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introduction-to-isis.md
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Trent Hare authored
3 links were updated, recently broken due to the refactor and release of Astropedia.
Trent Hare authored3 links were updated, recently broken due to the refactor and release of Astropedia.
model_maker.py 47.08 KiB
#!/usr/bin/env python3
# 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
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# A copy of the GNU General Public License is distributed along with
# this program in the COPYING file. If not, see: <https://www.gnu.org/licenses/>.
## @package model_maker
# \brief Script to build models from YAML configuration files.
#
# Script to assist in the creation of model input files starting
# from a YAML descriptor.
#
# The script requires python3.
import math
import multiprocessing
import numpy as np
import os
import pdb
import random
import yaml
allow_3d = True
try:
import pyvista as pv
except ModuleNotFoundError as ex:
print("WARNING: pyvista not found!")
allow_3d = False
from pathlib import Path
from sys import argv
## \brief Main execution code
#
# `main()` is the function that handles the creation of the code configuration.
# It returns an integer value as exit code, using 0 to signal successful execution.
#
# \returns result: `int` Number of detected error-level inconsistencies.
def main():
result = 0
config = parse_arguments()
if (config['help_mode'] or config['yml_file_name'] == ""):
print_help()
else:
sconf, gconf = load_model(config['yml_file_name'])
if (sconf is not None) and (gconf is not None):
result = write_legacy_sconf(sconf)
if (result == 0): result += write_legacy_gconf(gconf)
else:
print("ERROR: could not create configuration.")
result = 1
return result
## \brief Populate the dielectric constant data via interpolation
#
# \param sconf: `dict` Scatterer configuration dictionary.
# \return result: `int` An exit code (0 if successful).
def interpolate_constants(sconf):
result = 0
for i in range(sconf['configurations']):
for j in range(sconf['nshl'][i]):
file_idx = sconf['dielec_id'][i][j]
dielec_path = Path(sconf['dielec_path'], sconf['dielec_file'][int(file_idx) - 1])
file_name = str(dielec_path)
dielec_file = open(file_name, 'r')
wavelengths = []
rpart = []
ipart = []
str_line = dielec_file.readline()
while (str_line != ""):
if (not str_line.startswith('#')):
split_line = str_line.split(',')
if (len(split_line) == 3):
wavelengths.append(float(split_line[0]))
rpart.append(float(split_line[1]))
ipart.append(float(split_line[2]))
str_line = dielec_file.readline()
dielec_file.close()
wi = 0
x0 = 0.0
x1 = 0.0
ry0 = 0.0
iy0 = 0.0
ry1 = 0.0
iy1 = 0.0
for dci in range(sconf['nxi']):
w = sconf['vec_xi'][dci]
while (w > x1):
x0 = wavelengths[wi]
ry0 = rpart[wi]
iy0 = ipart[wi]
if (wi == len(wavelengths)):
print("ERROR: file %s does not cover requested wavelengths!"%file_name)
return 1
wi += 1
x1 = wavelengths[wi]
ry1 = rpart[wi]
iy1 = ipart[wi]
if (wi > 0):
x0 = wavelengths[wi - 1]
ry0 = rpart[wi - 1]
iy0 = ipart[wi - 1]
dx = w - x0
dry = (ry1 - ry0) / (x1 - x0) * dx
diy = (iy1 - iy0) / (x1 - x0) * dx
ry = ry0 + dry
iy = iy0 + diy
sconf['rdc0'][j][i][dci] = ry
sconf['idc0'][j][i][dci] = iy
else:
if (wavelengths[wi] == w):
sconf['rdc0'][j][i][dci] = rpart[0]
sconf['idc0'][j][i][dci] = ipart[0]
else:
print("ERROR: file %s does not cover requested wavelengths!"%file_name)
return 2
return result
## \brief Create tha calculation configuration structure from YAML input.
#
# \param model_file: `str` Full path to the YAML input file.
# \return sconf, gconf: `tuple` A dictionary tuple for scatterer and
# geometric configurations.
def load_model(model_file):
sconf = None
gconf = None
model = None
try:
with open(model_file, 'r') as stream:
model = yaml.safe_load(stream)
except yaml.YAMLError:
print("ERROR: " + model_file + " is not a valid YAML file!")
except FileNotFoundError:
print("ERROR: " + model_file + " was not found!")
if model is not None:
max_rad = 0.0
make_3d = False
try:
if model['system_settings']['make_3D'] == "0" else True
except KeyError:
make_3d = False
if (make_3d and not allow_3d):
print("WARNING: 3D visualization of models is not available. Disabling.")
