nothing

sbmy_control/analysis/power_spectrum.py

@@ -1,7 +1,7 @@
 import numpy as np
 import os
 
-nfirst_kmodes = 10
+kmin = 1e-1
 kmax = 2e0
 Nk = 50
 AliasingCorr=False
@@ -24,17 +24,12 @@ def crop_field(field, Ncrop):
         field.L2 = field.N2*d2
 
 
-def get_power_spectrum(field, nfirst_kmodes=nfirst_kmodes, kmax=kmax, Nk=Nk, G=None):
+def get_power_spectrum(field, kmin=kmin, kmax=kmax, Nk=Nk, G=None):
     from pysbmy.power import PowerSpectrum
     from pysbmy.fft import FourierGrid
     from pysbmy.correlations import get_autocorrelation
 
     if G is None:
-        default_k_modes = PowerSpectrum(field.L0,field.L1,field.L2,int(field.N0),int(field.N1),int(field.N2),).FourierGrid.k_modes
-        if kmax is None:
-            kmax = default_k_modes[-1]
-        if kmax > default_k_modes[-1]:
-            raise ValueError(f"kmax ({kmax}) is larger than the maximum k mode available in the field ({default_k_modes[-1]}).")
         G = FourierGrid(
             field.L0,
             field.L1,
@@ -42,8 +37,8 @@ def get_power_spectrum(field, nfirst_kmodes=nfirst_kmodes, kmax=kmax, Nk=Nk, G=N
             int(field.N0),
             int(field.N1),
             int(field.N2),
-            k_modes=np.concat([default_k_modes[:nfirst_kmodes],np.logspace(
-                np.log10(default_k_modes[nfirst_kmodes]),
+            k_modes=np.concat([PowerSpectrum(field.L0,field.L1,field.L2,int(field.N0),int(field.N1),int(field.N2),).FourierGrid.k_modes[:10],np.logspace(
+                np.log10(kmin),
                 np.log10(kmax),
                 Nk,
             )]),
@@ -56,18 +51,13 @@ def get_power_spectrum(field, nfirst_kmodes=nfirst_kmodes, kmax=kmax, Nk=Nk, G=N
     return G, k, Pk
 
 
-def get_cross_correlations(field_A, field_B, nfirst_kmodes=nfirst_kmodes, kmax=kmax, Nk=Nk, G=None):
+def get_cross_correlations(field_A, field_B, kmin=kmin, kmax=kmax, Nk=Nk, G=None):
     from pysbmy.power import PowerSpectrum
     from pysbmy.fft import FourierGrid
     from pysbmy.correlations import get_crosscorrelation
 
