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Revision Author Date Message Commit Date
cc5ca58 Final final metadata.conf + README.md ID edits I forgot about README. 04 July 2022, 12:48:37 UTC
5a062b5 Final metadata.conf edits (Zenodo ID, commit ID) before resubmission 04 July 2022, 12:05:59 UTC
060608a Minor copyediting This commit does some minor copyediting. The least trivial change is in 2.4.4 clarifying that we replace inv_I values rather than "insert" them. 04 July 2022, 11:42:41 UTC
36f11d4 Update README.md for resource usage This commit updates the README.md estimates of resource usage for the revised version of the paper. The biggest change is that wall clock time for the analysis/ step jumps from about 10 minutes to 2-3 hours. This is due to doing the different averaging layers in inhomog in a consistent way for all resolutions, including 128^3, and due to doing gevolution correctly at 128^3 as claimed (rather than 64^3). The wording is also changed to more consistently match the names of the Maneage commands and directories, and for more consistency between the two components. 01 July 2022, 22:23:14 UTC
5f58b23 Minor: system_resources script patch This commit makes some minor adjustments to a helper script that can optionally help to monitor RAM usage, at least during the calculation stage, and strengthens the warnings that it is not intended for automatic or out-of-the-box use. 01 July 2022, 17:39:17 UTC
362912c Fix Ncroot loop bug in analyse-plot.mk This commit fixes a bug in analyse-plot.mk, in which the list of values to loop through was set to Ncroot_inhomog_list instead of Ncroot_gevolution_list. The looping variable is also given a more descriptive name, Ncroot_letters, to distinguish between letter versions of numbers and digit versions of numbers; this makes the labelling more consistent throughout the related 'make' rules in analyse-plot.mk The md5sums are updated for the two gevolution output .dat files in this commit. 01 July 2022, 16:41:21 UTC
088934e Fix missing Ncroot string in runname This commit hopefully fixes a bug related to the recently introduced changes that generalised to output results for multiple simulation spatial resolutions. The bug seems to have been a missing Ncroot_gevolution string label that indicates the spatial resolution. This bug appears to have been missed in existing installs because earlier files remained in place. 30 June 2022, 22:35:43 UTC
8325570 Enable verification, add accuracy_parameters.dat, and update This commit re-enables the 'yes' parameter for md5sum verification checksums of the analyse-plot.tex macros and the .dat publishable results files; 'accuracy_parameters.dat' is added to the list of verified files; updates of the md5sums are done for several of the files, though not for the 'inhomog' outputs. 26 June 2022, 21:52:43 UTC
e8076d6 Table 2 URL; copyedit; rm obsolete texlive hack In this commit, the URL for a human-and-machine-readable version of Table 2 is added to the Table 2 caption; some copyediting is done of recent changes (e.g. better not break up "CECILL-compatible" for the footnote); and a hack in high-level.mk (which was temporarily needed for texlive) in the 'configure' stage is removed. This commits describes 'emergent' and 'effective' as synonyms. Although it's true that there are minor nuances between them in some contexts, they are effectively ;) the same from a computational (analytical + numerical) point of view. In principle, we could replace one of these two by the other throughout the text, to make things even clearer, although I don't think we have to. For me, 'emergent' tends to imply that a significant volume difference really *does* occur, while 'effective' describes whatever the result is, no matter whether any really 'emerges' or not. 'Synonyms' do not necessarily have exactly identical meanings, and the nuance seems to me to be enough to justify keeping both words. 26 June 2022, 21:44:48 UTC
323846b Clarify resolution effect; export Table 2 This commit splits a sentence in 4.3 in order to better explain why increasing spatial resolution for inhomog leads to less accuracy, via the automatic setting of the initial scale factor. This commit also exports the file .build/analysis/data-to-publish/accuracy_parameters.dat corresponding to Table 2 (with more precision in the case of gevolution: there is 'added value' in the machine-readable table compared to the published table). TODO: this table still needs to be referred to in the caption, and inclusion in the dist-* packages should be checked. 24 June 2022, 13:38:41 UTC