make_3d = False
# Create the sconf dict
sconf = {
'out_file': Path(
model['input_settings']['input_folder'],
model['input_settings']['spheres_file']
)
}
sconf['nsph'] = int(model['particle_settings']['n_spheres'])
sconf['application'] = model['particle_settings']['application']
sconf['ies'] = 1 if sconf['application'] == "INCLUSION" else 0
sconf['exdc'] = float(model['material_settings']['extern_diel'])
sconf['wp'] = float(model['radiation_settings']['wp'])
sconf['xip'] = float(model['radiation_settings']['xip'])
sconf['idfc'] = int(model['material_settings']['diel_flag'])
sconf['instpc'] = int(model['radiation_settings']['step_flag'])
sconf['xi_start'] = float(model['radiation_settings']['scale_start'])
sconf['xi_end'] = float(model['radiation_settings']['scale_end'])
sconf['xi_step'] = float(model['radiation_settings']['scale_step'])
sconf['configurations'] = int(model['particle_settings']['n_types'])
sconf['dielec_path'] = model['material_settings']['dielec_path']
sconf['dielec_file'] = model['material_settings']['dielec_file']
num_dielec = 0 # len(model['particle_settings']['dielec_id'])
if (sconf['idfc'] == -1):
num_dielec = len(model['material_settings']['diel_const'])
elif (sconf['idfc'] == 0):
num_dielec = len(model['particle_settings']['dielec_id'])
if (len(model['particle_settings']['n_layers']) != sconf['configurations']):
print("ERROR: Declared number of layers does not match number of types!")
return (None, None)
else:
sconf['nshl'] = [0 for i in range(sconf['configurations'])]
for i in range(sconf['configurations']):
sconf['nshl'][i] = int(model['particle_settings']['n_layers'][i])
max_layers = max(sconf['nshl'])
if (sconf['application'] == "INCLUSION"):
if (max_layers < sconf['nshl'][0] + 1):
max_layers = sconf['nshl'][0] + 1
if (num_dielec != sconf['configurations']):
print("ERROR: declared array of optical constants does not match configurations!")
return (None, None)
else:
if (sconf['idfc'] == 0):
sconf['dielec_id'] = [
[ 0 for j in range(max_layers)] for i in range(sconf['configurations'])
]
for i in range(sconf['configurations']):
expected_layer_num = 1 + int(sconf['nshl'][i] / 2)
if (sconf['application'] == "INCLUSION" and i == 0):
expected_layer_num += 1
if (len(model['particle_settings']['dielec_id'][i]) != expected_layer_num):
print("ERROR: Declared materials in type %d do not match the number of layers!"%(i + 1))
return (None, None)
else:
for j in range(1 + int(sconf['nshl'][i] / 2)):
sconf['dielec_id'][i][j] = float(model['particle_settings']['dielec_id'][i][j])
if (model['radiation_settings']['scale_name'] == "XI"):
sconf['insn'] = 1
sconf['nxi'] = 1 + int((sconf['xi_end'] - sconf['xi_start']) / sconf['xi_step'])
sconf['vec_xi'] = [0.0 for i in range(sconf['nxi'])]
for i in range(sconf['nxi']):
sconf['vec_xi'][i] = sconf['xi_start'] + i * sconf['xi_step']
# Set up dielectric constants
allow_dielec = True # TODO: define logic to check dielectric constants
if (not allow_dielec):
print("ERROR: delcared dielectric constants do not match number of sphere types!")
return (None, None)
else:
if (sconf['idfc'] == -1):
sconf['rdc0'] = [
[
[0.0 for k in range(1)] for j in range(sconf['configurations'])
] for i in range(max_layers)
]
sconf['idc0'] = [
[
[0.0 for k in range(1)] for j in range(sconf['configurations'])
] for i in range(max_layers)
]
for di in range(max_layers):
for dj in range(sconf['configurations']):
if (len(model['material_settings']['diel_const'][dj]) / 2 != sconf['nshl'][dj]):
print("ERROR: dielectric constants for type %d do not match number of layers!"%(dj + 1))
return (None, None)
else:
sconf['rdc0'][di][dj][0] = float(model['material_settings']['diel_const'][dj][2 * di])
sconf['idc0'][di][dj][0] = float(model['material_settings']['diel_const'][dj][2 * di + 1])
else: # sconf[idfc] != -1 and scaling on XI
print("ERROR: for scaling on XI, optical constants must be defined!")
return (None, None)
elif (model['radiation_settings']['scale_name'] == "WAVELENGTH"):
sconf['insn'] = 3
if (model['material_settings']['match_mode'] == "INTERPOLATE"):
sconf['nxi'] = 1 + int((sconf['xi_end'] - sconf['xi_start']) / sconf['xi_step'])
sconf['vec_xi'] = [0.0 for i in range(sconf['nxi'])]
for i in range(sconf['nxi']):
sconf['vec_xi'][i] = sconf['xi_start'] + i * sconf['xi_step']
# Set up the dielectric constants
if (sconf['idfc'] == 0):
sconf['rdc0'] = [
[
[0.0 for k in range(sconf['nxi'])] for j in range(sconf['configurations'])
] for i in range(max_layers)
]
sconf['idc0'] = [
[
[0.0 for k in range(sconf['nxi'])] for j in range(sconf['configurations'])
] for i in range(max_layers)
]
interpolate_constants(sconf)
else: # sconf[idfc] != 0 and scaling on wavelength
print("ERROR: for wavelength scaling, optical constants must be tabulated!")