 
     if G is None:
-        default_k_modes = PowerSpectrum(field_A.L0,field_A.L1,field_A.L2,int(field_A.N0),int(field_A.N1),int(field_A.N2),).FourierGrid.k_modes
-        if kmax is None:
-            kmax = default_k_modes[-1]
-        if kmax > default_k_modes[-1]:
-            raise ValueError(f"kmax ({kmax}) is larger than the maximum k mode available in the field ({default_k_modes[-1]}).")
         G = FourierGrid(
             field_A.L0,
             field_A.L1,
@@ -75,8 +65,8 @@ def get_cross_correlations(field_A, field_B, nfirst_kmodes=nfirst_kmodes, kmax=k
             int(field_A.N0),
             int(field_A.N1),
             int(field_A.N2),
-            k_modes=np.concat([default_k_modes[:nfirst_kmodes],np.logspace(
-                np.log10(default_k_modes[nfirst_kmodes]),
+            k_modes=np.concat([PowerSpectrum(field_A.L0,field_A.L1,field_A.L2,int(field_A.N0),int(field_A.N1),int(field_A.N2),).FourierGrid.k_modes[:10],np.logspace(
+                np.log10(kmin),
                 np.log10(kmax),
                 Nk,
             )]),
@@ -114,7 +104,7 @@ def plot_power_spectra(filenames,
                        yticks = np.linspace(0.9,1.1,11),
                        bound1=0.01,
                        bound2=0.02,
-                       nfirst_kmodes=nfirst_kmodes,
+                       kmin=kmin,
                        kmax=kmax,
                        Nk=Nk,
                        figsize=(8,4),
@@ -149,7 +139,7 @@ def plot_power_spectra(filenames,
                                                   color=colors[i],
                                                   linestyle=linestyles[i],
                                                   marker=markers[i],),
-                                   power_args=dict(nfirst_kmodes=nfirst_kmodes,
+                                   power_args=dict(kmin=kmin,
                                                    kmax=kmax,
                                                    Nk=Nk),
                                     )
@@ -188,7 +178,7 @@ def plot_cross_correlations(filenames_A,
                             yticks = np.linspace(0.99,1.001,12),
                             bound1=0.001,
                             bound2=0.002,
-                            nfirst_kmodes=nfirst_kmodes,
+                            kmin=kmin,
                             kmax=kmax,
                             Nk=Nk,
                             figsize=(8,4),
@@ -227,7 +217,7 @@ def plot_cross_correlations(filenames_A,
                                                        color=colors[i],
                                                        linestyle=linestyles[i],
                                                        marker=markers[i],),
-                                       power_args=dict(nfirst_kmodes=nfirst_kmodes,
+                                       power_args=dict(kmin=kmin,
                                                         kmax=kmax,
                                                         Nk=Nk),
                                         )   
@@ -293,15 +283,8 @@ def console_main():
     parser.add_argument('-yrp', '--ylim_power', type=float, nargs=2, default=[0.9,1.1], help='Y-axis limits.')
     parser.add_argument('-yrc', '--ylim_corr', type=float, nargs=2, default=[0.99,1.001], help='Y-axis limits.')
     parser.add_argument('--crop', type=int, default=None, help='Remove the outter N pixels of the fields.')
-    parser.add_argument('--nfirst_kmodes', type=float, default=10, help='First k modes from all available k modes to be used in the power spectrum before the geomspace part.')
-    parser.add_argument('--kmax', type=float, default=None, help='Maximum k value for the power spectrum geomspace part. If None, it will be set to the maximum k mode available in the field.')
-    parser.add_argument('--Nk', type=int, default=50, help='Number of k values for the power spectrum geomspace part.')
 
     args = parser.parse_args()
-    
-    nfirst_kmodes = args.nfirst_kmodes
-    kmax = args.kmax
-    Nk = args.Nk
 
     if not args.power_spectrum and not args.cross_correlation:
         print('You must choose between power_spectrum and cross_correlation.')
@@ -315,7 +298,7 @@ def console_main():
         from pysbmy.field import read_field
         F_ref = read_field(args.directory+args.reference)
         crop_field(F_ref, args.crop)
-        G, _, Pk_ref = get_power_spectrum(F_ref, nfirst_kmodes=nfirst_kmodes, kmax=kmax, Nk=Nk)
+        G, _, Pk_ref = get_power_spectrum(F_ref, kmin=kmin, kmax=kmax, Nk=Nk)
     else:
         Pk_ref = None
         G = None
@@ -342,7 +325,7 @@ def console_main():
                            yticks = yticks_power,
                            bound1=0.01,
                            bound2=0.02,
-                           nfirst_kmodes=nfirst_kmodes,
+                           kmin=kmin,
                            kmax=kmax,
                            Nk=Nk,
                            ax=axes[0],
@@ -361,7 +344,7 @@ def console_main():
                                 yticks = yticks_corr,
                                 bound1=0.001,
                                 bound2=0.002,
-                                nfirst_kmodes=nfirst_kmodes,
+                                kmin=kmin,
                                 kmax=kmax,
                                 Nk=Nk,
                                 ax=axes[1],
@@ -388,7 +371,7 @@ def console_main():
                                     yticks = yticks_power,
                                      bound1=0.01,
                                      bound2=0.02,
-                                     nfirst_kmodes=nfirst_kmodes,
+                                     kmin=kmin,
                                      kmax=kmax,
                                      Nk=Nk,
                                     Ncrop=args.crop,
@@ -409,7 +392,7 @@ def console_main():
                                         yticks = yticks_corr,
                                           bound1=0.001,
                                           bound2=0.002,
-                                          nfirst_kmodes=nfirst_kmodes,
+                                          kmin=kmin,
                                           kmax=kmax,
                                           Nk=Nk,
                                         Ncrop=args.crop,

