vs. ‘xy_set’? (AWS 07/18: This is apparently resolved.)
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Todo
In class tensor:
Future: Create an operator[] for tensor and not just tensor1?
Future: Could implement arithmetic operators + and - and some different products.
Future: Implement copies to and from vector and matrices
Future: Implement tensor contractions, i.e. tensor = tensor * tensor
Future: Could be interesting to write an iterator for this class.
Future: Try character and string tensors?
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Todo
Class tensor_grid: It is possible for the user to create a tensor_grid object, upcast it to a tensor object, and then use tensor::resize() to resize the tensor, failing to resize the grid. Following this, grid access functions will access random parts of memory or segfault. This can be fixed by ensuring that resize functions are virtual and have a version in tensor_grid which ensure that the grid and tensor data are matched. The problem is that the resize functions are templates, so they cannot be virtual.
Future: Create a swap function for the grid similar to the data swap function in the parent ref o2scl::tensor class?
Future: Only allocate space for grid if it is set.
Future: as with ref o2scl::tensor, generalize to other base data types.
Future: The function ref interp_linear_partial() appears to be a generalization of ref copy_table3d_interp_values_setxy(), so there may be some code duplication between the two that can be avoided.
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Todo
In set_grid_packed(): Define a more generic interface for matrix types
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Todo
In tensor_grid::interp_linear_partial(): Double check and document if the vector “ix_to_interp” needs to be ordered. I’m pretty sure it doesn’t, so long as the ordering in c val and c ix_to_interp are consistent.
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Todo
In class uniform_grid:
Future: Implement operator==, etc?
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Todo
Future: If all of the matrix elements are positive integers and scientific mode is not set, then we can avoid printing the extra spaces.
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Todo
Future: If all of the matrix elements are positive integers and scientific mode is not set, then we can avoid printing the extra spaces.
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Todo
In hfb_sp_load(): Document models 22 through 27.
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Todo
In tensor::index_spec_preprocess():
Future: Improve this to be more intelligent about whitespace and other characters between index specifications. Right now, this function fails if there are, e.g. two spaces between index specs.
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Todo
In tensor::rarrange_and_copy():
Future: Return a scalar if possible as a rank 1 tensor with 1 element.
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Todo
In function rebin_xy(): I’m not sure what the purpose of this function was originally.
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Todo
In function split_string(), the rules surrounding spaces and quotes are not well documented.
Future: Replace with a better algorithm. Should quotes be escaped?
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Todo
In function pair_calibrate()
Future: Create a version where the user specifies log vs. linear instead of autodetecting.
Future: Compare this algorithm to linear_or_log() and document the differences.
(The original entry is located in <breathe>, line 1.)
Todo
(Future) Create an HDF file I/O example
(The original entry is located in /home/awsteiner/wcs/o2scl/doc/o2scl/sphinx/hdf.rst, line 58.)
Todo
Create a 1- and 2-D histogram example.
(The original entry is located in /home/awsteiner/wcs/o2scl/doc/o2scl/sphinx/hist.rst, line 48.)
Todo
Fix the interpolation plot for this example.
(The original entry is located in /home/awsteiner/wcs/o2scl/doc/o2scl/sphinx/interp.rst, line 115.)
Todo
Global todo list:
examples:
add ex_string, ex_tensor, and ex_eos_had_rmf to the documentation
integ/multip
replace the old inte_exp_sinh and inte_tanh_sinh integrators with integ_double_exp_boost_multip
fix the docs for subdivisions in inte_adapt_cern
check to see if polylog.h classes need new integrators (done, created new polylog_multip)
make a most consistent interface for the multiprecision integrators and code reuse via, e.g. a parent class?
create multiprecision versions of the GSL integrators using the coefficients in the boost headers
part
improve and calibrate fermion_rel_ld and fermion_rel_cdf25
implement fermion_rel_ld in eos_lepton
etc
implement more code reuse in funct_multip_transform
move calc_utf8 and funct_strings classes down in the header file hierarchy so we can include polylogs and other related functions in calc_utf8
acol
document the cyl_bessel functions better
implement find for more types and fix the problem (what is it?) for size_t[]
sync read generic and output
more options for acol kde to-table, including the options to change the upper and lower x limits
(The original entry is located in /home/awsteiner/wcs/o2scl/doc/o2scl/sphinx/todos.rst, line 6.)
Todo
In yanic:
Need to fix function names in case where there is no namespace.
Simplify code duplication in parsing: reading global and member functions should be the same
Allow use of numpy.arange for uniform_grid arguments
Document .i format
Make sure data members named ‘del’ are properly renamed without hacking, e.g. with a py_name argument
Make sure negative size_t arguments are rejected in python
(The original entry is located in /home/awsteiner/wcs/o2scl/doc/o2scl/sphinx/yanic.rst, line 231.)