diff --git a/src/scripts/model_maker.py b/src/scripts/model_maker.py
index 6e2d3d50e20f538a528ba64cf1850ebda9ab21b2..4475a826aafa9a2cf053ac9c73ce94c59a7c7996 100755
--- a/src/scripts/model_maker.py
+++ b/src/scripts/model_maker.py
@@ -31,6 +31,7 @@ import pdb
import random
import yaml
+## \brief 3D software generation capability flag.
allow_3d = True
try:
import pyvista as pv
@@ -46,7 +47,7 @@ from sys import argv
# `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.
+# \returns result: `int` Exit code (0 = SUCCESS).
def main():
result = 0
config = parse_arguments()
@@ -68,63 +69,69 @@ def main():
# \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]))
+ err_arg = ""
+ try:
+ 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])
+ err_arg = str(dielec_path)
+ file_name = err_arg
+ dielec_file = open(file_name, 'r')
+ wavelengths = []
+ rpart = []
+ ipart = []
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]
+ 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:
- print("ERROR: file %s does not cover requested wavelengths!"%file_name)
- return 2
+ 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
+ except FileNotFoundError as ex:
+ print("ERROR: file not found %s!"%err_arg)
+ return 3
return result
## \brief Create tha calculation configuration structure from YAML input.
@@ -261,12 +268,16 @@ def load_model(model_file):
[0.0 for k in range(sconf['nxi'])] for j in range(sconf['configurations'])
] for i in range(max_layers)
]
- interpolate_constants(sconf)
+ check = interpolate_constants(sconf)
+ if (check != 0):
+ return (None, None)
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)
+ check = match_grid(sconf)
+ if (check != 0):
+ return(None, None)
else:
print("ERROR: %s is not a recognized match mode!"%(model['material_settings']['match_mode']))
return (None, None)
@@ -384,17 +395,25 @@ def load_model(model_file):
rnd_engine = "COMPACT"
if (rnd_engine == "COMPACT"):
check = random_compact(sconf, gconf, rnd_seed, max_rad)
- if (check == 1):
+ if (check == -1):
print("ERROR: compact random generator works only when all sphere types have the same radius.")
return (None, None)
+ elif (check == -2):
+ print("ERROR: sub-particle radius larger than particle radius.")
+ return (None, None)
+ elif (check == -3):
+ print("ERROR: requested number of spheres cannot fit in allowed volume.")
+ return (None, None)
elif (rnd_engine == "LOOSE"):
# random_aggregate() checks internally whether application is INCLUSION
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)
+ if (check != sconf['nsph']):
+ print("WARNING: placed only %d out of %d requested spheres."%(check, sconf['nsph']))
+ sconf['nsph'] = check
+ gconf['nsph'] = check
else:
if (len(model['geometry_settings']['x_coords']) != gconf['nsph']):
print("ERROR: coordinate vectors do not match the number of spheres!")
@@ -409,13 +428,16 @@ def load_model(model_file):
write_obj(sconf, gconf, max_rad)
try:
max_gpu_ram = int(model['system_settings']['max_gpu_ram'])
+ matrix_dim = 2 * gconf['nsph'] * gconf['li'] * (gconf['li'] + 2)
+ matrix_size_bytes = 16 * matrix_dim * matrix_dim
+ matrix_size_Gb = float(matrix_size_bytes) / 1024.0 / 1024.0 / 1024.0
+ print("INFO: estimated matrix size is {0:.3g} Gb.".format(matrix_size_Gb))
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)
+ print("INFO: only %d GPU processes allowed, if using refinement."%(max_gpu_processes / 3))
else:
print("WARNING: estimated matrix size is larger than available GPU memory!")
