Merge branch 'logl_dhmc_vs_bilby' into dev

Codes/main.py

@@ -554,7 +554,7 @@ if __name__ == '__main__':
         sampler.dict_of_trajectories = dict(
             H_p_logL_logP=[],
             pmom_trajs=[],
-            qpos=[],
+            qpos_traj=[],
             dlogL=[],
             dlogTrajPi_traj=[],
             lengths=[]
@@ -1147,7 +1147,7 @@ if __name__ == '__main__':
         # an empty file will be saved and the future load will see
         # sampler.samples = [] which will bug the derivations of scales
         # from the covariance matrix
-        if n_traj_already_run == sampler.n_traj_fit:
+        if sampler.n_traj_hmc_tot == sampler.n_traj_fit:
             cut.logger.info(f"Only Phase I and II were asked to be run as n_traj_fit = {sampler.n_traj_fit}. Quitting here.")
             sys.exit()
         cut.logger.info("----------------------------------------------------------------------------")
@@ -1448,7 +1448,7 @@ if __name__ == '__main__':
         if RUN_CONST.plot_traj:
             np.savetxt(sampler.plot_traj_dir + 'H_p_logL_logP.dat', sampler.dict_of_trajectories['H_p_logL_logP'])
             np.savetxt(sampler.plot_traj_dir + 'pmom_trajs.dat', sampler.dict_of_trajectories['pmom_trajs'])
-            np.savetxt(sampler.plot_traj_dir + 'qpos.dat', sampler.dict_of_trajectories['qpos'])
+            np.savetxt(sampler.plot_traj_dir + 'qpos_traj.dat', sampler.dict_of_trajectories['qpos_traj'])
             np.savetxt(sampler.plot_traj_dir + 'dlogL.dat', sampler.dict_of_trajectories['dlogL'])
             np.savetxt(sampler.plot_traj_dir + 'dlogTrajPi_traj.dat', sampler.dict_of_trajectories['dlogTrajPi_traj'])
             np.savetxt(sampler.plot_traj_dir + 'lengths.dat', sampler.dict_of_trajectories['lengths'], fmt='%.0f')

Tests/plot_trajectory.py

@@ -66,7 +66,7 @@ if os.path.isfile(outdir + 'config.ini'):
     config_parser = ConfigParser()
     config_parser.read(config_file_path)
     config_dict = pu.config_parser_to_dict(config_parser)
-    lengthT = config_dict['hmc']['length_num_traj']
+    # lengthT = config_dict['hmc']['length_num_traj']
 else:
     print("ERROR: COULD NOT FIND ANY SORT OF CONFIGURATION FILE")
     sys.exit()
@@ -88,6 +88,7 @@ dlogL_file = outdir_plot_traj + 'dlogL.dat'
 H_p_logL_logP_file = outdir_plot_traj + 'H_p_logL_logP.dat'
 pmom_trajs_file = outdir_plot_traj + 'pmom_trajs.dat'
 dlogTrajPi_trajs_file = outdir_plot_traj + 'dlogTrajPi_traj.dat'
+lengths_file = outdir_plot_traj + 'lengths.dat'
 
 # # Pb with np.loadtxt(): when there is only one index in the file, the resulting array has a shape = (), but size still equal to 1. Reshaping it puts it with shape = (1,) and hence it can be normally manipulated then
 # if search_parameter_indices.size == 1:
@@ -99,6 +100,7 @@ dlogL = np.loadtxt(dlogL_file).T
 H_p_logL_logP = np.loadtxt(H_p_logL_logP_file).T
 pmom_trajs = np.loadtxt(pmom_trajs_file).T
 dlogTrajPi_trajs = np.loadtxt(dlogTrajPi_trajs_file).T
+lengths = np.loadtxt(lengths_file).T
 if os.path.exists(outdir + 'sampler_state/phase1/scales.dat'):
     scale = np.loadtxt(outdir + 'sampler_state/phase1/scales.dat').T
 elif os.path.exists(outdir + 'sampler_state/scales.dat'):
@@ -109,6 +111,7 @@ else:
 # q_pos = pt_fit_traj[search_parameter_indices]
 # dlogL = dlogL_all[search_parameter_indices]
 # import IPython; IPython.embed();
+lengthT = int(lengths[trajectory_index])
 idx_start = trajectory_index * (lengthT + 1)
 idx_end = (trajectory_index +1) * (lengthT + 1)
 pt_fit_traj = pt_fit_traj[:, idx_start: idx_end]

examples/config_files/config_GW170817_IMRPhenomD_NRTidal.ini

@@ -2,13 +2,15 @@
 # Interferometers to run the analysis on.
 ifos = H1,L1,V1
 approximant = IMRPhenomD_NRTidal
-minimum_frequency = 30
+minimum_frequency_ifos = {H1: 30.0, L1: 30.0, V1: 30.0}
+; minimum_frequency = 30
 maximum_frequency = 2048.0
 reference_frequency = 20
 roq = False
 roq_b_matrix_directory = /Users/marcarene/roq/ROQ_data/IMRPhenomPv2/
 # 1: sets the PSDs from official GWTC-1 open PSD data; 2: computes PSDs using Welch methods from gwosc open strain data; 3: uses bilby's analytical pre-stored PSD files.
 psd = 1
+psds_single_file = /Users/marcarene/projects/python/gwhmc/__input_data/GWTC1_PSDs/GWTC1_GW170817_PSDs.dat
 phase_marginalization = True