Merge pull request #6 from thomasckng/thomas-edit

Sync after Journal Review

README.md

@@ -1,6 +1,6 @@
 Paper repository for _Constraining gravitational wave amplitude birefringence with GWTC-3_ by Ng, Isi, Wong & Farr (2023).
 
-The paper can be reproduced programmatically from this repo using [_showyourwork_](http://show-your.work). Scripts to produce figures and tables can be found in [src/scripts](src/scripts), and data in [zenodo](https://zenodo.org/record/7935107).
+The paper can be reproduced programmatically from this repo using [_showyourwork_](http://show-your.work). Scripts to produce figures and tables can be found in [src/scripts](src/scripts), and data in [Zenodo](https://zenodo.org/record/7935107).
 
 <p align="center">
 <a href="https://github.com/showyourwork/showyourwork">

Snakefile

@@ -27,6 +27,7 @@ rule compute_kappa_constraint_restricted:
         "src/tex/output/improvement_Okounkova.txt",
         "src/tex/output/restricted_absolute_kappa_90.txt",
         "src/tex/output/kappa_Wang.txt",
+        "src/tex/output/kappa_Zhu.txt",
         "src/tex/output/comparison_summary.txt"
     script:
         "src/scripts/kappa_constraint_restricted.py"

showyourwork.yml

@@ -53,11 +53,26 @@ dependencies:
         - src/data/GW191105_143521_GR.json.gz
         - src/data/samples_posterior_birefringence.feather
 
+    src/scripts/posterior_MPV.py:
+        - src/data/samples_posterior_birefringence.feather
+
     src/tex/ms.tex:
         - src/tex/output/mu_median.txt
         - src/tex/output/sigma_median.txt
-        - src/tex/output/restricted_kappa_median.txt
         - src/tex/output/generic_kappa_median.txt
+        - src/tex/output/M_PV_constraint.txt
+        - src/tex/output/restricted_kappa_median.txt
+        - src/tex/output/CL_kappa_0.txt
+        - src/tex/output/restricted_absolute_kappa_68.txt
+        - src/tex/output/improvement_Okounkova.txt
+        - src/tex/output/restricted_absolute_kappa_90.txt
+        - src/tex/output/kappa_Wang.txt
+        - src/tex/output/kappa_Zhu.txt
+        - src/tex/output/comparison_summary.txt
+        - src/tex/output/best_events_kappa.txt
+        - src/tex/output/GW170818_constraint.txt
+        - src/tex/output/GW200129_constraint.txt
+        - src/tex/output/bimodal_events_mass.txt
         - src/tex/bib.bib
 
 datasets:

src/scripts/birefringence.py

@@ -18,7 +18,7 @@
 # frequency array parameters
 df = 0.125
 f_min = 20
-f_max = 2048
+f_max = 2048*16 # using higher frequency to produce smoother TD waveform
 f_ref = 100
 
 # source parameters
@@ -81,7 +81,7 @@
 axs[0].loglog(freq, np.abs(hr_fd), ls=':', c=c2, label=r"R (GR)")
 axs[0].loglog(freq, np.abs(hl_bi_fd), c=c1, label=r"L (BR)")
 axs[0].loglog(freq, np.abs(hr_bi_fd), c=c2, label=r"R (BR)")
-axs[0].set_xlim(f_min+1,f_max-22)
+axs[0].set_xlim(f_min+1,2048-22) # force x_max to the max value for IMRPhenomD
 axs[0].set_ylim(1e-30,1e-20)
 axs[0].legend()
 axs[0].set_ylabel(r"$|\tilde{h}|$")

src/scripts/kappa_constraint_restricted.py

@@ -1,12 +1,13 @@
 import numpy as np
 import pandas as pd
+from bilby.gw.cosmology import get_cosmology
 import scipy
 import paths
 
 # constants
 h = 4.135667696e-15 # eV s
 c = 299792.458 # km/s
-H_0 = 68.3 # km/s/Mpc
+H_0 = get_cosmology().H0.value # km/s/Mpc
 
 result_dict = {}
 result_DataFrame = pd.read_feather(paths.data/"samples_posterior_birefringence.feather")
@@ -49,13 +50,12 @@
 with open(paths.output/"restricted_absolute_kappa_90.txt", "w") as f:
     f.write(f"$|\kappa| < {restricted_absolute_kappa_90:.2f} \\, \\mathrm{{Gpc}}^{{-1}}$")
 
