Add file with routines for reading EOS tables

Currently Compose and LALSim format are supported. The file contains an example routine for reading and plotting the EOS read from file, too.
ChunHuangPhy · Nov 8, 2024 · 4656397 · 4656397
1 parent 0c9a0fb
commit 4656397
Showing 1 changed file with 245 additions and 0 deletions.
diff --git a/EOSgenerators/Compose_eos.py b/EOSgenerators/Compose_eos.py
@@ -0,0 +1,245 @@
+"""
+MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+"""
+
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Version: 08/11/2024
+Adapated from parts of the CUTER tool, see https://zenodo.org/records/10781539 
+
+Module that reads tabulated EoS in Compose format or in LALSuite format
+"""
+
+import numpy as np
+#from TOVsolver.unit import g_cm_3, dyn_cm_2
+from pathlib import Path
+import sys
+import matplotlib.pyplot as plt
+from os import listdir
+from os.path import isfile, join
+
+c_si = 2.99792458E+8 	 #/< Velocity of light [m/s]
+mev_si =1.602176634E-13   #/< One MeV [J]
+MeVfm3_to_gcm3 = mev_si/(c_si*c_si)*1e42 # convert energy density from MeV/fm^3 to g/cm^3
+MeVfm3_to_dyncm2 = mev_si*1e46  # convert pressure from MeV/fm^3 to dyne/cm^2
+  # to convert from old Lal units to nuclear units (MeV/fm^3)
+lalpconvert = 755397844024.145 # pressure
+laleconvert = 755407089027.154 # energy density
+
+def read_compose(eosdir="./filesCompose/", eos_prefix="eos",nptsmin = 100): 
+
+    """
+    Routine which reads the data from the original EoS model, Compose format is assumed
+
+    One first check is performed on the data:
+    1. Minimum number of grid points > nptsmin (default is 100)
+
+    Args:
+      eosdir (character string): name of the directory where the EoS files are stored (default is filesCompose)
+      nptsmin (int): required minimum number of grid points
+      eos_prefix (character string): prefix of the eos file names, default is "eos"
+
+
+    Returns:
+       energy density (g/cm^3) : numpy array 
+       pressure (dyne/cm^2): numpy array
+       eosname: character string with name of the EoS stored in the table
+
+    """
+
+    # initialising the return variables
+    ntab = 1
+
+    nB_compose = np.zeros(ntab)
+    p_compose = np.zeros(ntab)
+    eps_compose = np.zeros(ntab)
+    temp = 0.
+
+    # Check if there is a temperature file, and if it is empty
+    if Path(eosdir+eos_prefix+".t").is_file():
+        with open(eosdir+eos_prefix+".t") as file_temp:
+          lines_t = file_temp.readlines()
+        ndimt = int(lines_t[1]) - int(lines_t[0])
+    else : ndimt = 0
+
+    if ndimt == 0 : # No temperature file or empty temperature file
+        with open(eosdir+eos_prefix+".nb") as file_nb:
+            lines_nb = file_nb.readlines()
+        with open(eosdir+eos_prefix+".thermo") as file_thermo:
+            lines_th = file_thermo.readlines()
+    else: # if temperature file not empty, check that the minimum T =0
+          temp = float(lines_t[2]) # lowest temperature entry of the EoS model
+          if(temp > 0.) :
+              sys.exit("\t Nonzero temperature in EoS, aborting...")
+          else:
+              with open(eosdir+eos_prefix+".nb") as file_nb:
+                  lines_nb = file_nb.readlines()
+              with open(eosdir+eos_prefix+".thermo") as file_thermo:
+                  lines_th = file_thermo.readlines()
+
+    ndim = int(lines_nb[1]) - int(lines_nb[0]) + 1
+    if(ndim <=nptsmin):
+          print("\t EoS table with",ndim,"lines is not sufficient, need at least ",nptsmin)
+          sys.exit()
+
+
+
+    nB_compose = np.zeros(ndim)
+    for i in range(ndim):
+          nB_compose[i] = float(lines_nb[i+2])
+
+    p_compose = np.zeros(ndim)
+    eps_compose = np.zeros(ndim)
+
+
+    # Reading the thermo file
+    tmp = lines_th[0].split()
+    m_n = float(tmp[0])
+    m_p = float(tmp[1])
+    print("\t Nucleon masses used within the CompOSE tables :\t m_n = %.5f MeV and m_p = %.5f MeV"%(m_n, m_p))
+
+    for i in range(ndim):
+          tmp = lines_th[i+1].split()
+          p_compose[i]=float(tmp[3])*nB_compose[i]  # pressure
+          eps_compose[i]=(float(tmp[9])+ 1.0)*m_n*nB_compose[i]  # energy density
+
+    eosname = read_README(eosdir)
+    eps_gcm3 = eps_compose*MeVfm3_to_gcm3
+    p_dyncm2 = p_compose*MeVfm3_to_dyncm2
+
+    return eps_gcm3,p_dyncm2,eosname
+
+
+
+def read_Lal(filename,eosdir = "./filesLaL/"):
+    """
+    Read the equation of state file in the LAL format, 
+    a number of tables is available at 
+    https://git.ligo.org/lscsoft/lalsuite/-/tree/master/lalsimulation/lib
+
+    Args:
+      eosdir (character string): name of the directory where the EoS files are stored (default is filesCompose)
+      filename: name of the LAL format equation of state file with extension
+    Returns:
+       energy density (g/cm^3) : numpy array 
+       pressure (dyne/cm^2): numpy array
+       eosname: character string with name of the EoS stored in the table
+
+    """
+    print("\n \t \t Reading the input table...")
