containers/docker/Dockerfile

@@ -15,7 +15,7 @@ RUN DEBIAN_FRONTEND=noninteractive apt -y upgrade
 RUN DEBIAN_FRONTEND=noninteractive apt -y install g++ gfortran gcc-offload-nvptx g++-12 gfortran-12 gcc-12-offload-nvptx g++-13 gfortran-13 gcc-13-offload-nvptx g++-14 gfortran-14 gcc-14-offload-nvptx clang libc++-dev libc++abi-dev clang-17 clang-18 clang-19 flang-17 flang-18 flang-19 libhdf5-dev make
 # install packages needed to test with Intel OneAPI compilers
 COPY --chown=root:root containers/docker/dockerstuff/intelcomps/oneapi-archive-keyring.gpg /usr/share/keyrings/
-COPY --chown=root:root containers/docker/dockerstuff/intelcomps/oneAPI.list /etc/apt/sources.list.d/
+COPY --chown=root:root containers/docker/dockerstuff/intelcomps/oneAPI.sources /etc/apt/sources.list.d/
 RUN apt update
 RUN DEBIAN_FRONTEND=noninteractive apt -y install intel-oneapi-compiler-fortran intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic intel-oneapi-compiler-dpcpp-cpp
 # install lapacke and its dependencies, both standard and the version with 64 bit integers

containers/docker/dockerstuff/intelcomps/oneAPI.list

-deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] http://apt.repos.intel.com/oneapi all main

containers/docker/dockerstuff/intelcomps/oneAPI.sources

+Types: deb
+Enabled: yes
+URIs: https://apt.repos.intel.com/oneapi
+Suites: all
+Components: main
+#Architectures: amd64
+Signed-By: /usr/share/keyrings/oneapi-archive-keyring.gpg
+Trusted: yes

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)

src/scripts/pycompare.py

-#!/bin/python3
+#!/usr/bin/env python3
 
-#   Copyright (C) 2024   INAF - Osservatorio Astronomico di Cagliari
+#   Copyright (C) 2025   INAF - Osservatorio Astronomico di Cagliari
 #
 #   This program is free software: you can redistribute it and/or modify
 #   it under the terms of the GNU General Public License as published by

src/scripts/pydynrange.py

-#!/bin/python3
+#!/usr/bin/env python3
 
-#   Copyright (C) 2024   INAF - Osservatorio Astronomico di Cagliari
+#   Copyright (C) 2025   INAF - Osservatorio Astronomico di Cagliari
 #
 #   This program is free software: you can redistribute it and/or modify
 #   it under the terms of the GNU General Public License as published by

src/scripts/pytiming.py

-#!/bin/python3
+#!/usr/bin/env python3
 
-#   Copyright (C) 2024   INAF - Osservatorio Astronomico di Cagliari
+#   Copyright (C) 2025   INAF - Osservatorio Astronomico di Cagliari
 #
 #   This program is free software: you can redistribute it and/or modify
 #   it under the terms of the GNU General Public License as published by