return (None, None)
elif (model['material_settings']['match_mode'] == "GRID"):
match_grid(sconf)
else:
print("ERROR: %s is not a recognized match mode!"%(model['material_settings']['match_mode']))
return (None, None)
else:
print("ERROR: %s is not a supported scaling mode!"%(model['radiation_settings']['scale_name']))
return (None, None)
sph_types = model['particle_settings']['sph_types']
if (len(sph_types) == sconf['nsph']):
sconf['vec_types'] = [int(str_typ) for str_typ in sph_types]
else:
if (len(sph_types) != 0):
print("ERROR: vector of sphere types does not match the declared number of spheres!")
return (None, None)
else: # len(sph_types) = 0
len_vec_x = len(model['geometry_settings']['x_coords'])
len_vec_y = len(model['geometry_settings']['y_coords'])
len_vec_z = len(model['geometry_settings']['z_coords'])
if (len_vec_x != 0 or len_vec_y != 0 or len_vec_z != 0):
print("ERROR: cannot assign random types with explicit sphere positions!")
return (None, None)
else:
sconf['vec_types'] = [0 for ti in range(sconf['nsph'])]
if (len(model['particle_settings']['radii']) != sconf['configurations']):
print("ERROR: Declared number of radii does not match number of types!")
return (None, None)
else:
sconf['ros'] = [0.0 for i in range(sconf['configurations'])]
for i in range(sconf['configurations']):
sconf['ros'][i] = float(model['particle_settings']['radii'][i])
if (len(model['particle_settings']['rad_frac']) != sconf['configurations']):
print("ERROR: Declared number of fractional radii does not match number of types!")
return (None, None)
else:
sconf['rcf'] = [
[0.0 for j in range(max_layers)] for i in range(sconf['configurations'])
]
for i in range(sconf['configurations']):
expected_radii = sconf['nshl'][i]
if (sconf['application'] == "INCLUSION" and i == 0):
expected_radii += 1
if (len(model['particle_settings']['rad_frac'][i]) != expected_radii):
print("ERROR: Declared transition radii in type %d do not match the number of layers!"%(i + 1))
return (None, None)
else:
expected_radii = sconf['nshl'][i]
if (sconf['application'] == "INCLUSION" and i == 0):
expected_radii += 1
for j in range(expected_radii):
sconf['rcf'][i][j] = float(model['particle_settings']['rad_frac'][i][j])
# Create the gconf dict
str_polar = model['radiation_settings']['polarization']
if (str_polar not in ["LINEAR", "CIRCULAR"]):
print("ERROR: %s is not a recognized polarization state."%str_polar)
return (None, None)
gconf = {
'out_file': Path(
model['input_settings']['input_folder'],
model['input_settings']['geometry_file']
)
}
gconf['nsph'] = sconf['nsph']
gconf['application'] = model['particle_settings']['application']
gconf['li'] = int(model['geometry_settings']['li'])
gconf['le'] = int(
gconf['li'] if gconf['application'] == "SPHERE" else model['geometry_settings']['le']
)
gconf['inpol'] = 0 if str_polar == "LINEAR" else 1
gconf['npnt'] = int(model['geometry_settings']['npnt'])
gconf['npntts'] = int(model['geometry_settings']['npntts'])
if (gconf['application'] != "SPHERE"):
gconf['iavm'] = int(model['geometry_settings']['iavm'])
gconf['isam'] = int(model['geometry_settings']['isam'])
gconf['jwtm'] = int(model['output_settings']['jwtm'])
gconf['th'] = float(model['geometry_settings']['in_th_start'])
gconf['thstp'] = float(model['geometry_settings']['in_th_step'])
gconf['thlst'] = float(model['geometry_settings']['in_th_end'])
gconf['ph'] = float(model['geometry_settings']['in_ph_start'])
gconf['phstp'] = float(model['geometry_settings']['in_ph_step'])
gconf['phlst'] = float(model['geometry_settings']['in_ph_end'])
gconf['ths'] = float(model['geometry_settings']['sc_th_start'])
gconf['thsstp'] = float(model['geometry_settings']['sc_th_step'])
gconf['thslst'] = float(model['geometry_settings']['sc_th_end'])
gconf['phs'] = float(model['geometry_settings']['sc_ph_start'])
gconf['phsstp'] = float(model['geometry_settings']['sc_ph_step'])
gconf['phslst'] = float(model['geometry_settings']['sc_ph_end'])
gconf['vec_sph_x'] = [0.0 for i in range(gconf['nsph'])]
gconf['vec_sph_y'] = [0.0 for i in range(gconf['nsph'])]
gconf['vec_sph_z'] = [0.0 for i in range(gconf['nsph'])]
if (gconf['application'] != "SPHERE" or gconf['nsph'] != 1):
len_vec_x = len(model['geometry_settings']['x_coords'])
len_vec_y = len(model['geometry_settings']['y_coords'])
len_vec_z = len(model['geometry_settings']['z_coords'])
if (len_vec_x != len_vec_y):
print("ERROR: X and Y coordinate vectors have different lengths!")
return (None, None)
if (len_vec_x != len_vec_z):
print("ERROR: X and Z coordinate vectors have different lengths!")
return (None, None)
if (len_vec_y != len_vec_z):
print("ERROR: Y and Z coordinate vectors have different lengths!")