sbmy_control/low_level.py

@@ -64,10 +64,14 @@ def stdout_redirector(stream):
     try:
         # Create a temporary file and redirect stdout to it
         tfile = tempfile.TemporaryFile(mode="w+b")
+
         _redirect_stdout(tfile.fileno())
+
         # Yield to caller, then redirect stdout back to the saved fd
         yield
+
         _redirect_stdout(saved_stdout_fd)
+
         # Copy contents of temporary file to the given stream
         tfile.flush()
         tfile.seek(0, io.SEEK_SET)
@@ -237,7 +241,7 @@ def progress_bar_from_logfile(filename:str, desc:str="", verbose:int=1, **kwargs
     from tqdm import tqdm
     from time import sleep
     k=0
-    limit=600
+    limit=6000
     update_interval=0.2
     wait_until_file_exists(filename, verbose=verbose, limit=limit)
     current_operation, total_operations = get_progress_from_logfile(filename)

sbmy_control/monofonic.py

@@ -32,7 +32,7 @@ def main_monofonic(parsed_args):
         print_message("Running monofonic in slurm mode.", 1, "monofonic", verbose=parsed_args.verbose)
         slurm_dict=parse_arguments_slurm(parsed_args)
         main_dict=parse_arguments_main(parsed_args)
-        slurm_script = slurm_dict["scripts"]+f"monofonic_{main_dict['simname']}.sh"
+        slurm_script = slurm_dict["scripts"]+"monofonic.sh"
 
         if not isfile(slurm_script) or parsed_args.force:
             print_message(f"SLURM script {slurm_script} does not exist (or forced). Creating it.", 2, "monofonic", verbose=parsed_args.verbose)

sbmy_control/parameters_card.py

@@ -47,6 +47,15 @@ def register_arguments_card(parser:ArgumentParser):
     parser.add_argument("--OutputFCsDensity", type=str, default=None, help="Output FCs density file.")
     parser.add_argument("--OutputFCsSnapshot", type=str, default=None, help="Output FCs snapshot file.")
     parser.add_argument("--OutputRngStateLPT", type=str, default=None, help="Output RNG state file.")
+    ## Tests with phiBCs and density
+    parser.add_argument("--WriteGravPot", type=bool, default=False, help="Write gravitational potential.")
+    parser.add_argument("--OutputGravitationalPotentialBase", type=str, default=None, help="Output gravitational potential base.")
+    parser.add_argument("--MeshGravPot", type=int, default=None, help="Mesh for gravitational potential.")
+    parser.add_argument("--WriteDensity", type=bool, default=False, help="Write density.")
+    parser.add_argument("--OutputDensityBase", type=str, default=None, help="Output density base.")
+    parser.add_argument("--MeshDensity", type=int, default=None, help="Mesh for density.")
+    parser.add_argument("--LoadPhiBCs", type=bool, default=False, help="Load phiBCs.")
+    parser.add_argument("--InputPhiBCsBase", type=str, default=None, help="Input phiBCs file base.")
     parser.add_argument("--WriteReferenceFrame", type=bool, default=False, help="Write reference frame (COCA).")
     parser.add_argument("--OutputMomentaBase", type=str, default=None, help="Output momenta base (COCA).")
     parser.add_argument("--ReadReferenceFrame", type=bool, default=False, help="Read reference frame (COCA).")
@@ -126,6 +135,16 @@ def parse_arguments_card(parsed_args):
             OutputFCsDensity=parsed_args.OutputFCsDensity,
             OutputFCsSnapshot=parsed_args.OutputFCsSnapshot,
             OutputRngStateLPT=parsed_args.OutputRngStateLPT,
+            ## Tests with phiBCs and density
+            WriteGravPot=parsed_args.WriteGravPot,
+            OutputGravitationalPotentialBase=parsed_args.OutputGravitationalPotentialBase,
+            MeshGravPot=parsed_args.MeshGravPot,
+            WriteDensity=parsed_args.WriteDensity,
+            OutputDensityBase=parsed_args.OutputDensityBase,
+            MeshDensity=parsed_args.MeshDensity,
+            LoadPhiBCs=parsed_args.LoadPhiBCs,
+            InputPhiBCsBase=parsed_args.InputPhiBCsBase,
+            ## Cosmological parameters
             h=cosmo_dict["h"],
             Omega_m=cosmo_dict["Omega_m"],
             Omega_b=cosmo_dict["Omega_b"],
@@ -211,6 +230,17 @@ def parse_arguments_card(parsed_args):
         card_dict["OutputFCsSnapshot"] = main_dict["resultdir"]+"final_particles_"+main_dict["simname"]+".gadget3"
     if card_dict["OutputRngStateLPT"] is None:
         card_dict["OutputRngStateLPT"] = main_dict["workdir"]+"rng_state.h5"
+    ## Tests with phiBCs and density
+    if card_dict["OutputGravitationalPotentialBase"] is None:
+        card_dict["OutputGravitationalPotentialBase"] = main_dict["workdir"]+"gravpot_"+main_dict["simname"]
+    if card_dict["MeshGravPot"] is None:
+        card_dict["MeshGravPot"] = card_dict["N_PM_mesh"]
+    if card_dict["OutputDensityBase"] is None:
+        card_dict["OutputDensityBase"] = main_dict["workdir"]+"density_"+main_dict["simname"]
+    if card_dict["MeshDensity"] is None:
+        card_dict["MeshDensity"] = card_dict["N_PM_mesh"]
+    if card_dict["InputPhiBCsBase"] is None:
+        card_dict["InputPhiBCsBase"] = main_dict["workdir"]+"gravpot_tCOLA"
     if card_dict["OutputMomentaBase"] is None:
         card_dict["OutputMomentaBase"] = main_dict["workdir"]+"momenta_"+main_dict["simname"]+"_"
     if card_dict["InputMomentaBase"] is None:
@@ -333,6 +363,15 @@ def create_parameter_card_dict(
                     OutputFCsDensity:str = 'fcs_density.h5',
                     OutputFCsSnapshot:str = 'fcs_particles.gadget3',
 
