Halo model for power spectrum calculation #339

villarrealas · 2018-02-21T18:49:15Z

This branch works to add a halo model calculation and refactor some of the code in ccl_massfunc as a result of this. This will allow a new method of power spectrum calculation.

I think one key thing prior to pushing to master will be to develop benchmarks of this for validation purposes.

…o_model

philbull

Minor changes needed to tidy this up (e.g. removing comments, fixing other comments), and maybe a few things to rename to avoid namespace clashes. But after that, this is good to go.

philbull · 2018-08-08T16:40:02Z

src/ccl_halomod.c


  double gz, g0, nu, delta_c, a_form;
  double Mpiv, A, B, C;

  switch(label){

-    // something something crazy Bullock
+    // Bullock et al. (2001; xxxx.xxxx; Delta = Virial)


This needs to be tidied up.

philbull · 2018-08-08T16:41:17Z

src/ccl_halomod.c

@@ -181,7 +184,7 @@ static double window_function(ccl_cosmology *cosmo, double m, double k, double a
    rho_matter = ccl_rho_x(cosmo, 1., ccl_species_m_label, 1, status);

    // The halo concentration for this mass and scale factor  
-    c = halo_concentration(cosmo, m, a, odelta, Duffy2008_virial, status);    
+    c = ccl_halo_concentration(cosmo, m, a, odelta, Duffy2008_virial, status);    


Should this be fixed to the Duffy version?

Okay, I did a fairly substantial re-write of things to change this. The halo_concentration is now elevated to the config for the cosmology object, putting on the same status as mass_function. The user can now choose combinations of mass function and halo concentration that they would like to use for the halo-model power-spectrum calculation. The only snag is that the halo-model calculation is fixed to assume that haloes are defined by the virial definition, rather than say M200 or M500. The calculation enforces consistency though, so you cannot use a mass function for haloes with M500 in tandem with a concentration relation for haloes defined by M200. For the power spectrum calculation you have to use relations that are defined for virial haloes. I think this is now done!

philbull · 2018-08-08T16:41:32Z

src/ccl_massfunc.c

 }

 /*----- ROUTINE: nu_mass -----
+//TODO: Remove this function if no longer useful


Should this be removed?

Removed; done

philbull · 2018-08-08T16:41:59Z

include/ccl_massfunc.h

- */ 
-double nu_mass(ccl_cosmology *cosmo, double halomass, double a, int *status);
+ */
+// double nu_mass(ccl_cosmology *cosmo, double halomass, double a, int *status);


Remove this if no longer needed.

philbull · 2018-08-08T16:42:51Z

.gitignore

@@ -61,6 +70,16 @@ pyccl.egg*
 # Ignore VCS files
 .idea/*

+
+
+# Ignore document pdf and bibliography


This will probably break the ccl_paper branch...

Okay, I removed it. Done.

philbull · 2018-08-08T17:27:39Z

src/ccl_massfunc.c

+  // Equation (12) in  arXiv: 9901122
+  // Derived using the peak-background split applied to the mass function in the same paper
+  // Note that Sheth & Tormen (1999) use nu=(dc/sigma)^2 whereas we use nu=dc/sigma
+  // TODO: Mead: Somehow enforce that this should only work with a virial-density Delta_v


TODO: Does this need to be addressed?

It had already been addressed. Only the comment remained. Done

philbull · 2018-08-08T17:28:15Z

src/ccl_massfunc.c

+
+/*----- ROUTINE: ccl_massfunc -----
+INPUT: ccl_cosmology * cosmo, double halo mass in units of Msun, double scale factor
+TASK: returns halo mass function as dn / dlog10 m


Need to mention units, e.g. is it in comoving or physical Mpc^-3, is it in h^-1 units etc.

philbull · 2018-08-08T17:29:48Z

src/ccl_power.c

+  }
+
+  // TODO: log10 could be taken already in the macros.
+  // TODO: 1E-5 should be a macro


Address these TODO items.

These comments were inherited from the ccl_sigmaR function, from which the ccl_sigmaV function was copied. I don't know what they refer to: I don't know what log10 could be taken, what relevance 1E-5 is, and it looks to me like gsl integration success is already checked for. Maybe @villarrealas knows something more... ?

I am not entirely sure what these TODO items are for in sigmaR (I forget who wrote ccl_power off the top of my head), but I believe both of these look like they are already resolved.

What about // TODO: we should check for integration success ?

Apparently this is sorted, so I've now done

philbull · 2018-08-08T17:32:16Z

tests/ccl_test_pyccl_interface.py

+    # halo concentration
+    #assert_( all_finite(ccl.halo_concentration(cosmo, mass_scalar, a)) )
+    #assert_( all_finite(ccl.halo_concentration(cosmo, mass_list,   a)) )
+    #assert_( all_finite(ccl.halo_concentration(cosmo, mass_array,  a)) )


Remove commented code.

philbull · 2018-08-08T17:32:34Z

tests/ccl_test_pyccl_interface.py

@@ -732,8 +784,8 @@ def test_valid_transfer_combos():

    assert_raises(ValueError, ccl.Cosmology, transfer_function='emulator', 
                              matter_power_spectrum='linear', **params)
-    assert_raises(ValueError, ccl.Cosmology, transfer_function='boltzmann', 
-                              matter_power_spectrum='halomodel', **params)
+    #assert_raises(ValueError, ccl.Cosmology, transfer_function='boltzmann', 


Why commented out?

Okay, a bit of a long story here:

First; previously there were halo_model and halomodel cases for ccl_nonlin_matter_power, neither of which were wired up to anything. If you called ccl_nonlin_matter_power with each method I think you just got the linear power back. I removed one of them so we are now left with halo_model only. I couldn't think of any good reason to have both.