d049c26 Clarification of acronyms, effective/expected models and others This commit introduces minor changes to the text, including the clarification of a confusing distinction between effective and expected models (introduced together with reference/effective model definition now), as well as several other remaining changes responding to the referee's acronym definition request. 24 June 2022, 13:17:52 UTC
3a08d76 Provide starting epochs to explain resolution effect This commit adds LaTeX macros for the initial scale factor for the inhomog runs for all resolutions, since these provide a credible explanation for dependence of the accuracy parameter \epsilon on the resolution. This has not (yet) been checked in --devmode. The text in Section 4.3 has been correspondingly updated. Thanks to the two referees are added in the acknowledgments. 20 June 2022, 16:54:59 UTC
7113085 Further improvements to 2.4.5.2 We didn't quite clearly enough say that there are two things: a projection and a discretisation, where the former constrains the latter. This commit aims to clarify this and further smooth the text. 20 June 2022, 13:13:34 UTC
0066a8f Further improvements (?) to 2.4.5.2 Attempt to improve the flow of the section; added an additional paragraph touching on more complicated cases and their general treatment in numerical relativity codes (before moving onto LATfield2 and gevolution) 20 June 2022, 12:12:55 UTC
0768b21 Proposed compresion of 2.4.5.2 This commit condenses the first three paragraphs of Section 2.4.5.2 "Choice of projection" into a single paragraph, so that the new first paragraph is mostly a general introduction, with only a brief mention of gevolution/LATfield2; while the case of gevolution/LATfield2 is discussed in what is now the second paragraph (essentially the old fourth paragraph). 20 June 2022, 11:22:53 UTC
a83d1e4 Fixes for Table 2 for full run This commit should work for Table 2 values for the full run (without --devmode); it fixes a few minor bugs remaining in the previous commit. 20 June 2022, 01:30:05 UTC
607d5a6 Referee 2 Point 1: resolution: done This commit responds to Referee 2 Point 1 by dropping the reporting on calculational accuracy from 3 to 2 significant figures (tiny changes in reproduce/analysis/make/analyse-plot.mk); and by adding a new section 4.3 in the discussion (shifting the old 4.3 and 4.4 to 4.4 and 4.5, respectively) and adding Table 2. The discussion will look a bit odd if you run this with --devmode, and needs the default (full) mode to obtain the correct values. Testing of this commit has only been done with --devmode. A fix will be made soon if it fails for the full calculation. 20 June 2022, 00:50:36 UTC
9d24dc1 Brief introduction of inhomog in 2.4.4 This commit gives a brief explanation of how inhomog runs in section 2.4.4, so that the reader knows enough for the analytical justification to make sense, prior to getting into the full numerical description later on in 2.5.1. 19 June 2022, 22:42:20 UTC
5eb4081 Small phrasing change in section 4.2 13 June 2022, 12:38:50 UTC
6151074 Extend Section 4.2 to inhomogeneous case This commit rewords paragraph 2 of Section 4.2, since the growing mode *is* likely to be relevant in structure collapse, even if it's not directly relevant to our homogeneous mode test. 13 June 2022, 12:16:02 UTC
ffbc5b1 Minor changes to 2.4.5.2 and App. A (better visibility of 4.2 ref.) 13 June 2022, 11:38:10 UTC
12a1e1b Minor copyedit of 2.4.5.2 on choice of sqrt This commit does a bit of copyediting of commit 200a646, which fixed the paragraph in 2.4.5.2 about the linearisation of the quadratic adopted by gevolution versus the generic solutions of the Hamiltonian constrant - a quadratic equation. 13 June 2022, 10:13:17 UTC
6e5bc21 Copyedit 2.4.5.1; fix minor bug in App A This commit does some minor language changes in 2.4.5.1, and fixes a formula error where we had \Phi instead of \Psi too early in Appendix A. These changes are only to paper.tex - there is no effect on calculations. 10 June 2022, 16:15:15 UTC
200a646 Improvement to the growing/decaying mode discussion (section 2.4.5) This commit introduces (the first iteration of) the improved double solution discussion (growing and decaying modes) in section 2.4.5, allowing the reader to get a basic understanding about it without referring to Appendix A. 10 June 2022, 16:06:18 UTC