+                    ## Tests with phiBCs and density
+                    WriteGravPot:bool = True,
+                    OutputGravitationalPotentialBase:str = 'gravitational_potential.h5',
+                    MeshGravPot:int = 128,
+                    WriteDensity:bool = False,
+                    OutputDensityBase:str = 'density.h5',
+                    MeshDensity:int = 128,
+                    LoadPhiBCs:bool = False,
+                    InputPhiBCsBase:str = 'gravitational_potential.h5',
                     ## COCA parameters
                     WriteReferenceFrame:bool = False,
                     OutputMomentaBase:str = 'momenta_',
@@ -403,6 +442,17 @@ def create_parameter_card_dict(
             OutputLPTPotential1=OutputLPTPotential1,
             OutputLPTPotential2=OutputLPTPotential2,
             OutputTilesBase=OutputTilesBase,
+
+            # Tests with phiBCs and density
+            WriteGravPot=int(WriteGravPot),
+            OutputGravitationalPotentialBase=OutputGravitationalPotentialBase,
+            MeshGravPot=MeshGravPot,
+            WriteDensity=int(WriteDensity),
+            OutputDensityBase=OutputDensityBase,
+            MeshDensity=MeshDensity,
+            LoadPhiBCs=int(LoadPhiBCs),
+            InputPhiBCsBase=InputPhiBCsBase,
+
             h=h,
             Omega_m=Omega_m,
             Omega_b=Omega_b,

sbmy_control/scripts/convert_snapshot_to_density.py

@@ -1,7 +1,9 @@
+from pysbmy.density import get_density_pm_snapshot
+from pysbmy.snapshot import read_snapshot
 import argparse
 
 
-def convert_snapshot_to_density(snapshot_path, output_path, N=None, corner=(0.0, 0.0, 0.0), time=1.0):
+def convert_snapshot_to_density(snapshot_path, output_path, N=None, corner=(0.0, 0.0, 0.0)):
     """
     Convert a snapshot to a density field.
 