-# Wang's constraint in kappa
+# Constraint comparison
 M_PV_Wang = 1e-22 # GeV
 kappa_Wang = (h*np.pi*H_0/c)*(1e3)*(100)*np.reciprocal(M_PV_Wang*1e9)
 with open(paths.output/"kappa_Wang.txt", "w") as f:
     f.write(f"$|\kappa| \lesssim {kappa_Wang:.2f} \, \mathrm{{Gpc}}^{{-1}}$")
 
-# Constraint comparison
 kappa_Okounkova = 0.74
 M_PV_Okounkova = (h*np.pi*H_0/c)*(1e3)*(100)*np.reciprocal(kappa_Okounkova)/1e9
 
@@ -64,6 +64,8 @@
 
 M_PV_Zhu = 4.1e-22 # GeV
 kappa_Zhu = (h*np.pi*H_0/c)*(1e3)*(100)*np.reciprocal(M_PV_Zhu*1e9)
+with open(paths.output/"kappa_Zhu.txt", "w") as f:
+    f.write(f"$|\kappa| \lesssim {kappa_Zhu:.2f} \, \mathrm{{Gpc}}^{{-1}}$")
 
 with open(paths.output/"M_PV_constraint.txt", "w") as f:
     f.write(rf"$M_{{\rm PV}} \gtrsim {M_PV_this_work/1e-21:.1f} \times 10^{{-21}}\, {{\rm GeV}}$")

src/scripts/posterior_MPV.py

@@ -0,0 +1,41 @@
+import matplotlib.pyplot as plt
+import matplotlib as mpl
+import pandas as pd
+import numpy as np
+import seaborn as sns
+from scipy.stats import gaussian_kde
+from bilby.gw.cosmology import get_cosmology
+import paths
+
+# constants
+h = 4.135667696e-15 # eV s
+c = 299792.458 # km/s
+H_0 = get_cosmology().H0.value # km/s/Mpc
+
+sns.set_theme(palette='colorblind', font_scale=1.2)
+
+plt.rcParams.update({
+    "text.usetex": True,
+    "font.family": "serif",
+    "font.serif": ["Computer Modern Roman"]
+})
+
+result_DataFrame = pd.read_feather(paths.data/"samples_posterior_birefringence.feather")
+events = result_DataFrame['event'].unique()
+
+M_PV_inv = np.linspace(0, 1.5e21, 1000)
+kappa = (h*np.pi*H_0/c)*(1e3)*(100)*(M_PV_inv)/1e9
+
+chosen_events = ['GW190727_060333', 'GW200112_155838', 'GW190513_205428', 'GW190915_235702', 'GW190803_022701', 'GW200311_115853']
+
+kernel_dict = {}
+for event in chosen_events:
+    kernel_dict[event] = gaussian_kde(result_DataFrame[result_DataFrame.event == event]['kappa'])
+    plt.plot(M_PV_inv, kernel_dict[event](kappa)+kernel_dict[event](-kappa), label=event)
+
+plt.legend(fontsize=14)
+plt.xlim(0, 1.5e21)
+plt.ylabel(r'$p\left(M_\mathrm{PV}^{-1}\right)$')
+plt.xlabel(r'$M_\mathrm{PV}^{-1}\, \left(\mathrm{GeV^{-1}}\right)$')
+
+plt.savefig(fname=paths.figures/"posterior_MPV.pdf", bbox_inches="tight", dpi=300)

src/scripts/reweighed_kappa.py

@@ -33,8 +33,9 @@
 norm_alpha = matplotlib.colors.Normalize(vmin=-1E-3, vmax=zscores.max()*1.1)
 for i, (z,line) in enumerate(zip(zscores, g.get_lines()[::-1])):
     line.set_alpha(norm_alpha(z))
-    if i < 3:
+    if zscores.index[i]=='GW170818':
       line.set_label(zscores.index[i].replace('_', r'\_'))
+      line.set_linestyle('--')
     else:
       line.set_label(None)
 g.legend(fontsize=14)

src/tex/bib.bib

@@ -253,6 +253,22 @@ @dataset{GWTC-2.1_dataset
   url          = {https://doi.org/10.5281/zenodo.6513631}
 }
 