01e7e68 Section 2.4.5 cleanup and added explanations This commit cleans up and explains unclear parts of section 2.4.5 (with the exception of "Choice of projection" subsection) to make it clearer for the readers from all backgrounds & allow for easier reading. The end of the section (last 3 paragraphs) is left for another commit, since it overlaps with the task of rewriting and/or expanding the discussion about growing/decaying modes (together with App. A and B) requested by the 1st referee. 30 May 2022, 10:53:10 UTC
fcd1cba Merge commit '1f84ef3' into gevcurvtest 30 May 2022, 09:17:03 UTC
ed324e5 Update checksum for R package called MASS The R-cran server source package MASS_7.3-54.tar.gz no longer matches the MASS_7.3-54.tar.gz package provided originally. The change is trivial: the time stamp in MASS/DESCRIPTION was changed by 50 seconds, from Date/Publication: 2021-05-03 09:03:50 UTC to Date/Publication: 2021-05-03 09:03:00 UTC and correspondingly changed the md5sum values in MASS/MD5. Maneage detected this change, so the Maneage checksum for MASS_7.3-54.tar.gz is updated in this commit, since the change is (obviously) quite safe. 24 May 2022, 22:10:43 UTC
61e87bf Merge branch 'Ncroot_loop' into gevcurvtest This merge commit brings the changes to run Ncroot loops into the main branch (called 'gevcurvtest'). Use the --devmode option (after './project make clean') for a fast, non-production run. 24 May 2022, 09:46:23 UTC
1f84ef3 Fix minor --devmode bug This commit fixes a minor bug in the previous commit for --devmode (the default is now 128^3 instead of 64^3, so the symlinks in the .build/analysis/tex/build/ directory had to be updated). This commit should work with --devmode. 22 May 2022, 15:37:12 UTC
db0d8de Include 128^3 as default resolution This commit uses 128^3 as the default resolution for both inhomog and gevolution, running through 32^3, 64^3 and 128^3 simulations successively. The resulting LaTeX macros are available for usage in the text, for an updated discussion of resolution (not yet provided). The use of --devmode for fast runs for 32^3 only. 22 May 2022, 15:10:31 UTC
67e1a4c Gevolution loop over resolution This commit implements the loop over particle/mesh for gevolution. This should work for both inhomog and gevolution, and for both with or without --devmode. However, the "best" resolution is currently 64, not 128. This will be fixed in a later commit. 22 May 2022, 11:33:04 UTC
cccc17c Introduce --devmode for fast checks This commit introduces the 'devmode' config file 'reproduce/analysis/config/Nbody-sim-params-devmode.conf' and the option --devmode for ./project that uses this configuration file. The aim is to be able to make fast calculations at 32^3 that allow the full chain to run, although the results are not the preferred 128^3 resolution results. For submittable versions, do *not* use the --devmode option. This commit appears to work correctly, either with or without --devmode. 21 May 2022, 18:56:34 UTC
2da5951 Inhomog step of Ncroot loop - multiple values This commit checks that the Ncroot loop for inhomog works for several values listed in Ncroot_inhomog_list. Comment: the writing of LaTeX macros needs some more automation and creative, sustainable solutions. Hardwiring decimal-digit numbers converted to lettered, CamelCased numbers is a short-term workaround, but is already getting messy. The gevolution loop is not yet done. 19 May 2022, 21:45:23 UTC
03a0361 Inhomog step of Ncroot loop This commit appears to correctly do the loop over the 'inhomog' part of the paper; currently it is set to use just one value of Ncroot_inhomog_list (the value 32 is transformed to the character string 'ThirtTwo' using the 'powers_two_macro' that was introduced in 'initialize.mk' in the previous commit). The 'gevolution' part so far only has a minimal intervention to allow full production of the final pdf. 18 May 2022, 20:15:36 UTC
9cd506d Minor copyedits of recent text changes This commit does some minor smoothing of the text of Jusytna's recent changes. See [1] for a useful guide (by A&A) for ways to avoid ambiguous adjectives in astro research papers; however, this doesn't handle the cosmological problem of perturbations/ fluctuations - spatial length scale (small/large) vs amplitude (weak/strong seems better to me than small/large). [1] https://www.aanda.org/for-authors/language-editing/9-measurements-and-their-descriptions 16 May 2022, 08:58:00 UTC
c705157 Referee response: reference vs effective terms (section 2) This commit adds a small change to better clarify the use of the "reference" and "effective" terms for the considered models. 16 May 2022, 07:39:17 UTC
cce5c4a Referee response: explaining the choice of models (EdS and LCDM) 16 May 2022, 07:29:45 UTC
