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Big docs update for v1.0.0
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@GordoNice
GordoNice committed Jul 2, 2020
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2 changes: 1 addition & 1 deletion docs/conf.py
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# The name of an image file (relative to this directory) to place at the top of
# the title page.
#latex_logo = None
latex_logo = 'images/logo.png'

# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
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179 changes: 179 additions & 0 deletions docs/examples/snake.inp
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[ Title ]
Example2b: Snake!
Illustrative example of FitsGeo usage
Shows how to create multiple (repeating) objects with some math laws

[ Parameters ]
icntl = 11 # (D=0) 3:ECH 5:ALL VOID 6:SRC 7,8:GSH 11:DSH 12:DUMP
#icntl = 0 # (D=0) 3:ECH 5:ALL VOID 6:SRC 7,8:GSH 11:DSH 12:DUMP
itall = 1
istdev = -1 # (D=0) Control parameter for statistical uncertainty calculation type and restart mode.
negs = 1

maxcas = 1000 # (D=10) number of particles per one batch
maxbch = 100000 # (D=10) number of batches

[ Source ]
s-type = 9
proj = proton
x0 = 2
y0 = 0
z0 = 0.132
e0 = 100.0
r0 = 0.0
dir = all

[ Material ]
mat[1] H 2.0 O 1.0 GAS=0 $ name: 'MAT_WATER'
mat[2] H -0.1 C -0.204 N -0.042 O -0.645 Na -0.002 P -0.001 S -0.002 Cl -0.003 K -0.001 GAS=0 $ name: 'MAT_SKIN_ICRP'
mat[3] H 4.0 C 2.0 GAS=0 $ name: 'MAT_POLYETHYLENE'

[ Mat Name Color ]
mat name size color
1 {MAT\_WATER} 1.00 blue
2 {MAT\_SKIN\_ICRP} 1.00 green
3 {MAT\_POLYETHYLENE} 1.00 blue