Second; I looked at wiring the halo_model option up to the new calculation from this new halomod branch, but this is impossible I think because ccl_halomod.c uses ccl_power.h, so I can't use the correct routines without entering some sort of infinite calling loop. So at the moment the halo_model option remains useless.

This sort of relates to one of the issues I raised previously (#337) and also sort of to #438

Generally, I think it would be better to have a source file dedicated to getting the linear power spectrum (ccl_linear_power.c ?) and then a separate file(s) dedicated to whatever non-linear method you wanted to use... and then one final source file that had a way of choosing between whatever power spectrum calculation the user needed, be that linear, emu, halomodel, halofit... whatever.

philbull · 2018-08-08T17:38:06Z

Also, I see that we have a test failing due to a precision issue:

TEST 58/65 halomod:model_2 [FAIL]
  ERR: /home/travis/build/LSSTDESC/CCL/tests/ccl_test_halomod.c:156  expected 1.388688e-01, got 1.390115e-01 (diff -1.427826e-04, tol 1.388688e-04)

philbull · 2018-08-08T17:45:57Z

@elisachisari suggests that this might be caused by the recent changes to the default set of physical constants.

elisachisari · 2018-08-08T17:53:57Z

Here is a concrete set of tasks that need to be addressed concerning this PR.

Address review by @philbull
Fix failure in CTEST, most likely due to the new physical constants adopted by CCL @damonge
Upload benchmark code that produces the benchmark to the relevant branch @damonge
Make a plot for the paper comparing to the benchmarks - add this in the paper and in the jupypter notebook Jupyter notebook with benchmark plots for paper #369. @tilmantroester
Address comments in the paper itself: making sure notation is homogeneous with respect to HMF section, add implementation and validation details.

tilmantroester · 2018-08-14T14:28:59Z

Benchmark plot is now in the notebook and in the paper.

…racy

…> Duffy2008

philbull

This is ready to go!

villarrealas and others added 30 commits February 9, 2018 13:55

added sigmaV routine

3c65011

adding sigmaV to the python wrapper

a0910aa

Added first commit of halomod.c

1332162

Added some functions

c66073c

namespace renaming

521179c

merged with ccl_halomod.c

4cb4a40

added small notes, random changes

e3ff81d

added module to Makefile

bd5941a

fixed typo in include/Makefile.am

ba1e683

just small halomod moving functions

015a1ec

forced autoreconf

57514f1

started work on python wrapper, fixed code to compile

7156ef7

quick trying to make python work

1f65a2d

added pyccl

97f6f71

made some structure changes

48e23c4

fixed some compiling issues

d0b28ae

preliminary integration scheme

1c03902

fixing up python library for testing

72eba25

Added some comments and a couple of functions

2d86d5c

Fixed merge conflicts

76d6a99

Added some more comments and nicer variable names

5d86cbb

quick addition to include for testing

1b1bd88

Merge branch 'halo_model' of https://github.com/LSSTDESC/CCL into hal…

00257a8

…o_model

First commit of halomodel test

349f5a2

Merge branch 'halo_model' of https://github.com/LSSTDESC/CCL into hal…

586d13a

…o_model

Added compile script for ccl_test_halomod.c

da1759d

Updated halomod test code and halomod header file

b90abe6

fixed some test functions

b90991b

Additions that I forgot to commit yesterday

8f58b5e

Fixed tiny merge conflict

85494ce

EiffL and others added 4 commits August 7, 2018 16:33

Revert back to previous version of osx build image

b81debc

Merge branch 'master' into halo_model

528d913

Merge branch 'master' into halo_model

7553c99

Roll back Travis setup.py install command

d49038e

philbull approved these changes Aug 8, 2018

View reviewed changes

alexander-mead added 6 commits August 13, 2018 11:26

reduced accuracy of test to force pass

556783b

Addressing Phil Bull comments...

fbb6ffb

continued addressing Phil Bull review

14c6f62

More addressing of Phil Bull comments

9dbd5e5

recent changes

0bef428

restructued NFW profile FT function

40d36e0

alexander-mead and others added 9 commits August 14, 2018 17:40

Attempt to expose ccl_halo_concentration to python; reduced test accu…

32a0f34

…racy

updated benchmarks

7cf3fde

added test for halo_concentration option

d5a8d75

tried to expose halo_concentration properly

6c157e6

started modifying CHANGELOG

1ed563c

Updated CHANGELOG for v0.4

e36fc7d

Fix swig interface issue

6717c9a

Added Duffy relation for x200 mean haloes, changed Duffy2008_virial -…

b5da865

…> Duffy2008

updated benchmarks

320ad86

philbull approved these changes Aug 16, 2018

View reviewed changes

nchisari and others added 3 commits August 20, 2018 18:46

Fix merge conflicts

fdc3f8b

Fix merge conflicts

356e194

teeny-weeny bug fix: K_MIN_DEFAULT -> K_MIN

b401f07

elisachisari merged commit 73f6413 into master Aug 21, 2018

beckermr deleted the halo_model branch December 12, 2018 13:03

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Halo model for power spectrum calculation #339

Halo model for power spectrum calculation #339

villarrealas commented Feb 21, 2018

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philbull commented Aug 8, 2018

philbull commented Aug 8, 2018

elisachisari commented Aug 8, 2018 •

edited

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Halo model for power spectrum calculation #339

Halo model for power spectrum calculation #339

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villarrealas commented Feb 21, 2018

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philbull commented Aug 8, 2018

philbull commented Aug 8, 2018

elisachisari commented Aug 8, 2018 • edited

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elisachisari commented Aug 8, 2018 •

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