be0e06e Steps towards an Ncroot loop This commit will not fully run. It includes changes that start the process of doing a loop of simulations for different resolutions. This commit is aimed to work for a loop over inhomog resolution values (Ncroot_...), but does not yet work. 15 May 2022, 17:43:56 UTC
58bd000 Use N_croot_gevolution in gevolution particle+mesh resolution Prior to this commit, Ncroot_gevolution was *not* used in the gevolution simulations; the particle and mesh resolution was hardwired to 64^3. This commit aims to match the particle and mesh resolution of gevolution to the value of Ncroot_gevolution. A subtlety of the 'pipefail' option to bash is also corrected in this commit, in analyse-plot.mk . The problem is that the tool "head" stops reading for input after it has read the required amount of lines; if this happens in a pipe, then the program feeding lines to "head" through a pipe no longer has anywhere to feed the lines to. So that program fails. If 'pipefail' is not enabled, then there's no problem, because the failure is irrelevant; if 'pipefail' is enabled, then it detects the failure and stops the script. This commit uses a sed script to replace the "head" commands. 13 May 2022, 12:09:12 UTC
4fc9cd4 Revert local change in Nbody-sim-params.conf This commit reverts to the default setting where USE_HW_THREADS = --use-hwthread-cpus is *disabled* in reproduce/analysis/config/Nbody-sim-params.conf . To prevent a new run after pulling this commit, you can hack the file with touch --date=2020-01-01 reproduce/analysis/config/Nbody-sim-params.conf or something similar. Do 'info touch' for more info about 'touch'. 09 May 2022, 09:08:33 UTC
05f6612 Highlighting postreferee changes; minor copyedit This commit prepares the option --highlight-new (as a slight variant from the default Maneage style) so that './project make --highlight-new' produces a form of the pdf with changes highlighted in a large bold red font. The normal form of the pdf is produced if --highlight-new is not given. 2.5 intro - minor wording changes. 09 May 2022, 08:53:49 UTC
f6bea9d Referee response: change of section 2.4 placement This commit answers one of the issues raised by the referees by introducing the codes (done previously in section 2.4) before the analytical discussion of changes in the code. The introduction is now section 2.3, while the more detailed technical discussion of the insertion of the perturbation in the codes is left in current section 2.5. 09 May 2022, 08:16:53 UTC
53b4464 Minor fix of old Zenodo DOI 10 January 2022, 10:54:11 UTC
a3e3a02 Last changes before re-submission This commit updates the IDs (Zenodo, arXiv, commit ID) to match the latest changes; it also adds small changes to the abstract and introduction sections of the paper. 10 January 2022, 10:34:20 UTC
fac1f7e Fixed email address 10 January 2022, 09:19:20 UTC
5b36a0a Update dist-arXiv and dist-journal rules This commit updates the dist-arXiv and dist-journal rules; and adds the ArXiv ID (and in a few places the missing first Zenodo ID) to README.md. 08 January 2022, 03:21:18 UTC
93e3aef Merge branch 'gevcurvtest' of galaxy:gevcurvtest into gevcurvtest 08 January 2022, 02:31:08 UTC
304362d Update style for resubmission This commit updates the style for a journal that is more likely to consider theoretical cosmology to be within the scope. The table of results had to be broken into subsections (still a single table) because it was too wide for this format. The original 'iopart.cls' has one footnote symbol '\|' which is buggy, and not enough footnotes, so 'iopart_footnotes.cls' removes '\|' and cycles through the symbols a second time. This is a hack which should work if there are no more than 16 footnotes (the documentation in the file was not updated). 08 January 2022, 02:20:17 UTC
a4c9261 Few-cpu machines - USE_HW_THREADS Prior to this commit, the parameter USE_HW_THREADS that can optionally be enabled in 'reproduce/analysis/config/Nbody-sim-params.conf', for running the project on a machine with only 2 cores but 2 threads per core, was not used in the 'mpgrafic' step. This commit enables this option to be effective for the mpgrafic step. 29 December 2021, 23:17:18 UTC
54398b7 Add Zenodo ID, update SWH commit ID This commit adds the Zenodo ID 5806028 and updates the general software heritage (swh) ID in the README.md file (and swh in metadata.conf). 28 December 2021, 12:14:17 UTC