[ Surface ]
1 SPH -1.3673469387755102 0 -0.7672719285390251 0.027723013645953594 $ name: 'SPH' (sphere) x0 y0 z0 R
2 SPH -1.2653061224489797 0 -0.6606685327429188 0.02829460213179771 $ name: 'SPH' (sphere) x0 y0 z0 R
3 SPH -1.163265306122449 0 -0.502391908191501 0.02887797553400489 $ name: 'SPH' (sphere) x0 y0 z0 R
4 SPH -1.0612244897959182 0 -0.31087406445720084 0.029473376832021225 $ name: 'SPH' (sphere) x0 y0 z0 R
5 SPH -0.9591836734693877 0 -0.10612250568576122 0.03008105401500263 $ name: 'SPH' (sphere) x0 y0 z0 R
6 SPH -0.8571428571428572 0 0.09222119831628449 0.0307012601851042 $ name: 'SPH' (sphere) x0 y0 z0 R
7 SPH -0.7551020408163263 0 0.26663740363716293 0.031334253662899186 $ name: 'SPH' (sphere) x0 y0 z0 R
8 SPH -0.6530612244897958 0 0.4031539294877735 0.031980298094971465 $ name: 'SPH' (sphere) x0 y0 z0 R
9 SPH -0.5510204081632653 0 0.49233751776643636 0.032639662563726336 $ name: 'SPH' (sphere) x0 y0 z0 R
10 SPH -0.44897959183673475 0 0.5297951558796689 0.033312621699465396 $ name: 'SPH' (sphere) x0 y0 z0 R
11 SPH -0.34693877551020424 0 0.516178133105813 0.03399945579477215 $ name: 'SPH' (sphere) x0 y0 z0 R
12 SPH -0.2448979591836733 0 0.4567274424263816 0.03470045092125597 $ name: 'SPH' (sphere) x0 y0 z0 R
13 SPH -0.1428571428571428 0 0.36043778735561943 0.035415899048703105 $ name: 'SPH' (sphere) x0 y0 z0 R
14 SPH -0.04081632653061229 0 0.23894605136204328 0.03614609816668431 $ name: 'SPH' (sphere) x0 y0 z0 R
15 SPH 0.06122448979591866 0 0.10526682529176924 0.03689135240866978 $ name: 'SPH' (sphere) x0 y0 z0 R
16 SPH 0.16326530612244916 0 -0.027498125343700826 0.03765197217870301 $ name: 'SPH' (sphere) x0 y0 z0 R
17 SPH 0.26530612244897966 0 -0.1473571496828118 0.03842827428068646 $ name: 'SPH' (sphere) x0 y0 z0 R
18 SPH 0.36734693877551017 0 -0.2444312783541894 0.03922058205033278 $ name: 'SPH' (sphere) x0 y0 z0 R
19 SPH 0.46938775510204067 0 -0.3116862365829553 0.040029225489836576 $ name: 'SPH' (sphere) x0 y0 z0 R
20 SPH 0.5714285714285716 0 -0.34534859980043214 0.040854541405322846 $ name: 'SPH' (sphere) x0 y0 z0 R
21 SPH 0.6734693877551021 0 -0.34499303885518234 0.04169687354712925 $ name: 'SPH' (sphere) x0 y0 z0 R
22 SPH 0.7755102040816326 0 -0.31331851066930916 0.04255657275298077 $ name: 'SPH' (sphere) x0 y0 z0 R
23 SPH 0.8775510204081636 0 -0.2556581135852169 0.04343399709411627 $ name: 'SPH' (sphere) x0 y0 z0 R
24 SPH 0.9795918367346941 0 -0.1792880209486128 0.04432951202442788 $ name: 'SPH' (sphere) x0 y0 z0 R
25 SPH 1.0816326530612246 0 -0.09261403493598512 0.04524349053267528 $ name: 'SPH' (sphere) x0 y0 z0 R
26 SPH 1.183673469387755 0 -0.004319265460356921 0.04617631329783845 $ name: 'SPH' (sphere) x0 y0 z0 R
27 SPH 1.2857142857142856 0 0.07744657465511029 0.04712836884767322 $ name: 'SPH' (sphere) x0 y0 z0 R
28 SPH 1.387755102040816 0 0.1457658580616131 0.04810005372053611 $ name: 'SPH' (sphere) x0 y0 z0 R
29 SPH 1.4897959183673475 0 0.1954850113560298 0.049091772630545545 $ name: 'SPH' (sphere) x0 y0 z0 R
30 SPH 1.591836734693878 0 0.22354449689276956 0.05010393863614837 $ name: 'SPH' (sphere) x0 y0 z0 R
31 SPH 1.6938775510204085 0 0.22909265869423243 0.051136973312161764 $ name: 'SPH' (sphere) x0 y0 z0 R
32 SPH 1.795918367346939 0 0.21339003096231585 0.052191306925362425 $ name: 'SPH' (sphere) x0 y0 z0 R
33 SPH 1.8979591836734695 0 0.17952922947672972 0.05326737861369591 $ name: 'SPH' (sphere) x0 y0 z0 R
34 SPH 2.0 0 0.1320103335494828 0.054365636569180906 $ name: 'SPH' (sphere) x0 y0 z0 R
35 TRC 2.0 0.054365636569180906 0.1320103335494828 0 0.07248751542557454 0 0.03624375771278727 1e-09 $ name: 'RCC' (truncated right-angle cone) [x0 y0 z0] [Hx Hy Hz] R_b R_t
36 RCC -1.4673469387755103 0 -0.7672719285390251 4 0 0 3 $ name: 'RCC' (cylinder) [x0 y0 z0] [Hx Hy Hz] R

[ Cell ]
100 -1 (36) $ name: 'Cell'