else:
@@ -454,72 +476,78 @@ def match_grid(sconf):
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]))
+ err_arg = ""
+ try:
+ 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])
+ err_arg = str(dielec_path)
+ file_name = err_arg
+ dielec_file = open(file_name, 'r')
+ wavelengths = []
+ rpart = []
+ ipart = []
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'] = [
- [
+ 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['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
+ [
+ 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
+ except FileNotFoundError as ex:
+ print("ERROR: file not found %s!"%err_arg)
+ return 3
return result
## \brief Parse the command line arguments.
@@ -587,15 +615,19 @@ def random_aggregate(scatterer, geometry, seed, max_rad, max_attempts=100):
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_types = []
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 (scatterer['application'] == "INCLUSION"):
+ scatterer['vec_types'][0] = 1
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]
+ vec_types.append(sph_type_index + 1)
placed_spheres = 1
attempts = 0
for i in range(1, nsph):
@@ -669,7 +701,9 @@ def random_aggregate(scatterer, geometry, seed, max_rad, max_attempts=100):
})
is_placed = True
placed_spheres += 1
+ vec_types.append(sph_type_index + 1)
attempts = 0
+ scatterer['vec_types'] = vec_types
sph_index = 0
for sphere in sorted(vec_spheres, key=lambda item: item['itype']):
scatterer['vec_types'][sph_index] = sphere['itype']
@@ -677,6 +711,7 @@ def random_aggregate(scatterer, geometry, seed, max_rad, max_attempts=100):
geometry['vec_sph_y'][sph_index] = sphere['y']
geometry['vec_sph_z'][sph_index] = sphere['z']
sph_index += 1
+ result = placed_spheres
return result
## \brief Generate a random compact cluster from YAML configuration options.
@@ -699,45 +734,30 @@ def random_compact(scatterer, geometry, seed, max_rad):
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
+ radius = scatterer['ros'][0]
+ # Return an error code if types have different radii
if (max(scatterer['ros']) != min(scatterer['ros'])):
- result = 1
+ result = -1
+ elif (radius > max_rad):
+ # Requested spheres are larger than the maximum allowed volume.
+ # End function with error code -2.
+ result = -2
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)
+ x_centers = np.arange(-1.0 * max_rad + 2.0 * radius, max_rad, 2.0 * radius)
+ x_size = len(x_centers)
+ y_size = int(2.0 * max_rad / ((1.0 + math.sqrt(3.0) / 3.0) * radius))
+ z_size = int(2.0 * max_rad / ((1.0 + 2.0 * math.sqrt(6.0) / 3.0) * radius))
tmp_spheres = []
- n_cells = len(x_centers) * len(y_centers) * len(z_centers)
+ n_cells = x_size * y_size * z_size
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]
+ k = 0
+ z = -max_rad + radius
+ while (z < max_rad - radius):
+ j = 0
+ y = -max_rad + radius
+ while (y < max_rad - radius):
+ for i in range(len(x_centers)):
+ x = (2 * (i + 1) + (j + k) % 2) * radius - max_rad
extent = radius + math.sqrt(x * x + y * y + z * z)
if (extent < max_rad):
tmp_spheres.append({
@@ -746,6 +766,11 @@ def random_compact(scatterer, geometry, seed, max_rad):
'y': y,
'z': z
})
+ #
+ j += 1
+ y = math.sqrt(3.0) * (j + (k % 2) / 3.0) * radius - max_rad + radius
+ k += 1
+ z = 2.0 / 3.0 * math.sqrt(6.0) * k * radius - max_rad + radius
#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)
@@ -777,20 +802,20 @@ def random_compact(scatterer, geometry, seed, max_rad):
current_n -= 1
vec_spheres = []
sph_index = 0
+ # Generate a vector of types if none is given
+ if (0 in scatterer['vec_types']):
+ tincrement = 1 if scatterer['application'] != "INCLUSION" else 2
+ for ti in range(current_n):
+ itype = tincrement + int(n_types * random.random())
+ scatterer['vec_types'][ti] = itype
+ if (scatterer['application'] == "INCLUSION"):
+ scatterer['vec_types'][0] = 1
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']
@@ -798,7 +823,7 @@ def random_compact(scatterer, geometry, seed, max_rad):
geometry['vec_sph_y'][sph_index] = sphere['y']
geometry['vec_sph_z'][sph_index] = sphere['z']
sph_index += 1
- return result
+ return current_n
## \brief Write the geometry configuration dictionary to legacy format.
#
@@ -952,9 +977,10 @@ def write_legacy_sconf(conf):
## \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.
+# This function exports the model as a single OBJ file, containing the
+# information to visualize the particle with 3D software tools. The model
+# file is associated with a MTL material libray file, used to assign colors
+# to spheres of different type.
#
# \param scatterer: `dict` Scatterer configuration dictionary (gets modified)
# \param geometry: `dict` Geometry configuration dictionary (gets modified)