74ff0f2 Hack to fix temporary LaTeX newtx bug The current version of the 'newtx' LaTeX package in CTAN [1] is version 1.7, which has a bug. The README file at CTAN [1] states that version 1.701 corrects the bug, but version 1.701 is not yet provided on the CTAN mirror servers. This commit provides a hack that should only have an effect if the the buggy file 'newtxtext.sty' (with an unclosed 'if' statement) is the same as in version 1.7 . This commit should be reverted once 1.701 or more recent versions that have fixed the bug are distributed by CTAN. [1] https://www.ctan.org/tex-archive/fonts/newtx 27 December 2021, 20:28:58 UTC
0ba4d10 Start finalising metadata This commit provides a tentative Zenodo ID; and softwareheritage IDs for the gevolution patch file. Footnote 10 should be correctly clickable now. 27 December 2021, 12:41:39 UTC
56849c3 Add missing LaTeX file This commit adds 'reproduce/analysis/bash/uncapitalise_De_bbl.sh', which operates on a bbl file instead of a tex file ('uncapitalise_De.sh' is for a tex file). 27 December 2021, 09:26:53 UTC
e90d195 Remove cubical-cell-volume calculations from 2.3.5.1 This commit removes the recently added paragraphs in Section 2.3.5.1 that compared flat to curved cubical cell volumes, since LATfield2/gevolution do not literally calculate the 3-volumes of cells, and instead perform more advanced flat-space averaging methods. This roughly reverts the section to its state in commit ab9e5fd, but makes several other changes aimed to improve the accuracy. 25 December 2021, 16:30:40 UTC
4306076 S^2 can be tiled by isometric squares This commit fixes an error in 2.3.5.1: S^2 *can* be tiled exactly by isometric squares, but the mesh is based on a single cube; three squares joining at a vertex (one of eight) gives a non-Cartesian mesh. 24 December 2021, 19:37:27 UTC
d0b99bb Finalise pre-submission scripts This commit fixes a few typos and updates the scripts for Zenodo/ArXiv/MNRAS submission. The following *should* work now: ./project make git-bundle ./project make git-snapshot ./project make dist-arXiv ./project make dist-journal ./project make dist-software # HUGE ./project make && mv -v gevcurvtest.pdf gevcurvtest-$(git describe --always --long --dirty).pdf A full run should be done to get the new commit label into the metadata of the *.dat files in .build/analysis/data-to-publish/ . These files will be labelled with a commit ID that is at least one commit behind the submittable commit. 23 December 2021, 18:56:40 UTC
b73f973 Clarifications following chat with Julian This commit makes changes mostly to Section 2.3.5.1 following a 4-hour text chat among Julian, Justyna and I. We switch to \gamma_{ij} for the components of the spatial part of the metric (we could define this to be comoving, but since this is just an illustrative argument, that would seem to be an unnecessary complication). This commit also switches to \mathbb for the style of H, E, S, T, following the common trend in the cosmic topology literature. Errors in (15) are fixed in this commit (thanks Julian :)). 23 December 2021, 01:04:55 UTC
5217219 Further minor tweaks of 2.3.5.1 This commit makes a few more minor tweaks of 2.3.5.1; and in 2.3.5.2 improves the notation of (23) + (24) to avoid literally stating that we have a changing constant. 20 December 2021, 10:16:21 UTC
37d58ea Changes to wording of section 2.3.5.1 Wording of section 2.3.5.1 has been changed to put emphasis that the problem we discuss may be inherent to all numerical relativity codes, not gevolution and LATfield2 alone (as was the intention from the start) 20 December 2021, 09:51:18 UTC
ab9e5fd Fine hone recent changes This commit makes some clarifications to several of the more recent changes to the text, to further improve clarity, in relation to discretisation and projection at the mesh cell level and the keyword "resolution", and the word "mode". 14 December 2021, 11:50:56 UTC
a3dbde9 Restore modes but clarify; other fixes This commit restores the 'mode' terminology, since the Raychaudhuri equation *is* a second order differential equation. However, it also clarifies a few things that are easy to check regarding the different solutions' properties, and points out that the flat growing mode solutions quite likely correspond to \Phi\ne\Psi. The algebra is left to the reader and future work. A few typos are fixed; Section 2.3.5.1 is adjusted a little, attempting to further clarify the text, although it's getting rather long. The Conclusions are updated to match the updated discussion about the decaying/growing modes. 13 December 2021, 17:06:55 UTC
282d0d6 Fix: chi not xi This commit fixes chi: = \Phi - \Psi. 11 December 2021, 02:07:38 UTC