return (None, None)
if (len_vec_x == 0):
# Generate random cluster
rnd_seed = int(model['system_settings']['rnd_seed'])
max_rad = float(model['particle_settings']['max_rad'])
# random_aggregate() checks internally whether application is INCLUSION
#random_aggregate(sconf, gconf, rnd_seed, max_rad)
rnd_engine = "COMPACT"
try:
rnd_engine = model['system_settings']['rnd_engine']
except KeyError:
# use compact generator, if no specification is given
rnd_engine = "COMPACT"
if (rnd_engine == "COMPACT"):
check = random_compact(sconf, gconf, rnd_seed, max_rad)
if (check == 1):
print("ERROR: compact random generator works only when all sphere types have the same radius.")
return (None, None)
elif (rnd_engine == "LOOSE"):
check = random_aggregate(sconf, gconf, rnd_seed, max_rad)
else:
print("ERROR: unrecognized random generator engine.")
return (None, None)
if (check != 0):
print("WARNING: %d sphere(s) could not be placed."%check)
else:
if (len(model['geometry_settings']['x_coords']) != gconf['nsph']):
print("ERROR: coordinate vectors do not match the number of spheres!")
return (None, None)
for si in range(gconf['nsph']):
gconf['vec_sph_x'][si] = float(model['geometry_settings']['x_coords'][si])
gconf['vec_sph_y'][si] = float(model['geometry_settings']['y_coords'][si])
gconf['vec_sph_z'][si] = float(model['geometry_settings']['z_coords'][si])
#
if (model['system_settings']['make_3D'] != "0" and allow_3d):
if (max_rad == 0.0):
max_rad = 20.0 * max(sconf['ros'])
write_obj(sconf, gconf, max_rad)
try:
max_gpu_ram = int(model['system_settings']['max_gpu_ram'])
if (max_gpu_ram > 0):
max_gpu_ram_bytes = max_gpu_ram * 1024 * 1024 * 1024
matrix_dim = 2 * gconf['nsph'] * gconf['li'] * (gconf['li'] + 2)
matrix_size_bytes = 16 * matrix_dim * matrix_dim
if (matrix_size_bytes < max_gpu_ram_bytes):
max_gpu_processes = int(max_gpu_ram_bytes / matrix_size_bytes)
print("INFO: system supports up to %d simultaneous processes on GPU."%max_gpu_processes)
else:
print("WARNING: estimated matrix size is larger than available GPU memory!")
else:
print("INFO: no GPU RAM declared.")
max_host_ram = int(model['system_settings']['max_host_ram'])
if (max_host_ram > 0):
max_host_ram_bytes = max_host_ram * 1024 * 1024 * 1024
matrix_dim = 2 * gconf['nsph'] * gconf['li'] * (gconf['li'] + 2)
matrix_size_bytes = 16 * matrix_dim * matrix_dim
if (matrix_size_bytes < max_host_ram_bytes):
max_host_processes = int(max_host_ram_bytes / matrix_size_bytes / 2)
print("INFO: system supports up to %d simultaneous processes."%max_host_processes)
else:
print("WARNING: estimated matrix size is larger than available host memory!")
else:
print("WARNING: no host RAM declared!")
except KeyError as ex:
print(ex)
print("WARNING: missing system description! Cannot estimate recommended execution.")
cpu_count = multiprocessing.cpu_count()
print("INFO: the number of detected CPUs is %d."%cpu_count)
else: # model is None
print("ERROR: could not parse " + model_file + "!")
return (sconf, gconf)
## \brief Populate the dielectric constant data matching a grid.
#
# Important note: if the configuration requests that more than one
# optical constants file should be used, all the files must provide
# their constants for the same vector of wavelengths.
#
# \param sconf: `dict` Scatterer configuration dictionary.
# \return result: `int` An exit code (0 if successful).
def match_grid(sconf):
result = 0
max_layers = 0
nxi = 0
sconf['vec_xi'] = []
for i in range(sconf['configurations']):
layers = sconf['nshl'][i]
if (sconf['application'] == "INCLUSION" and i == 0):
layers += 1
for j in range(layers):
file_idx = sconf['dielec_id'][i][j]
dielec_path = Path(sconf['dielec_path'], sconf['dielec_file'][int(file_idx) - 1])
file_name = str(dielec_path)
dielec_file = open(file_name, 'r')
wavelengths = []
rpart = []
ipart = []
str_line = dielec_file.readline()
while (str_line != ""):
if (not str_line.startswith('#')):
split_line = str_line.split(',')
if (len(split_line) == 3):
wavelengths.append(float(split_line[0]))
rpart.append(float(split_line[1]))
ipart.append(float(split_line[2]))
str_line = dielec_file.readline()
dielec_file.close()
if (max_layers == 0):
# This is executed only once
max_layers = max(sconf['nshl'])
if (sconf['application'] == "INCLUSION" and max_layers < sconf['nshl'][0] + 1):
max_layers = sconf['nshl'][0] + 1
w_start = sconf['xi_start']
w_end = sconf['xi_end']
for wi in range(len(wavelengths)):
w = wavelengths[wi]
if (w >= w_start and w <= w_end):
sconf['vec_xi'].append(w)
nxi += 1
sconf['rdc0'] = [
[
[
0.0 for dk in range(nxi)
] for dj in range(sconf['configurations'])
] for di in range(max_layers)
]
sconf['idc0'] = [
[
[
0.0 for dk in range(nxi)
] for dj in range(sconf['configurations'])
] for di in range(max_layers)
]
sconf['nxi'] = nxi
# This is executed for all layers in all configurations
wi = 0
x = wavelengths[wi]
ry = rpart[wi]
iy = ipart[wi]
for dci in range(sconf['nxi']):
w = sconf['vec_xi'][dci]
while (w > x):
x = wavelengths[wi]
ry = rpart[wi]
iy = ipart[wi]
if (wi == len(wavelengths)):
print("ERROR: file %s does not cover requested wavelengths!"%file_name)