+@article{LIGOScientific:2020tif,
+    author = "Abbott, R. and others",
+    collaboration = "LIGO Scientific, Virgo",
+    title = "{Tests of general relativity with binary black holes from the second LIGO-Virgo gravitational-wave transient catalog}",
+    eprint = "2010.14529",
+    archivePrefix = "arXiv",
+    primaryClass = "gr-qc",
+    reportNumber = "LIGO-P2000091",
+    doi = "10.1103/PhysRevD.103.122002",
+    journal = "Phys. Rev. D",
+    volume = "103",
+    number = "12",
+    pages = "122002",
+    year = "2021"
+}
+
 @dataset{GWTC-3_dataset,
   author       = {{LIGO Scientific Collaboration} and {Virgo Collaboration} and {KAGRA Collaboration}},
   title        = {{GWTC-3: Compact Binary Coalescences Observed by 
@@ -809,3 +825,75 @@ @ARTICLE{Yunes2009
       adsnote = {Provided by the SAO/NASA Astrophysics Data System}
 }
 
+@article{Wang:2021gqm,
+    author = "Wang, Yi-Fan and Brown, Stephanie M. and Shao, Lijing and Zhao, Wen",
+    title = "{Tests of gravitational-wave birefringence with the open gravitational-wave catalog}",
+    eprint = "2109.09718",
+    archivePrefix = "arXiv",
+    primaryClass = "astro-ph.HE",
+    doi = "10.1103/PhysRevD.106.084005",
+    journal = "Phys. Rev. D",
+    volume = "106",
+    number = "8",
+    pages = "084005",
+    year = "2022"
+}
+
+@article{Haegel:2022ymk,
+    author = {Haegel, Le\"\i{}la and O'Neal-Ault, Kellie and Bailey, Quentin G. and Tasson, Jay D. and Bloom, Malachy and Shao, Lijing},
+    title = "{Search for anisotropic, birefringent spacetime-symmetry breaking in gravitational wave propagation from GWTC-3}",
+    eprint = "2210.04481",
+    archivePrefix = "arXiv",
+    primaryClass = "gr-qc",
+    doi = "10.1103/PhysRevD.107.064031",
+    journal = "Phys. Rev. D",
+    volume = "107",
+    number = "6",
+    pages = "064031",
+    year = "2023"
+}
+
+@article{Jenks:2023pmk,
+    author = "Jenks, Leah and Choi, Lyla and Lagos, Macarena and Yunes, Nicol\'as",
+    title = "{Parameterized Parity Violation in Gravitational Wave Propagation}",
+    eprint = "2305.10478",
+    archivePrefix = "arXiv",
+    primaryClass = "gr-qc",
+    month = "5",
+    year = "2023"
+}
+
+@article{Chia:2020psj,
+    author = "Chia, Horng Sheng and Edwards, Thomas D. P.",
+    title = "{Searching for General Binary Inspirals with Gravitational Waves}",
+    eprint = "2004.06729",
+    archivePrefix = "arXiv",
+    primaryClass = "astro-ph.HE",
+    doi = "10.1088/1475-7516/2020/11/033",
+    journal = "JCAP",
+    volume = "11",
+    pages = "033",
+    year = "2020"
+}
+
+@unpublished{tgrsel},
+  author = {Magee, R and Isi, Max and Chatziioannou, Katerina and Vitale, Salvatore and Farr, Will and Pratten, Geraint},
+  title  = {Selection biases in tests of general relativity with gravitational waves},
+  year   = {in prep.}
+}
+
+@article{LIGOScientific:2019zcs,
+    author = "Abbott, B. P. and others",
+    collaboration = "LIGO Scientific, Virgo, VIRGO",
+    title = "{A Gravitational-wave Measurement of the Hubble Constant Following the Second Observing Run of Advanced LIGO and Virgo}",
+    eprint = "1908.06060",
+    archivePrefix = "arXiv",
+    primaryClass = "astro-ph.CO",
+    reportNumber = "LIGO-P1900015",
+    doi = "10.3847/1538-4357/abdcb7",
+    journal = "Astrophys. J.",
+    volume = "909",
+    number = "2",
+    pages = "218",
+    year = "2021"
+}