c989e98 More changes thanks to Julian This commit aims to respond to Julian's recent analysis of commit 653ed9c. 1. Section 2.3.5.1 is corrected to clarify that gevolution aims to be background-free; that small differences in a^r(t) vs a^e(6) would allow the reference model scale factor to not affect the accuracy too much; that the projection involved in discretisation to the mesh is to a flat space that is *not* the reference model, but is nevertheless a flat space; and explicit integrals and averaging are defined to clarify that a pointwise metric is not an averaged per-cell metric and that geometrical projections *are* a fundamental (and approximate) element of the calculation. 2. The word 'mode' is replaced by 'branch' or 'solution' to avoid confusion with the superposition of modes of a second order ODE (or PDE); the fact that the growing solution is not a collapsing universe is clarified; the physical relevance of the growing solution is discussed a little more. Minor: A sign error in a power in Eq (1) is fixed. A misleading statement about \Phi = \Psi is written more carefully. We forgot to add Julian in the acknowledgments - this is fixed! 11 December 2021, 01:22:49 UTC
4c37388 Minor wording changes; clarify source This commit removes 'within' in the abstract, since an accuracy 'within' (inside of) a negative value is more tricky to understand than the usual metaphor of being 'within' a certain (positive) accuracy (maximum absolute deviation); and replaces 'any' by 'each' in Section 2.3.5.1 so that the discussion is valid for individual charts for different coordinate patches, that together form an atlas that could, in principle, be used to prove that the spatial section is a manifold. The string 'exp' is changed to 'expected' in the R plotting scripts and the analyse-plot.mk analysis scripts, to avoid confusion with the exponential function e^x. The checksum for analyse-plot.mk is updated because of the change from 'exp' to 'expected'; the numbers remain identical (check this visually with diff or colordiff). 09 December 2021, 10:55:15 UTC
653ed9c Fix selection of max accuracy deviation This commit fixes the analysis in 'reproduce/analysis/make/analyse-plot.mk' of the 'accuracy' lines for gevolution results. The reverse sort of floating point numbers should only consider the third column -k3,3 (range of columns from the 3rd to the 3rd), and ignore the other columns and spacing details. The checksum is updated. This now appears to be consistent with the graphs. 04 December 2021, 11:16:58 UTC
e747d70 Merge branch 'gevcurvtest' of galaxy_git:gevcurvtest into gevcurvtest 04 December 2021, 10:59:09 UTC
69124a3 Section changes, rewordings, typo and minor calculation fixes This commit finishes the check of the paper text, includes additional subsections to better organise the text and fixes typos. Additional change is made to analyse-plot.mk for gevolution accuracy calculations - the percentages were not calculated correctly from the available data. 04 December 2021, 10:48:41 UTC
6bedd5c Fix checksum for analyse-plot.tex The previous commit generated checksums on a system that had not done a fresh run of the analysis step to use the most recent update of R commands for calculating the accuracy of the gevolution numerical code versus the analytical (cosmdist) expected results. This commit updates the checksum for analyse-plot.tex, which should now match calculations that are properly updated. 03 December 2021, 19:48:34 UTC
107fd86 Re-enable verification; update checksums This commit re-enables the verification of the numerical result tables. These are modified because the definition of \epsilon was changed since the last time verification was enabled; and because a few more values (gevolution accuracy estimates) were added to the LaTeX macro list. 03 December 2021, 14:33:04 UTC
0e5fce7 Add Appendix C for decaying/growing mode proof To counter the concern (Krzysztof Bolejko) that uniform perturbations might not have a growing mode, this commit adds Appendix C with an explicit algebraic/calculus calculation showing that both modes are possible in (at least) the EdS case (and the LCDM case has more complicated a(t) behaviour allowed by the extra parameter, making it more likely that multiple long-term trends are possible). A cross-link in the Discussion section 4.2, second para, is added. 02 December 2021, 14:21:17 UTC
785bd7d Fix missing Max in gevolution results This fixes a missing element in the names of the gevolution accuracy results - used in the abstract - the adjective 'Max', because we use the maximum absolute error. TODO: check that this is correctly described in the text... 02 December 2021, 11:38:16 UTC