return 1
wi += 1
sconf['rdc0'][j][i][dci] = ry
sconf['idc0'][j][i][dci] = iy
return result
## \brief Parse the command line arguments.
#
# The script behaviour can be modified through a set of optional arguments.
# The purpose of this function is to parse the command line in search for
# such arguments and prepare the execution accordingly.
#
# \returns config: `dict` A dictionary containing the script configuration.
def parse_arguments():
config = {
'yml_file_name': "",
'help_mode': False,
}
yml_set = False
for arg in argv[1:]:
if (arg.startswith("--help")):
config['help_mode'] = True
elif (not yml_set):
if (not arg.startswith("--")):
config['yml_file_name'] = arg
yml_set = True
else:
raise Exception("Unrecognized argument \'{0:s}\'".format(arg))
return config
## \brief Print a command-line help summary.
def print_help():
print("###############################################")
print("# #")
print("# NPtm_code MODEL_MAKER #")
print("# #")
print("###############################################")
print(" ")
print("Create input files for FORTRAN and C++ code. ")
print(" ")
print("Usage: \"./model_maker.py CONFIG [OPTIONS]\" ")
print(" ")
print("CONFIG must be a valid YAML configuration file.")
print(" ")
print("Valid options are: ")
print("--help Print this help and exit.")
print(" ")
## \brief Generate a random cluster aggregate from YAML configuration options.
#
# This function generates a random aggregate of spheres using radial ejection
# in random directions of new spheres until they become tangent to the
# outermost sphere existing in that direction. The result of the generated
# model is directly saved in the parameters of the scatterer and geometry
# configuration dictionaries.
#
# \param scatterer: `dict` Scatterer configuration dictionary (gets modified)
# \param geometry: `dict` Geometry configuration dictionary (gets modified)
# \param seed: `int` Seed for the random sequence generation
# \param max_rad: `float` Maximum allowed radial extension of the aggregate
# \param max_attempts: `int` Maximum number of attempts to place a particle in any direction
# \return result: `int` Function exit code (0 for success, otherwise number of
# spheres that could not be placed)
def random_aggregate(scatterer, geometry, seed, max_rad, max_attempts=100):
result = 0
random.seed(seed)
nsph = scatterer['nsph']
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)]
n_types = scatterer['configurations']
if (0 in scatterer['vec_types']):
tincrement = 1 if scatterer['application'] != "INCLUSION" else 2
for ti in range(nsph):
itype = tincrement + int(n_types * random.random())
scatterer['vec_types'][ti] = itype
sph_type_index = scatterer['vec_types'][0] - 1
vec_spheres = [{'itype': sph_type_index + 1, 'x': 0.0, 'y': 0.0, 'z': 0.0}]
vec_rads[0] = scatterer['ros'][sph_type_index]
placed_spheres = 1
attempts = 0
for i in range(1, nsph):
sph_type_index = scatterer['vec_types'][i] - 1
vec_rads[i] = scatterer['ros'][sph_type_index]
is_placed = False
while (not is_placed):
if (attempts > max_attempts):
result += 1
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_spheres[j]['x']) * (x - vec_spheres[j]['x'])
dy2 = (y - vec_spheres[j]['y']) * (y - vec_spheres[j]['y'])
dz2 = (z - vec_spheres[j]['z']) * (z - vec_spheres[j]['z'])
dist2 = dx2 + dy2 + dz2
rr2 = (vec_rads[i] + vec_rads[j]) * (vec_rads[i] + vec_rads[j])
if (dist2 < 0.9999 * 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.
# breakpoint()
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
)
D12 = math.sqrt(
vec_spheres[j]['x'] * vec_spheres[j]['x']
+ vec_spheres[j]['y'] * vec_spheres[j]['y']
+ vec_spheres[j]['z'] * vec_spheres[j]['z']
)
O1K = D12 * cosalpha
sinalpha = math.sqrt(1.0 - cosalpha * cosalpha)
sinbetaprime = D12 / (vec_rads[i] + vec_rads[j]) * sinalpha
cosbetaprime = math.sqrt(1.0 - sinbetaprime * sinbetaprime)
Op3K = (vec_rads[i] + vec_rads[j]) * cosbetaprime
rho = O1K + Op3K
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_spheres.append({
'itype': sph_type_index + 1,
'x': x,
'y': y,
'z': z
})
is_placed = True
placed_spheres += 1
attempts = 0
sph_index = 0
for sphere in sorted(vec_spheres, key=lambda item: item['itype']):
scatterer['vec_types'][sph_index] = sphere['itype']
geometry['vec_sph_x'][sph_index] = sphere['x']
geometry['vec_sph_y'][sph_index] = sphere['y']
geometry['vec_sph_z'][sph_index] = sphere['z']