@@ -16,9 +18,6 @@ def convert_snapshot_to_density(snapshot_path, output_path, N=None, corner=(0.0,
     corner : tuple of float
         Corner of the box (x, y, z).
     """
-    from pysbmy.density import get_density_pm_snapshot
-    from pysbmy.snapshot import read_snapshot
-
     # Read the snapshot
     print("Reading snapshot...")
     snap = read_snapshot(snapshot_path)
@@ -29,7 +28,6 @@ def convert_snapshot_to_density(snapshot_path, output_path, N=None, corner=(0.0,
     # Calculate density
     print("Calculating density...")
     F = get_density_pm_snapshot(snap, N, N, N, corner[0], corner[1], corner[2])
-    F.time = time  # Set the time for the field
 
     # Write density to file
     print("Writing density...")
@@ -38,7 +36,7 @@ def convert_snapshot_to_density(snapshot_path, output_path, N=None, corner=(0.0,
     print("Done.")
     
 
-def convert_snapshots_to_density(snapshot_base_path, output_path, N=None, corner=(0.0, 0.0, 0.0), time=1.0):
+def convert_snapshots_to_density(snapshot_base_path, output_path, N=None, corner=(0.0, 0.0, 0.0)):
     """
     Convert multiple snapshots to density fields.
 
@@ -53,57 +51,33 @@ def convert_snapshots_to_density(snapshot_base_path, output_path, N=None, corner
     corner : tuple of float
         Corner of the box (x, y, z).
     """
-    from pysbmy.density import get_density_pm, density_to_delta
-    from pysbmy.snapshot import read_snapshot
-    from pysbmy.field import Field
-    import numpy as np
-    
     # Get all snapshot files with path "snapshot_base_path*"
     import glob
-    
     snapshot_files = glob.glob(snapshot_base_path + "*")
     if not snapshot_files:
         raise FileNotFoundError(f"No snapshot files found at {snapshot_base_path}")
     
     A = None
-    L0 = L1 = L2 = None
-    d0 = d1 = d2 = None
+    F = None
     
     for snapshot_path in snapshot_files:
         # Read the snapshot
         print(f"Reading snapshot {snapshot_path}...")
         snap = read_snapshot(snapshot_path)
-        
+
         if N is None:
             N = snap.Np0
-        
-        if L0 is None:
-            # Get the grid parameters from the snapshot
-            L0 = snap.L0
-            L1 = snap.L1
-            L2 = snap.L2
-            d0 = L0 / N
-            d1 = L1 / N
-            d2 = L2 / N
-        else:
-            # Ensure the grid parameters match the first snapshot
-            if not (snap.L0 == L0 and snap.L1 == L1 and snap.L2 == L2):
-                raise ValueError(f"All snapshots must have the same grid parameters. Got {snap.L0}, {snap.L1}, {snap.L2} but expected {L0}, {L1}, {L2}.")
-        
-        if A is None:
-            # Initialize the density field
-            A = np.zeros((N, N, N), dtype=np.float32)
 
         # Calculate density
-        print("Calculating density for this snapshot...")
-        A = get_density_pm(snap.pos, A, d0=d0, d1=d1, d2=d2)
+        print("Calculating density...")
+        F = get_density_pm_snapshot(snap, N, N, N, corner[0], corner[1], corner[2])
+        
+        if A is None:
+            A = F.data
+        else:
+            A += F.data
     
-    # Convert density to delta field
-    print("Converting density to delta field...")
-    A = density_to_delta(A)
-    
-    # Create a Field object
-    F = Field(L0=L0,L1=L1,L2=L2,corner0=corner[0],corner1=corner[1],corner2=corner[2],rank=1,N0=N,N1=N,N2=N,time=time,data=A)
+    F.data = A # Combine densities from all snapshots
     # Write density to file
     print("Writing density...")
     F.write(output_path)

sbmy_control/simbelmyne.py

@@ -16,7 +16,7 @@ def main_simbelmyne(parsed_args):
 
         if isfile(log_file): # Remove the preexisting log file to allow for the progress_bar to be run normally
             from os import remove
-            remove(log_file)
+            oremove(log_file)
 
         command_args = ["simbelmyne", paramfile, log_file]