7c78a8e First set of abstract improvements, wording changes, typo corrections This commit fixes typos and errors in Latex macros, introduces some wording changes for certain sections and clarifies certain terms or aims for the discussions. The fixes are applied up to (not fully including) section 2.1.5.2 of the paper. 02 December 2021, 11:32:07 UTC
7b10560 Add maxima scripts; remove variable ambiguity This commit adds the two maxima scripts for calculating the 3-Ricci curvature and the Einstein tensor time-time part. These are not (currently) run automatically, and are provided as an extra for convenience of those interested. 'reproduce/analysis/maxima/Poisson_gauge_3R.max' 'reproduce/analysis/maxima/Poisson_gauge_Einstein_4D.max' The quadratic equation is also changed into variables alpha, beta, gamma unused elsewhere, and the confusion introduction of \beta for the shift covector is clarified. 01 December 2021, 14:39:12 UTC
da3b330 Julian objections handled: no growing mode This commit should, it seems to me, respond to all of Julian's very useful and detailed comments. There are changes throughout, clarifying that by linearising, gevolution omits the growing homogeneous modes. In the logical order of method through to results and conclusions, there are especially changes in Appendix A; in 2.1.5.2 significantly updating how we give and discuss the equations justifying our method; in 2.2.2 updating how we implement the method in our scripts; in 4.2 of the discussion saying why it would be nice in the future to allow the growing mode; the Conclusions have been split into intro, inhomog, gevolution, summary; the Abstract has been updated and is now around 247 words (the limit is "around 250"); and 'reproduce/analysis/make/run-simulations.mk' was updated so that the gevolution initial perturbation amplitude is written automatically to the abstract rather than by hand. 29 November 2021, 20:13:48 UTC
93b242f Presentation modifs mostly in Appendix A This commit mostly does some presentation style changes in Appendix A, along with fixing cross-refs to App B. The aim is to look good with \togglefalse{showDetailedDerivations} and to look reasonable with \toggletrue{showDetailedDerivations} (the reader of the detailed version should be less fussy about the style). 29 November 2021, 10:22:41 UTC
4c7124a Finished extrinsic curvature calculation This commit finishes the Appendix A extrinsic curvature calculation (with added detailed derivations) and cleans up the appendix a bit. 29 November 2021, 09:31:41 UTC
8da7f2a Fix minor spacing errors This commit fixes unedited minor merge conflicts that were in the previous commit. The previous commit included some more changes updating our handling of the gevolution case. 29 November 2021, 09:15:17 UTC
c84a2e8 Minor spacing This commit should just make some minor spacing changes in the normally hidden part of Appendix B. 29 November 2021, 09:09:13 UTC
b8f0b7f Further work on extrinsic curvature, cosmetic changes to Appendix B 25 November 2021, 11:10:25 UTC
ac6f5a3 Raychaudhuri appendix done If there are no errors, then this commit finishes off providing the Raychaudhuri equation for our setup, which will be used in the discussion - not for calculations. The current commit has \toggletrue{showDetailedRaychaudhuri} set so that the intermediate lines of calculating the derivative, substituting, and simplifying can be checked by hand; for a submittable version, the toggle should be disabled near the top of paper.tex, i.e. with \togglefalse{showDetailedRaychaudhuri}. Although we currently don't plan to use this, we obviously still want it to be correct. A few equation labels are set in this commit for the various forms of the extrinsic curvature in part A of the Appendix, since these are used in the derivation. 22 November 2021, 13:04:03 UTC
60b2fba Appendix A error fix #3 (I push faster than I think) 22 November 2021, 10:42:15 UTC
92659b9 ...missed a(t) power added to Appendix A... 22 November 2021, 10:16:05 UTC
57675c1 Fixed another error in Appendix A... 22 November 2021, 10:14:19 UTC
23bccdc Further changes to appendix A (K_ij calculation) 22 November 2021, 09:29:00 UTC
d191ee6 Appendix: Hamiltonian some corrections; start Raychaudhuri This commit does a few corrections to the Hamiltonian constraint part of the Appendix; and starts the Raychaudhuri equation part of the Appendix. A few other minor changes in the text are done. 19 November 2021, 00:25:40 UTC
a30ac71 Progress on appendix A 11 November 2021, 11:01:43 UTC