test_data/config_random_example.yml

+# EXAMPLE CONFIGURATION FILE TO BUILD A RANDOM CLUSTER WITH 100 SPHERES.
+
+system_settings:
+  # Limit on host RAM use in Gb (0 for no configuration limit)
+  max_host_ram : 24
+  # Limit on GPU RAM use in Gb (0 for no configuration limit)
+  max_gpu_ram  : 8
+  # Random seed (a positive integer number)
+  rnd_seed     : 105
+  # Random engine (COMPACT or LOOSE)
+  rnd_engine   : "COMPACT"
+  # OBJ model export flag (requires pyvista; 0 is FALSE)
+  make_3D      : 0
+
+input_settings:
+  # Folder to write the code input configuration files
+  input_folder : "."
+  # Name of the scatterer description file
+  spheres_file : "DEDFB_comp"
+  # Name of the geometry description file
+  geometry_file: "DCLU_comp"
+  
+output_settings:
+  # Folder for the code output storage
+  output_folder: "."
+  # Name of the main output file
+  output_name  : "c_OCLU"
+  # Requested output formats
+  formats      : [ "LEGACY", "HDF5" ]
+  # Index of the scale for transition matrix output
+  jwtm         : 1
+
+particle_settings:
+  # What application to use (SPHERE | CLUSTER | INCLUSION)
+  application : "CLUSTER"
+  # Number of spheres
+  n_spheres   : 100
+  # Number of sphere types
+  n_types     : 2
+  # Vector of sphere type identifiers (what type is each sphere)
+  # For random genration it can be empty (random sphere types),
+  # or contain "n_spheres" elements (random position with assigned
+  # types).
+  sph_types   : [ ]
+  # Vector of layers in types (how many layers in each type)
+  n_layers    : [ 1, 1 ]
+  # Spherical monomer radii in m (one size for each type)
+  radii       : [ 4.000e-8, 4.000e-8 ]
+  # Layer fractional radii (one per layer in each type)
+  rad_frac    : [ [ 1.0 ], [ 1.0 ] ]
+  # Index of the dielectric constants (one per layer in each type)
+  #
+  # 1 is first file in `dielec_file`, 2 is second ...
+  dielec_id   : [ [ 1 ], [ 1 ] ]
+  # Maximum radius for random particle size in m
+  max_rad     : 3.0e-7
+
+material_settings:
+  # Dielectric properties definition (-1 = scaled, 0 = tabulated)
+  diel_flag   : 0
+  # External medium dielectric constant
+  extern_diel : 1.00e+00
+  # Dielectric constant files folder
+  dielec_path : "../../ref_data"
+  # List of dielectric constant files (used if diel_flag = 0)
+  dielec_file : [ "eps_ashok_C.csv" ]
+  # Dielectric constant files format (same for all files)
+  dielec_fmt  : [ "CSV" ]
+  # Matching method between optical constants and radiation wavelengths
+  #
+  # INTERPOLATE: the constants are interpolated on wavelengths
+  # GRID: only the wavelengths with defined constants are computed
+  #
+  match_mode  : "GRID"
+  # Reference dielectric constants (used if diel_flag = -1)
+  #
+  # One real and one imaginary part for each layer in each type.
+  diel_const  : [ ]
+
+radiation_settings:
+  # Radiation field polarization (LINEAR | CIRCULAR)
+  polarization: "LINEAR"
+  # First scale to be used
+  scale_start : 1.00e-06
+  # Last scale to be used
+  scale_end   : 2.00e-05
+  # Calculation step (overridden if `match_mode` is GRID)
+  scale_step  : 5.00e-09
+  # Peak Omega
+  wp          : 2.99792e+08
+  # Peak scale
+  xip         : 1.00e+00
+  # Define scale explicitly (0) or in equal steps (1)
+  step_flag   : 0
+  # Type of scaling variable
+  scale_name  : "WAVELENGTH"
+
+geometry_settings:
+  # Maximum internal field expansion
+  li          : 6
+  # Maximum external field expansion (not used by SPHERE)
+  le          : 8
+  # Number of transition layer integration points
+  npnt        : 149
+  # Number of non transition layer integration points
+  npntts      : 300
+  # Averaging mode
+  iavm        : 0
+  # Meridional plane flag
+  isam        : 0
+  # Starting incidence azimuth angle
+  in_th_start : 0.0
+  # Incidence azimuth angle incremental step
+  in_th_step  : 0.0
+  # Ending incidence azimuth angle
+  in_th_end   : 0.0
+  # Starting incidence elevation angle
+  in_ph_start : 0.0
+  # Incidence elevation angle incremental step
+  in_ph_step  : 0.0
+  # Ending incidence elevation angle
+  in_ph_end   : 0.0
+  # Starting scattered azimuth angle
+  sc_th_start : 0.0
+  # Scattered azimuth angle incremental step
+  sc_th_step  : 0.0
+  # Ending scattered azimuth angle
+  sc_th_end   : 0.0
+  # Starting scattered elevation angle
+  sc_ph_start : 0.0
+  # Scattered elevation angle incremental step
+  sc_ph_step  : 0.0
+  # Ending scattered elevation angle
+  sc_ph_end   : 0.0
+  # Vector of sphere X coordinates (one per sphere or empty for random)
+  x_coords    : [ ]
+  # Vector of sphere Y coordinates (one per sphere or empty for random)
+  y_coords    : [ ]
+  # Vector of sphere Z coordinates (one per sphere or empty for random)
+  z_coords    : [ ]