Prepare a random generator script and a test configuration set

src/scripts/config_gen.yml

+system_settings:
+  max_host_ram : 0
+  max_gpu_ram  : 0
+
+input_settings:
+  input_folder : "."
+  spheres_file : "DEDFB"
+  geometry_file: "DCLU"
+  
+output_settings:
+  output_folder: "."
+  output_name  : "c_OCLU"
+  formats      : [ "LEGACY", "HDF5" ]
+  jwtm         : 1
+
+particle_settings:
+  application : "CLUSTER"
+  n_spheres   : 8
+  n_types     : 2
+  sph_types   : [ 1, 1, 1, 1, 2, 2, 2, 2 ]
+  n_layers    : [ 1, 1 ]
+  radii       : [ 6.000e-08, 4.000e-8 ]
+  rad_frac    : [ [ 1.0 ], [ 1.0 ] ]
+  dielec_id   : [ [ 1 ], [ 1 ] ]
+
+material_settings:
+  diel_flag   : 0
+  extern_diel : 1.00e+00
+  dielec_path : "../../ref_data"
+  dielec_file : [ "eps_ashok_C.csv" ]
+  dielec_fmt  : [ "CSV" ]
+  match_mode  : "GRID"
+  diel_const  : [ ]
+
+radiation_settings:
+  polarization: "LINEAR"
+  scale_start : 1.00e-06
+  scale_end   : 2.00e-05
+  scale_step  : 5.00e-09
+  wp          : 2.99792e+08
+  xip         : 1.00e+00
+  step_flag   : 0
+  scale_name  : "WAVELENGTH"
+
+geometry_settings:
+  li          : 4
+  le          : 8
+  npnt        : 149
+  npntts      : 300
+  iavm        : 0
+  isam        : 0
+  in_th_start : 0.0
+  in_th_step  : 0.0
+  in_th_end   : 0.0
+  in_ph_start : 0.0
+  in_ph_step  : 0.0
+  in_ph_end   : 0.0
+  sc_th_start : 0.0
+  sc_th_step  : 0.0
+  sc_th_end   : 0.0
+  sc_ph_start : 0.0
+  sc_ph_step  : 0.0
+  sc_ph_end   : 0.0
+  x_coords    : [
+    8.00e-08,
+    -8.00e-08,
+    0.00e+00,
+    0.00e+00,
+    0.00e+00,
+    0.00e+00,
+    0.00e+00,
+    0.00e+00
+    ]
+  y_coords    : [
+    0.00e+00,
+    0.00e+00,
+    8.00e-08,
+    -8.00e-08,
+    0.00e+00,
+    0.00e+00,
+    0.00e+00,
+    0.00e+00
+    ]
+  z_coords    : [
+    0.00e+00,
+    0.00e+00,
+    0.00e+00,
+    0.00e+00,
+    8.00e-08,
+    -8.00e-08,
+    16.00e-08,
+    -16.00e-08
+    ]

src/scripts/generator.py

+import math
+import random
+import yaml
+
+#import pdb
+
+from pathlib import PurePath
+from sys import argv
+
+seed = int(argv[1])
+
+random.seed(seed)
+
+config = {}
+with open('config.yml', 'r') as stream:
+    config = yaml.safe_load(stream)
+
+nsph = int(config['particle_settings']['n_spheres'])
+
+vec_thetas = [0.0 for i in range(nsph)]
+vec_phis = [0.0 for i in range(nsph)]
+vec_rads = [0.0 for i in range(nsph)]
+vec_sph_x = [0.0 for i in range(nsph)]
+vec_sph_y = [0.0 for i in range(nsph)]
+vec_sph_z = [0.0 for i in range(nsph)]
+
+sph_type_index = config['particle_settings']['sph_types'][0] - 1
+vec_rads[0] = config['particle_settings']['radii'][sph_type_index]
+max_rad = 20.0 * vec_rads[0]
+placed_spheres = 1
+attempts = 0
+max_attempts = 100
+for i in range(1, nsph):
+    sph_type_index = config['particle_settings']['sph_types'][i] - 1
+    vec_rads[i] = config['particle_settings']['radii'][sph_type_index]
+    is_placed = False
+    #breakpoint()
+    while (not is_placed):
+        if (attempts > max_attempts):
+            print("WARNING: could not place sphere %d in allowed radius!"%i)
+            break # while(not is_placed)
+        vec_thetas[i] = math.pi * random.random()
+        vec_phis[i] = 2.0 * math.pi * random.random()
+        rho = vec_rads[0] + vec_rads[i]
+        z = rho * math.cos(vec_thetas[i])
+        y = rho * math.sin(vec_thetas[i]) * math.sin(vec_phis[i])
+        x = rho * math.sin(vec_thetas[i]) * math.cos(vec_phis[i])
+        j = 0
+        while (j < i - 1):
+            j += 1
+            dx2 = (x - vec_sph_x[j]) * (x - vec_sph_x[j])
+            dy2 = (y - vec_sph_y[j]) * (y - vec_sph_y[j])
+            dz2 = (z - vec_sph_z[j]) * (z - vec_sph_z[j])
+            dist2 = dx2 + dy2 + dz2
+            rr2 = (vec_rads[i] + vec_rads[j]) * (vec_rads[i] + vec_rads[j])
+            if (dist2 < rr2):
+                # Spheres i and j are compenetrating.
+                # Sphere i is moved out radially until it becomes externally
+                # tangent to sphere j. Then the check is repeated, to verify
+                # that no other sphere was penetrated. The process is iterated
+                # until sphere i is placed or the maximum allowed radius is
+                # reached.
+                sinthi = math.sin(vec_thetas[i])
+                sinthj = math.sin(vec_thetas[j])
+                costhi = math.cos(vec_thetas[i])
+                costhj = math.cos(vec_thetas[j])
+                sinphi = math.sin(vec_phis[i])
+                sinphj = math.sin(vec_phis[j])
+                cosphi = math.cos(vec_phis[i])
+                cosphj = math.cos(vec_phis[j])
+                cosalpha = (
+                    sinthi * cosphi * sinthj * cosphj
+                    + sinthi * sinphi * sinthj * sinphj
+                    + costhi * costhj
+                )
+                rho += 2.0 * vec_rads[j] * cosalpha
+                z = rho * math.cos(vec_thetas[i])
+                y = rho * math.sin(vec_thetas[i]) * math.sin(vec_phis[i])
+                x = rho * math.sin(vec_thetas[i]) * math.cos(vec_phis[i])
+                j = 0
+                continue # while(j < i - 1)
+        if (rho + vec_rads[i] > max_rad):
+            # The current direction is filled. Try another one.
+            attempts += 1
+            continue # while(not is_placed)
+        vec_sph_x[i] = x
+        vec_sph_y[i] = y
+        vec_sph_z[i] = z
+        is_placed = True
+        placed_spheres += 1
+        attempts = 0
+
+print(vec_sph_x)
+print(vec_sph_y)
+print(vec_sph_z)