e6eb608 Merge branch 'gevcurvtest' of galaxy_git:gevcurvtest into gevcurvtest 11 November 2021, 09:21:45 UTC
355db95 Fix git diff for line element update This commit fixes the choice of git commits for showing the change in Poisson gauge line element from v1.0 to v1.1 of gevolution, and clarifying that the full tree git repository is needed to see the difference. 25 October 2021, 10:23:45 UTC
1b324f9 Merge branch 'gevcurvtest' of galaxy_git:gevcurvtest into gevcurvtest 21 October 2021, 10:25:14 UTC
5fe3493 Update of 5.1.2.1; Julian's points 3+4 This commit updates the text of section 5.1.2.1 and aims to handle Julian's comments 3 and 4. A re-read is still needed. 21 October 2021, 10:15:43 UTC
39d0957 Merge branch 'gevcurvtest' of galaxy_git:gevcurvtest into gevcurvtest 21 October 2021, 09:06:22 UTC
2dd3383 Tiny comment paper changes for merge reasons 21 October 2021, 09:05:43 UTC
8422725 Notation to clarify 2.0; TODO note on R dependencies This commit adds some algebraic notation into Sect 2.0 to clarify the different scales in our motivation and how these relate to the actual calculation; and adds a TODO note that there may be R dependencies missing that require a repeat of the 'configure' script when building. 21 October 2021, 09:00:27 UTC
73e7f7b Further work on Appendix A 14 October 2021, 08:23:01 UTC
439831c Fix bug detected by pipefail and improve fixes for aarch64 bugs This commit (1) fixes a bug detected by 'set -o pipefail'; (2) speeds up compilation of 'icu' by using -j${numthreads} for parallelisation in the 'make' rule in 'high-level.mk'; (3) fixes compilation bugs for coreutils and gcc in a cleaner way than before by upgrading to coreutils-9.0 and gcc-11.2.0 and removing the '--disable-multiarch' option for compiling gcc. A complete configure + make of this commit is expected to run fully on an aarch64 system, apart from the issue of vampires. A "vampire" is defined here as a job that is in the "R" (running) state, using nearly 95-100% of a cpu, for an extremely long time (hours), without producing any output to its log file, and is immune to being killed by the user or root with 'kill -9'. A reboot and relaunch of the './project configure --existing-conf' command is the only solution currently known for vampires. (1) The 'set -o pipefail' command leads to a correct failure of piping a long set of lines through 'head -n2'. This should fail because the command before 'head' does not succeed in outputting all its lines. See: https://stackoverflow.com/questions/62322597/how-to-use-head-in-a-script-with-pipefail-enabled https://stackoverflow.com/questions/41516177/bash-zcat-head-causes-pipefail This commit uses 'sed' to remove all except for the first two lines, so no failure occurs. A science change is that 'tail -n1' is also used, since otherwise the first line is effectively used instead of the second line. (2) The variable ${numthreads} during the configure cycle is the number given in the '-j' option if it is given to ./project configure, or by default, the number of all available cpus if the host system is sufficiently standard that the number is correctly calculated. (3) Coreutils-8.32 and gcc-10.2.0 have bugs in compilation on aarch64, and the --disable-multiarch option causes a bug, and in general should not be used, if the host system is Debian. This commit should fix these problems by removing the option and upgrading to more recent source packages. For details, see the two bug reports: https://savannah.nongnu.org/bugs/?61026 https://savannah.nongnu.org/bugs/?61240 12 October 2021, 20:39:44 UTC
22b11a7 Merge branch 'gevcurvtest' of galaxy_git:gevcurvtest into gevcurvtest 07 October 2021, 08:13:34 UTC
89f95cd Started on appendix A (work very much in progress) 07 October 2021, 08:10:32 UTC
c2538f5 Merge branch 'gevcurvtest' of galaxy:gevcurvtest into gevcurvtest 04 October 2021, 08:12:05 UTC
39f3230 Changes to Figs 5. and 6. Removed the first point from residuals in Figs 5. and 6. to improve readability; added text in captions explaining the change. Added a command stopping the pipeline in case the R plotting script fails for run-gevolution for easier debugging. 03 October 2021, 15:54:45 UTC
a4f04f4 Merge branch 'maneage' into gevcurvtest This updates gevcurvtest to the current commit 775fc036e0 of upstream Maneage, which includes a fix for interference between a system-level libunwind library and compilation of gcc. https://git.maneage.org/project.git/commit/?id=775fc036e0 01 October 2021, 15:27:02 UTC
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