101 2 1.09 (-1) $ name: 'Snake Part 0'
102 2 1.09 (-2) $ name: 'Snake Part 1'
103 2 1.09 (-3) $ name: 'Snake Part 2'
104 2 1.09 (-4) $ name: 'Snake Part 3'
105 2 1.09 (-5) $ name: 'Snake Part 4'
106 2 1.09 (-6) $ name: 'Snake Part 5'
107 2 1.09 (-7) $ name: 'Snake Part 6'
108 2 1.09 (-8) $ name: 'Snake Part 7'
109 2 1.09 (-9) $ name: 'Snake Part 8'
110 2 1.09 (-10) $ name: 'Snake Part 9'
111 2 1.09 (-11) $ name: 'Snake Part 10'
112 2 1.09 (-12) $ name: 'Snake Part 11'
113 2 1.09 (-13) $ name: 'Snake Part 12'
114 2 1.09 (-14) $ name: 'Snake Part 13'
115 2 1.09 (-15) $ name: 'Snake Part 14'
116 2 1.09 (-16) $ name: 'Snake Part 15'
117 2 1.09 (-17) $ name: 'Snake Part 16'
118 2 1.09 (-18) $ name: 'Snake Part 17'
119 2 1.09 (-19) $ name: 'Snake Part 18'
120 2 1.09 (-20) $ name: 'Snake Part 19'
121 2 1.09 (-21) $ name: 'Snake Part 20'
122 2 1.09 (-22) $ name: 'Snake Part 21'
123 2 1.09 (-23) $ name: 'Snake Part 22'
124 2 1.09 (-24) $ name: 'Snake Part 23'
125 2 1.09 (-25) $ name: 'Snake Part 24'
126 2 1.09 (-26) $ name: 'Snake Part 25'
127 2 1.09 (-27) $ name: 'Snake Part 26'
128 2 1.09 (-28) $ name: 'Snake Part 27'
129 2 1.09 (-29) $ name: 'Snake Part 28'
130 2 1.09 (-30) $ name: 'Snake Part 29'
131 2 1.09 (-31) $ name: 'Snake Part 30'
132 2 1.09 (-32) $ name: 'Snake Part 31'
133 2 1.09 (-33) $ name: 'Snake Part 32'
134 2 1.09 (-34) $ name: 'Snake Part 33'
135 3 0.93 (-35) $ name: 'Hat!'
136 0 (-36) (1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35) $ name: 'Vacuum'

[ T-Track ]
title = Track Detection in xyz mesh

mesh = xyz # mesh type is xyz scoring mesh
x-type = 2 # x-mesh is linear given by xmin, xmax and nx
nx = 240 # number of x-mesh points
xmin = -3.0 # minimum value of x-mesh points
xmax = 3.0 # maximum value of x-mesh points

y-type = 1 # y-mesh is given by the below data
ny = 1 # number of y-mesh points
-0.7 0.7 #

z-type = 2 # z-mesh is linear given by zmin, zmax and nz
nz = 240 # number of z-mesh points
zmin = -2.0 # minimum value of z-mesh points
zmax = 2.0 # maximum value of z-mesh points

axis = xz # axis of output

e-type = 1 # e-mesh is given by the below data
ne = 1 # number of e-mesh points
0.0 50.0 # number of l-mesh points

unit = 1 # unit is [1/cm^2/source] fluence
file = track_xyz-xz.out # file name of output for the above axis

part = all
part = electron
part = proton
part = neutron
part = photon

gshow = 1 # 0: no 1:bnd, 2:bnd+mat, 3:bnd+reg 4:bnd+lat
epsout = 1 # (D=0) generate eps file by ANGEL


[ T-3Dshow ]
title = Geometry 3D
x0 = 0
y0 = 0
z0 = 0

w-wdt = 1
w-hgt = 1
w-dst = 20

w-mnw = 400 # Number of meshes in horizontal direction.
w-mnh = 400 # Number of meshes in vertical direction.
w-ang = 0

e-the = 90
e-phi = 20
e-dst = 50

l-the = 80
l-phi = 140
l-dst = 200*100

file = snake_3D
output = 3 # (D=3) Region boundary + color
width = 0.5 # (D=0.5) The option defines the line thickness.
epsout = 1

[ E n d ]
37 changes: 18 additions & 19 deletions docs/examples/snake.py
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# Example 2b: Snake!
# Illustrative example of FitsGeo usage
# Shows how to easily create multiple (repeating) objects with some math laws
import fitsgeo
import fitsgeo as fg
from numpy import sin, exp, linspace # To use math functions

# Create laws for positions of snakes parts
x = linspace(0, 5, 50) # Create 50 evenly spaced x values from 0 to 5
y_p = [5*sin(3*x_i)*0.3*exp(-0.4*x_i) for x_i in x] # Law for y coordinate
y_r = [0.02*exp(0.2*x_i) for x_i in x] # Law for radius of spheres
# Law for z coordinate
z_p = [5 * sin(3 * x_i) * 0.3 * exp(-0.4 * x_i) for x_i in x]
r = [0.02 * exp(0.2 * x_i) for x_i in x] # Law for radius of spheres