sph_index += 1
return result
## \brief Generate a random compact cluster from YAML configuration options.
#
# This function generates a random aggregate of spheres using the maximum
# compactness packaging to fill a spherical volume with given maximum radius,
# then it proceeds by subtracting random spheres from the outer layers, until
# the aggregate is reduced to the desired number of spheres. The function
# can only be used if all sphere types have the same radius. The result of the
# generated model is directly saved in the parameters of the scatterer and
# geometry configuration dictionaries.
#
# \param scatterer: `dict` Scatterer configuration dictionary (gets modified)
# \param geometry: `dict` Geometry configuration dictionary (gets modified)
# \param seed: `int` Seed for the random sequence generation
# \param max_rad: `float` Maximum allowed radial extension of the aggregate
# \return result: `int` Function exit code (0 for success, otherwise error code)
def random_compact(scatterer, geometry, seed, max_rad):
result = 0
random.seed(seed)
nsph = scatterer['nsph']
n_types = scatterer['configurations']
if (0 in scatterer['vec_types']):
tincrement = 1 if scatterer['application'] != "INCLUSION" else 2
for ti in range(nsph):
itype = tincrement + int(n_types * random.random())
scatterer['vec_types'][ti] = itype
if (max(scatterer['ros']) != min(scatterer['ros'])):
result = 1
else:
radius = scatterer['ros'][0]
x_centers = np.arange(-1.0 * max_rad + radius, max_rad, 2.0 * radius)
y_centers = np.arange(-1.0 * max_rad + radius, max_rad, math.sqrt(3.0) * radius)
z_centers = np.arange(-1.0 * max_rad + radius, max_rad, math.sqrt(3.0) * radius)
x_offset = radius
y_offset = radius
x_layer_offset = radius
y_layer_offset = radius / math.sqrt(3.0)
tmp_spheres = []
n_cells = len(x_centers) * len(y_centers) * len(z_centers)
print("INFO: the cubic space would contain %d spheres."%n_cells)
n_max_spheres = int((max_rad / radius) * (max_rad / radius) * (max_rad / radius) * 0.74)
print("INFO: the maximum radius allows for %d spheres."%n_max_spheres)
for zi in range(len(z_centers)):
if (x_layer_offset == 0.0):
x_layer_offset = radius
else:
x_layer_offset = 0.0
if (y_offset == 0.0):
y_offset = radius
else:
y_offset = 0.0
for yi in range(len(y_centers)):
if (x_offset == 0.0):
x_offset = radius
else:
x_offset = 0.0
for xi in range(len(x_centers)):
x = x_centers[xi] + x_offset + x_layer_offset
y = y_centers[yi] + y_offset
z = z_centers[zi]
extent = radius + math.sqrt(x * x + y * y + z * z)
if (extent < max_rad):
tmp_spheres.append({
'itype': 1,
'x': x,
'y': y,
'z': z
})
#tmp_spheres = [{'itype': 1, 'x': 0.0, 'y': 0.0, 'z': 0.0}]
current_n = len(tmp_spheres)
print("INFO: before erosion there are %d spheres in use."%current_n)
rho = 10.0 * max_rad
discard_rad = 100.0 * max_rad
while (current_n > nsph):
theta = math.pi * random.random()
phi = 2.0 * math.pi * random.random()
x0 = rho * math.sin(theta) * math.cos(phi)
y0 = rho * math.sin(theta) * math.sin(phi)
z0 = rho * math.cos(theta)
closest_index = 0
minimum_distance = 1000.0 * max_rad
for di in range(len(tmp_spheres)):
x1 = tmp_spheres[di]['x']
if (x1 == discard_rad):
continue
y1 = tmp_spheres[di]['y']
z1 = tmp_spheres[di]['z']
distance = math.sqrt(
(x1 - x0) * (x1 - x0)
+ (y1 - y0) * (y1 - y0)
+ (z1 - z0) * (z1 - z0)
)
if (distance < minimum_distance):
closest_index = di
minimum_distance = distance
tmp_spheres[closest_index]['x'] = discard_rad
current_n -= 1
vec_spheres = []
sph_index = 0
for ti in range(len(tmp_spheres)):
sphere = tmp_spheres[ti]
if (sphere['x'] < max_rad):
sphere['itype'] = scatterer['vec_types'][sph_index]
sph_index += 1
vec_spheres.append(sphere)
#pl = pv.Plotter()
#for si in range(len(vec_spheres)):
# x = vec_spheres[si]['x'] / max_rad
# y = vec_spheres[si]['y'] / max_rad
# z = vec_spheres[si]['z'] / max_rad
# mesh = pv.Sphere(radius / max_rad, (x, y, z))
# pl.add_mesh(mesh)
#pl.export_obj("scene.obj")
sph_index = 0
for sphere in sorted(vec_spheres, key=lambda item: item['itype']):
scatterer['vec_types'][sph_index] = sphere['itype']
geometry['vec_sph_x'][sph_index] = sphere['x']
geometry['vec_sph_y'][sph_index] = sphere['y']
geometry['vec_sph_z'][sph_index] = sphere['z']
