Update run_pm_dmo_NFW_fixed_timestep.md

run_pm_dmo_NFW_fixed_timestep.md

@@ -16,86 +16,80 @@ from hotwheels_integrate import *
 from hotwheels_io import *
 
 #
-# step 1: config of components
-#
-# at this stage we do not allocate any resource, we just
-# pass the right config parameters to the constructors
-# in order to compile the underlying C libraries.
+# Step 1: Configure components
+# This stage configures components without allocating resources.
+# Configurations are passed to constructors to compile the underlying C libraries.
 #
 
-#call MPI_Init()
-mpi = hwc.MPI().init()
-#configure my malloc with 2GB
-mym = MyMalloc(alloc_bytes=int(2e9))
-#configure the default particle SoA with 1e5 particles
-p = SoA(maxpart=int(1e5), mem=mym)
-#add the particle soa to the multi-type particle SoAs
-soas = SoAs(p, mem=mym)
-# configure the timestep class to go from 0 to 1 Gyr
-# note: G=43007.1 in units of length=kpc, velocity=km/s, mass = 1e10Msun
-# if G=43007.1, masses are in 1e10Msun/h, and radii are in ckpc/h, then this
-# constant converts from Gyr to internal units. Not much to comment about it
+mpi = hwc.MPI().init() # Initialize MPI
+mym = MyMalloc(alloc_bytes=int(2e9)) # Configure memory allocator with 2GB
+p = SoA(maxpart=int(1e5), mem=mym) # Configure P to hold 1e5 particles
+soas = SoAs(p, mem=mym) # Add P to a multi-type SoA container
+# Set up a fixed time-step integrator from 0 to 1 Gyr
+# Conversion factor for Gyr to internal units
 gyr_to_cu = 3.086e+16 / (1e9 * 3600 * 24 * 365)
-ts = integrate.FixedTimeStep(soas, G=43007.1, t_from=0., t_to=1. * gyr_to_cu, MPI=mpi)
-ic = NFWIC(rs=100., rho0=1e-6, rs_factor=10.) #init the build of a NFW profile with R<10rs, (note that mass is in units of 1e10Msun)
-# init a refined PM grids with 7 stacked PLACEHIRESREGION at smaller and smaller scales
-# note that PM needs the time-step integrator class TS to attach its DriftTable and kick callbacks
-pm = SuperHiResPM(soas=soas, mem=mym, TS=ts, MPI=mpi, pmgrid=128, grids=8, dt_displacement_factor=0.25)
-#configure to compile all modules in the current folder
-build = make.Build('./', mpi, pm, ts, mym, *soas.values())
-#configure generate SoA headers
-headers = OnTheFly(build.build_name, *build.components, generate_user_c=True)
-
-#
-# step 2: build SoAs headers and compile C files
-#
-
-
-if mpi.rank == 0: #master rank compile and build headers
+ts = integrate.FixedTimeStep(
+    soas, 
+    G=43007.1,  # Gravitational constant in specific units
+    t_from=0., 
+    t_to=1. * gyr_to_cu, 
+    MPI=mpi
+)
+# Initialize a NFW profile with scale radius `rs=100` and density `rho0=1e-6`
+ic = NFWIC(rs=100., rho0=1e-6, rs_factor=10.)
+# Configure a refined PM grid with 7 stacked high-resolution regions
+pm = SuperHiResPM( #wrapper to the PM C library
+    soas=soas, 
+    mem=mym, 
+    TS=ts, #will use it to attach gravkick callback
+    MPI=mpi, 
+    pmgrid=128, 
+    grids=8, # number of grids to instantiate
+    dt_displacement_factor=0.25 #factor for DtDisplacement
+)
+build = make.Build('./', mpi, pm, ts, mym, *soas.values()) # Compile all modules in the current directory
+headers = OnTheFly(build.build_name, *build.components, generate_user_c=True) # Generate SoA headers
+
+if mpi.rank == 0:  # Master rank handles compilation
     headers.write()
     build.compile()
 
-
 #
-# step 3: allocate resources (e.g. MPI, MyMalloc, and allocations within it)
+# Step 2: Allocate resources
 #
 
-with (utils.Panic(Build=build) as panic, #attach panic handler to C calls
-      utils.Timer(Build=build) as timer, #attach timer handler to C calls
-      build.enter(debug=mpi.rank == 0), #parse the compiled object files
-      mpi.enter(pm), #attach MPI init info to PM module
-      mym.enter(*build.components), #actually allocates the 2GB of ram
-      p, #allocate the particle data stracture in the MyMalloc area
-      ic.enter(p, mpi.ranks, p.get_maxpart()), #sample the NFW in the particle SoA `p` fields
-      pm, #call pm_init() the PM regions
-      ts #compute DriftTables if necessary
+with (
+    utils.Panic(Build=build) as panic,  # Attach panic handler
+    utils.Timer(Build=build) as timer,  # Attach timer handler
+    build.enter(debug=mpi.rank == 0),  # Parse compiled objects
+    mpi.enter(pm),  # Initialize MPI in the PM module
+    mym.enter(*build.components),  # Allocate 2GB memory
+    p,  # Allocate particle data structure in MyMalloc
+    ic.enter(p, mpi.ranks, p.get_maxpart()),  # Sample NFW profile
+    pm,  # Initialize PM and compute first accelerations
+    ts  # Compute DriftTables if needed
 ):
 
-        pm.compute_accelerations() #first acc computation
-
-
     #
-        # step 4: the actual run
+    # Step 3: Main simulation loop
     #
 
+    while ts.time < ts.time_end:
+        ts.find_timesteps()  # Determine timesteps
+        ts.do_first_halfstep_kick()  # First kick (includes drift/kick callbacks)
+        ts.drift()  # Update particle positions
+        pm.compute_accelerations()  # Recompute accelerations
+        ts.do_second_halfstep_kick()  # Second kick
 
-        while ts.time < ts.time_end: #main run.c loop
-
-            ts.find_timesteps() #integrator will find timesteps
-            #integrator will call halfstep kick, including PM registered drift and kick callbacks
-            ts.do_first_halfstep_kick()
-            ts.drift() #integretor will drift
-            pm.compute_accelerations() #accelerations
-            #integrator will call halfstep kick, including PM registered drift and kick callbacks
-            ts.do_second_halfstep_kick()
-            
-            if mpi.rank == 0 and steps % 10 == 0: #sometimes, master rank will do a plot
-                f, ax = plt.subplots(1)
+        # Occasionally, generate plots on the master rank
+        if mpi.rank == 0 and ts.steps % 10 == 0:
+            fig, ax = plt.subplots(1)
             ax.hist2d(p['pos'][:, 0], p['pos'][:, 1], bins=128)
             ax.set_aspect('equal')
-                pat = os.path.join(os.getenv('HW_BUILD', '.'), 'snap%d_rank%d.png' % (steps, mpi.rank))
-                f.savefig(pat, bbox_inches='tight', dpi=200)
-                plt.close(f)
-
+            path = os.path.join(
+                os.getenv('HW_BUILD', '.'), f'snap{ts.steps}_rank{mpi.rank}.png'
+            )
+            fig.savefig(path, bbox_inches='tight', dpi=200)
+            plt.close(fig)
 
-print('simualtion finished')
+print('Simulation finished')
\ No newline at end of file