+    with open(eosdir+filename) as f:
+        line = f.readline()
+    ncolumns = len(line.split())
+    if ncolumns == 2: # old Lal format
+        ori_p,ori_eps = np.loadtxt(eosdir+filename,unpack=True)
+        ori_p = ori_p*lalpconvert*MeVfm3_to_dyncm2
+        ori_eps = ori_eps*laleconvert*MeVfm3_to_gcm3
+    else:    # new Lal format
+        ori_nb, ori_eps, ori_p, ori_mub, ori_mue, ori_yemu = np.loadtxt(eosdir+filename,usecols=(1,2,3,4,5,7), unpack =True, skiprows=8)
+    # nb[1/fm^3], eps[g/cm^3], P[dyn/cm^2], mu_B [MeV] mu_e [MeV]
+
+    print("\t \t ... done.")
+
+    # Define the list of strings that need to be replaced to get the name
+    # of the EoS from the filename
+    strings = ["LALSimNeutronStar",".dat"]
+    eosname = filename
+    for string in strings:
+        eosname = eosname.replace(string,"")
+
+
+    return ori_eps,ori_p,eosname
+
+
+def read_README(eosdir):
+  """
+  Routine to read the information about the EoS model from the README(.txt) file
+
+  Args:
+  eosdir: directory in which the README file is
+
+  Returns:
+  eosname: name of the eos.
+
+  """
+
+  if Path(eosdir+"/README").is_file():
+    file_eos_name = open(eosdir+"/README","r")
+    eosname = file_eos_name.readline()
+  else:
+    if Path(eosdir+"/README.txt").is_file():  
+      file_eos_name = open(eosdir+"/README.txt","r")
+      eosname = file_eos_name.readline()
+    else:
+      print("Warning: could not determine EoS name, README file missing")
+      print("README is in general contained in download of eos.zip from Compose")
+      print("Eosname is then set to default value = core_eos")
+      eosname = "core_eos"
+
+      # Define the list of strings that need to be replaced
+  strings = ['\n', "downloaded from ",'http://','https://','compose.obspm.fr','Original','with','electrons','references','cold NS',':','for','EoS','table','Table','model', 'Eos', 'cold','beta','equilibrated', 'equilibrium','neutron','star','in','star','unified', 'matter', 'NS',' ',')','.',',','crust']
+  for string in strings:
+    eosname = eosname.replace(string,"")
+  eosname = eosname.replace("(","_")
+  eosname = eosname.replace("-","_")
+  return eosname
+
+
+#### main for testing purposes only
+def test_read_eos_tables():
+    e_compose,p_compose,name_compose = read_compose()
+    lalpath = "./filesLaL/"
+
+    lalfiles = [f for f in listdir(lalpath) if isfile(join(lalpath, f))]
+    print("Will read the following files in LaL format:")
+    nlal = len(lalfiles)
+    if nlal > 0:
+        ii = 0
+        print(lalfiles[ii])
+        e_lal,p_lal,name_lal = read_Lal(filename=lalfiles[ii])
+        epslal = [e_lal] 
+        plal = [p_lal] 
+        namelal = [name_lal] 
+        for ii in range(1,nlal):
+            print(lalfiles[ii])
+            e_lal,p_lal,name_lal = read_Lal(filename=lalfiles[ii])
+            epslal.append(e_lal) 
+            plal.append(p_lal)
+            namelal.append(name_lal) 
+    else:
+        print("No file in LAL format found")
+
+    plt.yscale('log')
+    plt.xscale('log')
+
+    plt.plot(e_compose,p_compose,'-',color = 'blue',label=name_compose)
+    for ii in range(nlal):
+        plt.plot(epslal[ii],plal[ii],label=namelal[ii])
+
+    plt.legend()
+    plt.xlabel('energy density (g/cm$^3$)')
+    plt.ylabel('pressure (dyne/cm$^2$)')
+    savename = "testreadeos.pdf"
+    plt.savefig(savename,bbox_inches='tight')
+    plt.show()
+
+    return