sph_index += 1
return result
## \brief Write the geometry configuration dictionary to legacy format.
#
# \param conf: `dict` Geometry configuration dictionary.
# \return result: `int` An exit code (0 if successful).
def write_legacy_gconf(conf):
result = 0
out_file = str(conf['out_file'])
nsph = conf['nsph']
str_line = "INIT"
# Write legacy output
output = open(out_file, 'w')
if (conf['application'] == "SPHERE"):
str_line = " {0:4d} {1:4d} {2:4d} {3:4d} {4:4d} {5:4d}\n".format(
nsph, conf['li'], conf['inpol'], conf['npnt'], conf['npntts'], conf['isam']
)
output.write(str_line)
else:
mxndm = 2 * nsph * conf['li'] * (conf['li'] + 2)
str_line = " {0:4d} {1:4d} {2:4d} {3:4d} {4:4d} {5:4d} {6:4d} {7:4d} {8:4d}\n".format(
nsph, conf['li'], conf['le'], mxndm, conf['inpol'],
conf['npnt'], conf['npntts'], conf['iavm'], conf['isam']
)
output.write(str_line)
for si in range(nsph):
str_line = " {0:15.8E} {1:15.8E} {2:15.8E}\n".format(
conf['vec_sph_x'][si], conf['vec_sph_y'][si], conf['vec_sph_z'][si]
)
output.write(str_line)
str_line = " {0:7.2E} {1:7.2E} {2:7.2E} {3:7.2E} {4:7.2E} {5:7.2E}\n".format(
conf['th'], conf['thstp'], conf['thlst'],
conf['ph'], conf['phstp'], conf['phlst']
)
output.write(str_line)
str_line = " {0:7.2E} {1:7.2E} {2:7.2E} {3:7.2E} {4:7.2E} {5:7.2E}\n".format(
conf['ths'], conf['thsstp'], conf['thslst'],
conf['phs'], conf['phsstp'], conf['phslst']
)
output.write(str_line)
str_line = " {0:d}\n0\n".format(conf['jwtm'])
output.write(str_line)
output.close()
return result
## \brief Write the scatterer configuration dictionary to legacy format.
#
# \param conf: `dict` Scatterer configuration dictionary.
# \return result: `int` An exit code (0 if successful).
def write_legacy_sconf(conf):
result = 0
out_file = str(conf['out_file'])
nsph = conf['nsph']
ies = conf['ies']
exdc = conf['exdc']
wp = conf['wp']
xip = conf['xip']
idfc = conf['idfc']
instpc = conf['instpc']
xi_flag = 3
nxi = conf['nxi']
# Write legacy output
output = open(out_file, 'w')
str_line = " {0:3d}{1:3d}\n".format(nsph, ies)
output.write(str_line)
str_line = " {0:12.7E} {1:12.7E} {2:12.7E} {3:2d} {4:4d} {5:4d} {6:3d}\n".format(
exdc, wp, xip, idfc, nxi, instpc, xi_flag
)
output.write(str_line)
if (instpc == 0):
for ixi in range(nxi):
str_line = "{0:.3E}\n".format(conf['vec_xi'][ixi])
output.write(str_line)
else:
str_line = "{0:.3E} {1:.3E}\n".format(conf['xi_start'], conf['xi_step'])
output.write(str_line)
sphere_line_count = 0
placed_spheres = 0
last_type = 0
dedfb_type = 0
for si in range(nsph):
if (conf['vec_types'][si] > last_type):
dedfb_type = placed_spheres + 1
last_type = conf['vec_types'][si]
str_line = "{0:5d}".format(dedfb_type)
output.write(str_line)
sphere_line_count += 1
placed_spheres += 1
if (sphere_line_count == 16):
output.write("\n")
sphere_line_count = 0
if (sphere_line_count != 0):
output.write("\n")
for ci in range(conf['configurations']):
layers = conf['nshl'][ci]
str_line = "{0:3d} {1:15.7E}\n".format(layers, conf['ros'][ci])
output.write(str_line)
if (conf['application'] == "INCLUSION" and ci == 0):
layers += 1
for cj in range(layers):
str_line = " {0:.7E}\n".format(conf['rcf'][ci][cj])
output.write(str_line)
if (conf['application'] != "INCLUSION"):
if (conf['idfc'] == 0):
# Write all layers in each configuration for every wavelength
for xk in range(conf['nxi']):
for xi in range(conf['configurations']):
for xj in range(1 + int(conf['nshl'][xi] / 2)):
rdc0 = conf['rdc0'][xj][xi][xk]
idc0 = conf['idc0'][xj][xi][xk]
if (rdc0 != 0.0 or idc0 != 0.0):
str_line = "({0:11.5E},{1:11.5E})\n".format(rdc0, idc0)
output.write(str_line)
elif (conf['idfc'] == -1):
# Write reference scale constants for each layer in each configuration
for xi in range(conf['configurations']):
for xj in range(1 + int(conf['nshl'][xi] / 2)):
rdc0 = conf['rdc0'][xj][xi][0]
idc0 = conf['idc0'][xj][xi][0]
if (rdc0 != 0.0 or idc0 != 0.0):