# Define materials for snake and hat
snake_mat = fitsgeo.Material.database("MAT_SKIN_ICRP", color="green")
hat_mat = fitsgeo.Material.database("MAT_POLYETHYLENE", color="blue")

snake_mat = fg.Material.database("MAT_SKIN_ICRP", color="green")
hat_mat = fg.Material.database("MAT_POLYETHYLENE", color="blue")

snake = [] # List with all parts of snake
for i in range(16, len(x)): # Take x values starting from i=16
snake.append(
fitsgeo.SPH(xyz0=[x[i]-3, 0, y_p[i]], r=y_r[i], material=snake_mat))
fg.SPH(xyz0=[x[i] - 3, 0, z_p[i]], r=r[i], material=snake_mat))

last_part = snake[len(snake)-1]
hat = fitsgeo.TRC(
hat = fg.TRC(
xyz0=[
last_part.x0,
last_part.y0 + last_part.r,
Expand All @@ -29,35 +29,34 @@
r_1=last_part.r/1.5,
r_2=1e-9, material=hat_mat)

void = fitsgeo.RCC(
void = fg.RCC(
xyz0=[
snake[0].x0-0.1,
snake[0].y0,
snake[0].z0], h=[4, 0, 0], r=3, material=fitsgeo.MAT_VOID)

outer_void = fitsgeo.Cell([+void], material=fitsgeo.MAT_OUTER)
snake[0].z0], h=[4, 0, 0], r=3, material=fg.MAT_VOID)

# Define cells
outer_void = fg.Cell([+void], material=fg.MAT_OUTER)
cells = []
for i in range(len(snake)):
cells.append(
fitsgeo.Cell([-snake[i]], name=f"Snake Part {i}", material=snake_mat))
fg.Cell([-snake[i]], name=f"Snake Part {i}", material=snake_mat))
# Add a nice hat on head =)
hat_cell = fitsgeo.Cell([-hat], name="Hat!", material=hat_mat)
hat_cell = fg.Cell([-hat], name="Hat!", material=hat_mat)

text = ""
for s in snake:
text += +s

void_cell = fitsgeo.Cell(
[-void, " ", text + +hat], name="Vacuum", material=fitsgeo.MAT_VOID)
void_cell = fg.Cell(
[-void, " ", text + +hat], name="Vacuum", material=fg.MAT_VOID)

fitsgeo.create_scene(ax_length=5) # Create scene before draw
fg.create_scene(ax_length=5) # Create scene before draw

# Draw snake
for s in snake:
s.draw(label_center=True)
s.draw()
hat.draw(truncated=False) # Difficulties with truncated cone =(
void.draw()

fitsgeo.phits_export() # Export sections
fg.phits_export(to_file=True, inp_name="snake") # Export sections
92 changes: 92 additions & 0 deletions docs/examples/snowman.inp
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[ Title ]
Snowman (Example3): one more example of how to use FitsGeo module
Illustrative example of FitsGeo usage
Shows general workflow

[ Parameters ]
icntl = 11 # (D=0) 3:ECH 5:ALL VOID 6:SRC 7,8:GSH 11:DSH 12:DUMP

[ Source ]
s-type = 2 # mono-energetic rectangular source
e0 = 1 # energy of beam [MeV]
proj = proton # kind of incident particle

[ Material ]
mat[1] H 2.0 O 1.0 GAS=0 $ name: 'MAT_WATER'
mat[2] C 6.0 GAS=0 $ name: 'MAT_CARBON'
mat[3] H 2.0 C 1.0 GAS=0 $ name: 'MAT_PARAFFIN'

[ Mat Name Color ]
mat name size color
1 {MAT\_WATER} 1.00 lightgray
2 {MAT\_CARBON} 1.00 black
3 {MAT\_PARAFFIN} 1.00 orange

