minor changes

analysis/slices.py

@@ -82,6 +82,19 @@ def plot_imshow_with_reference( data_list,
         for i, data in enumerate(data_list):
             axes[1, i].text(0.5, 0.9, f"Score: {score(data, reference):.2e}", fontsize=10, transform=axes[1, i].transAxes, color='white')
         # plt.tight_layout()
+    else:
+
+        if len(data_list) == 1:
+            data_list = data_list[0]
+            im = axes.imshow(data_list, cmap=cmap, origin='lower', vmin=vmin, vmax=vmax)
+            axes.set_title(titles[0], fontsize=fs_titles)
+            axes.set_xticks(ticks[0])
+            axes.set_yticks(ticks[0])
+            axes.set_xticklabels(tick_labels[0])
+            axes.set_yticklabels(tick_labels[0])
+            axes.set_xlabel('Mpc/h')
+            fig.colorbar(im, ax=axes, orientation='vertical')
+
         else:
             for i, data in enumerate(data_list):
                 im = axes[i].imshow(data, cmap=cmap, origin='lower', vmin=vmin, vmax=vmax)

cosmo_params.py

@@ -19,7 +19,7 @@ def register_arguments_cosmo(parser:ArgumentParser):
     parser.add_argument("--m_nu3", type=float, default=0.0, help="Mass of the third neutrino species.")
     parser.add_argument("--w_0", type=float, default=-1.0, help="Dark energy equation of state parameter.")
     parser.add_argument("--w_a", type=float, default=0.0, help="Dark energy equation of state parameter.")
-    parser.add_argument("--fnl", type=float, default=100.0, help="Local non-Gaussianity parameter.")
+    parser.add_argument("--fnl", type=float, default=0.0, help="Local non-Gaussianity parameter.")
     parser.add_argument("--gnl", type=float, default=0.0, help="Equilateral non-Gaussianity parameter.")
 
 
@@ -84,7 +84,7 @@ cosmo_defaults = {
         "m_nu3": 0.0,
         "w_0": -1.0,
         "w_a": 0.0,
-        "fnl": 100.0,
+        "fnl": 0.0,
         "gnl": 0.0,
         "k_max":10.0, 
         "tau_reio":0.06,

main.py

@@ -136,7 +136,7 @@ def main(parsed_args):
             from parameters_card import parse_arguments_card, main_parameter_card
             from timestepping import main_timestepping
             from ICs import main_ICs
-            from scola import main_scola, main_pre_scola, main_post_scola
+            from scola import main_scola, main_pre_scola, main_post_scola, have_all_tiles
 
             card_dict = main_parameter_card(parsed_args)
 
@@ -177,7 +177,7 @@ def main(parsed_args):
             
             print_message("Running sCOLA.", 1, "control", verbose=parsed_args.verbose)
             main_scola(parsed_args)
-            if parsed_args.execution == "slurm":
+            if parsed_args.execution == "slurm" and not have_all_tiles(parsed_args):
                 from tqdm import tqdm
                 from low_level import progress_bar_from_logfile
                 for b in tqdm(range(1,parsed_args.N_tiles**3+1), desc="sCOLA", unit="box", disable=(parsed_args.verbose==0)):

monofonic.py

@@ -9,6 +9,7 @@ def main_monofonic(parsed_args):
     
     print_starting_module("monofonic", verbose=parsed_args.verbose)
     monofonic_dict=main_parameters_monofonic(parsed_args)
+    # raise SystemExit # Exit the program after writing the config file to avoid running monofonic
 
     if parsed_args.execution == "local":
         print_message("Running monofonic in local mode.", 1, "monofonic", verbose=parsed_args.verbose)

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.")
 
 
 def register_arguments_card_for_ICs(parser:ArgumentParser):
@@ -118,6 +127,16 @@ 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"],
@@ -203,6 +222,17 @@ 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"
     
     return card_dict
 
@@ -321,6 +351,16 @@ 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',
+
                     ## Cosmological parameters
                     h:float = 0.6732,
                     Omega_m:float = 0.302,
@@ -381,6 +421,17 @@ 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,

parameters_monofonic.py

@@ -140,7 +140,6 @@ def main_parameters_monofonic(parsed_args):
         return monofonic_dict
     create_monofonic_config(monofonic_dict["config"], get_config_from_dict(monofonic_dict))
     print_message(f"Configuration file written to {monofonic_dict["config"]}", 2, "monofonic", verbose=parsed_args.verbose)
-    
     return monofonic_dict