str_line = "({0:11.5E},{1:11.5E})\n".format(rdc0, idc0)
output.write(str_line)
else: # specialized output for INCLUSION
if (conf['idfc'] == 0):
# Write all layers in each configuration for every wavelength
for xk in range(conf['nxi']):
for xi in range(conf['configurations']):
layers = int(conf['nshl'][xi])
if (xi == 0):
layers += 1
for xj in range(layers):
rdc0 = conf['rdc0'][xj][xi][xk]
idc0 = conf['idc0'][xj][xi][xk]
if (rdc0 != 0.0 or idc0 != 0.0):
str_line = "({0:11.5E},{1:11.5E})\n".format(rdc0, idc0)
output.write(str_line)
elif (conf['idfc'] == -1):
# Write reference scale constants for each layer in each configuration
for xi in range(conf['configurations']):
layers = int(conf['nshl'][xi])
if (xi == 0):
layers += 1
for xj in range(layers):
rdc0 = conf['rdc0'][xj][xi][0]
idc0 = conf['idc0'][xj][xi][0]
if (rdc0 != 0.0 or idc0 != 0.0):
str_line = "({0:11.5E},{1:11.5E})\n".format(rdc0, idc0)
output.write(str_line)
output.write("0\n")
output.close()
return result
## \brief Export the model to a set of OBJ files for 3D visualization.
#
# This function exports the model as a set of OBJ files (one for every
# spherical unit, plus a single scene file) to allow for model visualization
# with 3D software tools.
#
# \param scatterer: `dict` Scatterer configuration dictionary (gets modified)
# \param geometry: `dict` Geometry configuration dictionary (gets modified)
# \param max_rad: `float` Maximum allowed radial extension of the aggregate
def write_obj(scatterer, geometry, max_rad):
out_dir = scatterer['out_file'].absolute().parent
out_model_path = Path(str(geometry['out_file']) + ".obj")
out_material_path = Path(str(geometry['out_file']) + ".mtl")
color_strings = [
"1.0 1.0 1.0\n", # white
"1.0 0.0 0.0\n", # red
"0.0 0.0 1.0\n", # blue
"0.0 1.0 0.0\n", # green
]
color_names = [
"white", "red", "blue", "green"
]
mtl_file = open(str(out_material_path), "w")
for mi in range(len(color_strings)):
mtl_line = "newmtl " + color_names[mi] + "\n"
mtl_file.write(mtl_line)
color_line = color_strings[mi]
mtl_file.write(" Ka " + color_line)
mtl_file.write(" Ks " + color_line)
mtl_file.write(" Kd " + color_line)
mtl_file.write(" Ns 100.0\n")
mtl_file.write(" Tr 0.0\n")
mtl_file.write(" illum 2\n\n")
mtl_file.close()
pl = pv.Plotter()
for si in range(scatterer['nsph']):
sph_type_index = scatterer['vec_types'][si]
# color_index = 1 + (sph_type_index % (len(color_strings) - 1))
# color_by_name = color_names[sph_type_index]
radius = scatterer['ros'][sph_type_index - 1] / max_rad
x = geometry['vec_sph_x'][si] / max_rad
y = geometry['vec_sph_y'][si] / max_rad
z = geometry['vec_sph_z'][si] / max_rad
mesh = pv.Sphere(radius, (x, y, z))
pl.add_mesh(mesh, color=None)
pl.export_obj(str(Path(str(out_dir), "TMP_MODEL.obj")))
tmp_model_file = open(str(Path(str(out_dir), "TMP_MODEL.obj")), "r")
out_model_file = open(str(out_model_path), "w")
mtl_line = "mtllib {0:s}\n".format(out_material_path.name)
sph_index = 0
sph_type_index = 0
old_sph_type_index = 0
str_line = tmp_model_file.readline()
while (str_line != ""):
if (str_line.startswith("mtllib")):
str_line = mtl_line
elif (str_line.startswith("g ")):
sph_index += 1
sph_type_index = scatterer['vec_types'][sph_index - 1]
if (sph_type_index == old_sph_type_index):
str_line = tmp_model_file.readline()
str_line = tmp_model_file.readline()
else:
old_sph_type_index = sph_type_index
color_index = sph_type_index % (len(color_names) - 1)
str_line = "g grp{0:04d}\n".format(sph_type_index)
out_model_file.write(str_line)
str_line = tmp_model_file.readline()
str_line = "usemtl {0:s}\n".format(color_names[color_index])
out_model_file.write(str_line)
str_line = tmp_model_file.readline()
out_model_file.close()
tmp_model_file.close()
os.remove(str(Path(str(out_dir), "TMP_MODEL.obj")))
os.remove(str(Path(str(out_dir), "TMP_MODEL.mtl")))
## \brief Exit code (0 for success)
exit_code = main()
exit(exit_code)