[ Surface ]
1 SPH 0 0 0 1 $ name: 'bottom' (sphere) x0 y0 z0 R
2 SPH 0 1 0 0.6666666666666666 $ name: 'middle' (sphere) x0 y0 z0 R
3 SPH 0 1.7999999999999998 0 0.4444444444444444 $ name: 'top' (sphere) x0 y0 z0 R
4 TRC 0 1.911111111111111 0.2222222222222222 0 0 0.7111111111111111 0.07407407407407407 0.001 $ name: 'RCC' (truncated right-angle cone) [x0 y0 z0] [Hx Hy Hz] R_b R_t
5 RCC 0 2.2444444444444445 0 0 0.09523809523809523 0 0.2962962962962963 $ name: 'Hat bottom' (cylinder) [x0 y0 z0] [Hx Hy Hz] R
6 RCC 0.0 2.3396825396825394 0.0 0.0 0.38095238095238093 0.0 0.19753086419753085 $ name: 'Hat top' (cylinder) [x0 y0 z0] [Hx Hy Hz] R
7 SPH -0.13333333333333333 2.022222222222222 0.35555555555555557 0.04444444444444444 $ name: 'Left Eye' (sphere) x0 y0 z0 R
8 SPH 0.13333333333333333 2.022222222222222 0.35555555555555557 0.04444444444444444 $ name: 'Right Eye' (sphere) x0 y0 z0 R
9 SPH 0 1.2666666666666666 0.6 0.05333333333333332 $ name: 'Button1' (sphere) x0 y0 z0 R
10 SPH 0 1 0.6666666666666666 0.05866666666666666 $ name: 'Button2' (sphere) x0 y0 z0 R
11 TZ 0 1.7099999999999997 0.4444444444444444 0.014814814814814814 0.006349206349206348 0.008888888888888887 $ name: 'Mouth 1' (torus, with z rotational axis) [x0 y0 z0] A(R) B C
12 TZ 0.04444444444444444 1.726296296296296 0.4444444444444444 0.014814814814814814 0.006349206349206348 0.008888888888888887 $ name: 'Mouth 2' (torus, with z rotational axis) [x0 y0 z0] A(R) B C
13 TZ -0.04444444444444444 1.726296296296296 0.4444444444444444 0.014814814814814814 0.006349206349206348 0.008888888888888887 $ name: 'Mouth 3' (torus, with z rotational axis) [x0 y0 z0] A(R) B C
14 TZ -0.08888888888888888 1.7485185185185181 0.4444444444444444 0.014814814814814814 0.006349206349206348 0.008888888888888887 $ name: 'Mouth 4' (torus, with z rotational axis) [x0 y0 z0] A(R) B C
15 TZ 0.08888888888888888 1.7485185185185181 0.4444444444444444 0.014814814814814814 0.006349206349206348 0.008888888888888887 $ name: 'Mouth 5' (torus, with z rotational axis) [x0 y0 z0] A(R) B C
16 SPH 0.0 0.0 0.0 3 $ name: 'Outer edge' (sphere) x0 y0 z0 R

[ Cell ]
100 -1 (16) $ name: 'Outer Void'

101 0 (-16 1 2 3 5 6 4 7 8 9 10 11 12 13 14 15) $ name: 'Inner Cell'

102 1 1.0 (-1 2) $ name: 'Bottom Cell'
103 1 1.0 (-2 9 10 3) $ name: 'Middle Cell'
104 1 1.0 (-3 4 7 8) $ name: 'Top Cell'
105 2 2.0 (-9) VOL=0.0006354549881038906 $ name: 'Button1 Cell'
106 2 2.0 (-10) VOL=0.0008457905891662785 $ name: 'Button2 Cell'
107 2 2.0 (-11) VOL=1.6504139569396266e-05 $ name: 'Mouth 1 Cell'
108 2 2.0 (-12) VOL=1.6504139569396266e-05 $ name: 'Mouth 2 Cell'
109 2 2.0 (-13) VOL=1.6504139569396266e-05 $ name: 'Mouth 3 Cell'
110 2 2.0 (-14) VOL=1.6504139569396266e-05 $ name: 'Mouth 4 Cell'
111 2 2.0 (-15) VOL=1.6504139569396266e-05 $ name: 'Mouth 5 Cell'
112 2 2.0 (-7) VOL=0.00036774015515271454 $ name: 'Left Eye Cell'
113 2 2.0 (-8) VOL=0.00036774015515271454 $ name: 'Right Eye Cell'
114 3 0.89 (-4) VOL=0.004141907421006144 $ name: 'Carrot Cell'
115 2 2.0 (-5) VOL=0.026267153939479614 $ name: 'Hat bottom Cell'
116 2 2.0 (-6) VOL=0.04669716255907488 $ name: 'Hat top Cell'

[ T-3Dshow ]
title = Geometry 3D
x0 = 0
y0 = 1
z0 = 0

w-wdt = 4
w-hgt = 4
w-dst = 10

w-mnw = 400 # Number of meshes in horizontal direction.
w-mnh = 400 # Number of meshes in vertical direction.
w-ang = 0

e-the = 40
e-phi = 120
e-dst = 100

l-the = 80
l-phi = 140
l-dst = 200*100

file = snowman_3D
output = 3 # (D=3) Region boundary + color
width = 0.5 # (D=0.5) The option defines the line thickness.

epsout = 1

[ E n d ]
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